Changes between Initial Version and Version 1 of Ticket #3712


Ignore:
Timestamp:
Sep 14, 2020, 8:56:31 AM (5 years ago)
Author:
Eric Pettersen
Comment:

Legend:

Unmodified
Added
Removed
Modified

  • Ticket #3712

    • Property Component Unassigned → Volume Data
    • Property Owner set to Tom Goddard
    • Property Platform → all
    • Property Project → ChimeraX
    • Property Status new → assigned
    • Property Summary ChimeraX bug report submission → volume command: overflow encountered in subtract

  • Ticket #3712 – Description

    initial v1  
    721721data = numpy.zeros(dim, numpy.uint8) 
    722722 
    723 See log for complete Python traceback. 
    724  
    725 Traceback (most recent call last): 
    726 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    727 packages/chimerax/core/triggerset.py", line 130, in invoke 
    728 return self._func(self._name, data) 
    729 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    730 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    731 self.set_surface_mask() 
    732 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    733 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    734 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    735 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    736 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    737 self._update_mask() 
    738 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    739 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    740 step=self.grid_step, pad=self.pad) 
    741 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    742 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    743 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    744 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    745 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    746 _generate_data_array 
    747 data = numpy.zeros(dim, numpy.uint8) 
    748 ValueError: negative dimensions are not allowed 
    749  
    750 Error processing trigger "atom coords updated": 
    751 ValueError: negative dimensions are not allowed 
    752  
    753 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    754 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    755 _generate_data_array 
    756 data = numpy.zeros(dim, numpy.uint8) 
    757  
    758 See log for complete Python traceback. 
    759  
    760 Traceback (most recent call last): 
    761 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    762 packages/chimerax/core/triggerset.py", line 130, in invoke 
    763 return self._func(self._name, data) 
    764 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    765 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    766 self.set_surface_mask() 
    767 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    768 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    769 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    770 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    771 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    772 self._update_mask() 
    773 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    774 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    775 step=self.grid_step, pad=self.pad) 
    776 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    777 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    778 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    779 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    780 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    781 _generate_data_array 
    782 data = numpy.zeros(dim, numpy.uint8) 
    783 ValueError: negative dimensions are not allowed 
    784  
    785 Error processing trigger "atom coords updated": 
    786 ValueError: negative dimensions are not allowed 
    787  
    788 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    789 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    790 _generate_data_array 
    791 data = numpy.zeros(dim, numpy.uint8) 
    792  
    793 See log for complete Python traceback. 
    794  
    795 Traceback (most recent call last): 
    796 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    797 packages/chimerax/core/triggerset.py", line 130, in invoke 
    798 return self._func(self._name, data) 
    799 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    800 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    801 self.set_surface_mask() 
    802 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    803 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    804 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    805 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    806 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    807 self._update_mask() 
    808 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    809 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    810 step=self.grid_step, pad=self.pad) 
    811 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    812 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    813 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    814 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    815 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    816 _generate_data_array 
    817 data = numpy.zeros(dim, numpy.uint8) 
    818 ValueError: negative dimensions are not allowed 
    819  
    820 Error processing trigger "atom coords updated": 
    821 ValueError: negative dimensions are not allowed 
    822  
    823 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    824 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    825 _generate_data_array 
    826 data = numpy.zeros(dim, numpy.uint8) 
    827  
    828 See log for complete Python traceback. 
    829  
    830 Traceback (most recent call last): 
    831 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    832 packages/chimerax/core/triggerset.py", line 130, in invoke 
    833 return self._func(self._name, data) 
    834 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    835 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    836 self.set_surface_mask() 
    837 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    838 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    839 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    840 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    841 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    842 self._update_mask() 
    843 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    844 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    845 step=self.grid_step, pad=self.pad) 
    846 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    847 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    848 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    849 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    850 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    851 _generate_data_array 
    852 data = numpy.zeros(dim, numpy.uint8) 
    853 ValueError: negative dimensions are not allowed 
    854  
    855 Error processing trigger "atom coords updated": 
    856 ValueError: negative dimensions are not allowed 
    857  
    858 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    859 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    860 _generate_data_array 
    861 data = numpy.zeros(dim, numpy.uint8) 
    862  
    863 See log for complete Python traceback. 
    864  
    865 Traceback (most recent call last): 
    866 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    867 packages/chimerax/core/triggerset.py", line 130, in invoke 
    868 return self._func(self._name, data) 
    869 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    870 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    871 self.set_surface_mask() 
    872 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    873 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    874 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    875 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    876 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    877 self._update_mask() 
    878 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    879 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    880 step=self.grid_step, pad=self.pad) 
    881 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    882 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    883 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    884 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    885 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    886 _generate_data_array 
    887 data = numpy.zeros(dim, numpy.uint8) 
    888 ValueError: negative dimensions are not allowed 
    889  
    890 Error processing trigger "atom coords updated": 
    891 ValueError: negative dimensions are not allowed 
    892  
    893 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    894 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    895 _generate_data_array 
    896 data = numpy.zeros(dim, numpy.uint8) 
    897  
    898 See log for complete Python traceback. 
    899  
    900 Traceback (most recent call last): 
    901 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    902 packages/chimerax/core/triggerset.py", line 130, in invoke 
    903 return self._func(self._name, data) 
    904 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    905 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    906 self.set_surface_mask() 
    907 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    908 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    909 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    910 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    911 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    912 self._update_mask() 
    913 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    914 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    915 step=self.grid_step, pad=self.pad) 
    916 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    917 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    918 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    919 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    920 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    921 _generate_data_array 
    922 data = numpy.zeros(dim, numpy.uint8) 
    923 ValueError: negative dimensions are not allowed 
    924  
    925 Error processing trigger "atom coords updated": 
    926 ValueError: negative dimensions are not allowed 
    927  
    928 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    929 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    930 _generate_data_array 
    931 data = numpy.zeros(dim, numpy.uint8) 
    932  
    933 See log for complete Python traceback. 
    934  
    935 Traceback (most recent call last): 
    936 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    937 packages/chimerax/core/triggerset.py", line 130, in invoke 
    938 return self._func(self._name, data) 
    939 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    940 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    941 self.set_surface_mask() 
    942 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    943 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    944 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    945 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    946 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    947 self._update_mask() 
    948 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    949 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    950 step=self.grid_step, pad=self.pad) 
    951 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    952 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    953 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    954 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    955 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    956 _generate_data_array 
    957 data = numpy.zeros(dim, numpy.uint8) 
    958 ValueError: negative dimensions are not allowed 
    959  
    960 Error processing trigger "atom coords updated": 
    961 ValueError: negative dimensions are not allowed 
    962  
    963 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    964 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    965 _generate_data_array 
    966 data = numpy.zeros(dim, numpy.uint8) 
    967  
    968 See log for complete Python traceback. 
    969  
    970 Traceback (most recent call last): 
    971 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    972 packages/chimerax/core/triggerset.py", line 130, in invoke 
    973 return self._func(self._name, data) 
    974 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    975 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    976 self.set_surface_mask() 
    977 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    978 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    979 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    980 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    981 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    982 self._update_mask() 
    983 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    984 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    985 step=self.grid_step, pad=self.pad) 
    986 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    987 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    988 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    989 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    990 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    991 _generate_data_array 
    992 data = numpy.zeros(dim, numpy.uint8) 
    993 ValueError: negative dimensions are not allowed 
    994  
    995 Error processing trigger "atom coords updated": 
    996 ValueError: negative dimensions are not allowed 
    997  
    998 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    999 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    1000 _generate_data_array 
    1001 data = numpy.zeros(dim, numpy.uint8) 
    1002  
    1003 See log for complete Python traceback. 
    1004  
    1005 Traceback (most recent call last): 
    1006 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    1007 packages/chimerax/core/triggerset.py", line 130, in invoke 
    1008 return self._func(self._name, data) 
    1009 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1010 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    1011 self.set_surface_mask() 
    1012 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1013 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    1014 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    1015 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1016 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    1017 self._update_mask() 
    1018 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1019 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    1020 step=self.grid_step, pad=self.pad) 
    1021 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1022 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    1023 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    1024 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1025 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    1026 _generate_data_array 
    1027 data = numpy.zeros(dim, numpy.uint8) 
    1028 ValueError: negative dimensions are not allowed 
    1029  
    1030 Error processing trigger "atom coords updated": 
    1031 ValueError: negative dimensions are not allowed 
    1032  
    1033 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1034 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    1035 _generate_data_array 
    1036 data = numpy.zeros(dim, numpy.uint8) 
    1037  
    1038 See log for complete Python traceback. 
    1039  
    1040 Traceback (most recent call last): 
    1041 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    1042 packages/chimerax/core/triggerset.py", line 130, in invoke 
    1043 return self._func(self._name, data) 
    1044 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1045 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    1046 self.set_surface_mask() 
    1047 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1048 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    1049 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    1050 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1051 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    1052 self._update_mask() 
    1053 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1054 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    1055 step=self.grid_step, pad=self.pad) 
    1056 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1057 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    1058 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    1059 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1060 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    1061 _generate_data_array 
    1062 data = numpy.zeros(dim, numpy.uint8) 
    1063 ValueError: negative dimensions are not allowed 
    1064  
    1065 Error processing trigger "atom coords updated": 
    1066 ValueError: negative dimensions are not allowed 
    1067  
    1068 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1069 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    1070 _generate_data_array 
    1071 data = numpy.zeros(dim, numpy.uint8) 
    1072  
    1073 See log for complete Python traceback. 
    1074  
    1075 Traceback (most recent call last): 
    1076 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    1077 packages/chimerax/core/triggerset.py", line 130, in invoke 
    1078 return self._func(self._name, data) 
    1079 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1080 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    1081 self.set_surface_mask() 
    1082 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1083 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    1084 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    1085 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1086 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    1087 self._update_mask() 
    1088 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1089 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    1090 step=self.grid_step, pad=self.pad) 
    1091 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1092 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    1093 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    1094 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1095 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    1096 _generate_data_array 
    1097 data = numpy.zeros(dim, numpy.uint8) 
    1098 ValueError: negative dimensions are not allowed 
    1099  
    1100 Error processing trigger "atom coords updated": 
    1101 ValueError: negative dimensions are not allowed 
    1102  
    1103 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1104 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    1105 _generate_data_array 
    1106 data = numpy.zeros(dim, numpy.uint8) 
    1107  
    1108 See log for complete Python traceback. 
    1109  
    1110 Traceback (most recent call last): 
    1111 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    1112 packages/chimerax/core/triggerset.py", line 130, in invoke 
    1113 return self._func(self._name, data) 
    1114 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1115 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    1116 self.set_surface_mask() 
    1117 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1118 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    1119 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    1120 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1121 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    1122 self._update_mask() 
    1123 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1124 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    1125 step=self.grid_step, pad=self.pad) 
    1126 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1127 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    1128 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    1129 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1130 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    1131 _generate_data_array 
    1132 data = numpy.zeros(dim, numpy.uint8) 
    1133 ValueError: negative dimensions are not allowed 
    1134  
    1135 Error processing trigger "atom coords updated": 
    1136 ValueError: negative dimensions are not allowed 
    1137  
    1138 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1139 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    1140 _generate_data_array 
    1141 data = numpy.zeros(dim, numpy.uint8) 
    1142  
    1143 See log for complete Python traceback. 
    1144  
    1145 Traceback (most recent call last): 
    1146 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    1147 packages/chimerax/core/triggerset.py", line 130, in invoke 
    1148 return self._func(self._name, data) 
    1149 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1150 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    1151 self.set_surface_mask() 
    1152 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1153 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    1154 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    1155 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1156 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    1157 self._update_mask() 
    1158 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1159 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    1160 step=self.grid_step, pad=self.pad) 
    1161 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1162 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    1163 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    1164 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1165 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    1166 _generate_data_array 
    1167 data = numpy.zeros(dim, numpy.uint8) 
    1168 ValueError: negative dimensions are not allowed 
    1169  
    1170 Error processing trigger "atom coords updated": 
    1171 ValueError: negative dimensions are not allowed 
    1172  
    1173 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1174 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    1175 _generate_data_array 
    1176 data = numpy.zeros(dim, numpy.uint8) 
    1177  
    1178 See log for complete Python traceback. 
    1179  
    1180 Traceback (most recent call last): 
    1181 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    1182 packages/chimerax/core/triggerset.py", line 130, in invoke 
    1183 return self._func(self._name, data) 
    1184 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1185 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    1186 self.set_surface_mask() 
    1187 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1188 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    1189 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    1190 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1191 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    1192 self._update_mask() 
    1193 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1194 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    1195 step=self.grid_step, pad=self.pad) 
    1196 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1197 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    1198 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    1199 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1200 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    1201 _generate_data_array 
    1202 data = numpy.zeros(dim, numpy.uint8) 
    1203 ValueError: negative dimensions are not allowed 
    1204  
    1205 Error processing trigger "atom coords updated": 
    1206 ValueError: negative dimensions are not allowed 
    1207  
    1208 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1209 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    1210 _generate_data_array 
    1211 data = numpy.zeros(dim, numpy.uint8) 
    1212  
    1213 See log for complete Python traceback. 
    1214  
    1215 Traceback (most recent call last): 
    1216 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    1217 packages/chimerax/core/triggerset.py", line 130, in invoke 
    1218 return self._func(self._name, data) 
    1219 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1220 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    1221 self.set_surface_mask() 
    1222 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1223 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    1224 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    1225 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1226 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    1227 self._update_mask() 
    1228 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1229 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    1230 step=self.grid_step, pad=self.pad) 
    1231 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1232 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    1233 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    1234 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1235 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    1236 _generate_data_array 
    1237 data = numpy.zeros(dim, numpy.uint8) 
    1238 ValueError: negative dimensions are not allowed 
    1239  
    1240 Error processing trigger "atom coords updated": 
    1241 ValueError: negative dimensions are not allowed 
    1242  
    1243 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1244 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    1245 _generate_data_array 
    1246 data = numpy.zeros(dim, numpy.uint8) 
    1247  
    1248 See log for complete Python traceback. 
    1249  
    1250 Traceback (most recent call last): 
    1251 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    1252 packages/chimerax/core/triggerset.py", line 130, in invoke 
    1253 return self._func(self._name, data) 
    1254 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1255 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    1256 self.set_surface_mask() 
    1257 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1258 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    1259 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    1260 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1261 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    1262 self._update_mask() 
    1263 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1264 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    1265 step=self.grid_step, pad=self.pad) 
    1266 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1267 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    1268 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    1269 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1270 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    1271 _generate_data_array 
    1272 data = numpy.zeros(dim, numpy.uint8) 
    1273 ValueError: negative dimensions are not allowed 
    1274  
    1275 Error processing trigger "atom coords updated": 
    1276 ValueError: negative dimensions are not allowed 
    1277  
    1278 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1279 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    1280 _generate_data_array 
    1281 data = numpy.zeros(dim, numpy.uint8) 
    1282  
    1283 See log for complete Python traceback. 
    1284  
    1285 Traceback (most recent call last): 
    1286 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    1287 packages/chimerax/core/triggerset.py", line 130, in invoke 
    1288 return self._func(self._name, data) 
    1289 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1290 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    1291 self.set_surface_mask() 
    1292 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1293 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    1294 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    1295 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1296 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    1297 self._update_mask() 
    1298 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1299 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    1300 step=self.grid_step, pad=self.pad) 
    1301 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1302 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    1303 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    1304 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1305 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    1306 _generate_data_array 
    1307 data = numpy.zeros(dim, numpy.uint8) 
    1308 ValueError: negative dimensions are not allowed 
    1309  
    1310 Error processing trigger "atom coords updated": 
    1311 ValueError: negative dimensions are not allowed 
    1312  
    1313 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1314 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    1315 _generate_data_array 
    1316 data = numpy.zeros(dim, numpy.uint8) 
    1317  
    1318 See log for complete Python traceback. 
    1319  
    1320 Traceback (most recent call last): 
    1321 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    1322 packages/chimerax/core/triggerset.py", line 130, in invoke 
    1323 return self._func(self._name, data) 
    1324 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1325 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    1326 self.set_surface_mask() 
    1327 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1328 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    1329 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    1330 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1331 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    1332 self._update_mask() 
    1333 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1334 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    1335 step=self.grid_step, pad=self.pad) 
    1336 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1337 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    1338 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    1339 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1340 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    1341 _generate_data_array 
    1342 data = numpy.zeros(dim, numpy.uint8) 
    1343 ValueError: negative dimensions are not allowed 
    1344  
    1345 Error processing trigger "atom coords updated": 
    1346 ValueError: negative dimensions are not allowed 
    1347  
    1348 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1349 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    1350 _generate_data_array 
    1351 data = numpy.zeros(dim, numpy.uint8) 
    1352  
    1353 See log for complete Python traceback. 
    1354  
    1355 Traceback (most recent call last): 
    1356 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    1357 packages/chimerax/core/triggerset.py", line 130, in invoke 
    1358 return self._func(self._name, data) 
    1359 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1360 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    1361 self.set_surface_mask() 
    1362 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1363 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    1364 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    1365 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1366 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    1367 self._update_mask() 
    1368 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1369 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    1370 step=self.grid_step, pad=self.pad) 
    1371 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1372 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    1373 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    1374 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1375 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    1376 _generate_data_array 
    1377 data = numpy.zeros(dim, numpy.uint8) 
    1378 ValueError: negative dimensions are not allowed 
    1379  
    1380 Error processing trigger "atom coords updated": 
    1381 ValueError: negative dimensions are not allowed 
    1382  
    1383 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1384 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    1385 _generate_data_array 
    1386 data = numpy.zeros(dim, numpy.uint8) 
    1387  
    1388 See log for complete Python traceback. 
    1389  
    1390 Traceback (most recent call last): 
    1391 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    1392 packages/chimerax/core/triggerset.py", line 130, in invoke 
    1393 return self._func(self._name, data) 
    1394 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1395 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    1396 self.set_surface_mask() 
    1397 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1398 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    1399 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    1400 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1401 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    1402 self._update_mask() 
    1403 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1404 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    1405 step=self.grid_step, pad=self.pad) 
    1406 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1407 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    1408 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    1409 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1410 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    1411 _generate_data_array 
    1412 data = numpy.zeros(dim, numpy.uint8) 
    1413 ValueError: negative dimensions are not allowed 
    1414  
    1415 Error processing trigger "atom coords updated": 
    1416 ValueError: negative dimensions are not allowed 
    1417  
    1418 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1419 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    1420 _generate_data_array 
    1421 data = numpy.zeros(dim, numpy.uint8) 
    1422  
    1423 See log for complete Python traceback. 
    1424  
    1425 Traceback (most recent call last): 
    1426 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    1427 packages/chimerax/core/triggerset.py", line 130, in invoke 
    1428 return self._func(self._name, data) 
    1429 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1430 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    1431 self.set_surface_mask() 
    1432 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1433 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    1434 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    1435 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1436 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    1437 self._update_mask() 
    1438 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1439 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    1440 step=self.grid_step, pad=self.pad) 
    1441 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1442 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    1443 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    1444 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1445 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    1446 _generate_data_array 
    1447 data = numpy.zeros(dim, numpy.uint8) 
    1448 ValueError: negative dimensions are not allowed 
    1449  
    1450 Error processing trigger "atom coords updated": 
    1451 ValueError: negative dimensions are not allowed 
    1452  
    1453 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1454 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    1455 _generate_data_array 
    1456 data = numpy.zeros(dim, numpy.uint8) 
    1457  
    1458 See log for complete Python traceback. 
    1459  
    1460 Traceback (most recent call last): 
    1461 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    1462 packages/chimerax/core/triggerset.py", line 130, in invoke 
    1463 return self._func(self._name, data) 
    1464 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1465 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    1466 self.set_surface_mask() 
    1467 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1468 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    1469 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    1470 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1471 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    1472 self._update_mask() 
    1473 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1474 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    1475 step=self.grid_step, pad=self.pad) 
    1476 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1477 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    1478 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    1479 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1480 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    1481 _generate_data_array 
    1482 data = numpy.zeros(dim, numpy.uint8) 
    1483 ValueError: negative dimensions are not allowed 
    1484  
    1485 Error processing trigger "atom coords updated": 
    1486 ValueError: negative dimensions are not allowed 
    1487  
    1488 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1489 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    1490 _generate_data_array 
    1491 data = numpy.zeros(dim, numpy.uint8) 
    1492  
    1493 See log for complete Python traceback. 
    1494  
    1495 Traceback (most recent call last): 
    1496 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    1497 packages/chimerax/core/triggerset.py", line 130, in invoke 
    1498 return self._func(self._name, data) 
    1499 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1500 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    1501 self.set_surface_mask() 
    1502 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1503 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    1504 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    1505 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1506 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    1507 self._update_mask() 
    1508 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1509 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    1510 step=self.grid_step, pad=self.pad) 
    1511 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1512 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    1513 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    1514 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1515 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    1516 _generate_data_array 
    1517 data = numpy.zeros(dim, numpy.uint8) 
    1518 ValueError: negative dimensions are not allowed 
    1519  
    1520 Error processing trigger "atom coords updated": 
    1521 ValueError: negative dimensions are not allowed 
    1522  
    1523 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1524 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    1525 _generate_data_array 
    1526 data = numpy.zeros(dim, numpy.uint8) 
    1527  
    1528 See log for complete Python traceback. 
    1529  
    1530 Traceback (most recent call last): 
    1531 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    1532 packages/chimerax/core/triggerset.py", line 130, in invoke 
    1533 return self._func(self._name, data) 
    1534 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1535 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    1536 self.set_surface_mask() 
    1537 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1538 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    1539 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    1540 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1541 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    1542 self._update_mask() 
    1543 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1544 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    1545 step=self.grid_step, pad=self.pad) 
    1546 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1547 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    1548 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    1549 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1550 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    1551 _generate_data_array 
    1552 data = numpy.zeros(dim, numpy.uint8) 
    1553 ValueError: negative dimensions are not allowed 
    1554  
    1555 Error processing trigger "atom coords updated": 
    1556 ValueError: negative dimensions are not allowed 
    1557  
    1558 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1559 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    1560 _generate_data_array 
    1561 data = numpy.zeros(dim, numpy.uint8) 
    1562  
    1563 See log for complete Python traceback. 
    1564  
    1565 Traceback (most recent call last): 
    1566 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    1567 packages/chimerax/core/triggerset.py", line 130, in invoke 
    1568 return self._func(self._name, data) 
    1569 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1570 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    1571 self.set_surface_mask() 
    1572 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1573 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    1574 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    1575 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1576 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    1577 self._update_mask() 
    1578 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1579 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    1580 step=self.grid_step, pad=self.pad) 
    1581 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1582 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    1583 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    1584 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1585 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    1586 _generate_data_array 
    1587 data = numpy.zeros(dim, numpy.uint8) 
    1588 ValueError: negative dimensions are not allowed 
    1589  
    1590 Error processing trigger "atom coords updated": 
    1591 ValueError: negative dimensions are not allowed 
    1592  
    1593 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1594 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    1595 _generate_data_array 
    1596 data = numpy.zeros(dim, numpy.uint8) 
    1597  
    1598 See log for complete Python traceback. 
    1599  
    1600 Traceback (most recent call last): 
    1601 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    1602 packages/chimerax/core/triggerset.py", line 130, in invoke 
    1603 return self._func(self._name, data) 
    1604 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1605 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    1606 self.set_surface_mask() 
    1607 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1608 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    1609 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    1610 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1611 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    1612 self._update_mask() 
    1613 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1614 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    1615 step=self.grid_step, pad=self.pad) 
    1616 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1617 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    1618 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    1619 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1620 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    1621 _generate_data_array 
    1622 data = numpy.zeros(dim, numpy.uint8) 
    1623 ValueError: negative dimensions are not allowed 
    1624  
    1625 Error processing trigger "atom coords updated": 
    1626 ValueError: negative dimensions are not allowed 
    1627  
    1628 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1629 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    1630 _generate_data_array 
    1631 data = numpy.zeros(dim, numpy.uint8) 
    1632  
    1633 See log for complete Python traceback. 
    1634  
    1635 Traceback (most recent call last): 
    1636 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    1637 packages/chimerax/core/triggerset.py", line 130, in invoke 
    1638 return self._func(self._name, data) 
    1639 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1640 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    1641 self.set_surface_mask() 
    1642 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1643 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    1644 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    1645 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1646 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    1647 self._update_mask() 
    1648 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1649 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    1650 step=self.grid_step, pad=self.pad) 
    1651 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1652 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    1653 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    1654 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1655 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    1656 _generate_data_array 
    1657 data = numpy.zeros(dim, numpy.uint8) 
    1658 ValueError: negative dimensions are not allowed 
    1659  
    1660 Error processing trigger "atom coords updated": 
    1661 ValueError: negative dimensions are not allowed 
    1662  
    1663 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1664 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    1665 _generate_data_array 
    1666 data = numpy.zeros(dim, numpy.uint8) 
    1667  
    1668 See log for complete Python traceback. 
    1669  
    1670 Traceback (most recent call last): 
    1671 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    1672 packages/chimerax/core/triggerset.py", line 130, in invoke 
    1673 return self._func(self._name, data) 
    1674 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1675 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    1676 self.set_surface_mask() 
    1677 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1678 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    1679 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    1680 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1681 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    1682 self._update_mask() 
    1683 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1684 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    1685 step=self.grid_step, pad=self.pad) 
    1686 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1687 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    1688 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    1689 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1690 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    1691 _generate_data_array 
    1692 data = numpy.zeros(dim, numpy.uint8) 
    1693 ValueError: negative dimensions are not allowed 
    1694  
    1695 Error processing trigger "atom coords updated": 
    1696 ValueError: negative dimensions are not allowed 
    1697  
    1698 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1699 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    1700 _generate_data_array 
    1701 data = numpy.zeros(dim, numpy.uint8) 
    1702  
    1703 See log for complete Python traceback. 
    1704  
    1705 Traceback (most recent call last): 
    1706 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    1707 packages/chimerax/core/triggerset.py", line 130, in invoke 
    1708 return self._func(self._name, data) 
    1709 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1710 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    1711 self.set_surface_mask() 
    1712 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1713 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    1714 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    1715 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1716 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    1717 self._update_mask() 
    1718 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1719 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    1720 step=self.grid_step, pad=self.pad) 
    1721 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1722 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    1723 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    1724 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1725 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    1726 _generate_data_array 
    1727 data = numpy.zeros(dim, numpy.uint8) 
    1728 ValueError: negative dimensions are not allowed 
    1729  
    1730 Error processing trigger "atom coords updated": 
    1731 ValueError: negative dimensions are not allowed 
    1732  
    1733 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1734 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    1735 _generate_data_array 
    1736 data = numpy.zeros(dim, numpy.uint8) 
    1737  
    1738 See log for complete Python traceback. 
    1739  
    1740 Traceback (most recent call last): 
    1741 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    1742 packages/chimerax/core/triggerset.py", line 130, in invoke 
    1743 return self._func(self._name, data) 
    1744 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1745 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    1746 self.set_surface_mask() 
    1747 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1748 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    1749 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    1750 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1751 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    1752 self._update_mask() 
    1753 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1754 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    1755 step=self.grid_step, pad=self.pad) 
    1756 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1757 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    1758 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    1759 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1760 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    1761 _generate_data_array 
    1762 data = numpy.zeros(dim, numpy.uint8) 
    1763 ValueError: negative dimensions are not allowed 
    1764  
    1765 Error processing trigger "atom coords updated": 
    1766 ValueError: negative dimensions are not allowed 
    1767  
    1768 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1769 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    1770 _generate_data_array 
    1771 data = numpy.zeros(dim, numpy.uint8) 
    1772  
    1773 See log for complete Python traceback. 
    1774  
    1775 Traceback (most recent call last): 
    1776 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    1777 packages/chimerax/core/triggerset.py", line 130, in invoke 
    1778 return self._func(self._name, data) 
    1779 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1780 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    1781 self.set_surface_mask() 
    1782 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1783 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    1784 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    1785 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1786 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    1787 self._update_mask() 
    1788 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1789 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    1790 step=self.grid_step, pad=self.pad) 
    1791 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1792 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    1793 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    1794 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1795 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    1796 _generate_data_array 
    1797 data = numpy.zeros(dim, numpy.uint8) 
    1798 ValueError: negative dimensions are not allowed 
    1799  
    1800 Error processing trigger "atom coords updated": 
    1801 ValueError: negative dimensions are not allowed 
    1802  
    1803 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1804 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    1805 _generate_data_array 
    1806 data = numpy.zeros(dim, numpy.uint8) 
    1807  
    1808 See log for complete Python traceback. 
    1809  
    1810 Traceback (most recent call last): 
    1811 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    1812 packages/chimerax/core/triggerset.py", line 130, in invoke 
    1813 return self._func(self._name, data) 
    1814 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1815 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    1816 self.set_surface_mask() 
    1817 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1818 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    1819 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    1820 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1821 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    1822 self._update_mask() 
    1823 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1824 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    1825 step=self.grid_step, pad=self.pad) 
    1826 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1827 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    1828 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    1829 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1830 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    1831 _generate_data_array 
    1832 data = numpy.zeros(dim, numpy.uint8) 
    1833 ValueError: negative dimensions are not allowed 
    1834  
    1835 Error processing trigger "atom coords updated": 
    1836 ValueError: negative dimensions are not allowed 
    1837  
    1838 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1839 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    1840 _generate_data_array 
    1841 data = numpy.zeros(dim, numpy.uint8) 
    1842  
    1843 See log for complete Python traceback. 
    1844  
    1845 Traceback (most recent call last): 
    1846 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    1847 packages/chimerax/core/triggerset.py", line 130, in invoke 
    1848 return self._func(self._name, data) 
    1849 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1850 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    1851 self.set_surface_mask() 
    1852 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1853 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    1854 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    1855 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1856 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    1857 self._update_mask() 
    1858 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1859 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    1860 step=self.grid_step, pad=self.pad) 
    1861 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1862 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    1863 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    1864 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1865 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    1866 _generate_data_array 
    1867 data = numpy.zeros(dim, numpy.uint8) 
    1868 ValueError: negative dimensions are not allowed 
    1869  
    1870 Error processing trigger "atom coords updated": 
    1871 ValueError: negative dimensions are not allowed 
    1872  
    1873 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1874 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    1875 _generate_data_array 
    1876 data = numpy.zeros(dim, numpy.uint8) 
    1877  
    1878 See log for complete Python traceback. 
    1879  
    1880 Traceback (most recent call last): 
    1881 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    1882 packages/chimerax/core/triggerset.py", line 130, in invoke 
    1883 return self._func(self._name, data) 
    1884 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1885 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    1886 self.set_surface_mask() 
    1887 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1888 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    1889 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    1890 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1891 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    1892 self._update_mask() 
    1893 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1894 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    1895 step=self.grid_step, pad=self.pad) 
    1896 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1897 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    1898 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    1899 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1900 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    1901 _generate_data_array 
    1902 data = numpy.zeros(dim, numpy.uint8) 
    1903 ValueError: negative dimensions are not allowed 
    1904  
    1905 Error processing trigger "atom coords updated": 
    1906 ValueError: negative dimensions are not allowed 
    1907  
    1908 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1909 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    1910 _generate_data_array 
    1911 data = numpy.zeros(dim, numpy.uint8) 
    1912  
    1913 See log for complete Python traceback. 
    1914  
    1915 Traceback (most recent call last): 
    1916 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    1917 packages/chimerax/core/triggerset.py", line 130, in invoke 
    1918 return self._func(self._name, data) 
    1919 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1920 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    1921 self.set_surface_mask() 
    1922 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1923 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    1924 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    1925 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1926 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    1927 self._update_mask() 
    1928 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1929 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    1930 step=self.grid_step, pad=self.pad) 
    1931 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1932 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    1933 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    1934 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1935 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    1936 _generate_data_array 
    1937 data = numpy.zeros(dim, numpy.uint8) 
    1938 ValueError: negative dimensions are not allowed 
    1939  
    1940 Error processing trigger "atom coords updated": 
    1941 ValueError: negative dimensions are not allowed 
    1942  
    1943 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1944 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    1945 _generate_data_array 
    1946 data = numpy.zeros(dim, numpy.uint8) 
    1947  
    1948 See log for complete Python traceback. 
    1949  
    1950 Traceback (most recent call last): 
    1951 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    1952 packages/chimerax/core/triggerset.py", line 130, in invoke 
    1953 return self._func(self._name, data) 
    1954 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1955 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    1956 self.set_surface_mask() 
    1957 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1958 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    1959 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    1960 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1961 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    1962 self._update_mask() 
    1963 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1964 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    1965 step=self.grid_step, pad=self.pad) 
    1966 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1967 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    1968 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    1969 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1970 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    1971 _generate_data_array 
    1972 data = numpy.zeros(dim, numpy.uint8) 
    1973 ValueError: negative dimensions are not allowed 
    1974  
    1975 Error processing trigger "atom coords updated": 
    1976 ValueError: negative dimensions are not allowed 
    1977  
    1978 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1979 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    1980 _generate_data_array 
    1981 data = numpy.zeros(dim, numpy.uint8) 
    1982  
    1983 See log for complete Python traceback. 
    1984  
    1985 Traceback (most recent call last): 
    1986 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    1987 packages/chimerax/core/triggerset.py", line 130, in invoke 
    1988 return self._func(self._name, data) 
    1989 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1990 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    1991 self.set_surface_mask() 
    1992 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1993 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    1994 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    1995 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1996 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    1997 self._update_mask() 
    1998 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    1999 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    2000 step=self.grid_step, pad=self.pad) 
    2001 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2002 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    2003 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    2004 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2005 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    2006 _generate_data_array 
    2007 data = numpy.zeros(dim, numpy.uint8) 
    2008 ValueError: negative dimensions are not allowed 
    2009  
    2010 Error processing trigger "atom coords updated": 
    2011 ValueError: negative dimensions are not allowed 
    2012  
    2013 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2014 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    2015 _generate_data_array 
    2016 data = numpy.zeros(dim, numpy.uint8) 
    2017  
    2018 See log for complete Python traceback. 
    2019  
    2020 Traceback (most recent call last): 
    2021 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    2022 packages/chimerax/core/triggerset.py", line 130, in invoke 
    2023 return self._func(self._name, data) 
    2024 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2025 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    2026 self.set_surface_mask() 
    2027 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2028 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    2029 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    2030 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2031 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    2032 self._update_mask() 
    2033 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2034 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    2035 step=self.grid_step, pad=self.pad) 
    2036 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2037 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    2038 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    2039 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2040 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    2041 _generate_data_array 
    2042 data = numpy.zeros(dim, numpy.uint8) 
    2043 ValueError: negative dimensions are not allowed 
    2044  
    2045 Error processing trigger "atom coords updated": 
    2046 ValueError: negative dimensions are not allowed 
    2047  
    2048 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2049 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    2050 _generate_data_array 
    2051 data = numpy.zeros(dim, numpy.uint8) 
    2052  
    2053 See log for complete Python traceback. 
    2054  
    2055 Traceback (most recent call last): 
    2056 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    2057 packages/chimerax/core/triggerset.py", line 130, in invoke 
    2058 return self._func(self._name, data) 
    2059 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2060 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    2061 self.set_surface_mask() 
    2062 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2063 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    2064 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    2065 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2066 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    2067 self._update_mask() 
    2068 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2069 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    2070 step=self.grid_step, pad=self.pad) 
    2071 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2072 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    2073 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    2074 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2075 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    2076 _generate_data_array 
    2077 data = numpy.zeros(dim, numpy.uint8) 
    2078 ValueError: negative dimensions are not allowed 
    2079  
    2080 Error processing trigger "atom coords updated": 
    2081 ValueError: negative dimensions are not allowed 
    2082  
    2083 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2084 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    2085 _generate_data_array 
    2086 data = numpy.zeros(dim, numpy.uint8) 
    2087  
    2088 See log for complete Python traceback. 
    2089  
    2090 Traceback (most recent call last): 
    2091 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    2092 packages/chimerax/core/triggerset.py", line 130, in invoke 
    2093 return self._func(self._name, data) 
    2094 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2095 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    2096 self.set_surface_mask() 
    2097 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2098 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    2099 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    2100 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2101 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    2102 self._update_mask() 
    2103 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2104 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    2105 step=self.grid_step, pad=self.pad) 
    2106 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2107 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    2108 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    2109 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2110 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    2111 _generate_data_array 
    2112 data = numpy.zeros(dim, numpy.uint8) 
    2113 ValueError: negative dimensions are not allowed 
    2114  
    2115 Error processing trigger "atom coords updated": 
    2116 ValueError: negative dimensions are not allowed 
    2117  
    2118 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2119 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    2120 _generate_data_array 
    2121 data = numpy.zeros(dim, numpy.uint8) 
    2122  
    2123 See log for complete Python traceback. 
    2124  
    2125 Traceback (most recent call last): 
    2126 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    2127 packages/chimerax/core/triggerset.py", line 130, in invoke 
    2128 return self._func(self._name, data) 
    2129 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2130 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    2131 self.set_surface_mask() 
    2132 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2133 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    2134 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    2135 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2136 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    2137 self._update_mask() 
    2138 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2139 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    2140 step=self.grid_step, pad=self.pad) 
    2141 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2142 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    2143 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    2144 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2145 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    2146 _generate_data_array 
    2147 data = numpy.zeros(dim, numpy.uint8) 
    2148 ValueError: negative dimensions are not allowed 
    2149  
    2150 Error processing trigger "atom coords updated": 
    2151 ValueError: negative dimensions are not allowed 
    2152  
    2153 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2154 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    2155 _generate_data_array 
    2156 data = numpy.zeros(dim, numpy.uint8) 
    2157  
    2158 See log for complete Python traceback. 
    2159  
    2160 Traceback (most recent call last): 
    2161 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    2162 packages/chimerax/core/triggerset.py", line 130, in invoke 
    2163 return self._func(self._name, data) 
    2164 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2165 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    2166 self.set_surface_mask() 
    2167 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2168 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    2169 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    2170 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2171 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    2172 self._update_mask() 
    2173 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2174 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    2175 step=self.grid_step, pad=self.pad) 
    2176 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2177 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    2178 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    2179 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2180 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    2181 _generate_data_array 
    2182 data = numpy.zeros(dim, numpy.uint8) 
    2183 ValueError: negative dimensions are not allowed 
    2184  
    2185 Error processing trigger "atom coords updated": 
    2186 ValueError: negative dimensions are not allowed 
    2187  
    2188 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2189 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    2190 _generate_data_array 
    2191 data = numpy.zeros(dim, numpy.uint8) 
    2192  
    2193 See log for complete Python traceback. 
    2194  
    2195 Traceback (most recent call last): 
    2196 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    2197 packages/chimerax/core/triggerset.py", line 130, in invoke 
    2198 return self._func(self._name, data) 
    2199 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2200 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    2201 self.set_surface_mask() 
    2202 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2203 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    2204 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    2205 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2206 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    2207 self._update_mask() 
    2208 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2209 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    2210 step=self.grid_step, pad=self.pad) 
    2211 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2212 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    2213 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    2214 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2215 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    2216 _generate_data_array 
    2217 data = numpy.zeros(dim, numpy.uint8) 
    2218 ValueError: negative dimensions are not allowed 
    2219  
    2220 Error processing trigger "atom coords updated": 
    2221 ValueError: negative dimensions are not allowed 
    2222  
    2223 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2224 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    2225 _generate_data_array 
    2226 data = numpy.zeros(dim, numpy.uint8) 
    2227  
    2228 See log for complete Python traceback. 
    2229  
    2230 Traceback (most recent call last): 
    2231 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    2232 packages/chimerax/core/triggerset.py", line 130, in invoke 
    2233 return self._func(self._name, data) 
    2234 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2235 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    2236 self.set_surface_mask() 
    2237 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2238 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    2239 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    2240 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2241 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    2242 self._update_mask() 
    2243 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2244 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    2245 step=self.grid_step, pad=self.pad) 
    2246 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2247 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    2248 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    2249 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2250 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    2251 _generate_data_array 
    2252 data = numpy.zeros(dim, numpy.uint8) 
    2253 ValueError: negative dimensions are not allowed 
    2254  
    2255 Error processing trigger "atom coords updated": 
    2256 ValueError: negative dimensions are not allowed 
    2257  
    2258 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2259 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    2260 _generate_data_array 
    2261 data = numpy.zeros(dim, numpy.uint8) 
    2262  
    2263 See log for complete Python traceback. 
    2264  
    2265 Traceback (most recent call last): 
    2266 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    2267 packages/chimerax/core/triggerset.py", line 130, in invoke 
    2268 return self._func(self._name, data) 
    2269 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2270 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    2271 self.set_surface_mask() 
    2272 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2273 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    2274 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    2275 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2276 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    2277 self._update_mask() 
    2278 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2279 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    2280 step=self.grid_step, pad=self.pad) 
    2281 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2282 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    2283 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    2284 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2285 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    2286 _generate_data_array 
    2287 data = numpy.zeros(dim, numpy.uint8) 
    2288 ValueError: negative dimensions are not allowed 
    2289  
    2290 Error processing trigger "atom coords updated": 
    2291 ValueError: negative dimensions are not allowed 
    2292  
    2293 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2294 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    2295 _generate_data_array 
    2296 data = numpy.zeros(dim, numpy.uint8) 
    2297  
    2298 See log for complete Python traceback. 
    2299  
    2300 Traceback (most recent call last): 
    2301 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    2302 packages/chimerax/core/triggerset.py", line 130, in invoke 
    2303 return self._func(self._name, data) 
    2304 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2305 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    2306 self.set_surface_mask() 
    2307 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2308 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    2309 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    2310 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2311 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    2312 self._update_mask() 
    2313 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2314 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    2315 step=self.grid_step, pad=self.pad) 
    2316 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2317 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    2318 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    2319 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2320 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    2321 _generate_data_array 
    2322 data = numpy.zeros(dim, numpy.uint8) 
    2323 ValueError: negative dimensions are not allowed 
    2324  
    2325 Error processing trigger "atom coords updated": 
    2326 ValueError: negative dimensions are not allowed 
    2327  
    2328 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2329 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    2330 _generate_data_array 
    2331 data = numpy.zeros(dim, numpy.uint8) 
    2332  
    2333 See log for complete Python traceback. 
    2334  
    2335 Traceback (most recent call last): 
    2336 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    2337 packages/chimerax/core/triggerset.py", line 130, in invoke 
    2338 return self._func(self._name, data) 
    2339 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2340 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    2341 self.set_surface_mask() 
    2342 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2343 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    2344 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    2345 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2346 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    2347 self._update_mask() 
    2348 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2349 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    2350 step=self.grid_step, pad=self.pad) 
    2351 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2352 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    2353 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    2354 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2355 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    2356 _generate_data_array 
    2357 data = numpy.zeros(dim, numpy.uint8) 
    2358 ValueError: negative dimensions are not allowed 
    2359  
    2360 Error processing trigger "atom coords updated": 
    2361 ValueError: negative dimensions are not allowed 
    2362  
    2363 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2364 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    2365 _generate_data_array 
    2366 data = numpy.zeros(dim, numpy.uint8) 
    2367  
    2368 See log for complete Python traceback. 
    2369  
    2370 Traceback (most recent call last): 
    2371 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    2372 packages/chimerax/core/triggerset.py", line 130, in invoke 
    2373 return self._func(self._name, data) 
    2374 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2375 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    2376 self.set_surface_mask() 
    2377 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2378 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    2379 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    2380 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2381 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    2382 self._update_mask() 
    2383 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2384 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    2385 step=self.grid_step, pad=self.pad) 
    2386 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2387 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    2388 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    2389 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2390 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    2391 _generate_data_array 
    2392 data = numpy.zeros(dim, numpy.uint8) 
    2393 ValueError: negative dimensions are not allowed 
    2394  
    2395 Error processing trigger "atom coords updated": 
    2396 ValueError: negative dimensions are not allowed 
    2397  
    2398 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2399 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    2400 _generate_data_array 
    2401 data = numpy.zeros(dim, numpy.uint8) 
    2402  
    2403 See log for complete Python traceback. 
    2404  
    2405 Traceback (most recent call last): 
    2406 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    2407 packages/chimerax/core/triggerset.py", line 130, in invoke 
    2408 return self._func(self._name, data) 
    2409 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2410 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    2411 self.set_surface_mask() 
    2412 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2413 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    2414 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    2415 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2416 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    2417 self._update_mask() 
    2418 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2419 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    2420 step=self.grid_step, pad=self.pad) 
    2421 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2422 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    2423 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    2424 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2425 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    2426 _generate_data_array 
    2427 data = numpy.zeros(dim, numpy.uint8) 
    2428 ValueError: negative dimensions are not allowed 
    2429  
    2430 Error processing trigger "atom coords updated": 
    2431 ValueError: negative dimensions are not allowed 
    2432  
    2433 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2434 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    2435 _generate_data_array 
    2436 data = numpy.zeros(dim, numpy.uint8) 
    2437  
    2438 See log for complete Python traceback. 
    2439  
    2440 Traceback (most recent call last): 
    2441 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    2442 packages/chimerax/core/triggerset.py", line 130, in invoke 
    2443 return self._func(self._name, data) 
    2444 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2445 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    2446 self.set_surface_mask() 
    2447 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2448 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    2449 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    2450 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2451 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    2452 self._update_mask() 
    2453 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2454 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    2455 step=self.grid_step, pad=self.pad) 
    2456 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2457 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    2458 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    2459 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2460 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    2461 _generate_data_array 
    2462 data = numpy.zeros(dim, numpy.uint8) 
    2463 ValueError: negative dimensions are not allowed 
    2464  
    2465 Error processing trigger "atom coords updated": 
    2466 ValueError: negative dimensions are not allowed 
    2467  
    2468 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2469 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    2470 _generate_data_array 
    2471 data = numpy.zeros(dim, numpy.uint8) 
    2472  
    2473 See log for complete Python traceback. 
    2474  
    2475 Traceback (most recent call last): 
    2476 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    2477 packages/chimerax/core/triggerset.py", line 130, in invoke 
    2478 return self._func(self._name, data) 
    2479 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2480 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    2481 self.set_surface_mask() 
    2482 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2483 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    2484 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    2485 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2486 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    2487 self._update_mask() 
    2488 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2489 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    2490 step=self.grid_step, pad=self.pad) 
    2491 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2492 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    2493 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    2494 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2495 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    2496 _generate_data_array 
    2497 data = numpy.zeros(dim, numpy.uint8) 
    2498 ValueError: negative dimensions are not allowed 
    2499  
    2500 Error processing trigger "atom coords updated": 
    2501 ValueError: negative dimensions are not allowed 
    2502  
    2503 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2504 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    2505 _generate_data_array 
    2506 data = numpy.zeros(dim, numpy.uint8) 
    2507  
    2508 See log for complete Python traceback. 
    2509  
    2510 Traceback (most recent call last): 
    2511 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    2512 packages/chimerax/core/triggerset.py", line 130, in invoke 
    2513 return self._func(self._name, data) 
    2514 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2515 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    2516 self.set_surface_mask() 
    2517 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2518 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    2519 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    2520 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2521 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    2522 self._update_mask() 
    2523 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2524 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    2525 step=self.grid_step, pad=self.pad) 
    2526 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2527 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    2528 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    2529 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2530 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    2531 _generate_data_array 
    2532 data = numpy.zeros(dim, numpy.uint8) 
    2533 ValueError: negative dimensions are not allowed 
    2534  
    2535 Error processing trigger "atom coords updated": 
    2536 ValueError: negative dimensions are not allowed 
    2537  
    2538 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2539 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    2540 _generate_data_array 
    2541 data = numpy.zeros(dim, numpy.uint8) 
    2542  
    2543 See log for complete Python traceback. 
    2544  
    2545 Traceback (most recent call last): 
    2546 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    2547 packages/chimerax/core/triggerset.py", line 130, in invoke 
    2548 return self._func(self._name, data) 
    2549 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2550 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    2551 self.set_surface_mask() 
    2552 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2553 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    2554 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    2555 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2556 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    2557 self._update_mask() 
    2558 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2559 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    2560 step=self.grid_step, pad=self.pad) 
    2561 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2562 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    2563 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    2564 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2565 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    2566 _generate_data_array 
    2567 data = numpy.zeros(dim, numpy.uint8) 
    2568 ValueError: negative dimensions are not allowed 
    2569  
    2570 Error processing trigger "atom coords updated": 
    2571 ValueError: negative dimensions are not allowed 
    2572  
    2573 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2574 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    2575 _generate_data_array 
    2576 data = numpy.zeros(dim, numpy.uint8) 
    2577  
    2578 See log for complete Python traceback. 
    2579  
    2580 Traceback (most recent call last): 
    2581 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    2582 packages/chimerax/core/triggerset.py", line 130, in invoke 
    2583 return self._func(self._name, data) 
    2584 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2585 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    2586 self.set_surface_mask() 
    2587 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2588 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    2589 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    2590 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2591 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    2592 self._update_mask() 
    2593 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2594 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    2595 step=self.grid_step, pad=self.pad) 
    2596 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2597 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    2598 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    2599 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2600 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    2601 _generate_data_array 
    2602 data = numpy.zeros(dim, numpy.uint8) 
    2603 ValueError: negative dimensions are not allowed 
    2604  
    2605 Error processing trigger "atom coords updated": 
    2606 ValueError: negative dimensions are not allowed 
    2607  
    2608 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2609 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    2610 _generate_data_array 
    2611 data = numpy.zeros(dim, numpy.uint8) 
    2612  
    2613 See log for complete Python traceback. 
    2614  
    2615 Traceback (most recent call last): 
    2616 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    2617 packages/chimerax/core/triggerset.py", line 130, in invoke 
    2618 return self._func(self._name, data) 
    2619 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2620 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    2621 self.set_surface_mask() 
    2622 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2623 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    2624 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    2625 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2626 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    2627 self._update_mask() 
    2628 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2629 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    2630 step=self.grid_step, pad=self.pad) 
    2631 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2632 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    2633 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    2634 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2635 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    2636 _generate_data_array 
    2637 data = numpy.zeros(dim, numpy.uint8) 
    2638 ValueError: negative dimensions are not allowed 
    2639  
    2640 Error processing trigger "atom coords updated": 
    2641 ValueError: negative dimensions are not allowed 
    2642  
    2643 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2644 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    2645 _generate_data_array 
    2646 data = numpy.zeros(dim, numpy.uint8) 
    2647  
    2648 See log for complete Python traceback. 
    2649  
    2650 Traceback (most recent call last): 
    2651 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    2652 packages/chimerax/core/triggerset.py", line 130, in invoke 
    2653 return self._func(self._name, data) 
    2654 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2655 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    2656 self.set_surface_mask() 
    2657 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2658 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    2659 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    2660 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2661 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    2662 self._update_mask() 
    2663 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2664 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    2665 step=self.grid_step, pad=self.pad) 
    2666 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2667 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    2668 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    2669 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2670 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    2671 _generate_data_array 
    2672 data = numpy.zeros(dim, numpy.uint8) 
    2673 ValueError: negative dimensions are not allowed 
    2674  
    2675 Error processing trigger "atom coords updated": 
    2676 ValueError: negative dimensions are not allowed 
    2677  
    2678 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2679 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    2680 _generate_data_array 
    2681 data = numpy.zeros(dim, numpy.uint8) 
    2682  
    2683 See log for complete Python traceback. 
    2684  
    2685 Traceback (most recent call last): 
    2686 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    2687 packages/chimerax/core/triggerset.py", line 130, in invoke 
    2688 return self._func(self._name, data) 
    2689 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2690 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    2691 self.set_surface_mask() 
    2692 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2693 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    2694 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    2695 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2696 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    2697 self._update_mask() 
    2698 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2699 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    2700 step=self.grid_step, pad=self.pad) 
    2701 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2702 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    2703 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    2704 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2705 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    2706 _generate_data_array 
    2707 data = numpy.zeros(dim, numpy.uint8) 
    2708 ValueError: negative dimensions are not allowed 
    2709  
    2710 Error processing trigger "atom coords updated": 
    2711 ValueError: negative dimensions are not allowed 
    2712  
    2713 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2714 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    2715 _generate_data_array 
    2716 data = numpy.zeros(dim, numpy.uint8) 
    2717  
    2718 See log for complete Python traceback. 
    2719  
    2720 Traceback (most recent call last): 
    2721 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    2722 packages/chimerax/core/triggerset.py", line 130, in invoke 
    2723 return self._func(self._name, data) 
    2724 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2725 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    2726 self.set_surface_mask() 
    2727 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2728 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    2729 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    2730 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2731 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    2732 self._update_mask() 
    2733 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2734 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    2735 step=self.grid_step, pad=self.pad) 
    2736 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2737 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    2738 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    2739 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2740 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    2741 _generate_data_array 
    2742 data = numpy.zeros(dim, numpy.uint8) 
    2743 ValueError: negative dimensions are not allowed 
    2744  
    2745 Error processing trigger "atom coords updated": 
    2746 ValueError: negative dimensions are not allowed 
    2747  
    2748 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2749 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    2750 _generate_data_array 
    2751 data = numpy.zeros(dim, numpy.uint8) 
    2752  
    2753 See log for complete Python traceback. 
    2754  
    2755 Traceback (most recent call last): 
    2756 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    2757 packages/chimerax/core/triggerset.py", line 130, in invoke 
    2758 return self._func(self._name, data) 
    2759 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2760 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    2761 self.set_surface_mask() 
    2762 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2763 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    2764 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    2765 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2766 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    2767 self._update_mask() 
    2768 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2769 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    2770 step=self.grid_step, pad=self.pad) 
    2771 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2772 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    2773 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    2774 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2775 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    2776 _generate_data_array 
    2777 data = numpy.zeros(dim, numpy.uint8) 
    2778 ValueError: negative dimensions are not allowed 
    2779  
    2780 Error processing trigger "atom coords updated": 
    2781 ValueError: negative dimensions are not allowed 
    2782  
    2783 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2784 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    2785 _generate_data_array 
    2786 data = numpy.zeros(dim, numpy.uint8) 
    2787  
    2788 See log for complete Python traceback. 
    2789  
    2790 Traceback (most recent call last): 
    2791 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    2792 packages/chimerax/core/triggerset.py", line 130, in invoke 
    2793 return self._func(self._name, data) 
    2794 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2795 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    2796 self.set_surface_mask() 
    2797 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2798 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    2799 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    2800 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2801 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    2802 self._update_mask() 
    2803 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2804 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    2805 step=self.grid_step, pad=self.pad) 
    2806 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2807 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    2808 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    2809 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2810 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    2811 _generate_data_array 
    2812 data = numpy.zeros(dim, numpy.uint8) 
    2813 ValueError: negative dimensions are not allowed 
    2814  
    2815 Error processing trigger "atom coords updated": 
    2816 ValueError: negative dimensions are not allowed 
    2817  
    2818 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2819 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    2820 _generate_data_array 
    2821 data = numpy.zeros(dim, numpy.uint8) 
    2822  
    2823 See log for complete Python traceback. 
    2824  
    2825 Traceback (most recent call last): 
    2826 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    2827 packages/chimerax/core/triggerset.py", line 130, in invoke 
    2828 return self._func(self._name, data) 
    2829 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2830 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    2831 self.set_surface_mask() 
    2832 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2833 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    2834 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    2835 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2836 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    2837 self._update_mask() 
    2838 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2839 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    2840 step=self.grid_step, pad=self.pad) 
    2841 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2842 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    2843 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    2844 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2845 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    2846 _generate_data_array 
    2847 data = numpy.zeros(dim, numpy.uint8) 
    2848 ValueError: negative dimensions are not allowed 
    2849  
    2850 Error processing trigger "atom coords updated": 
    2851 ValueError: negative dimensions are not allowed 
    2852  
    2853 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2854 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    2855 _generate_data_array 
    2856 data = numpy.zeros(dim, numpy.uint8) 
    2857  
    2858 See log for complete Python traceback. 
    2859  
    2860 Traceback (most recent call last): 
    2861 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    2862 packages/chimerax/core/triggerset.py", line 130, in invoke 
    2863 return self._func(self._name, data) 
    2864 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2865 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    2866 self.set_surface_mask() 
    2867 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2868 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    2869 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    2870 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2871 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    2872 self._update_mask() 
    2873 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2874 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    2875 step=self.grid_step, pad=self.pad) 
    2876 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2877 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    2878 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    2879 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2880 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    2881 _generate_data_array 
    2882 data = numpy.zeros(dim, numpy.uint8) 
    2883 ValueError: negative dimensions are not allowed 
    2884  
    2885 Error processing trigger "atom coords updated": 
    2886 ValueError: negative dimensions are not allowed 
    2887  
    2888 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2889 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    2890 _generate_data_array 
    2891 data = numpy.zeros(dim, numpy.uint8) 
    2892  
    2893 See log for complete Python traceback. 
    2894  
    2895 Traceback (most recent call last): 
    2896 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    2897 packages/chimerax/core/triggerset.py", line 130, in invoke 
    2898 return self._func(self._name, data) 
    2899 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2900 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    2901 self.set_surface_mask() 
    2902 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2903 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    2904 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    2905 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2906 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    2907 self._update_mask() 
    2908 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2909 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    2910 step=self.grid_step, pad=self.pad) 
    2911 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2912 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    2913 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    2914 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2915 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    2916 _generate_data_array 
    2917 data = numpy.zeros(dim, numpy.uint8) 
    2918 ValueError: negative dimensions are not allowed 
    2919  
    2920 Error processing trigger "atom coords updated": 
    2921 ValueError: negative dimensions are not allowed 
    2922  
    2923 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2924 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    2925 _generate_data_array 
    2926 data = numpy.zeros(dim, numpy.uint8) 
    2927  
    2928 See log for complete Python traceback. 
    2929  
    2930 Traceback (most recent call last): 
    2931 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    2932 packages/chimerax/core/triggerset.py", line 130, in invoke 
    2933 return self._func(self._name, data) 
    2934 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2935 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    2936 self.set_surface_mask() 
    2937 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2938 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    2939 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    2940 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2941 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    2942 self._update_mask() 
    2943 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2944 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    2945 step=self.grid_step, pad=self.pad) 
    2946 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2947 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    2948 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    2949 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2950 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    2951 _generate_data_array 
    2952 data = numpy.zeros(dim, numpy.uint8) 
    2953 ValueError: negative dimensions are not allowed 
    2954  
    2955 Error processing trigger "atom coords updated": 
    2956 ValueError: negative dimensions are not allowed 
    2957  
    2958 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2959 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    2960 _generate_data_array 
    2961 data = numpy.zeros(dim, numpy.uint8) 
    2962  
    2963 See log for complete Python traceback. 
    2964  
    2965 Traceback (most recent call last): 
    2966 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    2967 packages/chimerax/core/triggerset.py", line 130, in invoke 
    2968 return self._func(self._name, data) 
    2969 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2970 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    2971 self.set_surface_mask() 
    2972 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2973 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    2974 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    2975 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2976 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    2977 self._update_mask() 
    2978 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2979 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    2980 step=self.grid_step, pad=self.pad) 
    2981 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2982 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    2983 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    2984 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2985 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    2986 _generate_data_array 
    2987 data = numpy.zeros(dim, numpy.uint8) 
    2988 ValueError: negative dimensions are not allowed 
    2989  
    2990 Error processing trigger "atom coords updated": 
    2991 ValueError: negative dimensions are not allowed 
    2992  
    2993 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    2994 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    2995 _generate_data_array 
    2996 data = numpy.zeros(dim, numpy.uint8) 
    2997  
    2998 See log for complete Python traceback. 
    2999  
    3000 Traceback (most recent call last): 
    3001 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    3002 packages/chimerax/core/triggerset.py", line 130, in invoke 
    3003 return self._func(self._name, data) 
    3004 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3005 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    3006 self.set_surface_mask() 
    3007 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3008 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    3009 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    3010 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3011 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    3012 self._update_mask() 
    3013 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3014 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    3015 step=self.grid_step, pad=self.pad) 
    3016 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3017 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    3018 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    3019 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3020 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    3021 _generate_data_array 
    3022 data = numpy.zeros(dim, numpy.uint8) 
    3023 ValueError: negative dimensions are not allowed 
    3024  
    3025 Error processing trigger "atom coords updated": 
    3026 ValueError: negative dimensions are not allowed 
    3027  
    3028 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3029 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    3030 _generate_data_array 
    3031 data = numpy.zeros(dim, numpy.uint8) 
    3032  
    3033 See log for complete Python traceback. 
    3034  
    3035 Traceback (most recent call last): 
    3036 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    3037 packages/chimerax/core/triggerset.py", line 130, in invoke 
    3038 return self._func(self._name, data) 
    3039 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3040 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    3041 self.set_surface_mask() 
    3042 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3043 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    3044 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    3045 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3046 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    3047 self._update_mask() 
    3048 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3049 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    3050 step=self.grid_step, pad=self.pad) 
    3051 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3052 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    3053 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    3054 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3055 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    3056 _generate_data_array 
    3057 data = numpy.zeros(dim, numpy.uint8) 
    3058 ValueError: negative dimensions are not allowed 
    3059  
    3060 Error processing trigger "atom coords updated": 
    3061 ValueError: negative dimensions are not allowed 
    3062  
    3063 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3064 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    3065 _generate_data_array 
    3066 data = numpy.zeros(dim, numpy.uint8) 
    3067  
    3068 See log for complete Python traceback. 
    3069  
    3070 Traceback (most recent call last): 
    3071 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    3072 packages/chimerax/core/triggerset.py", line 130, in invoke 
    3073 return self._func(self._name, data) 
    3074 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3075 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    3076 self.set_surface_mask() 
    3077 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3078 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    3079 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    3080 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3081 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    3082 self._update_mask() 
    3083 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3084 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    3085 step=self.grid_step, pad=self.pad) 
    3086 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3087 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    3088 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    3089 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3090 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    3091 _generate_data_array 
    3092 data = numpy.zeros(dim, numpy.uint8) 
    3093 ValueError: negative dimensions are not allowed 
    3094  
    3095 Error processing trigger "atom coords updated": 
    3096 ValueError: negative dimensions are not allowed 
    3097  
    3098 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3099 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    3100 _generate_data_array 
    3101 data = numpy.zeros(dim, numpy.uint8) 
    3102  
    3103 See log for complete Python traceback. 
    3104  
    3105 Traceback (most recent call last): 
    3106 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    3107 packages/chimerax/core/triggerset.py", line 130, in invoke 
    3108 return self._func(self._name, data) 
    3109 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3110 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    3111 self.set_surface_mask() 
    3112 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3113 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    3114 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    3115 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3116 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    3117 self._update_mask() 
    3118 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3119 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    3120 step=self.grid_step, pad=self.pad) 
    3121 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3122 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    3123 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    3124 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3125 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    3126 _generate_data_array 
    3127 data = numpy.zeros(dim, numpy.uint8) 
    3128 ValueError: negative dimensions are not allowed 
    3129  
    3130 Error processing trigger "atom coords updated": 
    3131 ValueError: negative dimensions are not allowed 
    3132  
    3133 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3134 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    3135 _generate_data_array 
    3136 data = numpy.zeros(dim, numpy.uint8) 
    3137  
    3138 See log for complete Python traceback. 
    3139  
    3140 Traceback (most recent call last): 
    3141 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    3142 packages/chimerax/core/triggerset.py", line 130, in invoke 
    3143 return self._func(self._name, data) 
    3144 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3145 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    3146 self.set_surface_mask() 
    3147 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3148 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    3149 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    3150 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3151 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    3152 self._update_mask() 
    3153 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3154 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    3155 step=self.grid_step, pad=self.pad) 
    3156 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3157 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    3158 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    3159 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3160 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    3161 _generate_data_array 
    3162 data = numpy.zeros(dim, numpy.uint8) 
    3163 ValueError: negative dimensions are not allowed 
    3164  
    3165 Error processing trigger "atom coords updated": 
    3166 ValueError: negative dimensions are not allowed 
    3167  
    3168 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3169 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    3170 _generate_data_array 
    3171 data = numpy.zeros(dim, numpy.uint8) 
    3172  
    3173 See log for complete Python traceback. 
    3174  
    3175 Traceback (most recent call last): 
    3176 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    3177 packages/chimerax/core/triggerset.py", line 130, in invoke 
    3178 return self._func(self._name, data) 
    3179 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3180 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    3181 self.set_surface_mask() 
    3182 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3183 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    3184 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    3185 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3186 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    3187 self._update_mask() 
    3188 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3189 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    3190 step=self.grid_step, pad=self.pad) 
    3191 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3192 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    3193 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    3194 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3195 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    3196 _generate_data_array 
    3197 data = numpy.zeros(dim, numpy.uint8) 
    3198 ValueError: negative dimensions are not allowed 
    3199  
    3200 Error processing trigger "atom coords updated": 
    3201 ValueError: negative dimensions are not allowed 
    3202  
    3203 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3204 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    3205 _generate_data_array 
    3206 data = numpy.zeros(dim, numpy.uint8) 
    3207  
    3208 See log for complete Python traceback. 
    3209  
    3210 Traceback (most recent call last): 
    3211 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    3212 packages/chimerax/core/triggerset.py", line 130, in invoke 
    3213 return self._func(self._name, data) 
    3214 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3215 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    3216 self.set_surface_mask() 
    3217 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3218 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    3219 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    3220 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3221 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    3222 self._update_mask() 
    3223 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3224 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    3225 step=self.grid_step, pad=self.pad) 
    3226 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3227 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    3228 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    3229 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3230 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    3231 _generate_data_array 
    3232 data = numpy.zeros(dim, numpy.uint8) 
    3233 ValueError: negative dimensions are not allowed 
    3234  
    3235 Error processing trigger "atom coords updated": 
    3236 ValueError: negative dimensions are not allowed 
    3237  
    3238 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3239 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    3240 _generate_data_array 
    3241 data = numpy.zeros(dim, numpy.uint8) 
    3242  
    3243 See log for complete Python traceback. 
    3244  
    3245 Traceback (most recent call last): 
    3246 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    3247 packages/chimerax/core/triggerset.py", line 130, in invoke 
    3248 return self._func(self._name, data) 
    3249 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3250 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    3251 self.set_surface_mask() 
    3252 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3253 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    3254 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    3255 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3256 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    3257 self._update_mask() 
    3258 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3259 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    3260 step=self.grid_step, pad=self.pad) 
    3261 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3262 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    3263 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    3264 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3265 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    3266 _generate_data_array 
    3267 data = numpy.zeros(dim, numpy.uint8) 
    3268 ValueError: negative dimensions are not allowed 
    3269  
    3270 Error processing trigger "atom coords updated": 
    3271 ValueError: negative dimensions are not allowed 
    3272  
    3273 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3274 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    3275 _generate_data_array 
    3276 data = numpy.zeros(dim, numpy.uint8) 
    3277  
    3278 See log for complete Python traceback. 
    3279  
    3280 Traceback (most recent call last): 
    3281 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    3282 packages/chimerax/core/triggerset.py", line 130, in invoke 
    3283 return self._func(self._name, data) 
    3284 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3285 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    3286 self.set_surface_mask() 
    3287 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3288 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    3289 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    3290 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3291 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    3292 self._update_mask() 
    3293 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3294 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    3295 step=self.grid_step, pad=self.pad) 
    3296 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3297 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    3298 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    3299 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3300 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    3301 _generate_data_array 
    3302 data = numpy.zeros(dim, numpy.uint8) 
    3303 ValueError: negative dimensions are not allowed 
    3304  
    3305 Error processing trigger "atom coords updated": 
    3306 ValueError: negative dimensions are not allowed 
    3307  
    3308 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3309 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    3310 _generate_data_array 
    3311 data = numpy.zeros(dim, numpy.uint8) 
    3312  
    3313 See log for complete Python traceback. 
    3314  
    3315 Traceback (most recent call last): 
    3316 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    3317 packages/chimerax/core/triggerset.py", line 130, in invoke 
    3318 return self._func(self._name, data) 
    3319 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3320 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    3321 self.set_surface_mask() 
    3322 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3323 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    3324 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    3325 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3326 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    3327 self._update_mask() 
    3328 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3329 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    3330 step=self.grid_step, pad=self.pad) 
    3331 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3332 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    3333 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    3334 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3335 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    3336 _generate_data_array 
    3337 data = numpy.zeros(dim, numpy.uint8) 
    3338 ValueError: negative dimensions are not allowed 
    3339  
    3340 Error processing trigger "atom coords updated": 
    3341 ValueError: negative dimensions are not allowed 
    3342  
    3343 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3344 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    3345 _generate_data_array 
    3346 data = numpy.zeros(dim, numpy.uint8) 
    3347  
    3348 See log for complete Python traceback. 
    3349  
    3350 Traceback (most recent call last): 
    3351 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    3352 packages/chimerax/core/triggerset.py", line 130, in invoke 
    3353 return self._func(self._name, data) 
    3354 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3355 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    3356 self.set_surface_mask() 
    3357 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3358 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    3359 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    3360 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3361 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    3362 self._update_mask() 
    3363 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3364 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    3365 step=self.grid_step, pad=self.pad) 
    3366 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3367 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    3368 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    3369 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3370 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    3371 _generate_data_array 
    3372 data = numpy.zeros(dim, numpy.uint8) 
    3373 ValueError: negative dimensions are not allowed 
    3374  
    3375 Error processing trigger "atom coords updated": 
    3376 ValueError: negative dimensions are not allowed 
    3377  
    3378 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3379 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    3380 _generate_data_array 
    3381 data = numpy.zeros(dim, numpy.uint8) 
    3382  
    3383 See log for complete Python traceback. 
    3384  
    3385 Traceback (most recent call last): 
    3386 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    3387 packages/chimerax/core/triggerset.py", line 130, in invoke 
    3388 return self._func(self._name, data) 
    3389 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3390 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    3391 self.set_surface_mask() 
    3392 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3393 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    3394 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    3395 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3396 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    3397 self._update_mask() 
    3398 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3399 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    3400 step=self.grid_step, pad=self.pad) 
    3401 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3402 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    3403 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    3404 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3405 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    3406 _generate_data_array 
    3407 data = numpy.zeros(dim, numpy.uint8) 
    3408 ValueError: negative dimensions are not allowed 
    3409  
    3410 Error processing trigger "atom coords updated": 
    3411 ValueError: negative dimensions are not allowed 
    3412  
    3413 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3414 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    3415 _generate_data_array 
    3416 data = numpy.zeros(dim, numpy.uint8) 
    3417  
    3418 See log for complete Python traceback. 
    3419  
    3420 Traceback (most recent call last): 
    3421 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    3422 packages/chimerax/core/triggerset.py", line 130, in invoke 
    3423 return self._func(self._name, data) 
    3424 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3425 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    3426 self.set_surface_mask() 
    3427 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3428 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    3429 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    3430 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3431 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    3432 self._update_mask() 
    3433 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3434 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    3435 step=self.grid_step, pad=self.pad) 
    3436 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3437 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    3438 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    3439 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3440 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    3441 _generate_data_array 
    3442 data = numpy.zeros(dim, numpy.uint8) 
    3443 ValueError: negative dimensions are not allowed 
    3444  
    3445 Error processing trigger "atom coords updated": 
    3446 ValueError: negative dimensions are not allowed 
    3447  
    3448 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3449 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    3450 _generate_data_array 
    3451 data = numpy.zeros(dim, numpy.uint8) 
    3452  
    3453 See log for complete Python traceback. 
    3454  
    3455 Traceback (most recent call last): 
    3456 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    3457 packages/chimerax/core/triggerset.py", line 130, in invoke 
    3458 return self._func(self._name, data) 
    3459 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3460 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    3461 self.set_surface_mask() 
    3462 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3463 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    3464 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    3465 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3466 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    3467 self._update_mask() 
    3468 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3469 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    3470 step=self.grid_step, pad=self.pad) 
    3471 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3472 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    3473 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    3474 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3475 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    3476 _generate_data_array 
    3477 data = numpy.zeros(dim, numpy.uint8) 
    3478 ValueError: negative dimensions are not allowed 
    3479  
    3480 Error processing trigger "atom coords updated": 
    3481 ValueError: negative dimensions are not allowed 
    3482  
    3483 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3484 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    3485 _generate_data_array 
    3486 data = numpy.zeros(dim, numpy.uint8) 
    3487  
    3488 See log for complete Python traceback. 
    3489  
    3490 Traceback (most recent call last): 
    3491 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    3492 packages/chimerax/core/triggerset.py", line 130, in invoke 
    3493 return self._func(self._name, data) 
    3494 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3495 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    3496 self.set_surface_mask() 
    3497 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3498 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    3499 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    3500 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3501 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    3502 self._update_mask() 
    3503 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3504 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    3505 step=self.grid_step, pad=self.pad) 
    3506 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3507 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    3508 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    3509 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3510 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    3511 _generate_data_array 
    3512 data = numpy.zeros(dim, numpy.uint8) 
    3513 ValueError: negative dimensions are not allowed 
    3514  
    3515 Error processing trigger "atom coords updated": 
    3516 ValueError: negative dimensions are not allowed 
    3517  
    3518 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3519 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    3520 _generate_data_array 
    3521 data = numpy.zeros(dim, numpy.uint8) 
    3522  
    3523 See log for complete Python traceback. 
    3524  
    3525 Traceback (most recent call last): 
    3526 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    3527 packages/chimerax/core/triggerset.py", line 130, in invoke 
    3528 return self._func(self._name, data) 
    3529 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3530 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    3531 self.set_surface_mask() 
    3532 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3533 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    3534 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    3535 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3536 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    3537 self._update_mask() 
    3538 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3539 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    3540 step=self.grid_step, pad=self.pad) 
    3541 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3542 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    3543 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    3544 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3545 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    3546 _generate_data_array 
    3547 data = numpy.zeros(dim, numpy.uint8) 
    3548 ValueError: negative dimensions are not allowed 
    3549  
    3550 Error processing trigger "atom coords updated": 
    3551 ValueError: negative dimensions are not allowed 
    3552  
    3553 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3554 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    3555 _generate_data_array 
    3556 data = numpy.zeros(dim, numpy.uint8) 
    3557  
    3558 See log for complete Python traceback. 
    3559  
    3560 Traceback (most recent call last): 
    3561 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    3562 packages/chimerax/core/triggerset.py", line 130, in invoke 
    3563 return self._func(self._name, data) 
    3564 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3565 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    3566 self.set_surface_mask() 
    3567 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3568 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    3569 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    3570 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3571 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    3572 self._update_mask() 
    3573 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3574 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    3575 step=self.grid_step, pad=self.pad) 
    3576 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3577 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    3578 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    3579 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3580 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    3581 _generate_data_array 
    3582 data = numpy.zeros(dim, numpy.uint8) 
    3583 ValueError: negative dimensions are not allowed 
    3584  
    3585 Error processing trigger "atom coords updated": 
    3586 ValueError: negative dimensions are not allowed 
    3587  
    3588 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3589 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    3590 _generate_data_array 
    3591 data = numpy.zeros(dim, numpy.uint8) 
    3592  
    3593 See log for complete Python traceback. 
    3594  
    3595 Traceback (most recent call last): 
    3596 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    3597 packages/chimerax/core/triggerset.py", line 130, in invoke 
    3598 return self._func(self._name, data) 
    3599 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3600 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    3601 self.set_surface_mask() 
    3602 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3603 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    3604 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    3605 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3606 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    3607 self._update_mask() 
    3608 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3609 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    3610 step=self.grid_step, pad=self.pad) 
    3611 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3612 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    3613 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    3614 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3615 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    3616 _generate_data_array 
    3617 data = numpy.zeros(dim, numpy.uint8) 
    3618 ValueError: negative dimensions are not allowed 
    3619  
    3620 Error processing trigger "atom coords updated": 
    3621 ValueError: negative dimensions are not allowed 
    3622  
    3623 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3624 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    3625 _generate_data_array 
    3626 data = numpy.zeros(dim, numpy.uint8) 
    3627  
    3628 See log for complete Python traceback. 
    3629  
    3630 Traceback (most recent call last): 
    3631 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    3632 packages/chimerax/core/triggerset.py", line 130, in invoke 
    3633 return self._func(self._name, data) 
    3634 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3635 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    3636 self.set_surface_mask() 
    3637 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3638 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    3639 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    3640 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3641 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    3642 self._update_mask() 
    3643 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3644 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    3645 step=self.grid_step, pad=self.pad) 
    3646 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3647 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    3648 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    3649 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3650 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    3651 _generate_data_array 
    3652 data = numpy.zeros(dim, numpy.uint8) 
    3653 ValueError: negative dimensions are not allowed 
    3654  
    3655 Error processing trigger "atom coords updated": 
    3656 ValueError: negative dimensions are not allowed 
    3657  
    3658 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3659 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    3660 _generate_data_array 
    3661 data = numpy.zeros(dim, numpy.uint8) 
    3662  
    3663 See log for complete Python traceback. 
    3664  
    3665 Traceback (most recent call last): 
    3666 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    3667 packages/chimerax/core/triggerset.py", line 130, in invoke 
    3668 return self._func(self._name, data) 
    3669 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3670 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    3671 self.set_surface_mask() 
    3672 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3673 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    3674 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    3675 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3676 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    3677 self._update_mask() 
    3678 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3679 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    3680 step=self.grid_step, pad=self.pad) 
    3681 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3682 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    3683 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    3684 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3685 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    3686 _generate_data_array 
    3687 data = numpy.zeros(dim, numpy.uint8) 
    3688 ValueError: negative dimensions are not allowed 
    3689  
    3690 Error processing trigger "atom coords updated": 
    3691 ValueError: negative dimensions are not allowed 
    3692  
    3693 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3694 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    3695 _generate_data_array 
    3696 data = numpy.zeros(dim, numpy.uint8) 
    3697  
    3698 See log for complete Python traceback. 
    3699  
    3700 Traceback (most recent call last): 
    3701 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    3702 packages/chimerax/core/triggerset.py", line 130, in invoke 
    3703 return self._func(self._name, data) 
    3704 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3705 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    3706 self.set_surface_mask() 
    3707 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3708 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    3709 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    3710 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3711 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    3712 self._update_mask() 
    3713 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3714 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    3715 step=self.grid_step, pad=self.pad) 
    3716 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3717 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    3718 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    3719 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3720 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    3721 _generate_data_array 
    3722 data = numpy.zeros(dim, numpy.uint8) 
    3723 ValueError: negative dimensions are not allowed 
    3724  
    3725 Error processing trigger "atom coords updated": 
    3726 ValueError: negative dimensions are not allowed 
    3727  
    3728 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3729 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    3730 _generate_data_array 
    3731 data = numpy.zeros(dim, numpy.uint8) 
    3732  
    3733 See log for complete Python traceback. 
    3734  
    3735 Traceback (most recent call last): 
    3736 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    3737 packages/chimerax/core/triggerset.py", line 130, in invoke 
    3738 return self._func(self._name, data) 
    3739 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3740 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    3741 self.set_surface_mask() 
    3742 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3743 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    3744 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    3745 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3746 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    3747 self._update_mask() 
    3748 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3749 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    3750 step=self.grid_step, pad=self.pad) 
    3751 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3752 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    3753 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    3754 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3755 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    3756 _generate_data_array 
    3757 data = numpy.zeros(dim, numpy.uint8) 
    3758 ValueError: negative dimensions are not allowed 
    3759  
    3760 Error processing trigger "atom coords updated": 
    3761 ValueError: negative dimensions are not allowed 
    3762  
    3763 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3764 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    3765 _generate_data_array 
    3766 data = numpy.zeros(dim, numpy.uint8) 
    3767  
    3768 See log for complete Python traceback. 
    3769  
    3770 Traceback (most recent call last): 
    3771 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    3772 packages/chimerax/core/triggerset.py", line 130, in invoke 
    3773 return self._func(self._name, data) 
    3774 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3775 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    3776 self.set_surface_mask() 
    3777 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3778 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    3779 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    3780 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3781 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    3782 self._update_mask() 
    3783 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3784 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    3785 step=self.grid_step, pad=self.pad) 
    3786 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3787 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    3788 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    3789 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3790 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    3791 _generate_data_array 
    3792 data = numpy.zeros(dim, numpy.uint8) 
    3793 ValueError: negative dimensions are not allowed 
    3794  
    3795 Error processing trigger "atom coords updated": 
    3796 ValueError: negative dimensions are not allowed 
    3797  
    3798 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3799 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    3800 _generate_data_array 
    3801 data = numpy.zeros(dim, numpy.uint8) 
    3802  
    3803 See log for complete Python traceback. 
    3804  
    3805 Traceback (most recent call last): 
    3806 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    3807 packages/chimerax/core/triggerset.py", line 130, in invoke 
    3808 return self._func(self._name, data) 
    3809 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3810 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    3811 self.set_surface_mask() 
    3812 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3813 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    3814 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    3815 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3816 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    3817 self._update_mask() 
    3818 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3819 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    3820 step=self.grid_step, pad=self.pad) 
    3821 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3822 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    3823 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    3824 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3825 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    3826 _generate_data_array 
    3827 data = numpy.zeros(dim, numpy.uint8) 
    3828 ValueError: negative dimensions are not allowed 
    3829  
    3830 Error processing trigger "atom coords updated": 
    3831 ValueError: negative dimensions are not allowed 
    3832  
    3833 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3834 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    3835 _generate_data_array 
    3836 data = numpy.zeros(dim, numpy.uint8) 
    3837  
    3838 See log for complete Python traceback. 
    3839  
    3840 Traceback (most recent call last): 
    3841 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    3842 packages/chimerax/core/triggerset.py", line 130, in invoke 
    3843 return self._func(self._name, data) 
    3844 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3845 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    3846 self.set_surface_mask() 
    3847 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3848 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    3849 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    3850 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3851 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    3852 self._update_mask() 
    3853 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3854 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    3855 step=self.grid_step, pad=self.pad) 
    3856 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3857 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    3858 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    3859 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3860 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    3861 _generate_data_array 
    3862 data = numpy.zeros(dim, numpy.uint8) 
    3863 ValueError: negative dimensions are not allowed 
    3864  
    3865 Error processing trigger "atom coords updated": 
    3866 ValueError: negative dimensions are not allowed 
    3867  
    3868 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3869 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    3870 _generate_data_array 
    3871 data = numpy.zeros(dim, numpy.uint8) 
    3872  
    3873 See log for complete Python traceback. 
    3874  
    3875 Traceback (most recent call last): 
    3876 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    3877 packages/chimerax/core/triggerset.py", line 130, in invoke 
    3878 return self._func(self._name, data) 
    3879 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3880 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    3881 self.set_surface_mask() 
    3882 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3883 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    3884 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    3885 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3886 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    3887 self._update_mask() 
    3888 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3889 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    3890 step=self.grid_step, pad=self.pad) 
    3891 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3892 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    3893 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    3894 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3895 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    3896 _generate_data_array 
    3897 data = numpy.zeros(dim, numpy.uint8) 
    3898 ValueError: negative dimensions are not allowed 
    3899  
    3900 Error processing trigger "atom coords updated": 
    3901 ValueError: negative dimensions are not allowed 
    3902  
    3903 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3904 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    3905 _generate_data_array 
    3906 data = numpy.zeros(dim, numpy.uint8) 
    3907  
    3908 See log for complete Python traceback. 
    3909  
    3910 Traceback (most recent call last): 
    3911 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    3912 packages/chimerax/core/triggerset.py", line 130, in invoke 
    3913 return self._func(self._name, data) 
    3914 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3915 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    3916 self.set_surface_mask() 
    3917 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3918 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    3919 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    3920 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3921 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    3922 self._update_mask() 
    3923 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3924 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    3925 step=self.grid_step, pad=self.pad) 
    3926 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3927 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    3928 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    3929 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3930 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    3931 _generate_data_array 
    3932 data = numpy.zeros(dim, numpy.uint8) 
    3933 ValueError: negative dimensions are not allowed 
    3934  
    3935 Error processing trigger "atom coords updated": 
    3936 ValueError: negative dimensions are not allowed 
    3937  
    3938 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3939 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    3940 _generate_data_array 
    3941 data = numpy.zeros(dim, numpy.uint8) 
    3942  
    3943 See log for complete Python traceback. 
    3944  
    3945 Traceback (most recent call last): 
    3946 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    3947 packages/chimerax/core/triggerset.py", line 130, in invoke 
    3948 return self._func(self._name, data) 
    3949 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3950 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    3951 self.set_surface_mask() 
    3952 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3953 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    3954 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    3955 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3956 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    3957 self._update_mask() 
    3958 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3959 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    3960 step=self.grid_step, pad=self.pad) 
    3961 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3962 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    3963 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    3964 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3965 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    3966 _generate_data_array 
    3967 data = numpy.zeros(dim, numpy.uint8) 
    3968 ValueError: negative dimensions are not allowed 
    3969  
    3970 Error processing trigger "atom coords updated": 
    3971 ValueError: negative dimensions are not allowed 
    3972  
    3973 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3974 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    3975 _generate_data_array 
    3976 data = numpy.zeros(dim, numpy.uint8) 
    3977  
    3978 See log for complete Python traceback. 
    3979  
    3980 Traceback (most recent call last): 
    3981 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    3982 packages/chimerax/core/triggerset.py", line 130, in invoke 
    3983 return self._func(self._name, data) 
    3984 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3985 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    3986 self.set_surface_mask() 
    3987 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3988 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    3989 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    3990 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3991 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    3992 self._update_mask() 
    3993 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3994 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    3995 step=self.grid_step, pad=self.pad) 
    3996 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    3997 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    3998 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    3999 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4000 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    4001 _generate_data_array 
    4002 data = numpy.zeros(dim, numpy.uint8) 
    4003 ValueError: negative dimensions are not allowed 
    4004  
    4005 Error processing trigger "atom coords updated": 
    4006 ValueError: negative dimensions are not allowed 
    4007  
    4008 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4009 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    4010 _generate_data_array 
    4011 data = numpy.zeros(dim, numpy.uint8) 
    4012  
    4013 See log for complete Python traceback. 
    4014  
    4015 Traceback (most recent call last): 
    4016 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    4017 packages/chimerax/core/triggerset.py", line 130, in invoke 
    4018 return self._func(self._name, data) 
    4019 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4020 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    4021 self.set_surface_mask() 
    4022 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4023 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    4024 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    4025 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4026 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    4027 self._update_mask() 
    4028 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4029 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    4030 step=self.grid_step, pad=self.pad) 
    4031 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4032 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    4033 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    4034 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4035 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    4036 _generate_data_array 
    4037 data = numpy.zeros(dim, numpy.uint8) 
    4038 ValueError: negative dimensions are not allowed 
    4039  
    4040 Error processing trigger "atom coords updated": 
    4041 ValueError: negative dimensions are not allowed 
    4042  
    4043 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4044 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    4045 _generate_data_array 
    4046 data = numpy.zeros(dim, numpy.uint8) 
    4047  
    4048 See log for complete Python traceback. 
    4049  
    4050 Traceback (most recent call last): 
    4051 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    4052 packages/chimerax/core/triggerset.py", line 130, in invoke 
    4053 return self._func(self._name, data) 
    4054 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4055 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    4056 self.set_surface_mask() 
    4057 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4058 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    4059 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    4060 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4061 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    4062 self._update_mask() 
    4063 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4064 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    4065 step=self.grid_step, pad=self.pad) 
    4066 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4067 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    4068 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    4069 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4070 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    4071 _generate_data_array 
    4072 data = numpy.zeros(dim, numpy.uint8) 
    4073 ValueError: negative dimensions are not allowed 
    4074  
    4075 Error processing trigger "atom coords updated": 
    4076 ValueError: negative dimensions are not allowed 
    4077  
    4078 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4079 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    4080 _generate_data_array 
    4081 data = numpy.zeros(dim, numpy.uint8) 
    4082  
    4083 See log for complete Python traceback. 
    4084  
    4085 Traceback (most recent call last): 
    4086 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    4087 packages/chimerax/core/triggerset.py", line 130, in invoke 
    4088 return self._func(self._name, data) 
    4089 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4090 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    4091 self.set_surface_mask() 
    4092 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4093 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    4094 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    4095 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4096 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    4097 self._update_mask() 
    4098 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4099 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    4100 step=self.grid_step, pad=self.pad) 
    4101 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4102 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    4103 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    4104 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4105 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    4106 _generate_data_array 
    4107 data = numpy.zeros(dim, numpy.uint8) 
    4108 ValueError: negative dimensions are not allowed 
    4109  
    4110 Error processing trigger "atom coords updated": 
    4111 ValueError: negative dimensions are not allowed 
    4112  
    4113 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4114 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    4115 _generate_data_array 
    4116 data = numpy.zeros(dim, numpy.uint8) 
    4117  
    4118 See log for complete Python traceback. 
    4119  
    4120 Traceback (most recent call last): 
    4121 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    4122 packages/chimerax/core/triggerset.py", line 130, in invoke 
    4123 return self._func(self._name, data) 
    4124 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4125 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    4126 self.set_surface_mask() 
    4127 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4128 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    4129 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    4130 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4131 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    4132 self._update_mask() 
    4133 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4134 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    4135 step=self.grid_step, pad=self.pad) 
    4136 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4137 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    4138 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    4139 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4140 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    4141 _generate_data_array 
    4142 data = numpy.zeros(dim, numpy.uint8) 
    4143 ValueError: negative dimensions are not allowed 
    4144  
    4145 Error processing trigger "atom coords updated": 
    4146 ValueError: negative dimensions are not allowed 
    4147  
    4148 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4149 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    4150 _generate_data_array 
    4151 data = numpy.zeros(dim, numpy.uint8) 
    4152  
    4153 See log for complete Python traceback. 
    4154  
    4155 Traceback (most recent call last): 
    4156 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    4157 packages/chimerax/core/triggerset.py", line 130, in invoke 
    4158 return self._func(self._name, data) 
    4159 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4160 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    4161 self.set_surface_mask() 
    4162 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4163 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    4164 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    4165 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4166 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    4167 self._update_mask() 
    4168 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4169 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    4170 step=self.grid_step, pad=self.pad) 
    4171 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4172 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    4173 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    4174 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4175 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    4176 _generate_data_array 
    4177 data = numpy.zeros(dim, numpy.uint8) 
    4178 ValueError: negative dimensions are not allowed 
    4179  
    4180 Error processing trigger "atom coords updated": 
    4181 ValueError: negative dimensions are not allowed 
    4182  
    4183 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4184 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    4185 _generate_data_array 
    4186 data = numpy.zeros(dim, numpy.uint8) 
    4187  
    4188 See log for complete Python traceback. 
    4189  
    4190 Traceback (most recent call last): 
    4191 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    4192 packages/chimerax/core/triggerset.py", line 130, in invoke 
    4193 return self._func(self._name, data) 
    4194 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4195 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    4196 self.set_surface_mask() 
    4197 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4198 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    4199 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    4200 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4201 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    4202 self._update_mask() 
    4203 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4204 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    4205 step=self.grid_step, pad=self.pad) 
    4206 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4207 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    4208 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    4209 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4210 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    4211 _generate_data_array 
    4212 data = numpy.zeros(dim, numpy.uint8) 
    4213 ValueError: negative dimensions are not allowed 
    4214  
    4215 Error processing trigger "atom coords updated": 
    4216 ValueError: negative dimensions are not allowed 
    4217  
    4218 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4219 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    4220 _generate_data_array 
    4221 data = numpy.zeros(dim, numpy.uint8) 
    4222  
    4223 See log for complete Python traceback. 
    4224  
    4225 Traceback (most recent call last): 
    4226 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    4227 packages/chimerax/core/triggerset.py", line 130, in invoke 
    4228 return self._func(self._name, data) 
    4229 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4230 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    4231 self.set_surface_mask() 
    4232 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4233 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    4234 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    4235 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4236 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    4237 self._update_mask() 
    4238 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4239 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    4240 step=self.grid_step, pad=self.pad) 
    4241 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4242 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    4243 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    4244 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4245 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    4246 _generate_data_array 
    4247 data = numpy.zeros(dim, numpy.uint8) 
    4248 ValueError: negative dimensions are not allowed 
    4249  
    4250 Error processing trigger "atom coords updated": 
    4251 ValueError: negative dimensions are not allowed 
    4252  
    4253 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4254 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    4255 _generate_data_array 
    4256 data = numpy.zeros(dim, numpy.uint8) 
    4257  
    4258 See log for complete Python traceback. 
    4259  
    4260 Traceback (most recent call last): 
    4261 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    4262 packages/chimerax/core/triggerset.py", line 130, in invoke 
    4263 return self._func(self._name, data) 
    4264 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4265 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    4266 self.set_surface_mask() 
    4267 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4268 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    4269 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    4270 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4271 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    4272 self._update_mask() 
    4273 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4274 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    4275 step=self.grid_step, pad=self.pad) 
    4276 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4277 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    4278 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    4279 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4280 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    4281 _generate_data_array 
    4282 data = numpy.zeros(dim, numpy.uint8) 
    4283 ValueError: negative dimensions are not allowed 
    4284  
    4285 Error processing trigger "atom coords updated": 
    4286 ValueError: negative dimensions are not allowed 
    4287  
    4288 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4289 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    4290 _generate_data_array 
    4291 data = numpy.zeros(dim, numpy.uint8) 
    4292  
    4293 See log for complete Python traceback. 
    4294  
    4295 Traceback (most recent call last): 
    4296 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    4297 packages/chimerax/core/triggerset.py", line 130, in invoke 
    4298 return self._func(self._name, data) 
    4299 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4300 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    4301 self.set_surface_mask() 
    4302 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4303 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    4304 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    4305 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4306 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    4307 self._update_mask() 
    4308 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4309 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    4310 step=self.grid_step, pad=self.pad) 
    4311 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4312 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    4313 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    4314 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4315 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    4316 _generate_data_array 
    4317 data = numpy.zeros(dim, numpy.uint8) 
    4318 ValueError: negative dimensions are not allowed 
    4319  
    4320 Error processing trigger "atom coords updated": 
    4321 ValueError: negative dimensions are not allowed 
    4322  
    4323 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4324 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    4325 _generate_data_array 
    4326 data = numpy.zeros(dim, numpy.uint8) 
    4327  
    4328 See log for complete Python traceback. 
    4329  
    4330 Traceback (most recent call last): 
    4331 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    4332 packages/chimerax/core/triggerset.py", line 130, in invoke 
    4333 return self._func(self._name, data) 
    4334 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4335 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    4336 self.set_surface_mask() 
    4337 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4338 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    4339 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    4340 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4341 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    4342 self._update_mask() 
    4343 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4344 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    4345 step=self.grid_step, pad=self.pad) 
    4346 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4347 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    4348 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    4349 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4350 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    4351 _generate_data_array 
    4352 data = numpy.zeros(dim, numpy.uint8) 
    4353 ValueError: negative dimensions are not allowed 
    4354  
    4355 Error processing trigger "atom coords updated": 
    4356 ValueError: negative dimensions are not allowed 
    4357  
    4358 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4359 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    4360 _generate_data_array 
    4361 data = numpy.zeros(dim, numpy.uint8) 
    4362  
    4363 See log for complete Python traceback. 
    4364  
    4365 Traceback (most recent call last): 
    4366 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    4367 packages/chimerax/core/triggerset.py", line 130, in invoke 
    4368 return self._func(self._name, data) 
    4369 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4370 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    4371 self.set_surface_mask() 
    4372 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4373 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    4374 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    4375 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4376 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    4377 self._update_mask() 
    4378 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4379 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    4380 step=self.grid_step, pad=self.pad) 
    4381 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4382 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    4383 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    4384 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4385 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    4386 _generate_data_array 
    4387 data = numpy.zeros(dim, numpy.uint8) 
    4388 ValueError: negative dimensions are not allowed 
    4389  
    4390 Error processing trigger "atom coords updated": 
    4391 ValueError: negative dimensions are not allowed 
    4392  
    4393 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4394 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    4395 _generate_data_array 
    4396 data = numpy.zeros(dim, numpy.uint8) 
    4397  
    4398 See log for complete Python traceback. 
    4399  
    4400 Traceback (most recent call last): 
    4401 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    4402 packages/chimerax/core/triggerset.py", line 130, in invoke 
    4403 return self._func(self._name, data) 
    4404 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4405 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    4406 self.set_surface_mask() 
    4407 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4408 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    4409 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    4410 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4411 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    4412 self._update_mask() 
    4413 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4414 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    4415 step=self.grid_step, pad=self.pad) 
    4416 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4417 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    4418 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    4419 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4420 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    4421 _generate_data_array 
    4422 data = numpy.zeros(dim, numpy.uint8) 
    4423 ValueError: negative dimensions are not allowed 
    4424  
    4425 Error processing trigger "atom coords updated": 
    4426 ValueError: negative dimensions are not allowed 
    4427  
    4428 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4429 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    4430 _generate_data_array 
    4431 data = numpy.zeros(dim, numpy.uint8) 
    4432  
    4433 See log for complete Python traceback. 
    4434  
    4435 Traceback (most recent call last): 
    4436 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    4437 packages/chimerax/core/triggerset.py", line 130, in invoke 
    4438 return self._func(self._name, data) 
    4439 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4440 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    4441 self.set_surface_mask() 
    4442 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4443 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    4444 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    4445 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4446 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    4447 self._update_mask() 
    4448 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4449 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    4450 step=self.grid_step, pad=self.pad) 
    4451 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4452 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    4453 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    4454 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4455 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    4456 _generate_data_array 
    4457 data = numpy.zeros(dim, numpy.uint8) 
    4458 ValueError: negative dimensions are not allowed 
    4459  
    4460 Error processing trigger "atom coords updated": 
    4461 ValueError: negative dimensions are not allowed 
    4462  
    4463 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4464 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    4465 _generate_data_array 
    4466 data = numpy.zeros(dim, numpy.uint8) 
    4467  
    4468 See log for complete Python traceback. 
    4469  
    4470 Traceback (most recent call last): 
    4471 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    4472 packages/chimerax/core/triggerset.py", line 130, in invoke 
    4473 return self._func(self._name, data) 
    4474 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4475 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    4476 self.set_surface_mask() 
    4477 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4478 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    4479 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    4480 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4481 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    4482 self._update_mask() 
    4483 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4484 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    4485 step=self.grid_step, pad=self.pad) 
    4486 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4487 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    4488 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    4489 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4490 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    4491 _generate_data_array 
    4492 data = numpy.zeros(dim, numpy.uint8) 
    4493 ValueError: negative dimensions are not allowed 
    4494  
    4495 Error processing trigger "atom coords updated": 
    4496 ValueError: negative dimensions are not allowed 
    4497  
    4498 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4499 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    4500 _generate_data_array 
    4501 data = numpy.zeros(dim, numpy.uint8) 
    4502  
    4503 See log for complete Python traceback. 
    4504  
    4505 Traceback (most recent call last): 
    4506 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    4507 packages/chimerax/core/triggerset.py", line 130, in invoke 
    4508 return self._func(self._name, data) 
    4509 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4510 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    4511 self.set_surface_mask() 
    4512 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4513 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    4514 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    4515 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4516 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    4517 self._update_mask() 
    4518 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4519 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    4520 step=self.grid_step, pad=self.pad) 
    4521 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4522 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    4523 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    4524 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4525 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    4526 _generate_data_array 
    4527 data = numpy.zeros(dim, numpy.uint8) 
    4528 ValueError: negative dimensions are not allowed 
    4529  
    4530 Error processing trigger "atom coords updated": 
    4531 ValueError: negative dimensions are not allowed 
    4532  
    4533 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4534 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    4535 _generate_data_array 
    4536 data = numpy.zeros(dim, numpy.uint8) 
    4537  
    4538 See log for complete Python traceback. 
    4539  
    4540 Traceback (most recent call last): 
    4541 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    4542 packages/chimerax/core/triggerset.py", line 130, in invoke 
    4543 return self._func(self._name, data) 
    4544 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4545 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    4546 self.set_surface_mask() 
    4547 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4548 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    4549 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    4550 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4551 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    4552 self._update_mask() 
    4553 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4554 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    4555 step=self.grid_step, pad=self.pad) 
    4556 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4557 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    4558 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    4559 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4560 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    4561 _generate_data_array 
    4562 data = numpy.zeros(dim, numpy.uint8) 
    4563 ValueError: negative dimensions are not allowed 
    4564  
    4565 Error processing trigger "atom coords updated": 
    4566 ValueError: negative dimensions are not allowed 
    4567  
    4568 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4569 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    4570 _generate_data_array 
    4571 data = numpy.zeros(dim, numpy.uint8) 
    4572  
    4573 See log for complete Python traceback. 
    4574  
    4575 Traceback (most recent call last): 
    4576 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    4577 packages/chimerax/core/triggerset.py", line 130, in invoke 
    4578 return self._func(self._name, data) 
    4579 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4580 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    4581 self.set_surface_mask() 
    4582 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4583 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    4584 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    4585 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4586 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    4587 self._update_mask() 
    4588 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4589 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    4590 step=self.grid_step, pad=self.pad) 
    4591 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4592 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    4593 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    4594 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4595 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    4596 _generate_data_array 
    4597 data = numpy.zeros(dim, numpy.uint8) 
    4598 ValueError: negative dimensions are not allowed 
    4599  
    4600 Error processing trigger "atom coords updated": 
    4601 ValueError: negative dimensions are not allowed 
    4602  
    4603 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4604 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    4605 _generate_data_array 
    4606 data = numpy.zeros(dim, numpy.uint8) 
    4607  
    4608 See log for complete Python traceback. 
    4609  
    4610 Traceback (most recent call last): 
    4611 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    4612 packages/chimerax/core/triggerset.py", line 130, in invoke 
    4613 return self._func(self._name, data) 
    4614 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4615 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    4616 self.set_surface_mask() 
    4617 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4618 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    4619 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    4620 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4621 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    4622 self._update_mask() 
    4623 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4624 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    4625 step=self.grid_step, pad=self.pad) 
    4626 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4627 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    4628 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    4629 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4630 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    4631 _generate_data_array 
    4632 data = numpy.zeros(dim, numpy.uint8) 
    4633 ValueError: negative dimensions are not allowed 
    4634  
    4635 Error processing trigger "atom coords updated": 
    4636 ValueError: negative dimensions are not allowed 
    4637  
    4638 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4639 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    4640 _generate_data_array 
    4641 data = numpy.zeros(dim, numpy.uint8) 
    4642  
    4643 See log for complete Python traceback. 
    4644  
    4645 Traceback (most recent call last): 
    4646 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    4647 packages/chimerax/core/triggerset.py", line 130, in invoke 
    4648 return self._func(self._name, data) 
    4649 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4650 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    4651 self.set_surface_mask() 
    4652 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4653 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    4654 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    4655 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4656 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    4657 self._update_mask() 
    4658 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4659 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    4660 step=self.grid_step, pad=self.pad) 
    4661 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4662 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    4663 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    4664 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4665 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    4666 _generate_data_array 
    4667 data = numpy.zeros(dim, numpy.uint8) 
    4668 ValueError: negative dimensions are not allowed 
    4669  
    4670 Error processing trigger "atom coords updated": 
    4671 ValueError: negative dimensions are not allowed 
    4672  
    4673 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4674 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    4675 _generate_data_array 
    4676 data = numpy.zeros(dim, numpy.uint8) 
    4677  
    4678 See log for complete Python traceback. 
    4679  
    4680 Traceback (most recent call last): 
    4681 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    4682 packages/chimerax/core/triggerset.py", line 130, in invoke 
    4683 return self._func(self._name, data) 
    4684 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4685 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    4686 self.set_surface_mask() 
    4687 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4688 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    4689 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    4690 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4691 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    4692 self._update_mask() 
    4693 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4694 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    4695 step=self.grid_step, pad=self.pad) 
    4696 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4697 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    4698 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    4699 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4700 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    4701 _generate_data_array 
    4702 data = numpy.zeros(dim, numpy.uint8) 
    4703 ValueError: negative dimensions are not allowed 
    4704  
    4705 Error processing trigger "atom coords updated": 
    4706 ValueError: negative dimensions are not allowed 
    4707  
    4708 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4709 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    4710 _generate_data_array 
    4711 data = numpy.zeros(dim, numpy.uint8) 
    4712  
    4713 See log for complete Python traceback. 
    4714  
    4715 Traceback (most recent call last): 
    4716 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    4717 packages/chimerax/core/triggerset.py", line 130, in invoke 
    4718 return self._func(self._name, data) 
    4719 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4720 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    4721 self.set_surface_mask() 
    4722 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4723 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    4724 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    4725 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4726 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    4727 self._update_mask() 
    4728 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4729 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    4730 step=self.grid_step, pad=self.pad) 
    4731 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4732 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    4733 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    4734 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4735 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    4736 _generate_data_array 
    4737 data = numpy.zeros(dim, numpy.uint8) 
    4738 ValueError: negative dimensions are not allowed 
    4739  
    4740 Error processing trigger "atom coords updated": 
    4741 ValueError: negative dimensions are not allowed 
    4742  
    4743 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4744 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    4745 _generate_data_array 
    4746 data = numpy.zeros(dim, numpy.uint8) 
    4747  
    4748 See log for complete Python traceback. 
    4749  
    4750 Traceback (most recent call last): 
    4751 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    4752 packages/chimerax/core/triggerset.py", line 130, in invoke 
    4753 return self._func(self._name, data) 
    4754 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4755 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    4756 self.set_surface_mask() 
    4757 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4758 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    4759 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    4760 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4761 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    4762 self._update_mask() 
    4763 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4764 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    4765 step=self.grid_step, pad=self.pad) 
    4766 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4767 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    4768 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    4769 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4770 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    4771 _generate_data_array 
    4772 data = numpy.zeros(dim, numpy.uint8) 
    4773 ValueError: negative dimensions are not allowed 
    4774  
    4775 Error processing trigger "atom coords updated": 
    4776 ValueError: negative dimensions are not allowed 
    4777  
    4778 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4779 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    4780 _generate_data_array 
    4781 data = numpy.zeros(dim, numpy.uint8) 
    4782  
    4783 See log for complete Python traceback. 
    4784  
    4785 Traceback (most recent call last): 
    4786 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    4787 packages/chimerax/core/triggerset.py", line 130, in invoke 
    4788 return self._func(self._name, data) 
    4789 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4790 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    4791 self.set_surface_mask() 
    4792 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4793 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    4794 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    4795 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4796 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    4797 self._update_mask() 
    4798 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4799 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    4800 step=self.grid_step, pad=self.pad) 
    4801 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4802 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    4803 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    4804 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4805 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    4806 _generate_data_array 
    4807 data = numpy.zeros(dim, numpy.uint8) 
    4808 ValueError: negative dimensions are not allowed 
    4809  
    4810 Error processing trigger "atom coords updated": 
    4811 ValueError: negative dimensions are not allowed 
    4812  
    4813 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4814 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    4815 _generate_data_array 
    4816 data = numpy.zeros(dim, numpy.uint8) 
    4817  
    4818 See log for complete Python traceback. 
    4819  
    4820 Traceback (most recent call last): 
    4821 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    4822 packages/chimerax/core/triggerset.py", line 130, in invoke 
    4823 return self._func(self._name, data) 
    4824 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4825 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    4826 self.set_surface_mask() 
    4827 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4828 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    4829 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    4830 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4831 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    4832 self._update_mask() 
    4833 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4834 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    4835 step=self.grid_step, pad=self.pad) 
    4836 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4837 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    4838 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    4839 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4840 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    4841 _generate_data_array 
    4842 data = numpy.zeros(dim, numpy.uint8) 
    4843 ValueError: negative dimensions are not allowed 
    4844  
    4845 Error processing trigger "atom coords updated": 
    4846 ValueError: negative dimensions are not allowed 
    4847  
    4848 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4849 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    4850 _generate_data_array 
    4851 data = numpy.zeros(dim, numpy.uint8) 
    4852  
    4853 See log for complete Python traceback. 
    4854  
    4855 Traceback (most recent call last): 
    4856 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    4857 packages/chimerax/core/triggerset.py", line 130, in invoke 
    4858 return self._func(self._name, data) 
    4859 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4860 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    4861 self.set_surface_mask() 
    4862 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4863 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    4864 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    4865 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4866 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    4867 self._update_mask() 
    4868 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4869 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    4870 step=self.grid_step, pad=self.pad) 
    4871 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4872 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    4873 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    4874 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4875 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    4876 _generate_data_array 
    4877 data = numpy.zeros(dim, numpy.uint8) 
    4878 ValueError: negative dimensions are not allowed 
    4879  
    4880 Error processing trigger "atom coords updated": 
    4881 ValueError: negative dimensions are not allowed 
    4882  
    4883 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4884 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    4885 _generate_data_array 
    4886 data = numpy.zeros(dim, numpy.uint8) 
    4887  
    4888 See log for complete Python traceback. 
    4889  
    4890 Traceback (most recent call last): 
    4891 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    4892 packages/chimerax/core/triggerset.py", line 130, in invoke 
    4893 return self._func(self._name, data) 
    4894 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4895 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    4896 self.set_surface_mask() 
    4897 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4898 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    4899 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    4900 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4901 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    4902 self._update_mask() 
    4903 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4904 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    4905 step=self.grid_step, pad=self.pad) 
    4906 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4907 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    4908 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    4909 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4910 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    4911 _generate_data_array 
    4912 data = numpy.zeros(dim, numpy.uint8) 
    4913 ValueError: negative dimensions are not allowed 
    4914  
    4915 Error processing trigger "atom coords updated": 
    4916 ValueError: negative dimensions are not allowed 
    4917  
    4918 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4919 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    4920 _generate_data_array 
    4921 data = numpy.zeros(dim, numpy.uint8) 
    4922  
    4923 See log for complete Python traceback. 
    4924  
    4925 Traceback (most recent call last): 
    4926 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    4927 packages/chimerax/core/triggerset.py", line 130, in invoke 
    4928 return self._func(self._name, data) 
    4929 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4930 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    4931 self.set_surface_mask() 
    4932 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4933 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    4934 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    4935 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4936 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    4937 self._update_mask() 
    4938 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4939 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    4940 step=self.grid_step, pad=self.pad) 
    4941 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4942 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    4943 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    4944 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4945 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    4946 _generate_data_array 
    4947 data = numpy.zeros(dim, numpy.uint8) 
    4948 ValueError: negative dimensions are not allowed 
    4949  
    4950 Error processing trigger "atom coords updated": 
    4951 ValueError: negative dimensions are not allowed 
    4952  
    4953 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4954 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    4955 _generate_data_array 
    4956 data = numpy.zeros(dim, numpy.uint8) 
    4957  
    4958 See log for complete Python traceback. 
    4959  
    4960 Traceback (most recent call last): 
    4961 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    4962 packages/chimerax/core/triggerset.py", line 130, in invoke 
    4963 return self._func(self._name, data) 
    4964 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4965 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    4966 self.set_surface_mask() 
    4967 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4968 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    4969 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    4970 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4971 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    4972 self._update_mask() 
    4973 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4974 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    4975 step=self.grid_step, pad=self.pad) 
    4976 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4977 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    4978 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    4979 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4980 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    4981 _generate_data_array 
    4982 data = numpy.zeros(dim, numpy.uint8) 
    4983 ValueError: negative dimensions are not allowed 
    4984  
    4985 Error processing trigger "atom coords updated": 
    4986 ValueError: negative dimensions are not allowed 
    4987  
    4988 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    4989 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    4990 _generate_data_array 
    4991 data = numpy.zeros(dim, numpy.uint8) 
    4992  
    4993 See log for complete Python traceback. 
    4994  
    4995 Traceback (most recent call last): 
    4996 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    4997 packages/chimerax/core/triggerset.py", line 130, in invoke 
    4998 return self._func(self._name, data) 
    4999 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5000 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    5001 self.set_surface_mask() 
    5002 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5003 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    5004 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    5005 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5006 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    5007 self._update_mask() 
    5008 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5009 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    5010 step=self.grid_step, pad=self.pad) 
    5011 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5012 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    5013 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    5014 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5015 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    5016 _generate_data_array 
    5017 data = numpy.zeros(dim, numpy.uint8) 
    5018 ValueError: negative dimensions are not allowed 
    5019  
    5020 Error processing trigger "atom coords updated": 
    5021 ValueError: negative dimensions are not allowed 
    5022  
    5023 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5024 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    5025 _generate_data_array 
    5026 data = numpy.zeros(dim, numpy.uint8) 
    5027  
    5028 See log for complete Python traceback. 
    5029  
    5030 Traceback (most recent call last): 
    5031 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    5032 packages/chimerax/core/triggerset.py", line 130, in invoke 
    5033 return self._func(self._name, data) 
    5034 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5035 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    5036 self.set_surface_mask() 
    5037 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5038 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    5039 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    5040 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5041 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    5042 self._update_mask() 
    5043 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5044 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    5045 step=self.grid_step, pad=self.pad) 
    5046 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5047 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    5048 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    5049 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5050 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    5051 _generate_data_array 
    5052 data = numpy.zeros(dim, numpy.uint8) 
    5053 ValueError: negative dimensions are not allowed 
    5054  
    5055 Error processing trigger "atom coords updated": 
    5056 ValueError: negative dimensions are not allowed 
    5057  
    5058 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5059 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    5060 _generate_data_array 
    5061 data = numpy.zeros(dim, numpy.uint8) 
    5062  
    5063 See log for complete Python traceback. 
    5064  
    5065 Traceback (most recent call last): 
    5066 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    5067 packages/chimerax/core/triggerset.py", line 130, in invoke 
    5068 return self._func(self._name, data) 
    5069 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5070 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    5071 self.set_surface_mask() 
    5072 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5073 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    5074 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    5075 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5076 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    5077 self._update_mask() 
    5078 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5079 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    5080 step=self.grid_step, pad=self.pad) 
    5081 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5082 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    5083 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    5084 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5085 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    5086 _generate_data_array 
    5087 data = numpy.zeros(dim, numpy.uint8) 
    5088 ValueError: negative dimensions are not allowed 
    5089  
    5090 Error processing trigger "atom coords updated": 
    5091 ValueError: negative dimensions are not allowed 
    5092  
    5093 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5094 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    5095 _generate_data_array 
    5096 data = numpy.zeros(dim, numpy.uint8) 
    5097  
    5098 See log for complete Python traceback. 
    5099  
    5100 Traceback (most recent call last): 
    5101 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    5102 packages/chimerax/core/triggerset.py", line 130, in invoke 
    5103 return self._func(self._name, data) 
    5104 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5105 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    5106 self.set_surface_mask() 
    5107 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5108 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    5109 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    5110 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5111 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    5112 self._update_mask() 
    5113 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5114 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    5115 step=self.grid_step, pad=self.pad) 
    5116 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5117 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    5118 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    5119 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5120 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    5121 _generate_data_array 
    5122 data = numpy.zeros(dim, numpy.uint8) 
    5123 ValueError: negative dimensions are not allowed 
    5124  
    5125 Error processing trigger "atom coords updated": 
    5126 ValueError: negative dimensions are not allowed 
    5127  
    5128 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5129 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    5130 _generate_data_array 
    5131 data = numpy.zeros(dim, numpy.uint8) 
    5132  
    5133 See log for complete Python traceback. 
    5134  
    5135 Traceback (most recent call last): 
    5136 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    5137 packages/chimerax/core/triggerset.py", line 130, in invoke 
    5138 return self._func(self._name, data) 
    5139 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5140 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    5141 self.set_surface_mask() 
    5142 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5143 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    5144 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    5145 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5146 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    5147 self._update_mask() 
    5148 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5149 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    5150 step=self.grid_step, pad=self.pad) 
    5151 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5152 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    5153 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    5154 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5155 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    5156 _generate_data_array 
    5157 data = numpy.zeros(dim, numpy.uint8) 
    5158 ValueError: negative dimensions are not allowed 
    5159  
    5160 Error processing trigger "atom coords updated": 
    5161 ValueError: negative dimensions are not allowed 
    5162  
    5163 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5164 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    5165 _generate_data_array 
    5166 data = numpy.zeros(dim, numpy.uint8) 
    5167  
    5168 See log for complete Python traceback. 
    5169  
    5170 Traceback (most recent call last): 
    5171 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    5172 packages/chimerax/core/triggerset.py", line 130, in invoke 
    5173 return self._func(self._name, data) 
    5174 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5175 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    5176 self.set_surface_mask() 
    5177 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5178 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    5179 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    5180 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5181 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    5182 self._update_mask() 
    5183 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5184 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    5185 step=self.grid_step, pad=self.pad) 
    5186 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5187 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    5188 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    5189 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5190 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    5191 _generate_data_array 
    5192 data = numpy.zeros(dim, numpy.uint8) 
    5193 ValueError: negative dimensions are not allowed 
    5194  
    5195 Error processing trigger "atom coords updated": 
    5196 ValueError: negative dimensions are not allowed 
    5197  
    5198 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5199 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    5200 _generate_data_array 
    5201 data = numpy.zeros(dim, numpy.uint8) 
    5202  
    5203 See log for complete Python traceback. 
    5204  
    5205 Traceback (most recent call last): 
    5206 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    5207 packages/chimerax/core/triggerset.py", line 130, in invoke 
    5208 return self._func(self._name, data) 
    5209 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5210 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    5211 self.set_surface_mask() 
    5212 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5213 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    5214 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    5215 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5216 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    5217 self._update_mask() 
    5218 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5219 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    5220 step=self.grid_step, pad=self.pad) 
    5221 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5222 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    5223 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    5224 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5225 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    5226 _generate_data_array 
    5227 data = numpy.zeros(dim, numpy.uint8) 
    5228 ValueError: negative dimensions are not allowed 
    5229  
    5230 Error processing trigger "atom coords updated": 
    5231 ValueError: negative dimensions are not allowed 
    5232  
    5233 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5234 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    5235 _generate_data_array 
    5236 data = numpy.zeros(dim, numpy.uint8) 
    5237  
    5238 See log for complete Python traceback. 
    5239  
    5240 Traceback (most recent call last): 
    5241 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    5242 packages/chimerax/core/triggerset.py", line 130, in invoke 
    5243 return self._func(self._name, data) 
    5244 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5245 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    5246 self.set_surface_mask() 
    5247 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5248 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    5249 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    5250 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5251 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    5252 self._update_mask() 
    5253 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5254 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    5255 step=self.grid_step, pad=self.pad) 
    5256 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5257 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    5258 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    5259 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5260 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    5261 _generate_data_array 
    5262 data = numpy.zeros(dim, numpy.uint8) 
    5263 ValueError: negative dimensions are not allowed 
    5264  
    5265 Error processing trigger "atom coords updated": 
    5266 ValueError: negative dimensions are not allowed 
    5267  
    5268 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5269 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    5270 _generate_data_array 
    5271 data = numpy.zeros(dim, numpy.uint8) 
    5272  
    5273 See log for complete Python traceback. 
    5274  
    5275 Traceback (most recent call last): 
    5276 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    5277 packages/chimerax/core/triggerset.py", line 130, in invoke 
    5278 return self._func(self._name, data) 
    5279 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5280 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    5281 self.set_surface_mask() 
    5282 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5283 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    5284 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    5285 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5286 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    5287 self._update_mask() 
    5288 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5289 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    5290 step=self.grid_step, pad=self.pad) 
    5291 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5292 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    5293 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    5294 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5295 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    5296 _generate_data_array 
    5297 data = numpy.zeros(dim, numpy.uint8) 
    5298 ValueError: negative dimensions are not allowed 
    5299  
    5300 Error processing trigger "atom coords updated": 
    5301 ValueError: negative dimensions are not allowed 
    5302  
    5303 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5304 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    5305 _generate_data_array 
    5306 data = numpy.zeros(dim, numpy.uint8) 
    5307  
    5308 See log for complete Python traceback. 
    5309  
    5310 Traceback (most recent call last): 
    5311 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    5312 packages/chimerax/core/triggerset.py", line 130, in invoke 
    5313 return self._func(self._name, data) 
    5314 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5315 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    5316 self.set_surface_mask() 
    5317 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5318 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    5319 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    5320 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5321 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    5322 self._update_mask() 
    5323 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5324 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    5325 step=self.grid_step, pad=self.pad) 
    5326 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5327 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    5328 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    5329 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5330 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    5331 _generate_data_array 
    5332 data = numpy.zeros(dim, numpy.uint8) 
    5333 ValueError: negative dimensions are not allowed 
    5334  
    5335 Error processing trigger "atom coords updated": 
    5336 ValueError: negative dimensions are not allowed 
    5337  
    5338 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5339 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    5340 _generate_data_array 
    5341 data = numpy.zeros(dim, numpy.uint8) 
    5342  
    5343 See log for complete Python traceback. 
    5344  
    5345 Traceback (most recent call last): 
    5346 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    5347 packages/chimerax/core/triggerset.py", line 130, in invoke 
    5348 return self._func(self._name, data) 
    5349 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5350 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    5351 self.set_surface_mask() 
    5352 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5353 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    5354 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    5355 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5356 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    5357 self._update_mask() 
    5358 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5359 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    5360 step=self.grid_step, pad=self.pad) 
    5361 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5362 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    5363 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    5364 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5365 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    5366 _generate_data_array 
    5367 data = numpy.zeros(dim, numpy.uint8) 
    5368 ValueError: negative dimensions are not allowed 
    5369  
    5370 Error processing trigger "atom coords updated": 
    5371 ValueError: negative dimensions are not allowed 
    5372  
    5373 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5374 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    5375 _generate_data_array 
    5376 data = numpy.zeros(dim, numpy.uint8) 
    5377  
    5378 See log for complete Python traceback. 
    5379  
    5380 Traceback (most recent call last): 
    5381 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    5382 packages/chimerax/core/triggerset.py", line 130, in invoke 
    5383 return self._func(self._name, data) 
    5384 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5385 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    5386 self.set_surface_mask() 
    5387 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5388 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    5389 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    5390 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5391 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    5392 self._update_mask() 
    5393 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5394 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    5395 step=self.grid_step, pad=self.pad) 
    5396 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5397 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    5398 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    5399 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5400 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    5401 _generate_data_array 
    5402 data = numpy.zeros(dim, numpy.uint8) 
    5403 ValueError: negative dimensions are not allowed 
    5404  
    5405 Error processing trigger "atom coords updated": 
    5406 ValueError: negative dimensions are not allowed 
    5407  
    5408 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5409 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    5410 _generate_data_array 
    5411 data = numpy.zeros(dim, numpy.uint8) 
    5412  
    5413 See log for complete Python traceback. 
    5414  
    5415 Traceback (most recent call last): 
    5416 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    5417 packages/chimerax/core/triggerset.py", line 130, in invoke 
    5418 return self._func(self._name, data) 
    5419 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5420 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    5421 self.set_surface_mask() 
    5422 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5423 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    5424 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    5425 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5426 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    5427 self._update_mask() 
    5428 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5429 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    5430 step=self.grid_step, pad=self.pad) 
    5431 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5432 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    5433 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    5434 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5435 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    5436 _generate_data_array 
    5437 data = numpy.zeros(dim, numpy.uint8) 
    5438 ValueError: negative dimensions are not allowed 
    5439  
    5440 Error processing trigger "atom coords updated": 
    5441 ValueError: negative dimensions are not allowed 
    5442  
    5443 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5444 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    5445 _generate_data_array 
    5446 data = numpy.zeros(dim, numpy.uint8) 
    5447  
    5448 See log for complete Python traceback. 
    5449  
    5450 Traceback (most recent call last): 
    5451 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    5452 packages/chimerax/core/triggerset.py", line 130, in invoke 
    5453 return self._func(self._name, data) 
    5454 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5455 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    5456 self.set_surface_mask() 
    5457 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5458 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    5459 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    5460 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5461 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    5462 self._update_mask() 
    5463 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5464 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    5465 step=self.grid_step, pad=self.pad) 
    5466 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5467 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    5468 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    5469 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5470 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    5471 _generate_data_array 
    5472 data = numpy.zeros(dim, numpy.uint8) 
    5473 ValueError: negative dimensions are not allowed 
    5474  
    5475 Error processing trigger "atom coords updated": 
    5476 ValueError: negative dimensions are not allowed 
    5477  
    5478 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5479 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    5480 _generate_data_array 
    5481 data = numpy.zeros(dim, numpy.uint8) 
    5482  
    5483 See log for complete Python traceback. 
    5484  
    5485 Traceback (most recent call last): 
    5486 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    5487 packages/chimerax/core/triggerset.py", line 130, in invoke 
    5488 return self._func(self._name, data) 
    5489 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5490 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    5491 self.set_surface_mask() 
    5492 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5493 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    5494 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    5495 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5496 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    5497 self._update_mask() 
    5498 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5499 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    5500 step=self.grid_step, pad=self.pad) 
    5501 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5502 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    5503 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    5504 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5505 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    5506 _generate_data_array 
    5507 data = numpy.zeros(dim, numpy.uint8) 
    5508 ValueError: negative dimensions are not allowed 
    5509  
    5510 Error processing trigger "atom coords updated": 
    5511 ValueError: negative dimensions are not allowed 
    5512  
    5513 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5514 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    5515 _generate_data_array 
    5516 data = numpy.zeros(dim, numpy.uint8) 
    5517  
    5518 See log for complete Python traceback. 
    5519  
    5520 Traceback (most recent call last): 
    5521 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    5522 packages/chimerax/core/triggerset.py", line 130, in invoke 
    5523 return self._func(self._name, data) 
    5524 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5525 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    5526 self.set_surface_mask() 
    5527 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5528 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    5529 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    5530 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5531 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    5532 self._update_mask() 
    5533 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5534 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    5535 step=self.grid_step, pad=self.pad) 
    5536 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5537 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    5538 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    5539 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5540 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    5541 _generate_data_array 
    5542 data = numpy.zeros(dim, numpy.uint8) 
    5543 ValueError: negative dimensions are not allowed 
    5544  
    5545 Error processing trigger "atom coords updated": 
    5546 ValueError: negative dimensions are not allowed 
    5547  
    5548 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5549 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    5550 _generate_data_array 
    5551 data = numpy.zeros(dim, numpy.uint8) 
    5552  
    5553 See log for complete Python traceback. 
    5554  
    5555 Traceback (most recent call last): 
    5556 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    5557 packages/chimerax/core/triggerset.py", line 130, in invoke 
    5558 return self._func(self._name, data) 
    5559 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5560 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    5561 self.set_surface_mask() 
    5562 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5563 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    5564 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    5565 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5566 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    5567 self._update_mask() 
    5568 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5569 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    5570 step=self.grid_step, pad=self.pad) 
    5571 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5572 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    5573 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    5574 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5575 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    5576 _generate_data_array 
    5577 data = numpy.zeros(dim, numpy.uint8) 
    5578 ValueError: negative dimensions are not allowed 
    5579  
    5580 Error processing trigger "atom coords updated": 
    5581 ValueError: negative dimensions are not allowed 
    5582  
    5583 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5584 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    5585 _generate_data_array 
    5586 data = numpy.zeros(dim, numpy.uint8) 
    5587  
    5588 See log for complete Python traceback. 
    5589  
    5590 Traceback (most recent call last): 
    5591 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    5592 packages/chimerax/core/triggerset.py", line 130, in invoke 
    5593 return self._func(self._name, data) 
    5594 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5595 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    5596 self.set_surface_mask() 
    5597 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5598 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    5599 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    5600 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5601 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    5602 self._update_mask() 
    5603 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5604 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    5605 step=self.grid_step, pad=self.pad) 
    5606 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5607 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    5608 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    5609 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5610 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    5611 _generate_data_array 
    5612 data = numpy.zeros(dim, numpy.uint8) 
    5613 ValueError: negative dimensions are not allowed 
    5614  
    5615 Error processing trigger "atom coords updated": 
    5616 ValueError: negative dimensions are not allowed 
    5617  
    5618 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5619 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    5620 _generate_data_array 
    5621 data = numpy.zeros(dim, numpy.uint8) 
    5622  
    5623 See log for complete Python traceback. 
    5624  
    5625 Traceback (most recent call last): 
    5626 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    5627 packages/chimerax/core/triggerset.py", line 130, in invoke 
    5628 return self._func(self._name, data) 
    5629 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5630 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    5631 self.set_surface_mask() 
    5632 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5633 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    5634 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    5635 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5636 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    5637 self._update_mask() 
    5638 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5639 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    5640 step=self.grid_step, pad=self.pad) 
    5641 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5642 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    5643 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    5644 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5645 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    5646 _generate_data_array 
    5647 data = numpy.zeros(dim, numpy.uint8) 
    5648 ValueError: negative dimensions are not allowed 
    5649  
    5650 Error processing trigger "atom coords updated": 
    5651 ValueError: negative dimensions are not allowed 
    5652  
    5653 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5654 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    5655 _generate_data_array 
    5656 data = numpy.zeros(dim, numpy.uint8) 
    5657  
    5658 See log for complete Python traceback. 
    5659  
    5660 Traceback (most recent call last): 
    5661 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    5662 packages/chimerax/core/triggerset.py", line 130, in invoke 
    5663 return self._func(self._name, data) 
    5664 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5665 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    5666 self.set_surface_mask() 
    5667 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5668 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    5669 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    5670 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5671 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    5672 self._update_mask() 
    5673 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5674 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    5675 step=self.grid_step, pad=self.pad) 
    5676 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5677 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    5678 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    5679 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5680 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    5681 _generate_data_array 
    5682 data = numpy.zeros(dim, numpy.uint8) 
    5683 ValueError: negative dimensions are not allowed 
    5684  
    5685 Error processing trigger "atom coords updated": 
    5686 ValueError: negative dimensions are not allowed 
    5687  
    5688 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5689 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    5690 _generate_data_array 
    5691 data = numpy.zeros(dim, numpy.uint8) 
    5692  
    5693 See log for complete Python traceback. 
    5694  
    5695 Traceback (most recent call last): 
    5696 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    5697 packages/chimerax/core/triggerset.py", line 130, in invoke 
    5698 return self._func(self._name, data) 
    5699 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5700 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    5701 self.set_surface_mask() 
    5702 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5703 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    5704 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    5705 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5706 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    5707 self._update_mask() 
    5708 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5709 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    5710 step=self.grid_step, pad=self.pad) 
    5711 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5712 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    5713 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    5714 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5715 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    5716 _generate_data_array 
    5717 data = numpy.zeros(dim, numpy.uint8) 
    5718 ValueError: negative dimensions are not allowed 
    5719  
    5720 Error processing trigger "atom coords updated": 
    5721 ValueError: negative dimensions are not allowed 
    5722  
    5723 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5724 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    5725 _generate_data_array 
    5726 data = numpy.zeros(dim, numpy.uint8) 
    5727  
    5728 See log for complete Python traceback. 
    5729  
    5730 Traceback (most recent call last): 
    5731 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    5732 packages/chimerax/core/triggerset.py", line 130, in invoke 
    5733 return self._func(self._name, data) 
    5734 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5735 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    5736 self.set_surface_mask() 
    5737 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5738 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    5739 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    5740 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5741 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    5742 self._update_mask() 
    5743 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5744 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    5745 step=self.grid_step, pad=self.pad) 
    5746 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5747 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    5748 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    5749 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5750 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    5751 _generate_data_array 
    5752 data = numpy.zeros(dim, numpy.uint8) 
    5753 ValueError: negative dimensions are not allowed 
    5754  
    5755 Error processing trigger "atom coords updated": 
    5756 ValueError: negative dimensions are not allowed 
    5757  
    5758 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5759 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    5760 _generate_data_array 
    5761 data = numpy.zeros(dim, numpy.uint8) 
    5762  
    5763 See log for complete Python traceback. 
    5764  
    5765 Traceback (most recent call last): 
    5766 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    5767 packages/chimerax/core/triggerset.py", line 130, in invoke 
    5768 return self._func(self._name, data) 
    5769 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5770 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    5771 self.set_surface_mask() 
    5772 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5773 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    5774 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    5775 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5776 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    5777 self._update_mask() 
    5778 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5779 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    5780 step=self.grid_step, pad=self.pad) 
    5781 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5782 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    5783 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    5784 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5785 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    5786 _generate_data_array 
    5787 data = numpy.zeros(dim, numpy.uint8) 
    5788 ValueError: negative dimensions are not allowed 
    5789  
    5790 Error processing trigger "atom coords updated": 
    5791 ValueError: negative dimensions are not allowed 
    5792  
    5793 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5794 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    5795 _generate_data_array 
    5796 data = numpy.zeros(dim, numpy.uint8) 
    5797  
    5798 See log for complete Python traceback. 
    5799  
    5800 Traceback (most recent call last): 
    5801 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    5802 packages/chimerax/core/triggerset.py", line 130, in invoke 
    5803 return self._func(self._name, data) 
    5804 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5805 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    5806 self.set_surface_mask() 
    5807 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5808 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    5809 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    5810 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5811 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    5812 self._update_mask() 
    5813 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5814 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    5815 step=self.grid_step, pad=self.pad) 
    5816 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5817 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    5818 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    5819 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5820 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    5821 _generate_data_array 
    5822 data = numpy.zeros(dim, numpy.uint8) 
    5823 ValueError: negative dimensions are not allowed 
    5824  
    5825 Error processing trigger "atom coords updated": 
    5826 ValueError: negative dimensions are not allowed 
    5827  
    5828 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5829 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    5830 _generate_data_array 
    5831 data = numpy.zeros(dim, numpy.uint8) 
    5832  
    5833 See log for complete Python traceback. 
    5834  
    5835 Traceback (most recent call last): 
    5836 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    5837 packages/chimerax/core/triggerset.py", line 130, in invoke 
    5838 return self._func(self._name, data) 
    5839 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5840 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    5841 self.set_surface_mask() 
    5842 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5843 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    5844 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    5845 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5846 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    5847 self._update_mask() 
    5848 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5849 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    5850 step=self.grid_step, pad=self.pad) 
    5851 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5852 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    5853 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    5854 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5855 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    5856 _generate_data_array 
    5857 data = numpy.zeros(dim, numpy.uint8) 
    5858 ValueError: negative dimensions are not allowed 
    5859  
    5860 Error processing trigger "atom coords updated": 
    5861 ValueError: negative dimensions are not allowed 
    5862  
    5863 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5864 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    5865 _generate_data_array 
    5866 data = numpy.zeros(dim, numpy.uint8) 
    5867  
    5868 See log for complete Python traceback. 
    5869  
    5870 Traceback (most recent call last): 
    5871 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    5872 packages/chimerax/core/triggerset.py", line 130, in invoke 
    5873 return self._func(self._name, data) 
    5874 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5875 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    5876 self.set_surface_mask() 
    5877 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5878 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    5879 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    5880 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5881 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    5882 self._update_mask() 
    5883 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5884 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    5885 step=self.grid_step, pad=self.pad) 
    5886 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5887 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    5888 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    5889 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5890 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    5891 _generate_data_array 
    5892 data = numpy.zeros(dim, numpy.uint8) 
    5893 ValueError: negative dimensions are not allowed 
    5894  
    5895 Error processing trigger "atom coords updated": 
    5896 ValueError: negative dimensions are not allowed 
    5897  
    5898 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5899 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    5900 _generate_data_array 
    5901 data = numpy.zeros(dim, numpy.uint8) 
    5902  
    5903 See log for complete Python traceback. 
    5904  
    5905 Traceback (most recent call last): 
    5906 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    5907 packages/chimerax/core/triggerset.py", line 130, in invoke 
    5908 return self._func(self._name, data) 
    5909 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5910 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    5911 self.set_surface_mask() 
    5912 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5913 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    5914 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    5915 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5916 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    5917 self._update_mask() 
    5918 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5919 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    5920 step=self.grid_step, pad=self.pad) 
    5921 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5922 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    5923 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    5924 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5925 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    5926 _generate_data_array 
    5927 data = numpy.zeros(dim, numpy.uint8) 
    5928 ValueError: negative dimensions are not allowed 
    5929  
    5930 Error processing trigger "atom coords updated": 
    5931 ValueError: negative dimensions are not allowed 
    5932  
    5933 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5934 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    5935 _generate_data_array 
    5936 data = numpy.zeros(dim, numpy.uint8) 
    5937  
    5938 See log for complete Python traceback. 
    5939  
    5940 Traceback (most recent call last): 
    5941 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    5942 packages/chimerax/core/triggerset.py", line 130, in invoke 
    5943 return self._func(self._name, data) 
    5944 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5945 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    5946 self.set_surface_mask() 
    5947 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5948 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    5949 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    5950 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5951 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    5952 self._update_mask() 
    5953 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5954 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    5955 step=self.grid_step, pad=self.pad) 
    5956 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5957 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    5958 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    5959 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5960 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    5961 _generate_data_array 
    5962 data = numpy.zeros(dim, numpy.uint8) 
    5963 ValueError: negative dimensions are not allowed 
    5964  
    5965 Error processing trigger "atom coords updated": 
    5966 ValueError: negative dimensions are not allowed 
    5967  
    5968 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5969 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    5970 _generate_data_array 
    5971 data = numpy.zeros(dim, numpy.uint8) 
    5972  
    5973 See log for complete Python traceback. 
    5974  
    5975 Traceback (most recent call last): 
    5976 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    5977 packages/chimerax/core/triggerset.py", line 130, in invoke 
    5978 return self._func(self._name, data) 
    5979 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5980 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    5981 self.set_surface_mask() 
    5982 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5983 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    5984 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    5985 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5986 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    5987 self._update_mask() 
    5988 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5989 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    5990 step=self.grid_step, pad=self.pad) 
    5991 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5992 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    5993 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    5994 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    5995 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    5996 _generate_data_array 
    5997 data = numpy.zeros(dim, numpy.uint8) 
    5998 ValueError: negative dimensions are not allowed 
    5999  
    6000 Error processing trigger "atom coords updated": 
    6001 ValueError: negative dimensions are not allowed 
    6002  
    6003 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6004 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    6005 _generate_data_array 
    6006 data = numpy.zeros(dim, numpy.uint8) 
    6007  
    6008 See log for complete Python traceback. 
    6009  
    6010 Traceback (most recent call last): 
    6011 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    6012 packages/chimerax/core/triggerset.py", line 130, in invoke 
    6013 return self._func(self._name, data) 
    6014 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6015 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    6016 self.set_surface_mask() 
    6017 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6018 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    6019 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    6020 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6021 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    6022 self._update_mask() 
    6023 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6024 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    6025 step=self.grid_step, pad=self.pad) 
    6026 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6027 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    6028 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    6029 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6030 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    6031 _generate_data_array 
    6032 data = numpy.zeros(dim, numpy.uint8) 
    6033 ValueError: negative dimensions are not allowed 
    6034  
    6035 Error processing trigger "atom coords updated": 
    6036 ValueError: negative dimensions are not allowed 
    6037  
    6038 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6039 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    6040 _generate_data_array 
    6041 data = numpy.zeros(dim, numpy.uint8) 
    6042  
    6043 See log for complete Python traceback. 
    6044  
    6045 Traceback (most recent call last): 
    6046 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    6047 packages/chimerax/core/triggerset.py", line 130, in invoke 
    6048 return self._func(self._name, data) 
    6049 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6050 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    6051 self.set_surface_mask() 
    6052 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6053 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    6054 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    6055 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6056 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    6057 self._update_mask() 
    6058 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6059 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    6060 step=self.grid_step, pad=self.pad) 
    6061 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6062 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    6063 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    6064 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6065 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    6066 _generate_data_array 
    6067 data = numpy.zeros(dim, numpy.uint8) 
    6068 ValueError: negative dimensions are not allowed 
    6069  
    6070 Error processing trigger "atom coords updated": 
    6071 ValueError: negative dimensions are not allowed 
    6072  
    6073 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6074 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    6075 _generate_data_array 
    6076 data = numpy.zeros(dim, numpy.uint8) 
    6077  
    6078 See log for complete Python traceback. 
    6079  
    6080 Traceback (most recent call last): 
    6081 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    6082 packages/chimerax/core/triggerset.py", line 130, in invoke 
    6083 return self._func(self._name, data) 
    6084 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6085 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    6086 self.set_surface_mask() 
    6087 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6088 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    6089 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    6090 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6091 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    6092 self._update_mask() 
    6093 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6094 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    6095 step=self.grid_step, pad=self.pad) 
    6096 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6097 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    6098 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    6099 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6100 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    6101 _generate_data_array 
    6102 data = numpy.zeros(dim, numpy.uint8) 
    6103 ValueError: negative dimensions are not allowed 
    6104  
    6105 Error processing trigger "atom coords updated": 
    6106 ValueError: negative dimensions are not allowed 
    6107  
    6108 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6109 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    6110 _generate_data_array 
    6111 data = numpy.zeros(dim, numpy.uint8) 
    6112  
    6113 See log for complete Python traceback. 
    6114  
    6115 Traceback (most recent call last): 
    6116 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    6117 packages/chimerax/core/triggerset.py", line 130, in invoke 
    6118 return self._func(self._name, data) 
    6119 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6120 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    6121 self.set_surface_mask() 
    6122 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6123 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    6124 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    6125 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6126 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    6127 self._update_mask() 
    6128 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6129 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    6130 step=self.grid_step, pad=self.pad) 
    6131 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6132 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    6133 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    6134 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6135 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    6136 _generate_data_array 
    6137 data = numpy.zeros(dim, numpy.uint8) 
    6138 ValueError: negative dimensions are not allowed 
    6139  
    6140 Error processing trigger "atom coords updated": 
    6141 ValueError: negative dimensions are not allowed 
    6142  
    6143 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6144 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    6145 _generate_data_array 
    6146 data = numpy.zeros(dim, numpy.uint8) 
    6147  
    6148 See log for complete Python traceback. 
    6149  
    6150 Traceback (most recent call last): 
    6151 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    6152 packages/chimerax/core/triggerset.py", line 130, in invoke 
    6153 return self._func(self._name, data) 
    6154 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6155 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    6156 self.set_surface_mask() 
    6157 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6158 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    6159 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    6160 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6161 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    6162 self._update_mask() 
    6163 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6164 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    6165 step=self.grid_step, pad=self.pad) 
    6166 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6167 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    6168 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    6169 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6170 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    6171 _generate_data_array 
    6172 data = numpy.zeros(dim, numpy.uint8) 
    6173 ValueError: negative dimensions are not allowed 
    6174  
    6175 Error processing trigger "atom coords updated": 
    6176 ValueError: negative dimensions are not allowed 
    6177  
    6178 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6179 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    6180 _generate_data_array 
    6181 data = numpy.zeros(dim, numpy.uint8) 
    6182  
    6183 See log for complete Python traceback. 
    6184  
    6185 Traceback (most recent call last): 
    6186 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    6187 packages/chimerax/core/triggerset.py", line 130, in invoke 
    6188 return self._func(self._name, data) 
    6189 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6190 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    6191 self.set_surface_mask() 
    6192 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6193 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    6194 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    6195 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6196 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    6197 self._update_mask() 
    6198 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6199 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    6200 step=self.grid_step, pad=self.pad) 
    6201 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6202 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    6203 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    6204 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6205 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    6206 _generate_data_array 
    6207 data = numpy.zeros(dim, numpy.uint8) 
    6208 ValueError: negative dimensions are not allowed 
    6209  
    6210 Error processing trigger "atom coords updated": 
    6211 ValueError: negative dimensions are not allowed 
    6212  
    6213 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6214 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    6215 _generate_data_array 
    6216 data = numpy.zeros(dim, numpy.uint8) 
    6217  
    6218 See log for complete Python traceback. 
    6219  
    6220 Traceback (most recent call last): 
    6221 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    6222 packages/chimerax/core/triggerset.py", line 130, in invoke 
    6223 return self._func(self._name, data) 
    6224 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6225 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    6226 self.set_surface_mask() 
    6227 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6228 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    6229 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    6230 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6231 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    6232 self._update_mask() 
    6233 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6234 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    6235 step=self.grid_step, pad=self.pad) 
    6236 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6237 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    6238 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    6239 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6240 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    6241 _generate_data_array 
    6242 data = numpy.zeros(dim, numpy.uint8) 
    6243 ValueError: negative dimensions are not allowed 
    6244  
    6245 Error processing trigger "atom coords updated": 
    6246 ValueError: negative dimensions are not allowed 
    6247  
    6248 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6249 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    6250 _generate_data_array 
    6251 data = numpy.zeros(dim, numpy.uint8) 
    6252  
    6253 See log for complete Python traceback. 
    6254  
    6255 Traceback (most recent call last): 
    6256 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    6257 packages/chimerax/core/triggerset.py", line 130, in invoke 
    6258 return self._func(self._name, data) 
    6259 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6260 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    6261 self.set_surface_mask() 
    6262 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6263 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    6264 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    6265 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6266 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    6267 self._update_mask() 
    6268 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6269 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    6270 step=self.grid_step, pad=self.pad) 
    6271 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6272 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    6273 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    6274 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6275 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    6276 _generate_data_array 
    6277 data = numpy.zeros(dim, numpy.uint8) 
    6278 ValueError: negative dimensions are not allowed 
    6279  
    6280 Error processing trigger "atom coords updated": 
    6281 ValueError: negative dimensions are not allowed 
    6282  
    6283 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6284 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    6285 _generate_data_array 
    6286 data = numpy.zeros(dim, numpy.uint8) 
    6287  
    6288 See log for complete Python traceback. 
    6289  
    6290 Traceback (most recent call last): 
    6291 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    6292 packages/chimerax/core/triggerset.py", line 130, in invoke 
    6293 return self._func(self._name, data) 
    6294 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6295 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    6296 self.set_surface_mask() 
    6297 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6298 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    6299 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    6300 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6301 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    6302 self._update_mask() 
    6303 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6304 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    6305 step=self.grid_step, pad=self.pad) 
    6306 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6307 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    6308 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    6309 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6310 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    6311 _generate_data_array 
    6312 data = numpy.zeros(dim, numpy.uint8) 
    6313 ValueError: negative dimensions are not allowed 
    6314  
    6315 Error processing trigger "atom coords updated": 
    6316 ValueError: negative dimensions are not allowed 
    6317  
    6318 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6319 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    6320 _generate_data_array 
    6321 data = numpy.zeros(dim, numpy.uint8) 
    6322  
    6323 See log for complete Python traceback. 
    6324  
    6325 Traceback (most recent call last): 
    6326 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    6327 packages/chimerax/core/triggerset.py", line 130, in invoke 
    6328 return self._func(self._name, data) 
    6329 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6330 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    6331 self.set_surface_mask() 
    6332 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6333 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    6334 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    6335 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6336 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    6337 self._update_mask() 
    6338 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6339 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    6340 step=self.grid_step, pad=self.pad) 
    6341 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6342 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    6343 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    6344 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6345 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    6346 _generate_data_array 
    6347 data = numpy.zeros(dim, numpy.uint8) 
    6348 ValueError: negative dimensions are not allowed 
    6349  
    6350 Error processing trigger "atom coords updated": 
    6351 ValueError: negative dimensions are not allowed 
    6352  
    6353 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6354 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    6355 _generate_data_array 
    6356 data = numpy.zeros(dim, numpy.uint8) 
    6357  
    6358 See log for complete Python traceback. 
    6359  
    6360 Traceback (most recent call last): 
    6361 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    6362 packages/chimerax/core/triggerset.py", line 130, in invoke 
    6363 return self._func(self._name, data) 
    6364 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6365 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    6366 self.set_surface_mask() 
    6367 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6368 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    6369 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    6370 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6371 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    6372 self._update_mask() 
    6373 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6374 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    6375 step=self.grid_step, pad=self.pad) 
    6376 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6377 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    6378 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    6379 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6380 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    6381 _generate_data_array 
    6382 data = numpy.zeros(dim, numpy.uint8) 
    6383 ValueError: negative dimensions are not allowed 
    6384  
    6385 Error processing trigger "atom coords updated": 
    6386 ValueError: negative dimensions are not allowed 
    6387  
    6388 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6389 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    6390 _generate_data_array 
    6391 data = numpy.zeros(dim, numpy.uint8) 
    6392  
    6393 See log for complete Python traceback. 
    6394  
    6395 Traceback (most recent call last): 
    6396 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    6397 packages/chimerax/core/triggerset.py", line 130, in invoke 
    6398 return self._func(self._name, data) 
    6399 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6400 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    6401 self.set_surface_mask() 
    6402 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6403 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    6404 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    6405 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6406 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    6407 self._update_mask() 
    6408 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6409 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    6410 step=self.grid_step, pad=self.pad) 
    6411 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6412 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    6413 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    6414 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6415 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    6416 _generate_data_array 
    6417 data = numpy.zeros(dim, numpy.uint8) 
    6418 ValueError: negative dimensions are not allowed 
    6419  
    6420 Error processing trigger "atom coords updated": 
    6421 ValueError: negative dimensions are not allowed 
    6422  
    6423 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6424 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    6425 _generate_data_array 
    6426 data = numpy.zeros(dim, numpy.uint8) 
    6427  
    6428 See log for complete Python traceback. 
    6429  
    6430 Traceback (most recent call last): 
    6431 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    6432 packages/chimerax/core/triggerset.py", line 130, in invoke 
    6433 return self._func(self._name, data) 
    6434 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6435 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    6436 self.set_surface_mask() 
    6437 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6438 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    6439 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    6440 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6441 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    6442 self._update_mask() 
    6443 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6444 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    6445 step=self.grid_step, pad=self.pad) 
    6446 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6447 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    6448 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    6449 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6450 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    6451 _generate_data_array 
    6452 data = numpy.zeros(dim, numpy.uint8) 
    6453 ValueError: negative dimensions are not allowed 
    6454  
    6455 Error processing trigger "atom coords updated": 
    6456 ValueError: negative dimensions are not allowed 
    6457  
    6458 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6459 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    6460 _generate_data_array 
    6461 data = numpy.zeros(dim, numpy.uint8) 
    6462  
    6463 See log for complete Python traceback. 
    6464  
    6465 Traceback (most recent call last): 
    6466 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    6467 packages/chimerax/core/triggerset.py", line 130, in invoke 
    6468 return self._func(self._name, data) 
    6469 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6470 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    6471 self.set_surface_mask() 
    6472 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6473 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    6474 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    6475 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6476 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    6477 self._update_mask() 
    6478 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6479 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    6480 step=self.grid_step, pad=self.pad) 
    6481 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6482 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    6483 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    6484 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6485 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    6486 _generate_data_array 
    6487 data = numpy.zeros(dim, numpy.uint8) 
    6488 ValueError: negative dimensions are not allowed 
    6489  
    6490 Error processing trigger "atom coords updated": 
    6491 ValueError: negative dimensions are not allowed 
    6492  
    6493 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6494 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    6495 _generate_data_array 
    6496 data = numpy.zeros(dim, numpy.uint8) 
    6497  
    6498 See log for complete Python traceback. 
    6499  
    6500 Traceback (most recent call last): 
    6501 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    6502 packages/chimerax/core/triggerset.py", line 130, in invoke 
    6503 return self._func(self._name, data) 
    6504 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6505 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    6506 self.set_surface_mask() 
    6507 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6508 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    6509 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    6510 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6511 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    6512 self._update_mask() 
    6513 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6514 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    6515 step=self.grid_step, pad=self.pad) 
    6516 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6517 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    6518 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    6519 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6520 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    6521 _generate_data_array 
    6522 data = numpy.zeros(dim, numpy.uint8) 
    6523 ValueError: negative dimensions are not allowed 
    6524  
    6525 Error processing trigger "atom coords updated": 
    6526 ValueError: negative dimensions are not allowed 
    6527  
    6528 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6529 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    6530 _generate_data_array 
    6531 data = numpy.zeros(dim, numpy.uint8) 
    6532  
    6533 See log for complete Python traceback. 
    6534  
    6535 Traceback (most recent call last): 
    6536 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    6537 packages/chimerax/core/triggerset.py", line 130, in invoke 
    6538 return self._func(self._name, data) 
    6539 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6540 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    6541 self.set_surface_mask() 
    6542 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6543 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    6544 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    6545 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6546 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    6547 self._update_mask() 
    6548 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6549 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    6550 step=self.grid_step, pad=self.pad) 
    6551 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6552 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    6553 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    6554 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6555 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    6556 _generate_data_array 
    6557 data = numpy.zeros(dim, numpy.uint8) 
    6558 ValueError: negative dimensions are not allowed 
    6559  
    6560 Error processing trigger "atom coords updated": 
    6561 ValueError: negative dimensions are not allowed 
    6562  
    6563 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6564 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    6565 _generate_data_array 
    6566 data = numpy.zeros(dim, numpy.uint8) 
    6567  
    6568 See log for complete Python traceback. 
    6569  
    6570 Traceback (most recent call last): 
    6571 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    6572 packages/chimerax/core/triggerset.py", line 130, in invoke 
    6573 return self._func(self._name, data) 
    6574 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6575 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    6576 self.set_surface_mask() 
    6577 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6578 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    6579 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    6580 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6581 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    6582 self._update_mask() 
    6583 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6584 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    6585 step=self.grid_step, pad=self.pad) 
    6586 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6587 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    6588 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    6589 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6590 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    6591 _generate_data_array 
    6592 data = numpy.zeros(dim, numpy.uint8) 
    6593 ValueError: negative dimensions are not allowed 
    6594  
    6595 Error processing trigger "atom coords updated": 
    6596 ValueError: negative dimensions are not allowed 
    6597  
    6598 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6599 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    6600 _generate_data_array 
    6601 data = numpy.zeros(dim, numpy.uint8) 
    6602  
    6603 See log for complete Python traceback. 
    6604  
    6605 Traceback (most recent call last): 
    6606 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    6607 packages/chimerax/core/triggerset.py", line 130, in invoke 
    6608 return self._func(self._name, data) 
    6609 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6610 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    6611 self.set_surface_mask() 
    6612 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6613 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    6614 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    6615 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6616 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    6617 self._update_mask() 
    6618 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6619 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    6620 step=self.grid_step, pad=self.pad) 
    6621 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6622 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    6623 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    6624 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6625 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    6626 _generate_data_array 
    6627 data = numpy.zeros(dim, numpy.uint8) 
    6628 ValueError: negative dimensions are not allowed 
    6629  
    6630 Error processing trigger "atom coords updated": 
    6631 ValueError: negative dimensions are not allowed 
    6632  
    6633 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6634 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    6635 _generate_data_array 
    6636 data = numpy.zeros(dim, numpy.uint8) 
    6637  
    6638 See log for complete Python traceback. 
    6639  
    6640 Traceback (most recent call last): 
    6641 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    6642 packages/chimerax/core/triggerset.py", line 130, in invoke 
    6643 return self._func(self._name, data) 
    6644 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6645 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    6646 self.set_surface_mask() 
    6647 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6648 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    6649 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    6650 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6651 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    6652 self._update_mask() 
    6653 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6654 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    6655 step=self.grid_step, pad=self.pad) 
    6656 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6657 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    6658 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    6659 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6660 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    6661 _generate_data_array 
    6662 data = numpy.zeros(dim, numpy.uint8) 
    6663 ValueError: negative dimensions are not allowed 
    6664  
    6665 Error processing trigger "atom coords updated": 
    6666 ValueError: negative dimensions are not allowed 
    6667  
    6668 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6669 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    6670 _generate_data_array 
    6671 data = numpy.zeros(dim, numpy.uint8) 
    6672  
    6673 See log for complete Python traceback. 
    6674  
    6675 Traceback (most recent call last): 
    6676 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    6677 packages/chimerax/core/triggerset.py", line 130, in invoke 
    6678 return self._func(self._name, data) 
    6679 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6680 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    6681 self.set_surface_mask() 
    6682 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6683 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    6684 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    6685 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6686 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    6687 self._update_mask() 
    6688 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6689 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    6690 step=self.grid_step, pad=self.pad) 
    6691 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6692 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    6693 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    6694 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6695 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    6696 _generate_data_array 
    6697 data = numpy.zeros(dim, numpy.uint8) 
    6698 ValueError: negative dimensions are not allowed 
    6699  
    6700 Error processing trigger "atom coords updated": 
    6701 ValueError: negative dimensions are not allowed 
    6702  
    6703 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6704 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    6705 _generate_data_array 
    6706 data = numpy.zeros(dim, numpy.uint8) 
    6707  
    6708 See log for complete Python traceback. 
    6709  
    6710 Traceback (most recent call last): 
    6711 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    6712 packages/chimerax/core/triggerset.py", line 130, in invoke 
    6713 return self._func(self._name, data) 
    6714 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6715 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    6716 self.set_surface_mask() 
    6717 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6718 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    6719 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    6720 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6721 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    6722 self._update_mask() 
    6723 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6724 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    6725 step=self.grid_step, pad=self.pad) 
    6726 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6727 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    6728 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    6729 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6730 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    6731 _generate_data_array 
    6732 data = numpy.zeros(dim, numpy.uint8) 
    6733 ValueError: negative dimensions are not allowed 
    6734  
    6735 Error processing trigger "atom coords updated": 
    6736 ValueError: negative dimensions are not allowed 
    6737  
    6738 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6739 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    6740 _generate_data_array 
    6741 data = numpy.zeros(dim, numpy.uint8) 
    6742  
    6743 See log for complete Python traceback. 
    6744  
    6745 Traceback (most recent call last): 
    6746 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    6747 packages/chimerax/core/triggerset.py", line 130, in invoke 
    6748 return self._func(self._name, data) 
    6749 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6750 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    6751 self.set_surface_mask() 
    6752 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6753 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    6754 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    6755 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6756 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    6757 self._update_mask() 
    6758 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6759 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    6760 step=self.grid_step, pad=self.pad) 
    6761 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6762 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    6763 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    6764 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6765 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    6766 _generate_data_array 
    6767 data = numpy.zeros(dim, numpy.uint8) 
    6768 ValueError: negative dimensions are not allowed 
    6769  
    6770 Error processing trigger "atom coords updated": 
    6771 ValueError: negative dimensions are not allowed 
    6772  
    6773 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6774 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    6775 _generate_data_array 
    6776 data = numpy.zeros(dim, numpy.uint8) 
    6777  
    6778 See log for complete Python traceback. 
    6779  
    6780 Traceback (most recent call last): 
    6781 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    6782 packages/chimerax/core/triggerset.py", line 130, in invoke 
    6783 return self._func(self._name, data) 
    6784 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6785 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    6786 self.set_surface_mask() 
    6787 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6788 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    6789 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    6790 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6791 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    6792 self._update_mask() 
    6793 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6794 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    6795 step=self.grid_step, pad=self.pad) 
    6796 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6797 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    6798 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    6799 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6800 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    6801 _generate_data_array 
    6802 data = numpy.zeros(dim, numpy.uint8) 
    6803 ValueError: negative dimensions are not allowed 
    6804  
    6805 Error processing trigger "atom coords updated": 
    6806 ValueError: negative dimensions are not allowed 
    6807  
    6808 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6809 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    6810 _generate_data_array 
    6811 data = numpy.zeros(dim, numpy.uint8) 
    6812  
    6813 See log for complete Python traceback. 
    6814  
    6815 Traceback (most recent call last): 
    6816 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    6817 packages/chimerax/core/triggerset.py", line 130, in invoke 
    6818 return self._func(self._name, data) 
    6819 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6820 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    6821 self.set_surface_mask() 
    6822 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6823 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    6824 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    6825 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6826 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    6827 self._update_mask() 
    6828 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6829 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    6830 step=self.grid_step, pad=self.pad) 
    6831 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6832 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    6833 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    6834 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6835 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    6836 _generate_data_array 
    6837 data = numpy.zeros(dim, numpy.uint8) 
    6838 ValueError: negative dimensions are not allowed 
    6839  
    6840 Error processing trigger "atom coords updated": 
    6841 ValueError: negative dimensions are not allowed 
    6842  
    6843 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6844 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    6845 _generate_data_array 
    6846 data = numpy.zeros(dim, numpy.uint8) 
    6847  
    6848 See log for complete Python traceback. 
    6849  
    6850 Traceback (most recent call last): 
    6851 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    6852 packages/chimerax/core/triggerset.py", line 130, in invoke 
    6853 return self._func(self._name, data) 
    6854 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6855 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    6856 self.set_surface_mask() 
    6857 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6858 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    6859 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    6860 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6861 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    6862 self._update_mask() 
    6863 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6864 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    6865 step=self.grid_step, pad=self.pad) 
    6866 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6867 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    6868 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    6869 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6870 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    6871 _generate_data_array 
    6872 data = numpy.zeros(dim, numpy.uint8) 
    6873 ValueError: negative dimensions are not allowed 
    6874  
    6875 Error processing trigger "atom coords updated": 
    6876 ValueError: negative dimensions are not allowed 
    6877  
    6878 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6879 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    6880 _generate_data_array 
    6881 data = numpy.zeros(dim, numpy.uint8) 
    6882  
    6883 See log for complete Python traceback. 
    6884  
    6885 Traceback (most recent call last): 
    6886 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    6887 packages/chimerax/core/triggerset.py", line 130, in invoke 
    6888 return self._func(self._name, data) 
    6889 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6890 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    6891 self.set_surface_mask() 
    6892 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6893 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    6894 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    6895 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6896 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    6897 self._update_mask() 
    6898 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6899 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    6900 step=self.grid_step, pad=self.pad) 
    6901 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6902 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    6903 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    6904 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6905 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    6906 _generate_data_array 
    6907 data = numpy.zeros(dim, numpy.uint8) 
    6908 ValueError: negative dimensions are not allowed 
    6909  
    6910 Error processing trigger "atom coords updated": 
    6911 ValueError: negative dimensions are not allowed 
    6912  
    6913 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6914 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    6915 _generate_data_array 
    6916 data = numpy.zeros(dim, numpy.uint8) 
    6917  
    6918 See log for complete Python traceback. 
    6919  
    6920 Traceback (most recent call last): 
    6921 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    6922 packages/chimerax/core/triggerset.py", line 130, in invoke 
    6923 return self._func(self._name, data) 
    6924 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6925 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    6926 self.set_surface_mask() 
    6927 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6928 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    6929 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    6930 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6931 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    6932 self._update_mask() 
    6933 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6934 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    6935 step=self.grid_step, pad=self.pad) 
    6936 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6937 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    6938 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    6939 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6940 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    6941 _generate_data_array 
    6942 data = numpy.zeros(dim, numpy.uint8) 
    6943 ValueError: negative dimensions are not allowed 
    6944  
    6945 Error processing trigger "atom coords updated": 
    6946 ValueError: negative dimensions are not allowed 
    6947  
    6948 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6949 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    6950 _generate_data_array 
    6951 data = numpy.zeros(dim, numpy.uint8) 
    6952  
    6953 See log for complete Python traceback. 
    6954  
    6955 Traceback (most recent call last): 
    6956 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    6957 packages/chimerax/core/triggerset.py", line 130, in invoke 
    6958 return self._func(self._name, data) 
    6959 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6960 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    6961 self.set_surface_mask() 
    6962 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6963 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    6964 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    6965 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6966 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    6967 self._update_mask() 
    6968 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6969 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    6970 step=self.grid_step, pad=self.pad) 
    6971 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6972 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    6973 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    6974 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6975 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    6976 _generate_data_array 
    6977 data = numpy.zeros(dim, numpy.uint8) 
    6978 ValueError: negative dimensions are not allowed 
    6979  
    6980 Error processing trigger "atom coords updated": 
    6981 ValueError: negative dimensions are not allowed 
    6982  
    6983 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6984 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    6985 _generate_data_array 
    6986 data = numpy.zeros(dim, numpy.uint8) 
    6987  
    6988 See log for complete Python traceback. 
    6989  
    6990 Traceback (most recent call last): 
    6991 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    6992 packages/chimerax/core/triggerset.py", line 130, in invoke 
    6993 return self._func(self._name, data) 
    6994 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6995 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    6996 self.set_surface_mask() 
    6997 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    6998 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    6999 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    7000 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7001 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    7002 self._update_mask() 
    7003 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7004 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    7005 step=self.grid_step, pad=self.pad) 
    7006 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7007 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    7008 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    7009 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7010 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    7011 _generate_data_array 
    7012 data = numpy.zeros(dim, numpy.uint8) 
    7013 ValueError: negative dimensions are not allowed 
    7014  
    7015 Error processing trigger "atom coords updated": 
    7016 ValueError: negative dimensions are not allowed 
    7017  
    7018 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7019 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    7020 _generate_data_array 
    7021 data = numpy.zeros(dim, numpy.uint8) 
    7022  
    7023 See log for complete Python traceback. 
    7024  
    7025 Traceback (most recent call last): 
    7026 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    7027 packages/chimerax/core/triggerset.py", line 130, in invoke 
    7028 return self._func(self._name, data) 
    7029 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7030 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    7031 self.set_surface_mask() 
    7032 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7033 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    7034 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    7035 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7036 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    7037 self._update_mask() 
    7038 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7039 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    7040 step=self.grid_step, pad=self.pad) 
    7041 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7042 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    7043 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    7044 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7045 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    7046 _generate_data_array 
    7047 data = numpy.zeros(dim, numpy.uint8) 
    7048 ValueError: negative dimensions are not allowed 
    7049  
    7050 Error processing trigger "atom coords updated": 
    7051 ValueError: negative dimensions are not allowed 
    7052  
    7053 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7054 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    7055 _generate_data_array 
    7056 data = numpy.zeros(dim, numpy.uint8) 
    7057  
    7058 See log for complete Python traceback. 
    7059  
    7060 Traceback (most recent call last): 
    7061 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    7062 packages/chimerax/core/triggerset.py", line 130, in invoke 
    7063 return self._func(self._name, data) 
    7064 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7065 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    7066 self.set_surface_mask() 
    7067 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7068 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    7069 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    7070 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7071 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    7072 self._update_mask() 
    7073 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7074 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    7075 step=self.grid_step, pad=self.pad) 
    7076 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7077 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    7078 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    7079 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7080 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    7081 _generate_data_array 
    7082 data = numpy.zeros(dim, numpy.uint8) 
    7083 ValueError: negative dimensions are not allowed 
    7084  
    7085 Error processing trigger "atom coords updated": 
    7086 ValueError: negative dimensions are not allowed 
    7087  
    7088 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7089 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    7090 _generate_data_array 
    7091 data = numpy.zeros(dim, numpy.uint8) 
    7092  
    7093 See log for complete Python traceback. 
    7094  
    7095 Traceback (most recent call last): 
    7096 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    7097 packages/chimerax/core/triggerset.py", line 130, in invoke 
    7098 return self._func(self._name, data) 
    7099 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7100 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    7101 self.set_surface_mask() 
    7102 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7103 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    7104 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    7105 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7106 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    7107 self._update_mask() 
    7108 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7109 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    7110 step=self.grid_step, pad=self.pad) 
    7111 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7112 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    7113 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    7114 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7115 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    7116 _generate_data_array 
    7117 data = numpy.zeros(dim, numpy.uint8) 
    7118 ValueError: negative dimensions are not allowed 
    7119  
    7120 Error processing trigger "atom coords updated": 
    7121 ValueError: negative dimensions are not allowed 
    7122  
    7123 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7124 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    7125 _generate_data_array 
    7126 data = numpy.zeros(dim, numpy.uint8) 
    7127  
    7128 See log for complete Python traceback. 
    7129  
    7130 Traceback (most recent call last): 
    7131 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    7132 packages/chimerax/core/triggerset.py", line 130, in invoke 
    7133 return self._func(self._name, data) 
    7134 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7135 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    7136 self.set_surface_mask() 
    7137 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7138 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    7139 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    7140 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7141 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    7142 self._update_mask() 
    7143 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7144 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    7145 step=self.grid_step, pad=self.pad) 
    7146 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7147 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    7148 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    7149 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7150 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    7151 _generate_data_array 
    7152 data = numpy.zeros(dim, numpy.uint8) 
    7153 ValueError: negative dimensions are not allowed 
    7154  
    7155 Error processing trigger "atom coords updated": 
    7156 ValueError: negative dimensions are not allowed 
    7157  
    7158 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7159 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    7160 _generate_data_array 
    7161 data = numpy.zeros(dim, numpy.uint8) 
    7162  
    7163 See log for complete Python traceback. 
    7164  
    7165 Traceback (most recent call last): 
    7166 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    7167 packages/chimerax/core/triggerset.py", line 130, in invoke 
    7168 return self._func(self._name, data) 
    7169 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7170 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    7171 self.set_surface_mask() 
    7172 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7173 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    7174 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    7175 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7176 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    7177 self._update_mask() 
    7178 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7179 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    7180 step=self.grid_step, pad=self.pad) 
    7181 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7182 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    7183 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    7184 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7185 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    7186 _generate_data_array 
    7187 data = numpy.zeros(dim, numpy.uint8) 
    7188 ValueError: negative dimensions are not allowed 
    7189  
    7190 Error processing trigger "atom coords updated": 
    7191 ValueError: negative dimensions are not allowed 
    7192  
    7193 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7194 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    7195 _generate_data_array 
    7196 data = numpy.zeros(dim, numpy.uint8) 
    7197  
    7198 See log for complete Python traceback. 
    7199  
    7200 Traceback (most recent call last): 
    7201 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    7202 packages/chimerax/core/triggerset.py", line 130, in invoke 
    7203 return self._func(self._name, data) 
    7204 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7205 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    7206 self.set_surface_mask() 
    7207 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7208 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    7209 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    7210 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7211 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    7212 self._update_mask() 
    7213 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7214 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    7215 step=self.grid_step, pad=self.pad) 
    7216 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7217 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    7218 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    7219 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7220 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    7221 _generate_data_array 
    7222 data = numpy.zeros(dim, numpy.uint8) 
    7223 ValueError: negative dimensions are not allowed 
    7224  
    7225 Error processing trigger "atom coords updated": 
    7226 ValueError: negative dimensions are not allowed 
    7227  
    7228 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7229 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    7230 _generate_data_array 
    7231 data = numpy.zeros(dim, numpy.uint8) 
    7232  
    7233 See log for complete Python traceback. 
    7234  
    7235 Traceback (most recent call last): 
    7236 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    7237 packages/chimerax/core/triggerset.py", line 130, in invoke 
    7238 return self._func(self._name, data) 
    7239 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7240 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    7241 self.set_surface_mask() 
    7242 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7243 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    7244 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    7245 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7246 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    7247 self._update_mask() 
    7248 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7249 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    7250 step=self.grid_step, pad=self.pad) 
    7251 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7252 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    7253 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    7254 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7255 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    7256 _generate_data_array 
    7257 data = numpy.zeros(dim, numpy.uint8) 
    7258 ValueError: negative dimensions are not allowed 
    7259  
    7260 Error processing trigger "atom coords updated": 
    7261 ValueError: negative dimensions are not allowed 
    7262  
    7263 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7264 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    7265 _generate_data_array 
    7266 data = numpy.zeros(dim, numpy.uint8) 
    7267  
    7268 See log for complete Python traceback. 
    7269  
    7270 Traceback (most recent call last): 
    7271 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    7272 packages/chimerax/core/triggerset.py", line 130, in invoke 
    7273 return self._func(self._name, data) 
    7274 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7275 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    7276 self.set_surface_mask() 
    7277 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7278 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    7279 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    7280 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7281 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    7282 self._update_mask() 
    7283 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7284 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    7285 step=self.grid_step, pad=self.pad) 
    7286 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7287 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    7288 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    7289 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7290 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    7291 _generate_data_array 
    7292 data = numpy.zeros(dim, numpy.uint8) 
    7293 ValueError: negative dimensions are not allowed 
    7294  
    7295 Error processing trigger "atom coords updated": 
    7296 ValueError: negative dimensions are not allowed 
    7297  
    7298 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7299 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    7300 _generate_data_array 
    7301 data = numpy.zeros(dim, numpy.uint8) 
    7302  
    7303 See log for complete Python traceback. 
    7304  
    7305 Traceback (most recent call last): 
    7306 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    7307 packages/chimerax/core/triggerset.py", line 130, in invoke 
    7308 return self._func(self._name, data) 
    7309 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7310 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    7311 self.set_surface_mask() 
    7312 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7313 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    7314 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    7315 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7316 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    7317 self._update_mask() 
    7318 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7319 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    7320 step=self.grid_step, pad=self.pad) 
    7321 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7322 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    7323 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    7324 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7325 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    7326 _generate_data_array 
    7327 data = numpy.zeros(dim, numpy.uint8) 
    7328 ValueError: negative dimensions are not allowed 
    7329  
    7330 Error processing trigger "atom coords updated": 
    7331 ValueError: negative dimensions are not allowed 
    7332  
    7333 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7334 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    7335 _generate_data_array 
    7336 data = numpy.zeros(dim, numpy.uint8) 
    7337  
    7338 See log for complete Python traceback. 
    7339  
    7340 Traceback (most recent call last): 
    7341 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    7342 packages/chimerax/core/triggerset.py", line 130, in invoke 
    7343 return self._func(self._name, data) 
    7344 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7345 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    7346 self.set_surface_mask() 
    7347 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7348 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    7349 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    7350 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7351 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    7352 self._update_mask() 
    7353 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7354 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    7355 step=self.grid_step, pad=self.pad) 
    7356 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7357 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    7358 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    7359 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7360 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    7361 _generate_data_array 
    7362 data = numpy.zeros(dim, numpy.uint8) 
    7363 ValueError: negative dimensions are not allowed 
    7364  
    7365 Error processing trigger "atom coords updated": 
    7366 ValueError: negative dimensions are not allowed 
    7367  
    7368 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7369 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    7370 _generate_data_array 
    7371 data = numpy.zeros(dim, numpy.uint8) 
    7372  
    7373 See log for complete Python traceback. 
    7374  
    7375 Traceback (most recent call last): 
    7376 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    7377 packages/chimerax/core/triggerset.py", line 130, in invoke 
    7378 return self._func(self._name, data) 
    7379 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7380 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    7381 self.set_surface_mask() 
    7382 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7383 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    7384 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    7385 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7386 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    7387 self._update_mask() 
    7388 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7389 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    7390 step=self.grid_step, pad=self.pad) 
    7391 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7392 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    7393 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    7394 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7395 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    7396 _generate_data_array 
    7397 data = numpy.zeros(dim, numpy.uint8) 
    7398 ValueError: negative dimensions are not allowed 
    7399  
    7400 Error processing trigger "atom coords updated": 
    7401 ValueError: negative dimensions are not allowed 
    7402  
    7403 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7404 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    7405 _generate_data_array 
    7406 data = numpy.zeros(dim, numpy.uint8) 
    7407  
    7408 See log for complete Python traceback. 
    7409  
    7410 Traceback (most recent call last): 
    7411 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    7412 packages/chimerax/core/triggerset.py", line 130, in invoke 
    7413 return self._func(self._name, data) 
    7414 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7415 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    7416 self.set_surface_mask() 
    7417 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7418 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    7419 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    7420 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7421 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    7422 self._update_mask() 
    7423 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7424 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    7425 step=self.grid_step, pad=self.pad) 
    7426 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7427 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    7428 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    7429 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7430 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    7431 _generate_data_array 
    7432 data = numpy.zeros(dim, numpy.uint8) 
    7433 ValueError: negative dimensions are not allowed 
    7434  
    7435 Error processing trigger "atom coords updated": 
    7436 ValueError: negative dimensions are not allowed 
    7437  
    7438 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7439 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    7440 _generate_data_array 
    7441 data = numpy.zeros(dim, numpy.uint8) 
    7442  
    7443 See log for complete Python traceback. 
    7444  
    7445 Traceback (most recent call last): 
    7446 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    7447 packages/chimerax/core/triggerset.py", line 130, in invoke 
    7448 return self._func(self._name, data) 
    7449 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7450 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    7451 self.set_surface_mask() 
    7452 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7453 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    7454 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    7455 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7456 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    7457 self._update_mask() 
    7458 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7459 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    7460 step=self.grid_step, pad=self.pad) 
    7461 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7462 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    7463 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    7464 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7465 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    7466 _generate_data_array 
    7467 data = numpy.zeros(dim, numpy.uint8) 
    7468 ValueError: negative dimensions are not allowed 
    7469  
    7470 Error processing trigger "atom coords updated": 
    7471 ValueError: negative dimensions are not allowed 
    7472  
    7473 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7474 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    7475 _generate_data_array 
    7476 data = numpy.zeros(dim, numpy.uint8) 
    7477  
    7478 See log for complete Python traceback. 
    7479  
    7480 Traceback (most recent call last): 
    7481 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    7482 packages/chimerax/core/triggerset.py", line 130, in invoke 
    7483 return self._func(self._name, data) 
    7484 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7485 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    7486 self.set_surface_mask() 
    7487 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7488 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    7489 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    7490 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7491 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    7492 self._update_mask() 
    7493 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7494 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    7495 step=self.grid_step, pad=self.pad) 
    7496 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7497 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    7498 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    7499 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7500 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    7501 _generate_data_array 
    7502 data = numpy.zeros(dim, numpy.uint8) 
    7503 ValueError: negative dimensions are not allowed 
    7504  
    7505 Error processing trigger "atom coords updated": 
    7506 ValueError: negative dimensions are not allowed 
    7507  
    7508 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7509 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    7510 _generate_data_array 
    7511 data = numpy.zeros(dim, numpy.uint8) 
    7512  
    7513 See log for complete Python traceback. 
    7514  
    7515 Traceback (most recent call last): 
    7516 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    7517 packages/chimerax/core/triggerset.py", line 130, in invoke 
    7518 return self._func(self._name, data) 
    7519 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7520 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    7521 self.set_surface_mask() 
    7522 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7523 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    7524 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    7525 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7526 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    7527 self._update_mask() 
    7528 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7529 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    7530 step=self.grid_step, pad=self.pad) 
    7531 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7532 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    7533 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    7534 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7535 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    7536 _generate_data_array 
    7537 data = numpy.zeros(dim, numpy.uint8) 
    7538 ValueError: negative dimensions are not allowed 
    7539  
    7540 Error processing trigger "atom coords updated": 
    7541 ValueError: negative dimensions are not allowed 
    7542  
    7543 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7544 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    7545 _generate_data_array 
    7546 data = numpy.zeros(dim, numpy.uint8) 
    7547  
    7548 See log for complete Python traceback. 
    7549  
    7550 Traceback (most recent call last): 
    7551 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    7552 packages/chimerax/core/triggerset.py", line 130, in invoke 
    7553 return self._func(self._name, data) 
    7554 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7555 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    7556 self.set_surface_mask() 
    7557 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7558 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    7559 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    7560 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7561 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    7562 self._update_mask() 
    7563 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7564 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    7565 step=self.grid_step, pad=self.pad) 
    7566 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7567 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    7568 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    7569 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7570 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    7571 _generate_data_array 
    7572 data = numpy.zeros(dim, numpy.uint8) 
    7573 ValueError: negative dimensions are not allowed 
    7574  
    7575 Error processing trigger "atom coords updated": 
    7576 ValueError: negative dimensions are not allowed 
    7577  
    7578 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7579 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    7580 _generate_data_array 
    7581 data = numpy.zeros(dim, numpy.uint8) 
    7582  
    7583 See log for complete Python traceback. 
    7584  
    7585 Traceback (most recent call last): 
    7586 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    7587 packages/chimerax/core/triggerset.py", line 130, in invoke 
    7588 return self._func(self._name, data) 
    7589 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7590 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    7591 self.set_surface_mask() 
    7592 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7593 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    7594 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    7595 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7596 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    7597 self._update_mask() 
    7598 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7599 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    7600 step=self.grid_step, pad=self.pad) 
    7601 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7602 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    7603 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    7604 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7605 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    7606 _generate_data_array 
    7607 data = numpy.zeros(dim, numpy.uint8) 
    7608 ValueError: negative dimensions are not allowed 
    7609  
    7610 Error processing trigger "atom coords updated": 
    7611 ValueError: negative dimensions are not allowed 
    7612  
    7613 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7614 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    7615 _generate_data_array 
    7616 data = numpy.zeros(dim, numpy.uint8) 
    7617  
    7618 See log for complete Python traceback. 
    7619  
    7620 Traceback (most recent call last): 
    7621 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    7622 packages/chimerax/core/triggerset.py", line 130, in invoke 
    7623 return self._func(self._name, data) 
    7624 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7625 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    7626 self.set_surface_mask() 
    7627 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7628 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    7629 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    7630 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7631 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    7632 self._update_mask() 
    7633 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7634 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    7635 step=self.grid_step, pad=self.pad) 
    7636 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7637 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    7638 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    7639 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7640 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    7641 _generate_data_array 
    7642 data = numpy.zeros(dim, numpy.uint8) 
    7643 ValueError: negative dimensions are not allowed 
    7644  
    7645 Error processing trigger "atom coords updated": 
    7646 ValueError: negative dimensions are not allowed 
    7647  
    7648 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7649 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    7650 _generate_data_array 
    7651 data = numpy.zeros(dim, numpy.uint8) 
    7652  
    7653 See log for complete Python traceback. 
    7654  
    7655 Traceback (most recent call last): 
    7656 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    7657 packages/chimerax/core/triggerset.py", line 130, in invoke 
    7658 return self._func(self._name, data) 
    7659 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7660 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    7661 self.set_surface_mask() 
    7662 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7663 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    7664 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    7665 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7666 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    7667 self._update_mask() 
    7668 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7669 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    7670 step=self.grid_step, pad=self.pad) 
    7671 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7672 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    7673 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    7674 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7675 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    7676 _generate_data_array 
    7677 data = numpy.zeros(dim, numpy.uint8) 
    7678 ValueError: negative dimensions are not allowed 
    7679  
    7680 Error processing trigger "atom coords updated": 
    7681 ValueError: negative dimensions are not allowed 
    7682  
    7683 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7684 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    7685 _generate_data_array 
    7686 data = numpy.zeros(dim, numpy.uint8) 
    7687  
    7688 See log for complete Python traceback. 
    7689  
    7690 Traceback (most recent call last): 
    7691 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    7692 packages/chimerax/core/triggerset.py", line 130, in invoke 
    7693 return self._func(self._name, data) 
    7694 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7695 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    7696 self.set_surface_mask() 
    7697 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7698 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    7699 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    7700 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7701 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    7702 self._update_mask() 
    7703 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7704 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    7705 step=self.grid_step, pad=self.pad) 
    7706 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7707 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    7708 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    7709 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7710 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    7711 _generate_data_array 
    7712 data = numpy.zeros(dim, numpy.uint8) 
    7713 ValueError: negative dimensions are not allowed 
    7714  
    7715 Error processing trigger "atom coords updated": 
    7716 ValueError: negative dimensions are not allowed 
    7717  
    7718 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7719 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    7720 _generate_data_array 
    7721 data = numpy.zeros(dim, numpy.uint8) 
    7722  
    7723 See log for complete Python traceback. 
    7724  
    7725 Traceback (most recent call last): 
    7726 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    7727 packages/chimerax/core/triggerset.py", line 130, in invoke 
    7728 return self._func(self._name, data) 
    7729 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7730 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    7731 self.set_surface_mask() 
    7732 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7733 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    7734 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    7735 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7736 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    7737 self._update_mask() 
    7738 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7739 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    7740 step=self.grid_step, pad=self.pad) 
    7741 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7742 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    7743 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    7744 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7745 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    7746 _generate_data_array 
    7747 data = numpy.zeros(dim, numpy.uint8) 
    7748 ValueError: negative dimensions are not allowed 
    7749  
    7750 Error processing trigger "atom coords updated": 
    7751 ValueError: negative dimensions are not allowed 
    7752  
    7753 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7754 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    7755 _generate_data_array 
    7756 data = numpy.zeros(dim, numpy.uint8) 
    7757  
    7758 See log for complete Python traceback. 
    7759  
    7760 Traceback (most recent call last): 
    7761 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    7762 packages/chimerax/core/triggerset.py", line 130, in invoke 
    7763 return self._func(self._name, data) 
    7764 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7765 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    7766 self.set_surface_mask() 
    7767 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7768 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    7769 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    7770 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7771 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    7772 self._update_mask() 
    7773 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7774 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    7775 step=self.grid_step, pad=self.pad) 
    7776 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7777 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    7778 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    7779 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7780 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    7781 _generate_data_array 
    7782 data = numpy.zeros(dim, numpy.uint8) 
    7783 ValueError: negative dimensions are not allowed 
    7784  
    7785 Error processing trigger "atom coords updated": 
    7786 ValueError: negative dimensions are not allowed 
    7787  
    7788 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7789 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    7790 _generate_data_array 
    7791 data = numpy.zeros(dim, numpy.uint8) 
    7792  
    7793 See log for complete Python traceback. 
    7794  
    7795 Traceback (most recent call last): 
    7796 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    7797 packages/chimerax/core/triggerset.py", line 130, in invoke 
    7798 return self._func(self._name, data) 
    7799 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7800 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    7801 self.set_surface_mask() 
    7802 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7803 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    7804 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    7805 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7806 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    7807 self._update_mask() 
    7808 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7809 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    7810 step=self.grid_step, pad=self.pad) 
    7811 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7812 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    7813 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    7814 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7815 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    7816 _generate_data_array 
    7817 data = numpy.zeros(dim, numpy.uint8) 
    7818 ValueError: negative dimensions are not allowed 
    7819  
    7820 Error processing trigger "atom coords updated": 
    7821 ValueError: negative dimensions are not allowed 
    7822  
    7823 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7824 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    7825 _generate_data_array 
    7826 data = numpy.zeros(dim, numpy.uint8) 
    7827  
    7828 See log for complete Python traceback. 
    7829  
    7830 Traceback (most recent call last): 
    7831 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    7832 packages/chimerax/core/triggerset.py", line 130, in invoke 
    7833 return self._func(self._name, data) 
    7834 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7835 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    7836 self.set_surface_mask() 
    7837 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7838 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    7839 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    7840 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7841 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    7842 self._update_mask() 
    7843 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7844 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    7845 step=self.grid_step, pad=self.pad) 
    7846 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7847 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    7848 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    7849 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7850 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    7851 _generate_data_array 
    7852 data = numpy.zeros(dim, numpy.uint8) 
    7853 ValueError: negative dimensions are not allowed 
    7854  
    7855 Error processing trigger "atom coords updated": 
    7856 ValueError: negative dimensions are not allowed 
    7857  
    7858 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7859 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    7860 _generate_data_array 
    7861 data = numpy.zeros(dim, numpy.uint8) 
    7862  
    7863 See log for complete Python traceback. 
    7864  
    7865 Traceback (most recent call last): 
    7866 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    7867 packages/chimerax/core/triggerset.py", line 130, in invoke 
    7868 return self._func(self._name, data) 
    7869 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7870 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    7871 self.set_surface_mask() 
    7872 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7873 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    7874 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    7875 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7876 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    7877 self._update_mask() 
    7878 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7879 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    7880 step=self.grid_step, pad=self.pad) 
    7881 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7882 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    7883 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    7884 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7885 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    7886 _generate_data_array 
    7887 data = numpy.zeros(dim, numpy.uint8) 
    7888 ValueError: negative dimensions are not allowed 
    7889  
    7890 Error processing trigger "atom coords updated": 
    7891 ValueError: negative dimensions are not allowed 
    7892  
    7893 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7894 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    7895 _generate_data_array 
    7896 data = numpy.zeros(dim, numpy.uint8) 
    7897  
    7898 See log for complete Python traceback. 
    7899  
    7900 Traceback (most recent call last): 
    7901 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    7902 packages/chimerax/core/triggerset.py", line 130, in invoke 
    7903 return self._func(self._name, data) 
    7904 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7905 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    7906 self.set_surface_mask() 
    7907 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7908 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    7909 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    7910 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7911 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    7912 self._update_mask() 
    7913 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7914 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    7915 step=self.grid_step, pad=self.pad) 
    7916 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7917 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    7918 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    7919 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7920 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    7921 _generate_data_array 
    7922 data = numpy.zeros(dim, numpy.uint8) 
    7923 ValueError: negative dimensions are not allowed 
    7924  
    7925 Error processing trigger "atom coords updated": 
    7926 ValueError: negative dimensions are not allowed 
    7927  
    7928 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7929 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    7930 _generate_data_array 
    7931 data = numpy.zeros(dim, numpy.uint8) 
    7932  
    7933 See log for complete Python traceback. 
    7934  
    7935 Traceback (most recent call last): 
    7936 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    7937 packages/chimerax/core/triggerset.py", line 130, in invoke 
    7938 return self._func(self._name, data) 
    7939 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7940 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    7941 self.set_surface_mask() 
    7942 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7943 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    7944 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    7945 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7946 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    7947 self._update_mask() 
    7948 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7949 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    7950 step=self.grid_step, pad=self.pad) 
    7951 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7952 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    7953 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    7954 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7955 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    7956 _generate_data_array 
    7957 data = numpy.zeros(dim, numpy.uint8) 
    7958 ValueError: negative dimensions are not allowed 
    7959  
    7960 Error processing trigger "atom coords updated": 
    7961 ValueError: negative dimensions are not allowed 
    7962  
    7963 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7964 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    7965 _generate_data_array 
    7966 data = numpy.zeros(dim, numpy.uint8) 
    7967  
    7968 See log for complete Python traceback. 
    7969  
    7970 Traceback (most recent call last): 
    7971 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    7972 packages/chimerax/core/triggerset.py", line 130, in invoke 
    7973 return self._func(self._name, data) 
    7974 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7975 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    7976 self.set_surface_mask() 
    7977 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7978 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    7979 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    7980 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7981 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    7982 self._update_mask() 
    7983 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7984 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    7985 step=self.grid_step, pad=self.pad) 
    7986 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7987 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    7988 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    7989 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7990 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    7991 _generate_data_array 
    7992 data = numpy.zeros(dim, numpy.uint8) 
    7993 ValueError: negative dimensions are not allowed 
    7994  
    7995 Error processing trigger "atom coords updated": 
    7996 ValueError: negative dimensions are not allowed 
    7997  
    7998 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    7999 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    8000 _generate_data_array 
    8001 data = numpy.zeros(dim, numpy.uint8) 
    8002  
    8003 See log for complete Python traceback. 
    8004  
    8005 Traceback (most recent call last): 
    8006 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    8007 packages/chimerax/core/triggerset.py", line 130, in invoke 
    8008 return self._func(self._name, data) 
    8009 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8010 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    8011 self.set_surface_mask() 
    8012 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8013 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    8014 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    8015 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8016 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    8017 self._update_mask() 
    8018 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8019 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    8020 step=self.grid_step, pad=self.pad) 
    8021 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8022 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    8023 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    8024 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8025 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    8026 _generate_data_array 
    8027 data = numpy.zeros(dim, numpy.uint8) 
    8028 ValueError: negative dimensions are not allowed 
    8029  
    8030 Error processing trigger "atom coords updated": 
    8031 ValueError: negative dimensions are not allowed 
    8032  
    8033 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8034 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    8035 _generate_data_array 
    8036 data = numpy.zeros(dim, numpy.uint8) 
    8037  
    8038 See log for complete Python traceback. 
    8039  
    8040 Traceback (most recent call last): 
    8041 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    8042 packages/chimerax/core/triggerset.py", line 130, in invoke 
    8043 return self._func(self._name, data) 
    8044 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8045 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    8046 self.set_surface_mask() 
    8047 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8048 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    8049 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    8050 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8051 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    8052 self._update_mask() 
    8053 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8054 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    8055 step=self.grid_step, pad=self.pad) 
    8056 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8057 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    8058 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    8059 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8060 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    8061 _generate_data_array 
    8062 data = numpy.zeros(dim, numpy.uint8) 
    8063 ValueError: negative dimensions are not allowed 
    8064  
    8065 Error processing trigger "atom coords updated": 
    8066 ValueError: negative dimensions are not allowed 
    8067  
    8068 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8069 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    8070 _generate_data_array 
    8071 data = numpy.zeros(dim, numpy.uint8) 
    8072  
    8073 See log for complete Python traceback. 
    8074  
    8075 Traceback (most recent call last): 
    8076 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    8077 packages/chimerax/core/triggerset.py", line 130, in invoke 
    8078 return self._func(self._name, data) 
    8079 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8080 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    8081 self.set_surface_mask() 
    8082 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8083 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    8084 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    8085 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8086 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    8087 self._update_mask() 
    8088 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8089 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    8090 step=self.grid_step, pad=self.pad) 
    8091 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8092 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    8093 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    8094 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8095 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    8096 _generate_data_array 
    8097 data = numpy.zeros(dim, numpy.uint8) 
    8098 ValueError: negative dimensions are not allowed 
    8099  
    8100 Error processing trigger "atom coords updated": 
    8101 ValueError: negative dimensions are not allowed 
    8102  
    8103 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8104 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    8105 _generate_data_array 
    8106 data = numpy.zeros(dim, numpy.uint8) 
    8107  
    8108 See log for complete Python traceback. 
    8109  
    8110 Traceback (most recent call last): 
    8111 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    8112 packages/chimerax/core/triggerset.py", line 130, in invoke 
    8113 return self._func(self._name, data) 
    8114 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8115 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    8116 self.set_surface_mask() 
    8117 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8118 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    8119 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    8120 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8121 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    8122 self._update_mask() 
    8123 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8124 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    8125 step=self.grid_step, pad=self.pad) 
    8126 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8127 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    8128 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    8129 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8130 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    8131 _generate_data_array 
    8132 data = numpy.zeros(dim, numpy.uint8) 
    8133 ValueError: negative dimensions are not allowed 
    8134  
    8135 Error processing trigger "atom coords updated": 
    8136 ValueError: negative dimensions are not allowed 
    8137  
    8138 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8139 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    8140 _generate_data_array 
    8141 data = numpy.zeros(dim, numpy.uint8) 
    8142  
    8143 See log for complete Python traceback. 
    8144  
    8145 Traceback (most recent call last): 
    8146 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    8147 packages/chimerax/core/triggerset.py", line 130, in invoke 
    8148 return self._func(self._name, data) 
    8149 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8150 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    8151 self.set_surface_mask() 
    8152 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8153 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    8154 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    8155 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8156 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    8157 self._update_mask() 
    8158 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8159 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    8160 step=self.grid_step, pad=self.pad) 
    8161 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8162 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    8163 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    8164 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8165 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    8166 _generate_data_array 
    8167 data = numpy.zeros(dim, numpy.uint8) 
    8168 ValueError: negative dimensions are not allowed 
    8169  
    8170 Error processing trigger "atom coords updated": 
    8171 ValueError: negative dimensions are not allowed 
    8172  
    8173 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8174 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    8175 _generate_data_array 
    8176 data = numpy.zeros(dim, numpy.uint8) 
    8177  
    8178 See log for complete Python traceback. 
    8179  
    8180 Traceback (most recent call last): 
    8181 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    8182 packages/chimerax/core/triggerset.py", line 130, in invoke 
    8183 return self._func(self._name, data) 
    8184 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8185 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    8186 self.set_surface_mask() 
    8187 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8188 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    8189 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    8190 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8191 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    8192 self._update_mask() 
    8193 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8194 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    8195 step=self.grid_step, pad=self.pad) 
    8196 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8197 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    8198 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    8199 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8200 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    8201 _generate_data_array 
    8202 data = numpy.zeros(dim, numpy.uint8) 
    8203 ValueError: negative dimensions are not allowed 
    8204  
    8205 Error processing trigger "atom coords updated": 
    8206 ValueError: negative dimensions are not allowed 
    8207  
    8208 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8209 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    8210 _generate_data_array 
    8211 data = numpy.zeros(dim, numpy.uint8) 
    8212  
    8213 See log for complete Python traceback. 
    8214  
    8215 Traceback (most recent call last): 
    8216 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    8217 packages/chimerax/core/triggerset.py", line 130, in invoke 
    8218 return self._func(self._name, data) 
    8219 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8220 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    8221 self.set_surface_mask() 
    8222 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8223 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    8224 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    8225 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8226 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    8227 self._update_mask() 
    8228 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8229 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    8230 step=self.grid_step, pad=self.pad) 
    8231 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8232 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    8233 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    8234 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8235 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    8236 _generate_data_array 
    8237 data = numpy.zeros(dim, numpy.uint8) 
    8238 ValueError: negative dimensions are not allowed 
    8239  
    8240 Error processing trigger "atom coords updated": 
    8241 ValueError: negative dimensions are not allowed 
    8242  
    8243 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8244 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    8245 _generate_data_array 
    8246 data = numpy.zeros(dim, numpy.uint8) 
    8247  
    8248 See log for complete Python traceback. 
    8249  
    8250 Traceback (most recent call last): 
    8251 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    8252 packages/chimerax/core/triggerset.py", line 130, in invoke 
    8253 return self._func(self._name, data) 
    8254 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8255 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    8256 self.set_surface_mask() 
    8257 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8258 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    8259 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    8260 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8261 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    8262 self._update_mask() 
    8263 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8264 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    8265 step=self.grid_step, pad=self.pad) 
    8266 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8267 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    8268 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    8269 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8270 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    8271 _generate_data_array 
    8272 data = numpy.zeros(dim, numpy.uint8) 
    8273 ValueError: negative dimensions are not allowed 
    8274  
    8275 Error processing trigger "atom coords updated": 
    8276 ValueError: negative dimensions are not allowed 
    8277  
    8278 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8279 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    8280 _generate_data_array 
    8281 data = numpy.zeros(dim, numpy.uint8) 
    8282  
    8283 See log for complete Python traceback. 
    8284  
    8285 Traceback (most recent call last): 
    8286 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    8287 packages/chimerax/core/triggerset.py", line 130, in invoke 
    8288 return self._func(self._name, data) 
    8289 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8290 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    8291 self.set_surface_mask() 
    8292 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8293 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    8294 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    8295 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8296 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    8297 self._update_mask() 
    8298 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8299 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    8300 step=self.grid_step, pad=self.pad) 
    8301 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8302 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    8303 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    8304 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8305 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    8306 _generate_data_array 
    8307 data = numpy.zeros(dim, numpy.uint8) 
    8308 ValueError: negative dimensions are not allowed 
    8309  
    8310 Error processing trigger "atom coords updated": 
    8311 ValueError: negative dimensions are not allowed 
    8312  
    8313 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8314 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    8315 _generate_data_array 
    8316 data = numpy.zeros(dim, numpy.uint8) 
    8317  
    8318 See log for complete Python traceback. 
    8319  
    8320 Traceback (most recent call last): 
    8321 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    8322 packages/chimerax/core/triggerset.py", line 130, in invoke 
    8323 return self._func(self._name, data) 
    8324 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8325 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    8326 self.set_surface_mask() 
    8327 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8328 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    8329 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    8330 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8331 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    8332 self._update_mask() 
    8333 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8334 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    8335 step=self.grid_step, pad=self.pad) 
    8336 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8337 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    8338 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    8339 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8340 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    8341 _generate_data_array 
    8342 data = numpy.zeros(dim, numpy.uint8) 
    8343 ValueError: negative dimensions are not allowed 
    8344  
    8345 Error processing trigger "atom coords updated": 
    8346 ValueError: negative dimensions are not allowed 
    8347  
    8348 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8349 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    8350 _generate_data_array 
    8351 data = numpy.zeros(dim, numpy.uint8) 
    8352  
    8353 See log for complete Python traceback. 
    8354  
    8355 Traceback (most recent call last): 
    8356 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    8357 packages/chimerax/core/triggerset.py", line 130, in invoke 
    8358 return self._func(self._name, data) 
    8359 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8360 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    8361 self.set_surface_mask() 
    8362 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8363 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    8364 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    8365 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8366 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    8367 self._update_mask() 
    8368 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8369 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    8370 step=self.grid_step, pad=self.pad) 
    8371 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8372 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    8373 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    8374 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8375 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    8376 _generate_data_array 
    8377 data = numpy.zeros(dim, numpy.uint8) 
    8378 ValueError: negative dimensions are not allowed 
    8379  
    8380 Error processing trigger "atom coords updated": 
    8381 ValueError: negative dimensions are not allowed 
    8382  
    8383 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8384 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    8385 _generate_data_array 
    8386 data = numpy.zeros(dim, numpy.uint8) 
    8387  
    8388 See log for complete Python traceback. 
    8389  
    8390 Traceback (most recent call last): 
    8391 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    8392 packages/chimerax/core/triggerset.py", line 130, in invoke 
    8393 return self._func(self._name, data) 
    8394 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8395 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    8396 self.set_surface_mask() 
    8397 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8398 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    8399 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    8400 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8401 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    8402 self._update_mask() 
    8403 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8404 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    8405 step=self.grid_step, pad=self.pad) 
    8406 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8407 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    8408 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    8409 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8410 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    8411 _generate_data_array 
    8412 data = numpy.zeros(dim, numpy.uint8) 
    8413 ValueError: negative dimensions are not allowed 
    8414  
    8415 Error processing trigger "atom coords updated": 
    8416 ValueError: negative dimensions are not allowed 
    8417  
    8418 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8419 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    8420 _generate_data_array 
    8421 data = numpy.zeros(dim, numpy.uint8) 
    8422  
    8423 See log for complete Python traceback. 
    8424  
    8425 Traceback (most recent call last): 
    8426 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    8427 packages/chimerax/core/triggerset.py", line 130, in invoke 
    8428 return self._func(self._name, data) 
    8429 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8430 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    8431 self.set_surface_mask() 
    8432 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8433 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    8434 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    8435 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8436 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    8437 self._update_mask() 
    8438 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8439 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    8440 step=self.grid_step, pad=self.pad) 
    8441 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8442 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    8443 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    8444 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8445 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    8446 _generate_data_array 
    8447 data = numpy.zeros(dim, numpy.uint8) 
    8448 ValueError: negative dimensions are not allowed 
    8449  
    8450 Error processing trigger "atom coords updated": 
    8451 ValueError: negative dimensions are not allowed 
    8452  
    8453 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8454 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    8455 _generate_data_array 
    8456 data = numpy.zeros(dim, numpy.uint8) 
    8457  
    8458 See log for complete Python traceback. 
    8459  
    8460 Traceback (most recent call last): 
    8461 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    8462 packages/chimerax/core/triggerset.py", line 130, in invoke 
    8463 return self._func(self._name, data) 
    8464 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8465 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    8466 self.set_surface_mask() 
    8467 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8468 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    8469 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    8470 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8471 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    8472 self._update_mask() 
    8473 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8474 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    8475 step=self.grid_step, pad=self.pad) 
    8476 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8477 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    8478 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    8479 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8480 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    8481 _generate_data_array 
    8482 data = numpy.zeros(dim, numpy.uint8) 
    8483 ValueError: negative dimensions are not allowed 
    8484  
    8485 Error processing trigger "atom coords updated": 
    8486 ValueError: negative dimensions are not allowed 
    8487  
    8488 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8489 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    8490 _generate_data_array 
    8491 data = numpy.zeros(dim, numpy.uint8) 
    8492  
    8493 See log for complete Python traceback. 
    8494  
    8495 Traceback (most recent call last): 
    8496 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    8497 packages/chimerax/core/triggerset.py", line 130, in invoke 
    8498 return self._func(self._name, data) 
    8499 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8500 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    8501 self.set_surface_mask() 
    8502 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8503 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    8504 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    8505 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8506 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    8507 self._update_mask() 
    8508 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8509 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    8510 step=self.grid_step, pad=self.pad) 
    8511 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8512 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    8513 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    8514 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8515 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    8516 _generate_data_array 
    8517 data = numpy.zeros(dim, numpy.uint8) 
    8518 ValueError: negative dimensions are not allowed 
    8519  
    8520 Error processing trigger "atom coords updated": 
    8521 ValueError: negative dimensions are not allowed 
    8522  
    8523 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8524 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    8525 _generate_data_array 
    8526 data = numpy.zeros(dim, numpy.uint8) 
    8527  
    8528 See log for complete Python traceback. 
    8529  
    8530 Traceback (most recent call last): 
    8531 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    8532 packages/chimerax/core/triggerset.py", line 130, in invoke 
    8533 return self._func(self._name, data) 
    8534 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8535 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    8536 self.set_surface_mask() 
    8537 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8538 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    8539 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    8540 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8541 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    8542 self._update_mask() 
    8543 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8544 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    8545 step=self.grid_step, pad=self.pad) 
    8546 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8547 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    8548 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    8549 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8550 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    8551 _generate_data_array 
    8552 data = numpy.zeros(dim, numpy.uint8) 
    8553 ValueError: negative dimensions are not allowed 
    8554  
    8555 Error processing trigger "atom coords updated": 
    8556 ValueError: negative dimensions are not allowed 
    8557  
    8558 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8559 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    8560 _generate_data_array 
    8561 data = numpy.zeros(dim, numpy.uint8) 
    8562  
    8563 See log for complete Python traceback. 
    8564  
    8565 Traceback (most recent call last): 
    8566 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    8567 packages/chimerax/core/triggerset.py", line 130, in invoke 
    8568 return self._func(self._name, data) 
    8569 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8570 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    8571 self.set_surface_mask() 
    8572 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8573 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    8574 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    8575 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8576 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    8577 self._update_mask() 
    8578 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8579 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    8580 step=self.grid_step, pad=self.pad) 
    8581 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8582 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    8583 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    8584 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8585 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    8586 _generate_data_array 
    8587 data = numpy.zeros(dim, numpy.uint8) 
    8588 ValueError: negative dimensions are not allowed 
    8589  
    8590 Error processing trigger "atom coords updated": 
    8591 ValueError: negative dimensions are not allowed 
    8592  
    8593 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8594 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    8595 _generate_data_array 
    8596 data = numpy.zeros(dim, numpy.uint8) 
    8597  
    8598 See log for complete Python traceback. 
    8599  
    8600 Traceback (most recent call last): 
    8601 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    8602 packages/chimerax/core/triggerset.py", line 130, in invoke 
    8603 return self._func(self._name, data) 
    8604 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8605 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    8606 self.set_surface_mask() 
    8607 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8608 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    8609 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    8610 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8611 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    8612 self._update_mask() 
    8613 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8614 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    8615 step=self.grid_step, pad=self.pad) 
    8616 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8617 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    8618 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    8619 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8620 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    8621 _generate_data_array 
    8622 data = numpy.zeros(dim, numpy.uint8) 
    8623 ValueError: negative dimensions are not allowed 
    8624  
    8625 Error processing trigger "atom coords updated": 
    8626 ValueError: negative dimensions are not allowed 
    8627  
    8628 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8629 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    8630 _generate_data_array 
    8631 data = numpy.zeros(dim, numpy.uint8) 
    8632  
    8633 See log for complete Python traceback. 
    8634  
    8635 Traceback (most recent call last): 
    8636 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    8637 packages/chimerax/core/triggerset.py", line 130, in invoke 
    8638 return self._func(self._name, data) 
    8639 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8640 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    8641 self.set_surface_mask() 
    8642 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8643 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    8644 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    8645 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8646 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    8647 self._update_mask() 
    8648 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8649 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    8650 step=self.grid_step, pad=self.pad) 
    8651 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8652 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    8653 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    8654 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8655 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    8656 _generate_data_array 
    8657 data = numpy.zeros(dim, numpy.uint8) 
    8658 ValueError: negative dimensions are not allowed 
    8659  
    8660 Error processing trigger "atom coords updated": 
    8661 ValueError: negative dimensions are not allowed 
    8662  
    8663 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8664 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    8665 _generate_data_array 
    8666 data = numpy.zeros(dim, numpy.uint8) 
    8667  
    8668 See log for complete Python traceback. 
    8669  
    8670 Traceback (most recent call last): 
    8671 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    8672 packages/chimerax/core/triggerset.py", line 130, in invoke 
    8673 return self._func(self._name, data) 
    8674 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8675 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    8676 self.set_surface_mask() 
    8677 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8678 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    8679 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    8680 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8681 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    8682 self._update_mask() 
    8683 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8684 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    8685 step=self.grid_step, pad=self.pad) 
    8686 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8687 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    8688 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    8689 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8690 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    8691 _generate_data_array 
    8692 data = numpy.zeros(dim, numpy.uint8) 
    8693 ValueError: negative dimensions are not allowed 
    8694  
    8695 Error processing trigger "atom coords updated": 
    8696 ValueError: negative dimensions are not allowed 
    8697  
    8698 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8699 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    8700 _generate_data_array 
    8701 data = numpy.zeros(dim, numpy.uint8) 
    8702  
    8703 See log for complete Python traceback. 
    8704  
    8705 Traceback (most recent call last): 
    8706 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    8707 packages/chimerax/core/triggerset.py", line 130, in invoke 
    8708 return self._func(self._name, data) 
    8709 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8710 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    8711 self.set_surface_mask() 
    8712 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8713 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    8714 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    8715 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8716 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    8717 self._update_mask() 
    8718 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8719 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    8720 step=self.grid_step, pad=self.pad) 
    8721 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8722 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    8723 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    8724 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8725 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    8726 _generate_data_array 
    8727 data = numpy.zeros(dim, numpy.uint8) 
    8728 ValueError: negative dimensions are not allowed 
    8729  
    8730 Error processing trigger "atom coords updated": 
    8731 ValueError: negative dimensions are not allowed 
    8732  
    8733 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8734 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    8735 _generate_data_array 
    8736 data = numpy.zeros(dim, numpy.uint8) 
    8737  
    8738 See log for complete Python traceback. 
    8739  
    8740 Traceback (most recent call last): 
    8741 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    8742 packages/chimerax/core/triggerset.py", line 130, in invoke 
    8743 return self._func(self._name, data) 
    8744 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8745 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    8746 self.set_surface_mask() 
    8747 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8748 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    8749 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    8750 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8751 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    8752 self._update_mask() 
    8753 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8754 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    8755 step=self.grid_step, pad=self.pad) 
    8756 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8757 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    8758 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    8759 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8760 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    8761 _generate_data_array 
    8762 data = numpy.zeros(dim, numpy.uint8) 
    8763 ValueError: negative dimensions are not allowed 
    8764  
    8765 Error processing trigger "atom coords updated": 
    8766 ValueError: negative dimensions are not allowed 
    8767  
    8768 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8769 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    8770 _generate_data_array 
    8771 data = numpy.zeros(dim, numpy.uint8) 
    8772  
    8773 See log for complete Python traceback. 
    8774  
    8775 Traceback (most recent call last): 
    8776 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    8777 packages/chimerax/core/triggerset.py", line 130, in invoke 
    8778 return self._func(self._name, data) 
    8779 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8780 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    8781 self.set_surface_mask() 
    8782 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8783 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    8784 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    8785 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8786 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    8787 self._update_mask() 
    8788 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8789 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    8790 step=self.grid_step, pad=self.pad) 
    8791 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8792 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    8793 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    8794 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8795 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    8796 _generate_data_array 
    8797 data = numpy.zeros(dim, numpy.uint8) 
    8798 ValueError: negative dimensions are not allowed 
    8799  
    8800 Error processing trigger "atom coords updated": 
    8801 ValueError: negative dimensions are not allowed 
    8802  
    8803 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8804 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    8805 _generate_data_array 
    8806 data = numpy.zeros(dim, numpy.uint8) 
    8807  
    8808 See log for complete Python traceback. 
    8809  
    8810 Traceback (most recent call last): 
    8811 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    8812 packages/chimerax/core/triggerset.py", line 130, in invoke 
    8813 return self._func(self._name, data) 
    8814 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8815 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    8816 self.set_surface_mask() 
    8817 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8818 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    8819 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    8820 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8821 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    8822 self._update_mask() 
    8823 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8824 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    8825 step=self.grid_step, pad=self.pad) 
    8826 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8827 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    8828 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    8829 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8830 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    8831 _generate_data_array 
    8832 data = numpy.zeros(dim, numpy.uint8) 
    8833 ValueError: negative dimensions are not allowed 
    8834  
    8835 Error processing trigger "atom coords updated": 
    8836 ValueError: negative dimensions are not allowed 
    8837  
    8838 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8839 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    8840 _generate_data_array 
    8841 data = numpy.zeros(dim, numpy.uint8) 
    8842  
    8843 See log for complete Python traceback. 
    8844  
    8845 Traceback (most recent call last): 
    8846 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    8847 packages/chimerax/core/triggerset.py", line 130, in invoke 
    8848 return self._func(self._name, data) 
    8849 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8850 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    8851 self.set_surface_mask() 
    8852 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8853 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    8854 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    8855 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8856 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    8857 self._update_mask() 
    8858 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8859 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    8860 step=self.grid_step, pad=self.pad) 
    8861 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8862 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    8863 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    8864 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8865 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    8866 _generate_data_array 
    8867 data = numpy.zeros(dim, numpy.uint8) 
    8868 ValueError: negative dimensions are not allowed 
    8869  
    8870 Error processing trigger "atom coords updated": 
    8871 ValueError: negative dimensions are not allowed 
    8872  
    8873 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8874 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    8875 _generate_data_array 
    8876 data = numpy.zeros(dim, numpy.uint8) 
    8877  
    8878 See log for complete Python traceback. 
    8879  
    8880 Traceback (most recent call last): 
    8881 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    8882 packages/chimerax/core/triggerset.py", line 130, in invoke 
    8883 return self._func(self._name, data) 
    8884 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8885 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    8886 self.set_surface_mask() 
    8887 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8888 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    8889 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    8890 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8891 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    8892 self._update_mask() 
    8893 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8894 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    8895 step=self.grid_step, pad=self.pad) 
    8896 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8897 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    8898 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    8899 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8900 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    8901 _generate_data_array 
    8902 data = numpy.zeros(dim, numpy.uint8) 
    8903 ValueError: negative dimensions are not allowed 
    8904  
    8905 Error processing trigger "atom coords updated": 
    8906 ValueError: negative dimensions are not allowed 
    8907  
    8908 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8909 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    8910 _generate_data_array 
    8911 data = numpy.zeros(dim, numpy.uint8) 
    8912  
    8913 See log for complete Python traceback. 
    8914  
    8915 Traceback (most recent call last): 
    8916 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    8917 packages/chimerax/core/triggerset.py", line 130, in invoke 
    8918 return self._func(self._name, data) 
    8919 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8920 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    8921 self.set_surface_mask() 
    8922 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8923 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    8924 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    8925 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8926 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    8927 self._update_mask() 
    8928 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8929 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    8930 step=self.grid_step, pad=self.pad) 
    8931 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8932 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    8933 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    8934 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8935 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    8936 _generate_data_array 
    8937 data = numpy.zeros(dim, numpy.uint8) 
    8938 ValueError: negative dimensions are not allowed 
    8939  
    8940 Error processing trigger "atom coords updated": 
    8941 ValueError: negative dimensions are not allowed 
    8942  
    8943 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8944 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    8945 _generate_data_array 
    8946 data = numpy.zeros(dim, numpy.uint8) 
    8947  
    8948 See log for complete Python traceback. 
    8949  
    8950 Traceback (most recent call last): 
    8951 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    8952 packages/chimerax/core/triggerset.py", line 130, in invoke 
    8953 return self._func(self._name, data) 
    8954 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8955 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    8956 self.set_surface_mask() 
    8957 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8958 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    8959 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    8960 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8961 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    8962 self._update_mask() 
    8963 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8964 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    8965 step=self.grid_step, pad=self.pad) 
    8966 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8967 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    8968 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    8969 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8970 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    8971 _generate_data_array 
    8972 data = numpy.zeros(dim, numpy.uint8) 
    8973 ValueError: negative dimensions are not allowed 
    8974  
    8975 Error processing trigger "atom coords updated": 
    8976 ValueError: negative dimensions are not allowed 
    8977  
    8978 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8979 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    8980 _generate_data_array 
    8981 data = numpy.zeros(dim, numpy.uint8) 
    8982  
    8983 See log for complete Python traceback. 
    8984  
    8985 Traceback (most recent call last): 
    8986 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    8987 packages/chimerax/core/triggerset.py", line 130, in invoke 
    8988 return self._func(self._name, data) 
    8989 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8990 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    8991 self.set_surface_mask() 
    8992 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8993 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    8994 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    8995 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8996 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    8997 self._update_mask() 
    8998 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    8999 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    9000 step=self.grid_step, pad=self.pad) 
    9001 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9002 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    9003 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    9004 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9005 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    9006 _generate_data_array 
    9007 data = numpy.zeros(dim, numpy.uint8) 
    9008 ValueError: negative dimensions are not allowed 
    9009  
    9010 Error processing trigger "atom coords updated": 
    9011 ValueError: negative dimensions are not allowed 
    9012  
    9013 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9014 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    9015 _generate_data_array 
    9016 data = numpy.zeros(dim, numpy.uint8) 
    9017  
    9018 See log for complete Python traceback. 
    9019  
    9020 Traceback (most recent call last): 
    9021 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    9022 packages/chimerax/core/triggerset.py", line 130, in invoke 
    9023 return self._func(self._name, data) 
    9024 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9025 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    9026 self.set_surface_mask() 
    9027 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9028 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    9029 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    9030 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9031 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    9032 self._update_mask() 
    9033 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9034 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    9035 step=self.grid_step, pad=self.pad) 
    9036 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9037 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    9038 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    9039 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9040 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    9041 _generate_data_array 
    9042 data = numpy.zeros(dim, numpy.uint8) 
    9043 ValueError: negative dimensions are not allowed 
    9044  
    9045 Error processing trigger "atom coords updated": 
    9046 ValueError: negative dimensions are not allowed 
    9047  
    9048 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9049 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    9050 _generate_data_array 
    9051 data = numpy.zeros(dim, numpy.uint8) 
    9052  
    9053 See log for complete Python traceback. 
    9054  
    9055 Traceback (most recent call last): 
    9056 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    9057 packages/chimerax/core/triggerset.py", line 130, in invoke 
    9058 return self._func(self._name, data) 
    9059 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9060 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    9061 self.set_surface_mask() 
    9062 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9063 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    9064 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    9065 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9066 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    9067 self._update_mask() 
    9068 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9069 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    9070 step=self.grid_step, pad=self.pad) 
    9071 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9072 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    9073 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    9074 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9075 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    9076 _generate_data_array 
    9077 data = numpy.zeros(dim, numpy.uint8) 
    9078 ValueError: negative dimensions are not allowed 
    9079  
    9080 Error processing trigger "atom coords updated": 
    9081 ValueError: negative dimensions are not allowed 
    9082  
    9083 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9084 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    9085 _generate_data_array 
    9086 data = numpy.zeros(dim, numpy.uint8) 
    9087  
    9088 See log for complete Python traceback. 
    9089  
    9090 Traceback (most recent call last): 
    9091 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    9092 packages/chimerax/core/triggerset.py", line 130, in invoke 
    9093 return self._func(self._name, data) 
    9094 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9095 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    9096 self.set_surface_mask() 
    9097 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9098 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    9099 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    9100 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9101 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    9102 self._update_mask() 
    9103 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9104 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    9105 step=self.grid_step, pad=self.pad) 
    9106 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9107 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    9108 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    9109 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9110 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    9111 _generate_data_array 
    9112 data = numpy.zeros(dim, numpy.uint8) 
    9113 ValueError: negative dimensions are not allowed 
    9114  
    9115 Error processing trigger "atom coords updated": 
    9116 ValueError: negative dimensions are not allowed 
    9117  
    9118 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9119 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    9120 _generate_data_array 
    9121 data = numpy.zeros(dim, numpy.uint8) 
    9122  
    9123 See log for complete Python traceback. 
    9124  
    9125 Traceback (most recent call last): 
    9126 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    9127 packages/chimerax/core/triggerset.py", line 130, in invoke 
    9128 return self._func(self._name, data) 
    9129 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9130 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    9131 self.set_surface_mask() 
    9132 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9133 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    9134 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    9135 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9136 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    9137 self._update_mask() 
    9138 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9139 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    9140 step=self.grid_step, pad=self.pad) 
    9141 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9142 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    9143 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    9144 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9145 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    9146 _generate_data_array 
    9147 data = numpy.zeros(dim, numpy.uint8) 
    9148 ValueError: negative dimensions are not allowed 
    9149  
    9150 Error processing trigger "atom coords updated": 
    9151 ValueError: negative dimensions are not allowed 
    9152  
    9153 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9154 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    9155 _generate_data_array 
    9156 data = numpy.zeros(dim, numpy.uint8) 
    9157  
    9158 See log for complete Python traceback. 
    9159  
    9160 Traceback (most recent call last): 
    9161 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    9162 packages/chimerax/core/triggerset.py", line 130, in invoke 
    9163 return self._func(self._name, data) 
    9164 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9165 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    9166 self.set_surface_mask() 
    9167 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9168 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    9169 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    9170 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9171 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    9172 self._update_mask() 
    9173 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9174 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    9175 step=self.grid_step, pad=self.pad) 
    9176 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9177 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    9178 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    9179 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9180 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    9181 _generate_data_array 
    9182 data = numpy.zeros(dim, numpy.uint8) 
    9183 ValueError: negative dimensions are not allowed 
    9184  
    9185 Error processing trigger "atom coords updated": 
    9186 ValueError: negative dimensions are not allowed 
    9187  
    9188 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9189 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    9190 _generate_data_array 
    9191 data = numpy.zeros(dim, numpy.uint8) 
    9192  
    9193 See log for complete Python traceback. 
    9194  
    9195 Traceback (most recent call last): 
    9196 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    9197 packages/chimerax/core/triggerset.py", line 130, in invoke 
    9198 return self._func(self._name, data) 
    9199 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9200 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    9201 self.set_surface_mask() 
    9202 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9203 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    9204 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    9205 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9206 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    9207 self._update_mask() 
    9208 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9209 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    9210 step=self.grid_step, pad=self.pad) 
    9211 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9212 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    9213 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    9214 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9215 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    9216 _generate_data_array 
    9217 data = numpy.zeros(dim, numpy.uint8) 
    9218 ValueError: negative dimensions are not allowed 
    9219  
    9220 Error processing trigger "atom coords updated": 
    9221 ValueError: negative dimensions are not allowed 
    9222  
    9223 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9224 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    9225 _generate_data_array 
    9226 data = numpy.zeros(dim, numpy.uint8) 
    9227  
    9228 See log for complete Python traceback. 
    9229  
    9230 Traceback (most recent call last): 
    9231 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    9232 packages/chimerax/core/triggerset.py", line 130, in invoke 
    9233 return self._func(self._name, data) 
    9234 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9235 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    9236 self.set_surface_mask() 
    9237 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9238 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    9239 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    9240 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9241 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    9242 self._update_mask() 
    9243 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9244 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    9245 step=self.grid_step, pad=self.pad) 
    9246 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9247 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    9248 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    9249 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9250 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    9251 _generate_data_array 
    9252 data = numpy.zeros(dim, numpy.uint8) 
    9253 ValueError: negative dimensions are not allowed 
    9254  
    9255 Error processing trigger "atom coords updated": 
    9256 ValueError: negative dimensions are not allowed 
    9257  
    9258 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9259 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    9260 _generate_data_array 
    9261 data = numpy.zeros(dim, numpy.uint8) 
    9262  
    9263 See log for complete Python traceback. 
    9264  
    9265 Traceback (most recent call last): 
    9266 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    9267 packages/chimerax/core/triggerset.py", line 130, in invoke 
    9268 return self._func(self._name, data) 
    9269 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9270 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    9271 self.set_surface_mask() 
    9272 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9273 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    9274 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    9275 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9276 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    9277 self._update_mask() 
    9278 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9279 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    9280 step=self.grid_step, pad=self.pad) 
    9281 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9282 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    9283 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    9284 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9285 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    9286 _generate_data_array 
    9287 data = numpy.zeros(dim, numpy.uint8) 
    9288 ValueError: negative dimensions are not allowed 
    9289  
    9290 Error processing trigger "atom coords updated": 
    9291 ValueError: negative dimensions are not allowed 
    9292  
    9293 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9294 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    9295 _generate_data_array 
    9296 data = numpy.zeros(dim, numpy.uint8) 
    9297  
    9298 See log for complete Python traceback. 
    9299  
    9300 Traceback (most recent call last): 
    9301 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    9302 packages/chimerax/core/triggerset.py", line 130, in invoke 
    9303 return self._func(self._name, data) 
    9304 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9305 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    9306 self.set_surface_mask() 
    9307 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9308 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    9309 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    9310 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9311 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    9312 self._update_mask() 
    9313 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9314 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    9315 step=self.grid_step, pad=self.pad) 
    9316 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9317 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    9318 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    9319 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9320 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    9321 _generate_data_array 
    9322 data = numpy.zeros(dim, numpy.uint8) 
    9323 ValueError: negative dimensions are not allowed 
    9324  
    9325 Error processing trigger "atom coords updated": 
    9326 ValueError: negative dimensions are not allowed 
    9327  
    9328 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9329 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    9330 _generate_data_array 
    9331 data = numpy.zeros(dim, numpy.uint8) 
    9332  
    9333 See log for complete Python traceback. 
    9334  
    9335 Traceback (most recent call last): 
    9336 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    9337 packages/chimerax/core/triggerset.py", line 130, in invoke 
    9338 return self._func(self._name, data) 
    9339 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9340 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    9341 self.set_surface_mask() 
    9342 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9343 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    9344 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    9345 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9346 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    9347 self._update_mask() 
    9348 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9349 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    9350 step=self.grid_step, pad=self.pad) 
    9351 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9352 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    9353 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    9354 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9355 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    9356 _generate_data_array 
    9357 data = numpy.zeros(dim, numpy.uint8) 
    9358 ValueError: negative dimensions are not allowed 
    9359  
    9360 Error processing trigger "atom coords updated": 
    9361 ValueError: negative dimensions are not allowed 
    9362  
    9363 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9364 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    9365 _generate_data_array 
    9366 data = numpy.zeros(dim, numpy.uint8) 
    9367  
    9368 See log for complete Python traceback. 
    9369  
    9370 Traceback (most recent call last): 
    9371 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    9372 packages/chimerax/core/triggerset.py", line 130, in invoke 
    9373 return self._func(self._name, data) 
    9374 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9375 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    9376 self.set_surface_mask() 
    9377 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9378 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    9379 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    9380 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9381 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    9382 self._update_mask() 
    9383 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9384 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    9385 step=self.grid_step, pad=self.pad) 
    9386 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9387 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    9388 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    9389 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9390 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    9391 _generate_data_array 
    9392 data = numpy.zeros(dim, numpy.uint8) 
    9393 ValueError: negative dimensions are not allowed 
    9394  
    9395 Error processing trigger "atom coords updated": 
    9396 ValueError: negative dimensions are not allowed 
    9397  
    9398 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9399 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    9400 _generate_data_array 
    9401 data = numpy.zeros(dim, numpy.uint8) 
    9402  
    9403 See log for complete Python traceback. 
    9404  
    9405 Traceback (most recent call last): 
    9406 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    9407 packages/chimerax/core/triggerset.py", line 130, in invoke 
    9408 return self._func(self._name, data) 
    9409 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9410 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    9411 self.set_surface_mask() 
    9412 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9413 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    9414 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    9415 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9416 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    9417 self._update_mask() 
    9418 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9419 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    9420 step=self.grid_step, pad=self.pad) 
    9421 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9422 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    9423 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    9424 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9425 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    9426 _generate_data_array 
    9427 data = numpy.zeros(dim, numpy.uint8) 
    9428 ValueError: negative dimensions are not allowed 
    9429  
    9430 Error processing trigger "atom coords updated": 
    9431 ValueError: negative dimensions are not allowed 
    9432  
    9433 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9434 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    9435 _generate_data_array 
    9436 data = numpy.zeros(dim, numpy.uint8) 
    9437  
    9438 See log for complete Python traceback. 
    9439  
    9440 Traceback (most recent call last): 
    9441 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    9442 packages/chimerax/core/triggerset.py", line 130, in invoke 
    9443 return self._func(self._name, data) 
    9444 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9445 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    9446 self.set_surface_mask() 
    9447 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9448 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    9449 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    9450 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9451 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    9452 self._update_mask() 
    9453 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9454 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    9455 step=self.grid_step, pad=self.pad) 
    9456 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9457 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    9458 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    9459 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9460 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    9461 _generate_data_array 
    9462 data = numpy.zeros(dim, numpy.uint8) 
    9463 ValueError: negative dimensions are not allowed 
    9464  
    9465 Error processing trigger "atom coords updated": 
    9466 ValueError: negative dimensions are not allowed 
    9467  
    9468 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9469 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    9470 _generate_data_array 
    9471 data = numpy.zeros(dim, numpy.uint8) 
    9472  
    9473 See log for complete Python traceback. 
    9474  
    9475 Traceback (most recent call last): 
    9476 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    9477 packages/chimerax/core/triggerset.py", line 130, in invoke 
    9478 return self._func(self._name, data) 
    9479 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9480 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    9481 self.set_surface_mask() 
    9482 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9483 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    9484 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    9485 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9486 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    9487 self._update_mask() 
    9488 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9489 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    9490 step=self.grid_step, pad=self.pad) 
    9491 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9492 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    9493 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    9494 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9495 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    9496 _generate_data_array 
    9497 data = numpy.zeros(dim, numpy.uint8) 
    9498 ValueError: negative dimensions are not allowed 
    9499  
    9500 Error processing trigger "atom coords updated": 
    9501 ValueError: negative dimensions are not allowed 
    9502  
    9503 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9504 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    9505 _generate_data_array 
    9506 data = numpy.zeros(dim, numpy.uint8) 
    9507  
    9508 See log for complete Python traceback. 
    9509  
    9510 Traceback (most recent call last): 
    9511 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    9512 packages/chimerax/core/triggerset.py", line 130, in invoke 
    9513 return self._func(self._name, data) 
    9514 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9515 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    9516 self.set_surface_mask() 
    9517 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9518 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    9519 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    9520 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9521 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    9522 self._update_mask() 
    9523 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9524 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    9525 step=self.grid_step, pad=self.pad) 
    9526 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9527 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    9528 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    9529 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9530 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    9531 _generate_data_array 
    9532 data = numpy.zeros(dim, numpy.uint8) 
    9533 ValueError: negative dimensions are not allowed 
    9534  
    9535 Error processing trigger "atom coords updated": 
    9536 ValueError: negative dimensions are not allowed 
    9537  
    9538 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9539 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    9540 _generate_data_array 
    9541 data = numpy.zeros(dim, numpy.uint8) 
    9542  
    9543 See log for complete Python traceback. 
    9544  
    9545 Traceback (most recent call last): 
    9546 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    9547 packages/chimerax/core/triggerset.py", line 130, in invoke 
    9548 return self._func(self._name, data) 
    9549 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9550 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    9551 self.set_surface_mask() 
    9552 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9553 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    9554 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    9555 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9556 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    9557 self._update_mask() 
    9558 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9559 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    9560 step=self.grid_step, pad=self.pad) 
    9561 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9562 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    9563 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    9564 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9565 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    9566 _generate_data_array 
    9567 data = numpy.zeros(dim, numpy.uint8) 
    9568 ValueError: negative dimensions are not allowed 
    9569  
    9570 Error processing trigger "atom coords updated": 
    9571 ValueError: negative dimensions are not allowed 
    9572  
    9573 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9574 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    9575 _generate_data_array 
    9576 data = numpy.zeros(dim, numpy.uint8) 
    9577  
    9578 See log for complete Python traceback. 
    9579  
    9580 Traceback (most recent call last): 
    9581 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    9582 packages/chimerax/core/triggerset.py", line 130, in invoke 
    9583 return self._func(self._name, data) 
    9584 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9585 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    9586 self.set_surface_mask() 
    9587 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9588 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    9589 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    9590 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9591 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    9592 self._update_mask() 
    9593 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9594 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    9595 step=self.grid_step, pad=self.pad) 
    9596 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9597 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    9598 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    9599 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9600 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    9601 _generate_data_array 
    9602 data = numpy.zeros(dim, numpy.uint8) 
    9603 ValueError: negative dimensions are not allowed 
    9604  
    9605 Error processing trigger "atom coords updated": 
    9606 ValueError: negative dimensions are not allowed 
    9607  
    9608 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9609 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    9610 _generate_data_array 
    9611 data = numpy.zeros(dim, numpy.uint8) 
    9612  
    9613 See log for complete Python traceback. 
    9614  
    9615 Traceback (most recent call last): 
    9616 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    9617 packages/chimerax/core/triggerset.py", line 130, in invoke 
    9618 return self._func(self._name, data) 
    9619 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9620 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    9621 self.set_surface_mask() 
    9622 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9623 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    9624 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    9625 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9626 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    9627 self._update_mask() 
    9628 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9629 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    9630 step=self.grid_step, pad=self.pad) 
    9631 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9632 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    9633 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    9634 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9635 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    9636 _generate_data_array 
    9637 data = numpy.zeros(dim, numpy.uint8) 
    9638 ValueError: negative dimensions are not allowed 
    9639  
    9640 Error processing trigger "atom coords updated": 
    9641 ValueError: negative dimensions are not allowed 
    9642  
    9643 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9644 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    9645 _generate_data_array 
    9646 data = numpy.zeros(dim, numpy.uint8) 
    9647  
    9648 See log for complete Python traceback. 
    9649  
    9650 Traceback (most recent call last): 
    9651 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    9652 packages/chimerax/core/triggerset.py", line 130, in invoke 
    9653 return self._func(self._name, data) 
    9654 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9655 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    9656 self.set_surface_mask() 
    9657 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9658 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    9659 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    9660 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9661 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    9662 self._update_mask() 
    9663 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9664 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    9665 step=self.grid_step, pad=self.pad) 
    9666 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9667 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    9668 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    9669 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9670 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    9671 _generate_data_array 
    9672 data = numpy.zeros(dim, numpy.uint8) 
    9673 ValueError: negative dimensions are not allowed 
    9674  
    9675 Error processing trigger "atom coords updated": 
    9676 ValueError: negative dimensions are not allowed 
    9677  
    9678 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9679 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    9680 _generate_data_array 
    9681 data = numpy.zeros(dim, numpy.uint8) 
    9682  
    9683 See log for complete Python traceback. 
    9684  
    9685 Traceback (most recent call last): 
    9686 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    9687 packages/chimerax/core/triggerset.py", line 130, in invoke 
    9688 return self._func(self._name, data) 
    9689 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9690 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    9691 self.set_surface_mask() 
    9692 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9693 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    9694 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    9695 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9696 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    9697 self._update_mask() 
    9698 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9699 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    9700 step=self.grid_step, pad=self.pad) 
    9701 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9702 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    9703 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    9704 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9705 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    9706 _generate_data_array 
    9707 data = numpy.zeros(dim, numpy.uint8) 
    9708 ValueError: negative dimensions are not allowed 
    9709  
    9710 Error processing trigger "atom coords updated": 
    9711 ValueError: negative dimensions are not allowed 
    9712  
    9713 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9714 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    9715 _generate_data_array 
    9716 data = numpy.zeros(dim, numpy.uint8) 
    9717  
    9718 See log for complete Python traceback. 
    9719  
    9720 Traceback (most recent call last): 
    9721 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    9722 packages/chimerax/core/triggerset.py", line 130, in invoke 
    9723 return self._func(self._name, data) 
    9724 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9725 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    9726 self.set_surface_mask() 
    9727 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9728 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    9729 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    9730 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9731 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    9732 self._update_mask() 
    9733 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9734 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    9735 step=self.grid_step, pad=self.pad) 
    9736 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9737 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    9738 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    9739 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9740 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    9741 _generate_data_array 
    9742 data = numpy.zeros(dim, numpy.uint8) 
    9743 ValueError: negative dimensions are not allowed 
    9744  
    9745 Error processing trigger "atom coords updated": 
    9746 ValueError: negative dimensions are not allowed 
    9747  
    9748 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9749 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    9750 _generate_data_array 
    9751 data = numpy.zeros(dim, numpy.uint8) 
    9752  
    9753 See log for complete Python traceback. 
    9754  
    9755 Traceback (most recent call last): 
    9756 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    9757 packages/chimerax/core/triggerset.py", line 130, in invoke 
    9758 return self._func(self._name, data) 
    9759 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9760 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    9761 self.set_surface_mask() 
    9762 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9763 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    9764 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    9765 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9766 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    9767 self._update_mask() 
    9768 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9769 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    9770 step=self.grid_step, pad=self.pad) 
    9771 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9772 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    9773 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    9774 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9775 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    9776 _generate_data_array 
    9777 data = numpy.zeros(dim, numpy.uint8) 
    9778 ValueError: negative dimensions are not allowed 
    9779  
    9780 Error processing trigger "atom coords updated": 
    9781 ValueError: negative dimensions are not allowed 
    9782  
    9783 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9784 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    9785 _generate_data_array 
    9786 data = numpy.zeros(dim, numpy.uint8) 
    9787  
    9788 See log for complete Python traceback. 
    9789  
    9790 Traceback (most recent call last): 
    9791 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    9792 packages/chimerax/core/triggerset.py", line 130, in invoke 
    9793 return self._func(self._name, data) 
    9794 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9795 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    9796 self.set_surface_mask() 
    9797 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9798 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    9799 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    9800 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9801 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    9802 self._update_mask() 
    9803 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9804 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    9805 step=self.grid_step, pad=self.pad) 
    9806 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9807 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    9808 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    9809 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9810 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    9811 _generate_data_array 
    9812 data = numpy.zeros(dim, numpy.uint8) 
    9813 ValueError: negative dimensions are not allowed 
    9814  
    9815 Error processing trigger "atom coords updated": 
    9816 ValueError: negative dimensions are not allowed 
    9817  
    9818 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9819 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    9820 _generate_data_array 
    9821 data = numpy.zeros(dim, numpy.uint8) 
    9822  
    9823 See log for complete Python traceback. 
    9824  
    9825 Traceback (most recent call last): 
    9826 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    9827 packages/chimerax/core/triggerset.py", line 130, in invoke 
    9828 return self._func(self._name, data) 
    9829 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9830 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    9831 self.set_surface_mask() 
    9832 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9833 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    9834 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    9835 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9836 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    9837 self._update_mask() 
    9838 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9839 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    9840 step=self.grid_step, pad=self.pad) 
    9841 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9842 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    9843 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    9844 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9845 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    9846 _generate_data_array 
    9847 data = numpy.zeros(dim, numpy.uint8) 
    9848 ValueError: negative dimensions are not allowed 
    9849  
    9850 Error processing trigger "atom coords updated": 
    9851 ValueError: negative dimensions are not allowed 
    9852  
    9853 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9854 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    9855 _generate_data_array 
    9856 data = numpy.zeros(dim, numpy.uint8) 
    9857  
    9858 See log for complete Python traceback. 
    9859  
    9860 Traceback (most recent call last): 
    9861 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    9862 packages/chimerax/core/triggerset.py", line 130, in invoke 
    9863 return self._func(self._name, data) 
    9864 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9865 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    9866 self.set_surface_mask() 
    9867 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9868 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    9869 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    9870 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9871 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    9872 self._update_mask() 
    9873 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9874 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    9875 step=self.grid_step, pad=self.pad) 
    9876 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9877 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    9878 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    9879 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9880 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    9881 _generate_data_array 
    9882 data = numpy.zeros(dim, numpy.uint8) 
    9883 ValueError: negative dimensions are not allowed 
    9884  
    9885 Error processing trigger "atom coords updated": 
    9886 ValueError: negative dimensions are not allowed 
    9887  
    9888 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9889 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    9890 _generate_data_array 
    9891 data = numpy.zeros(dim, numpy.uint8) 
    9892  
    9893 See log for complete Python traceback. 
    9894  
    9895 Traceback (most recent call last): 
    9896 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    9897 packages/chimerax/core/triggerset.py", line 130, in invoke 
    9898 return self._func(self._name, data) 
    9899 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9900 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    9901 self.set_surface_mask() 
    9902 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9903 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    9904 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    9905 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9906 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    9907 self._update_mask() 
    9908 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9909 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    9910 step=self.grid_step, pad=self.pad) 
    9911 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9912 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    9913 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    9914 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9915 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    9916 _generate_data_array 
    9917 data = numpy.zeros(dim, numpy.uint8) 
    9918 ValueError: negative dimensions are not allowed 
    9919  
    9920 Error processing trigger "atom coords updated": 
    9921 ValueError: negative dimensions are not allowed 
    9922  
    9923 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9924 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    9925 _generate_data_array 
    9926 data = numpy.zeros(dim, numpy.uint8) 
    9927  
    9928 See log for complete Python traceback. 
    9929  
    9930 Traceback (most recent call last): 
    9931 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    9932 packages/chimerax/core/triggerset.py", line 130, in invoke 
    9933 return self._func(self._name, data) 
    9934 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9935 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    9936 self.set_surface_mask() 
    9937 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9938 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    9939 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    9940 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9941 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    9942 self._update_mask() 
    9943 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9944 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    9945 step=self.grid_step, pad=self.pad) 
    9946 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9947 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    9948 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    9949 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9950 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    9951 _generate_data_array 
    9952 data = numpy.zeros(dim, numpy.uint8) 
    9953 ValueError: negative dimensions are not allowed 
    9954  
    9955 Error processing trigger "atom coords updated": 
    9956 ValueError: negative dimensions are not allowed 
    9957  
    9958 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9959 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    9960 _generate_data_array 
    9961 data = numpy.zeros(dim, numpy.uint8) 
    9962  
    9963 See log for complete Python traceback. 
    9964  
    9965 Traceback (most recent call last): 
    9966 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    9967 packages/chimerax/core/triggerset.py", line 130, in invoke 
    9968 return self._func(self._name, data) 
    9969 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9970 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    9971 self.set_surface_mask() 
    9972 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9973 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    9974 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    9975 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9976 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    9977 self._update_mask() 
    9978 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9979 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    9980 step=self.grid_step, pad=self.pad) 
    9981 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9982 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    9983 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    9984 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9985 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    9986 _generate_data_array 
    9987 data = numpy.zeros(dim, numpy.uint8) 
    9988 ValueError: negative dimensions are not allowed 
    9989  
    9990 Error processing trigger "atom coords updated": 
    9991 ValueError: negative dimensions are not allowed 
    9992  
    9993 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    9994 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    9995 _generate_data_array 
    9996 data = numpy.zeros(dim, numpy.uint8) 
    9997  
    9998 See log for complete Python traceback. 
    9999  
    10000 Traceback (most recent call last): 
    10001 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    10002 packages/chimerax/core/triggerset.py", line 130, in invoke 
    10003 return self._func(self._name, data) 
    10004 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10005 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    10006 self.set_surface_mask() 
    10007 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10008 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    10009 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    10010 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10011 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    10012 self._update_mask() 
    10013 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10014 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    10015 step=self.grid_step, pad=self.pad) 
    10016 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10017 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    10018 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    10019 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10020 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    10021 _generate_data_array 
    10022 data = numpy.zeros(dim, numpy.uint8) 
    10023 ValueError: negative dimensions are not allowed 
    10024  
    10025 Error processing trigger "atom coords updated": 
    10026 ValueError: negative dimensions are not allowed 
    10027  
    10028 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10029 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    10030 _generate_data_array 
    10031 data = numpy.zeros(dim, numpy.uint8) 
    10032  
    10033 See log for complete Python traceback. 
    10034  
    10035 Traceback (most recent call last): 
    10036 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    10037 packages/chimerax/core/triggerset.py", line 130, in invoke 
    10038 return self._func(self._name, data) 
    10039 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10040 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    10041 self.set_surface_mask() 
    10042 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10043 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    10044 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    10045 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10046 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    10047 self._update_mask() 
    10048 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10049 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    10050 step=self.grid_step, pad=self.pad) 
    10051 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10052 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    10053 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    10054 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10055 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    10056 _generate_data_array 
    10057 data = numpy.zeros(dim, numpy.uint8) 
    10058 ValueError: negative dimensions are not allowed 
    10059  
    10060 Error processing trigger "atom coords updated": 
    10061 ValueError: negative dimensions are not allowed 
    10062  
    10063 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10064 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    10065 _generate_data_array 
    10066 data = numpy.zeros(dim, numpy.uint8) 
    10067  
    10068 See log for complete Python traceback. 
    10069  
    10070 Traceback (most recent call last): 
    10071 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    10072 packages/chimerax/core/triggerset.py", line 130, in invoke 
    10073 return self._func(self._name, data) 
    10074 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10075 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    10076 self.set_surface_mask() 
    10077 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10078 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    10079 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    10080 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10081 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    10082 self._update_mask() 
    10083 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10084 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    10085 step=self.grid_step, pad=self.pad) 
    10086 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10087 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    10088 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    10089 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10090 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    10091 _generate_data_array 
    10092 data = numpy.zeros(dim, numpy.uint8) 
    10093 ValueError: negative dimensions are not allowed 
    10094  
    10095 Error processing trigger "atom coords updated": 
    10096 ValueError: negative dimensions are not allowed 
    10097  
    10098 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10099 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    10100 _generate_data_array 
    10101 data = numpy.zeros(dim, numpy.uint8) 
    10102  
    10103 See log for complete Python traceback. 
    10104  
    10105 Traceback (most recent call last): 
    10106 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    10107 packages/chimerax/core/triggerset.py", line 130, in invoke 
    10108 return self._func(self._name, data) 
    10109 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10110 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    10111 self.set_surface_mask() 
    10112 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10113 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    10114 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    10115 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10116 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    10117 self._update_mask() 
    10118 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10119 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    10120 step=self.grid_step, pad=self.pad) 
    10121 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10122 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    10123 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    10124 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10125 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    10126 _generate_data_array 
    10127 data = numpy.zeros(dim, numpy.uint8) 
    10128 ValueError: negative dimensions are not allowed 
    10129  
    10130 Error processing trigger "atom coords updated": 
    10131 ValueError: negative dimensions are not allowed 
    10132  
    10133 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10134 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    10135 _generate_data_array 
    10136 data = numpy.zeros(dim, numpy.uint8) 
    10137  
    10138 See log for complete Python traceback. 
    10139  
    10140 Traceback (most recent call last): 
    10141 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    10142 packages/chimerax/core/triggerset.py", line 130, in invoke 
    10143 return self._func(self._name, data) 
    10144 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10145 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    10146 self.set_surface_mask() 
    10147 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10148 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    10149 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    10150 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10151 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    10152 self._update_mask() 
    10153 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10154 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    10155 step=self.grid_step, pad=self.pad) 
    10156 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10157 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    10158 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    10159 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10160 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    10161 _generate_data_array 
    10162 data = numpy.zeros(dim, numpy.uint8) 
    10163 ValueError: negative dimensions are not allowed 
    10164  
    10165 Error processing trigger "atom coords updated": 
    10166 ValueError: negative dimensions are not allowed 
    10167  
    10168 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10169 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    10170 _generate_data_array 
    10171 data = numpy.zeros(dim, numpy.uint8) 
    10172  
    10173 See log for complete Python traceback. 
    10174  
    10175 Traceback (most recent call last): 
    10176 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    10177 packages/chimerax/core/triggerset.py", line 130, in invoke 
    10178 return self._func(self._name, data) 
    10179 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10180 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    10181 self.set_surface_mask() 
    10182 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10183 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    10184 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    10185 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10186 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    10187 self._update_mask() 
    10188 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10189 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    10190 step=self.grid_step, pad=self.pad) 
    10191 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10192 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    10193 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    10194 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10195 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    10196 _generate_data_array 
    10197 data = numpy.zeros(dim, numpy.uint8) 
    10198 ValueError: negative dimensions are not allowed 
    10199  
    10200 Error processing trigger "atom coords updated": 
    10201 ValueError: negative dimensions are not allowed 
    10202  
    10203 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10204 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    10205 _generate_data_array 
    10206 data = numpy.zeros(dim, numpy.uint8) 
    10207  
    10208 See log for complete Python traceback. 
    10209  
    10210 Traceback (most recent call last): 
    10211 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    10212 packages/chimerax/core/triggerset.py", line 130, in invoke 
    10213 return self._func(self._name, data) 
    10214 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10215 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    10216 self.set_surface_mask() 
    10217 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10218 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    10219 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    10220 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10221 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    10222 self._update_mask() 
    10223 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10224 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    10225 step=self.grid_step, pad=self.pad) 
    10226 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10227 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    10228 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    10229 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10230 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    10231 _generate_data_array 
    10232 data = numpy.zeros(dim, numpy.uint8) 
    10233 ValueError: negative dimensions are not allowed 
    10234  
    10235 Error processing trigger "atom coords updated": 
    10236 ValueError: negative dimensions are not allowed 
    10237  
    10238 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10239 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    10240 _generate_data_array 
    10241 data = numpy.zeros(dim, numpy.uint8) 
    10242  
    10243 See log for complete Python traceback. 
    10244  
    10245 Traceback (most recent call last): 
    10246 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    10247 packages/chimerax/core/triggerset.py", line 130, in invoke 
    10248 return self._func(self._name, data) 
    10249 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10250 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    10251 self.set_surface_mask() 
    10252 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10253 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    10254 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    10255 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10256 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    10257 self._update_mask() 
    10258 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10259 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    10260 step=self.grid_step, pad=self.pad) 
    10261 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10262 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    10263 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    10264 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10265 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    10266 _generate_data_array 
    10267 data = numpy.zeros(dim, numpy.uint8) 
    10268 ValueError: negative dimensions are not allowed 
    10269  
    10270 Error processing trigger "atom coords updated": 
    10271 ValueError: negative dimensions are not allowed 
    10272  
    10273 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10274 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    10275 _generate_data_array 
    10276 data = numpy.zeros(dim, numpy.uint8) 
    10277  
    10278 See log for complete Python traceback. 
    10279  
    10280 Traceback (most recent call last): 
    10281 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    10282 packages/chimerax/core/triggerset.py", line 130, in invoke 
    10283 return self._func(self._name, data) 
    10284 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10285 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    10286 self.set_surface_mask() 
    10287 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10288 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    10289 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    10290 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10291 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    10292 self._update_mask() 
    10293 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10294 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    10295 step=self.grid_step, pad=self.pad) 
    10296 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10297 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    10298 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    10299 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10300 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    10301 _generate_data_array 
    10302 data = numpy.zeros(dim, numpy.uint8) 
    10303 ValueError: negative dimensions are not allowed 
    10304  
    10305 Error processing trigger "atom coords updated": 
    10306 ValueError: negative dimensions are not allowed 
    10307  
    10308 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10309 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    10310 _generate_data_array 
    10311 data = numpy.zeros(dim, numpy.uint8) 
    10312  
    10313 See log for complete Python traceback. 
    10314  
    10315 Traceback (most recent call last): 
    10316 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    10317 packages/chimerax/core/triggerset.py", line 130, in invoke 
    10318 return self._func(self._name, data) 
    10319 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10320 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    10321 self.set_surface_mask() 
    10322 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10323 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    10324 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    10325 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10326 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    10327 self._update_mask() 
    10328 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10329 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    10330 step=self.grid_step, pad=self.pad) 
    10331 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10332 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    10333 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    10334 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10335 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    10336 _generate_data_array 
    10337 data = numpy.zeros(dim, numpy.uint8) 
    10338 ValueError: negative dimensions are not allowed 
    10339  
    10340 Error processing trigger "atom coords updated": 
    10341 ValueError: negative dimensions are not allowed 
    10342  
    10343 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10344 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    10345 _generate_data_array 
    10346 data = numpy.zeros(dim, numpy.uint8) 
    10347  
    10348 See log for complete Python traceback. 
    10349  
    10350 Traceback (most recent call last): 
    10351 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    10352 packages/chimerax/core/triggerset.py", line 130, in invoke 
    10353 return self._func(self._name, data) 
    10354 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10355 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    10356 self.set_surface_mask() 
    10357 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10358 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    10359 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    10360 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10361 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    10362 self._update_mask() 
    10363 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10364 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    10365 step=self.grid_step, pad=self.pad) 
    10366 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10367 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    10368 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    10369 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10370 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    10371 _generate_data_array 
    10372 data = numpy.zeros(dim, numpy.uint8) 
    10373 ValueError: negative dimensions are not allowed 
    10374  
    10375 Error processing trigger "atom coords updated": 
    10376 ValueError: negative dimensions are not allowed 
    10377  
    10378 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10379 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    10380 _generate_data_array 
    10381 data = numpy.zeros(dim, numpy.uint8) 
    10382  
    10383 See log for complete Python traceback. 
    10384  
    10385 Traceback (most recent call last): 
    10386 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    10387 packages/chimerax/core/triggerset.py", line 130, in invoke 
    10388 return self._func(self._name, data) 
    10389 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10390 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    10391 self.set_surface_mask() 
    10392 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10393 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    10394 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    10395 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10396 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    10397 self._update_mask() 
    10398 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10399 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    10400 step=self.grid_step, pad=self.pad) 
    10401 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10402 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    10403 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    10404 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10405 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    10406 _generate_data_array 
    10407 data = numpy.zeros(dim, numpy.uint8) 
    10408 ValueError: negative dimensions are not allowed 
    10409  
    10410 Error processing trigger "atom coords updated": 
    10411 ValueError: negative dimensions are not allowed 
    10412  
    10413 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10414 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    10415 _generate_data_array 
    10416 data = numpy.zeros(dim, numpy.uint8) 
    10417  
    10418 See log for complete Python traceback. 
    10419  
    10420 Traceback (most recent call last): 
    10421 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    10422 packages/chimerax/core/triggerset.py", line 130, in invoke 
    10423 return self._func(self._name, data) 
    10424 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10425 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    10426 self.set_surface_mask() 
    10427 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10428 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    10429 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    10430 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10431 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    10432 self._update_mask() 
    10433 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10434 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    10435 step=self.grid_step, pad=self.pad) 
    10436 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10437 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    10438 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    10439 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10440 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    10441 _generate_data_array 
    10442 data = numpy.zeros(dim, numpy.uint8) 
    10443 ValueError: negative dimensions are not allowed 
    10444  
    10445 Error processing trigger "atom coords updated": 
    10446 ValueError: negative dimensions are not allowed 
    10447  
    10448 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10449 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    10450 _generate_data_array 
    10451 data = numpy.zeros(dim, numpy.uint8) 
    10452  
    10453 See log for complete Python traceback. 
    10454  
    10455 Traceback (most recent call last): 
    10456 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    10457 packages/chimerax/core/triggerset.py", line 130, in invoke 
    10458 return self._func(self._name, data) 
    10459 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10460 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    10461 self.set_surface_mask() 
    10462 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10463 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    10464 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    10465 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10466 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    10467 self._update_mask() 
    10468 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10469 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    10470 step=self.grid_step, pad=self.pad) 
    10471 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10472 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    10473 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    10474 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10475 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    10476 _generate_data_array 
    10477 data = numpy.zeros(dim, numpy.uint8) 
    10478 ValueError: negative dimensions are not allowed 
    10479  
    10480 Error processing trigger "atom coords updated": 
    10481 ValueError: negative dimensions are not allowed 
    10482  
    10483 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10484 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    10485 _generate_data_array 
    10486 data = numpy.zeros(dim, numpy.uint8) 
    10487  
    10488 See log for complete Python traceback. 
    10489  
    10490 Traceback (most recent call last): 
    10491 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    10492 packages/chimerax/core/triggerset.py", line 130, in invoke 
    10493 return self._func(self._name, data) 
    10494 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10495 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    10496 self.set_surface_mask() 
    10497 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10498 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    10499 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    10500 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10501 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    10502 self._update_mask() 
    10503 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10504 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    10505 step=self.grid_step, pad=self.pad) 
    10506 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10507 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    10508 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    10509 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10510 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    10511 _generate_data_array 
    10512 data = numpy.zeros(dim, numpy.uint8) 
    10513 ValueError: negative dimensions are not allowed 
    10514  
    10515 Error processing trigger "atom coords updated": 
    10516 ValueError: negative dimensions are not allowed 
    10517  
    10518 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10519 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    10520 _generate_data_array 
    10521 data = numpy.zeros(dim, numpy.uint8) 
    10522  
    10523 See log for complete Python traceback. 
    10524  
    10525 Traceback (most recent call last): 
    10526 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    10527 packages/chimerax/core/triggerset.py", line 130, in invoke 
    10528 return self._func(self._name, data) 
    10529 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10530 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    10531 self.set_surface_mask() 
    10532 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10533 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    10534 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    10535 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10536 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    10537 self._update_mask() 
    10538 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10539 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    10540 step=self.grid_step, pad=self.pad) 
    10541 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10542 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    10543 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    10544 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10545 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    10546 _generate_data_array 
    10547 data = numpy.zeros(dim, numpy.uint8) 
    10548 ValueError: negative dimensions are not allowed 
    10549  
    10550 Error processing trigger "atom coords updated": 
    10551 ValueError: negative dimensions are not allowed 
    10552  
    10553 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10554 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    10555 _generate_data_array 
    10556 data = numpy.zeros(dim, numpy.uint8) 
    10557  
    10558 See log for complete Python traceback. 
    10559  
    10560 Traceback (most recent call last): 
    10561 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    10562 packages/chimerax/core/triggerset.py", line 130, in invoke 
    10563 return self._func(self._name, data) 
    10564 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10565 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    10566 self.set_surface_mask() 
    10567 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10568 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    10569 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    10570 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10571 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    10572 self._update_mask() 
    10573 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10574 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    10575 step=self.grid_step, pad=self.pad) 
    10576 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10577 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    10578 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    10579 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10580 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    10581 _generate_data_array 
    10582 data = numpy.zeros(dim, numpy.uint8) 
    10583 ValueError: negative dimensions are not allowed 
    10584  
    10585 Error processing trigger "atom coords updated": 
    10586 ValueError: negative dimensions are not allowed 
    10587  
    10588 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10589 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    10590 _generate_data_array 
    10591 data = numpy.zeros(dim, numpy.uint8) 
    10592  
    10593 See log for complete Python traceback. 
    10594  
    10595 Traceback (most recent call last): 
    10596 File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site-
    10597 packages/chimerax/core/triggerset.py", line 130, in invoke 
    10598 return self._func(self._name, data) 
    10599 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10600 packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb 
    10601 self.set_surface_mask() 
    10602 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10603 packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask 
    10604 indices = numpy.where(self.mgr.get_vertex_mask(v))[0] 
    10605 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10606 packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask 
    10607 self._update_mask() 
    10608 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10609 packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask 
    10610 step=self.grid_step, pad=self.pad) 
    10611 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10612 packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask 
    10613 self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) 
    10614 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10615 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    10616 _generate_data_array 
    10617 data = numpy.zeros(dim, numpy.uint8) 
    10618 ValueError: negative dimensions are not allowed 
    10619  
    10620 Error processing trigger "atom coords updated": 
    10621 ValueError: negative dimensions are not allowed 
    10622  
    10623 File "/home/lad58072/.local/share/ChimeraX/1.0/site-
    10624 packages/chimerax/clipper/maps/mask_handler.py", line 236, in
    10625 _generate_data_array 
    10626 data = numpy.zeros(dim, numpy.uint8) 
    10627  
     723[many repetitions of this error deleted] 
     724
    10628725See log for complete Python traceback. 
    10629726