Changes between Initial Version and Version 1 of Ticket #9541


Ignore:
Timestamp:
Aug 8, 2023, 11:00:39 AM (2 years ago)
Author:
Eric Pettersen
Comment:

Legend:

Unmodified
Added
Removed
Modified

  • Ticket #9541

    • Property Component Unassigned → Input/Output
    • Property Owner set to Greg Couch
    • Property Platform → all
    • Property Project → ChimeraX
    • Property Status new → assigned
    • Property Summary ChimeraX bug report submission → MemoryError open mmCIF

  • Ticket #9541 – Description

    initial v1  
    548548> color #16-19 #a7ff7eff
    549549
    550 > color #16-19 #b2ff7eff
    551 
    552 > color #16-19 #b8ff7eff
    553 
    554 > color #16-19 #c3ff7eff
    555 
    556 > color #16-19 #cbff7eff
    557 
    558 > color #16-19 #ceff7eff
    559 
    560 > color #16-19 #c7ff7eff
    561 
    562 > color #16-19 #c3ff7eff
    563 
    564 > color #16-19 #bcff7eff
    565 
    566 > color #16-19 #b8ff7eff
    567 
    568 > color #16-19 #b6ff7eff
    569 
    570 > color #16-19 #b2ff7eff
    571 
    572 > volume level 0.0034
    573 
    574 Drag select of 16 run_it025_class004.mrc , 18 run_it025_class002.mrc 
    575 
    576 > ui mousemode right "translate selected models"
    577 
    578 > view matrix models
    579 > #16,-0.6562,-0.45162,0.60451,183.48,0.02297,-0.81271,-0.58222,328.58,0.75423,-0.36817,0.54368,6.3905,#18,-0.6562,-0.45162,0.60451,180.08,0.02297,-0.81271,-0.58222,284.5,0.75423,-0.36817,0.54368,15.049
    580 
    581 > select clear
    582 
    583 Drag select of 17 run_it025_class003.mrc , 19 run_it025_class001.mrc 
    584 
    585 > view matrix models
    586 > #17,-0.6562,-0.45162,0.60451,251.73,0.02297,-0.81271,-0.58222,328.24,0.75423,-0.36817,0.54368,16.337,#19,-0.6562,-0.45162,0.60451,252.14,0.02297,-0.81271,-0.58222,284.47,0.75423,-0.36817,0.54368,17.484
    587 
    588 > select clear
    589 
    590 > save C:\Users\lilyh\Desktop\image110.png supersample 3
    591 
    592 > show #!15 models
    593 
    594 > show #!14 models
    595 
    596 > show #!13 models
    597 
    598 > show #!12 models
    599 
    600 > tile
    601 
    602 8 models tiled 
    603 
    604 > hide #!12 models
    605 
    606 > show #!12 models
    607 
    608 > hide #!13 models
    609 
    610 > show #!13 models
    611 
    612 > hide #!14 models
    613 
    614 > show #!14 models
    615 
    616 > hide #!15 models
    617 
    618 > show #!15 models
    619 
    620 > hide #!15 models
    621 
    622 > show #!15 models
    623 
    624 > hide #!16 models
    625 
    626 > show #!16 models
    627 
    628 > hide #!16 models
    629 
    630 > show #!16 models
    631 
    632 > hide #!17 models
    633 
    634 > show #!17 models
    635 
    636 > hide #17.1 models
    637 
    638 > show #17.1 models
    639 
    640 > hide #!18 models
    641 
    642 > show #!18 models
    643 
    644 > hide #!19 models
    645 
    646 > show #!19 models
    647 
    648 > lighting soft
    649 
    650 > lighting flat
    651 
    652 > lighting soft
    653 
    654 > lighting shadows true intensity 0.5
    655 
    656 > lighting soft
    657 
    658 > save C:\Users\lilyh\Desktop\image111.png supersample 3
    659 
    660 > hide #!12 models
    661 
    662 > hide #!13 models
    663 
    664 > hide #!14 models
    665 
    666 > hide #!15 models
    667 
    668 > hide #!16 models
    669 
    670 > hide #17.1 models
    671 
    672 > hide #!17 models
    673 
    674 > hide #!18 models
    675 
    676 > hide #!19 models
    677 
    678 > open C:/Users/lilyh/Downloads/Refine3D_Job156/run_class001.mrc
    679 
    680 Opened run_class001.mrc as #20, grid size 256,256,256, pixel 1.09, shown at
    681 level 0.000529, step 1, values float32 
    682 
    683 > volume #20 level 0.003905
    684 
    685 > volume #20 level 0.006828
    686 
    687 > close #20
    688 
    689 > open C:/Users/lilyh/Downloads/Class3D_Job155/run_it025_class004.mrc
    690 
    691 Opened run_it025_class004.mrc as #20, grid size 256,256,256, pixel 1.09, shown
    692 at level 1.56e-06, step 1, values float32 
    693 
    694 > open C:/Users/lilyh/Downloads/Class3D_Job155/run_it025_class003.mrc
    695 
    696 Opened run_it025_class003.mrc as #21, grid size 256,256,256, pixel 1.09, shown
    697 at level 3.1e-07, step 1, values float32 
    698 
    699 > open C:/Users/lilyh/Downloads/Class3D_Job155/run_it025_class002.mrc
    700 
    701 Opened run_it025_class002.mrc as #22, grid size 256,256,256, pixel 1.09, shown
    702 at level 7.18e-07, step 1, values float32 
    703 
    704 > open C:/Users/lilyh/Downloads/Class3D_Job155/run_it025_class001.mrc
    705 
    706 Opened run_it025_class001.mrc as #23, grid size 256,256,256, pixel 1.09, shown
    707 at level 5.85e-07, step 1, values float32 
    708 
    709 > volume level 0.0034
    710 
    711 > color #20-23 #aaffffff
    712 
    713 > tile
    714 
    715 4 models tiled 
    716 
    717 > lighting full
    718 
    719 [Repeated 1 time(s)]
    720 
    721 > lighting soft
    722 
    723 > show #!1 models
    724 
    725 > show #!2 models
    726 
    727 > show #!3 models
    728 
    729 > show #!4 models
    730 
    731 > tile
    732 
    733 8 models tiled 
    734 Drag select of 1 run_it025_class001.mrc , 2 run_it025_class004.mrc , 3
    735 run_it025_class003.mrc 
    736 Drag select of 24 run_it025_class001.mrc , 22 run_it025_class004.mrc , 24
    737 run_it025_class003.mrc , 26 run_it025_class002.mrc 
    738 
    739 > lighting soft
    740 
    741 > lighting shadows true intensity 0.5
    742 
    743 > lighting flat
    744 
    745 > lighting soft
    746 
    747 > select clear
    748 
    749 > save C:\Users\lilyh\Desktop\image112.png supersample 3
    750 
    751 > hide #!4 models
    752 
    753 > hide #!3 models
    754 
    755 > hide #!2 models
    756 
    757 > hide #!1 models
    758 
    759 > hide #!21 models
    760 
    761 > hide #!20 models
    762 
    763 > hide #!22 models
    764 
    765 > hide #!23 models
    766 
    767 > open C:/Users/lilyh/Downloads/Class3D_Job157/run_it025_class001.mrc
    768 
    769 Opened run_it025_class001.mrc as #24, grid size 256,256,256, pixel 1.09, shown
    770 at level 1.46e-06, step 1, values float32 
    771 
    772 > open C:/Users/lilyh/Downloads/Class3D_Job157/run_it025_class004.mrc
    773 
    774 Opened run_it025_class004.mrc as #25, grid size 256,256,256, pixel 1.09, shown
    775 at level 7.72e-07, step 1, values float32 
    776 
    777 > open C:/Users/lilyh/Downloads/Class3D_Job157/run_it025_class003.mrc
    778 
    779 Opened run_it025_class003.mrc as #26, grid size 256,256,256, pixel 1.09, shown
    780 at level 6.08e-07, step 1, values float32 
    781 
    782 > open C:/Users/lilyh/Downloads/Class3D_Job157/run_it025_class002.mrc
    783 
    784 Opened run_it025_class002.mrc as #27, grid size 256,256,256, pixel 1.09, shown
    785 at level 1.24e-07, step 1, values float32 
    786 
    787 > tile
    788 
    789 4 models tiled 
    790 
    791 > lighting soft
    792 
    793 > color #24-27 medium blue
    794 
    795 > color #24-27 cornflower blue
    796 
    797 > volume level 0.0034
    798 
    799 > hide #!24 models
    800 
    801 > show #!24 models
    802 
    803 > close #24
    804 
    805 > close #25
    806 
    807 > close #27
    808 
    809 > close #26
    810 
    811 > open C:/Users/lilyh/Downloads/Class3D_Job159/run_it025_class004.mrc
    812 
    813 Opened run_it025_class004.mrc as #24, grid size 256,256,256, pixel 1.09, shown
    814 at level 5.08e-07, step 1, values float32 
    815 
    816 > open C:/Users/lilyh/Downloads/Class3D_Job159/run_it025_class003.mrc
    817 
    818 Opened run_it025_class003.mrc as #25, grid size 256,256,256, pixel 1.09, shown
    819 at level 1.05e-06, step 1, values float32 
    820 
    821 > open C:/Users/lilyh/Downloads/Class3D_Job159/run_it025_class002.mrc
    822 
    823 Opened run_it025_class002.mrc as #26, grid size 256,256,256, pixel 1.09, shown
    824 at level 1.65e-07, step 1, values float32 
    825 
    826 > open C:/Users/lilyh/Downloads/Class3D_Job159/run_it025_class001.mrc
    827 
    828 Opened run_it025_class001.mrc as #27, grid size 256,256,256, pixel 1.09, shown
    829 at level 6.48e-07, step 1, values float32 
    830 
    831 > volume level 0.0034
    832 
    833 > tile
    834 
    835 4 models tiled 
    836 
    837 > lighting soft
    838 
    839 Drag select of 24 run_it025_class004.mrc , 26 run_it025_class002.mrc 
    840 
    841 > ui mousemode right "translate selected models"
    842 
    843 > view matrix models
    844 > #24,0.047067,0.35787,0.93259,-78.153,-0.47244,-0.81462,0.33644,248.36,0.88011,-0.45642,0.13073,75.285,#26,0.047067,0.35787,0.93259,-79.854,-0.47244,-0.81462,0.33644,205.82,0.88011,-0.45642,0.13073,77.026
    845 
    846 Drag select of 25 run_it025_class003.mrc , 27 run_it025_class001.mrc 
    847 
    848 > view matrix models
    849 > #25,0.047067,0.35787,0.93259,-19.723,-0.47244,-0.81462,0.33644,246.64,0.88011,-0.45642,0.13073,78.834,#27,0.047067,0.35787,0.93259,-21.918,-0.47244,-0.81462,0.33644,206.87,0.88011,-0.45642,0.13073,83.489
    850 
    851 > select clear
    852 
    853 Drag select of 24 run_it025_class004.mrc , 25 run_it025_class003.mrc , 26
    854 run_it025_class002.mrc , 27 run_it025_class001.mrc 
    855 No visible atoms or bonds selected 
    856 Drag select of 24 run_it025_class004.mrc , 25 run_it025_class003.mrc , 26
    857 run_it025_class002.mrc , 27 run_it025_class001.mrc 
    858 No visible atoms or bonds selected 
    859 
    860 > select add #24
    861 
    862 8 models selected 
    863 
    864 > select add #25
    865 
    866 8 models selected 
    867 
    868 > select add #26
    869 
    870 8 models selected 
    871 
    872 > select add #27
    873 
    874 8 models selected 
    875 No visible atoms or bonds selected 
    876 [Repeated 2 time(s)]
    877 
    878 > ui tool show "Color Actions"
    879 
    880 > color #24.1#25.1#26.1#27.1 cornflower blue
    881 
    882 > select clear
    883 
    884 > save C:\Users\lilyh\Desktop\image113.png supersample 3
    885 
    886 > show #!16 models
    887 
    888 > show #!18 models
    889 
    890 > hide #!18 models
    891 
    892 > hide #!16 models
    893 
    894 > show #!16 models
    895 
    896 > hide #!16 models
    897 
    898 > hide #!27 models
    899 
    900 > hide #!26 models
    901 
    902 > hide #!25 models
    903 
    904 > hide #!24 models
    905 
    906 > open C:/Users/lilyh/Downloads/Class3D_Job160/run_it025_class004.mrc
    907 
    908 Opened run_it025_class004.mrc as #28, grid size 256,256,256, pixel 1.09, shown
    909 at level 1.09e-07, step 1, values float32 
    910 
    911 > open C:/Users/lilyh/Downloads/Class3D_Job160/run_it025_class003.mrc
    912 
    913 Opened run_it025_class003.mrc as #29, grid size 256,256,256, pixel 1.09, shown
    914 at level 7.5e-07, step 1, values float32 
    915 
    916 > open C:/Users/lilyh/Downloads/Class3D_Job160/run_it025_class002.mrc
    917 
    918 Opened run_it025_class002.mrc as #30, grid size 256,256,256, pixel 1.09, shown
    919 at level 1.35e-07, step 1, values float32 
    920 
    921 > open C:/Users/lilyh/Downloads/Class3D_Job160/run_it025_class001.mrc
    922 
    923 Opened run_it025_class001.mrc as #31, grid size 256,256,256, pixel 1.09, shown
    924 at level 1.45e-06, step 1, values float32 
    925 
    926 > tile
    927 
    928 4 models tiled 
    929 
    930 > volume level 0.0034
    931 
    932 > lighting simple
    933 
    934 > lighting soft
    935 
    936 > lighting flat
    937 
    938 > lighting soft
    939 
    940 > lighting shadows true intensity 0.5
    941 
    942 > lighting simple
    943 
    944 [Repeated 1 time(s)]
    945 
    946 > lighting soft
    947 
    948 > color #28-31 #0055ffff
    949 
    950 > color #28-31 #aa55ffff
    951 
    952 > select clear
    953 
    954 Drag select of 28 run_it025_class004.mrc 
    955 
    956 > ui mousemode right "translate selected models"
    957 
    958 > view matrix models
    959 > #28,-0.5539,-0.11417,0.82472,109.62,-0.36195,-0.85903,-0.36202,348.85,0.74979,-0.49903,0.43449,48.626
    960 
    961 > select clear
    962 
    963 > save C:\Users\lilyh\Desktop\image114.png supersample 3
    964 
    965 > show #!27 models
    966 
    967 > show #!26 models
    968 
    969 > show #!25 models
    970 
    971 > show #!24 models
    972 
    973 > show #!16 models
    974 
    975 > tile
    976 
    977 9 models tiled 
    978 Drag select of 68 run_it025_class004.mrc , 54 run_it025_class003.mrc , 56
    979 run_it025_class002.mrc , 58 run_it025_class001.mrc 
    980 
    981 > lighting full
    982 
    983 > lighting soft
    984 
    985 > lighting full
    986 
    987 > lighting soft
    988 
    989 > select clear
    990 
    991 > save C:\Users\lilyh\Desktop\image115.png supersample 3
    992 
    993 > show volume
    994 
    995 Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
    996 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword 
    997 
    998 > show all
    999 
    1000 > tile
    1001 
    1002 31 models tiled 
    1003 
    1004 > hide #!9 models
    1005 
    1006 > hide #!10 models
    1007 
    1008 > close #9
    1009 
    1010 > close #10
    1011 
    1012 > close #11
    1013 
    1014 > tile
    1015 
    1016 28 models tiled 
    1017 
    1018 > close #6
    1019 
    1020 > close #7
    1021 
    1022 > close #8
    1023 
    1024 > tile
    1025 
    1026 25 models tiled 
    1027 
    1028 > close #5
    1029 
    1030 > tile
    1031 
    1032 24 models tiled 
    1033 
    1034 > lighting soft
    1035 
    1036 > graphics silhouettes false
    1037 
    1038 > graphics silhouettes true
    1039 
    1040 > lighting shadows true intensity 0.5
    1041 
    1042 > lighting shadows false
    1043 
    1044 > lighting flat
    1045 
    1046 [Repeated 1 time(s)]
    1047 
    1048 > lighting full
    1049 
    1050 > lighting soft
    1051 
    1052 [Repeated 1 time(s)]
    1053 
    1054 > select clear
    1055 
    1056 [Repeated 1 time(s)]
    1057 
    1058 > close #20
    1059 
    1060 > close #21
    1061 
    1062 > close #22
    1063 
    1064 > close #23
    1065 
    1066 > tile
    1067 
    1068 20 models tiled 
    1069 
    1070 > lighting soft
    1071 
    1072 > select clear
    1073 
    1074 > save C:/Users/lilyh/Desktop/Vac17_focused_3D_Relion.cxs includeMaps true
    1075 
    1076 > save C:\Users\lilyh\Desktop\image116.png supersample 3
    1077 
    1078 > open C:/Users/lilyh/Downloads/cryosparc_P122_J540_class_00_00031_volume.mrc
    1079 
    1080 Opened cryosparc_P122_J540_class_00_00031_volume.mrc as #5, grid size
    1081 100,100,100, pixel 2.78, shown at level 0.0542, step 1, values float32 
    1082 
    1083 > open C:/Users/lilyh/Downloads/cryosparc_P122_J541_class_02_00031_volume.mrc
    1084 
    1085 Opened cryosparc_P122_J541_class_02_00031_volume.mrc as #6, grid size
    1086 100,100,100, pixel 2.78, shown at level 0.0674, step 1, values float32 
    1087 
    1088 > open C:/Users/lilyh/Downloads/cryosparc_P122_J541_class_01_00031_volume.mrc
    1089 
    1090 Opened cryosparc_P122_J541_class_01_00031_volume.mrc as #7, grid size
    1091 100,100,100, pixel 2.78, shown at level 0.0663, step 1, values float32 
    1092 
    1093 > open C:/Users/lilyh/Downloads/cryosparc_P122_J541_class_00_00031_volume.mrc
    1094 
    1095 Opened cryosparc_P122_J541_class_00_00031_volume.mrc as #8, grid size
    1096 100,100,100, pixel 2.78, shown at level 0.0729, step 1, values float32 
    1097 
    1098 > open C:/Users/lilyh/Downloads/cryosparc_P122_J540_class_01_00031_volume.mrc
    1099 
    1100 Opened cryosparc_P122_J540_class_01_00031_volume.mrc as #9, grid size
    1101 100,100,100, pixel 2.78, shown at level 0.0571, step 1, values float32 
    1102 
    1103 > open C:/Users/lilyh/Downloads/cryosparc_P122_J540_class_02_00031_volume.mrc
    1104 
    1105 Opened cryosparc_P122_J540_class_02_00031_volume.mrc as #10, grid size
    1106 100,100,100, pixel 2.78, shown at level 0.0555, step 1, values float32 
    1107 
    1108 > ~tile
    1109 
    1110 > volume level 0.35
    1111 
    1112 > close #5
    1113 
    1114 > close #6
    1115 
    1116 > close #7
    1117 
    1118 > close #10
    1119 
    1120 > close #9
    1121 
    1122 > close #8
    1123 
    1124 > open C:/Users/lilyh/Downloads/cryosparc_P122_J521_004_volume_map_sharp.mrc
    1125 
    1126 Opened cryosparc_P122_J521_004_volume_map_sharp.mrc as #5, grid size
    1127 256,256,256, pixel 1.09, shown at level 0.0396, step 1, values float32 
    1128 
    1129 > open C:/Users/lilyh/Downloads/cryosparc_P122_J482_003_volume_map_sharp.mrc
    1130 
    1131 Opened cryosparc_P122_J482_003_volume_map_sharp.mrc as #6, grid size
    1132 256,256,256, pixel 1.09, shown at level 0.0359, step 1, values float32 
    1133 
    1134 > volume level 0.35
    1135 
    1136 > volume #5 level 0.4689
    1137 
    1138 > open "C:/Users/lilyh/Downloads/cryosparc_P122_J482_003_volume_map (1).mrc"
    1139 
    1140 Opened cryosparc_P122_J482_003_volume_map (1).mrc as #7, grid size
    1141 256,256,256, pixel 1.09, shown at level 0.00334, step 1, values float32 
    1142 
    1143 > volume #7 level 0.1708
    1144 
    1145 > volume #7 level 0.2
    1146 
    1147 > volume #7 level 0.1556
    1148 
    1149 > volume #6 level 0.2471
    1150 
    1151 > volume #5 level 0.4635
    1152 
    1153 > hide #!1 models
    1154 
    1155 > show #!1 models
    1156 
    1157 > close session
    1158 
    1159 > open "C:/Users/lilyh/Downloads/cryosparc_P122_J482_003_volume_map (1).mrc"
    1160 
    1161 Opened cryosparc_P122_J482_003_volume_map (1).mrc as #1, grid size
    1162 256,256,256, pixel 1.09, shown at level 0.00334, step 1, values float32 
    1163 
    1164 > open C:/Users/lilyh/Downloads/cryosparc_P122_J521_004_volume_map_sharp.mrc
    1165 
    1166 Opened cryosparc_P122_J521_004_volume_map_sharp.mrc as #2, grid size
    1167 256,256,256, pixel 1.09, shown at level 0.0396, step 1, values float32 
    1168 
    1169 > open C:/Users/lilyh/Downloads/cryosparc_P122_J482_003_volume_map_sharp.mrc
    1170 
    1171 Opened cryosparc_P122_J482_003_volume_map_sharp.mrc as #3, grid size
    1172 256,256,256, pixel 1.09, shown at level 0.0359, step 1, values float32 
    1173 
    1174 > open C:/Users/lilyh/Downloads/Class3D_Job151/run_it025_class001.mrc
    1175 
    1176 Opened run_it025_class001.mrc as #4, grid size 256,256,256, pixel 1.09, shown
    1177 at level 6.64e-08, step 1, values float32 
    1178 
    1179 > open C:/Users/lilyh/Downloads/Class3D_Job151/run_it025_class004.mrc
    1180 
    1181 Opened run_it025_class004.mrc as #5, grid size 256,256,256, pixel 1.09, shown
    1182 at level 1.52e-06, step 1, values float32 
    1183 
    1184 > open C:/Users/lilyh/Downloads/Class3D_Job151/run_it025_class003.mrc
    1185 
    1186 Opened run_it025_class003.mrc as #6, grid size 256,256,256, pixel 1.09, shown
    1187 at level 5.8e-07, step 1, values float32 
    1188 
    1189 > open C:/Users/lilyh/Downloads/Class3D_Job151/run_it025_class002.mrc
    1190 
    1191 Opened run_it025_class002.mrc as #7, grid size 256,256,256, pixel 1.09, shown
    1192 at level 1.22e-06, step 1, values float32 
    1193 
    1194 > ~tile
    1195 
    1196 > volume level 0.3
    1197 
    1198 > hide #!3 models
    1199 
    1200 > show #!3 models
    1201 
    1202 > hide #!3 models
    1203 
    1204 > volume #2 level 0.4567
    1205 
    1206 > volume #1 level 0.1934
    1207 
    1208 > volume #3 level 0.2255
    1209 
    1210 > volume #2 level 0.4675
    1211 
    1212 > volume #3 color #7a7a7a
    1213 
    1214 > volume #!2-7 appearance chest
    1215 
    1216 > lighting soft
    1217 
    1218 > lighting shadows true intensity 0.5
    1219 
    1220 > lighting soft
    1221 
    1222 > style ball
    1223 
    1224 Changed 0 atom styles 
    1225 
    1226 > set bgColor white
    1227 
    1228 > volume #2 color #aaff7f
    1229 
    1230 > volume #4 level 0.01084
    1231 
    1232 > volume #4 level 0.005243
    1233 
    1234 > volume #5 level 0.00524
    1235 
    1236 > volume #6 level 0.00524
    1237 
    1238 > volume #7 level 0.00524
    1239 
    1240 > volume #7 level 0.0034
    1241 
    1242 > volume #6 level 0.0034
    1243 
    1244 > volume #5 level 0.0034
    1245 
    1246 > volume #4 level 0.0034
    1247 
    1248 > volume #1 level 0.1071
    1249 
    1250 > select #1
    1251 
    1252 2 models selected 
    1253 
    1254 > transparency #1.1 50
    1255 
    1256 > select clear
    1257 
    1258 [Repeated 1 time(s)]
    1259 
    1260 > hide #!4 models
    1261 
    1262 > show #!4 models
    1263 
    1264 > hide #!4 models
    1265 
    1266 > hide #!5 models
    1267 
    1268 > hide #!6 models
    1269 
    1270 > hide #!7 models
    1271 
    1272 > hide #!2 models
    1273 
    1274 > lighting flat
    1275 
    1276 > lighting simple
    1277 
    1278 > lighting soft
    1279 
    1280 > lighting shadows true intensity 0.5
    1281 
    1282 > lighting shadows false
    1283 
    1284 > lighting full
    1285 
    1286 > lighting soft
    1287 
    1288 > show #!7 models
    1289 
    1290 > show #!6 models
    1291 
    1292 > hide #!7 models
    1293 
    1294 > hide #!6 models
    1295 
    1296 > show #!5 models
    1297 
    1298 > show #!4 models
    1299 
    1300 > hide #!5 models
    1301 
    1302 > hide #5.1 models
    1303 
    1304 > hide #!4 models
    1305 
    1306 > show #!4 models
    1307 
    1308 > show #!2 models
    1309 
    1310 > hide #!4 models
    1311 
    1312 > hide #!2 models
    1313 
    1314 > show #!4 models
    1315 
    1316 > show #!5 models
    1317 
    1318 > hide #!5 models
    1319 
    1320 > show #!5 models
    1321 
    1322 > hide #!5 models
    1323 
    1324 > show #5.1 models
    1325 
    1326 > hide #!4 models
    1327 
    1328 > show #!4 models
    1329 
    1330 > show #!6 models
    1331 
    1332 > show #!7 models
    1333 
    1334 > show #!2 models
    1335 
    1336 > hide #!7 models
    1337 
    1338 > hide #!6 models
    1339 
    1340 > hide #5.1 models
    1341 
    1342 > hide #!5 models
    1343 
    1344 > hide #!4 models
    1345 
    1346 > open
    1347 > C:/Users/lilyh/Desktop/output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
    1348 
    1349 Chain information for
    1350 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
    1351 #8 
    1352 --- 
    1353 Chain | Description 
    1354 B | No description available 
    1355 C | No description available 
    1356  
    1357 
    1358 > open
    1359 > C:/Users/lilyh/Desktop/output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
    1360 
    1361 Chain information for
    1362 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
    1363 #9 
    1364 --- 
    1365 Chain | Description 
    1366 B | No description available 
    1367 C | No description available 
    1368  
    1369 Drag select of 260 residues 
    1370 
    1371 > ui mousemode right "translate selected models"
    1372 
    1373 > view matrix models
    1374 > #8,1,0,0,48.272,0,1,0,164.59,0,0,1,125.11,#9,1,0,0,48.272,0,1,0,164.59,0,0,1,125.11
    1375 
    1376 > ui mousemode right "rotate selected models"
    1377 
    1378 > view matrix models
    1379 > #8,0.79558,0.33084,-0.50755,47.489,0.60106,-0.32581,0.72978,163.29,0.076068,-0.88566,-0.45806,124.13,#9,0.79558,0.33084,-0.50755,47.489,0.60106,-0.32581,0.72978,163.29,0.076068,-0.88566,-0.45806,124.13
    1380 
    1381 Drag select of 13 residues 
    1382 
    1383 > view matrix models
    1384 > #8,-0.68742,0.37563,-0.62157,42.22,-0.72534,-0.39814,0.56157,158.83,-0.036534,0.83689,0.54615,119.84
    1385 
    1386 Drag select of 35 residues 
    1387 
    1388 > ui mousemode right "translate selected models"
    1389 
    1390 > view matrix models
    1391 > #8,-0.68742,0.37563,-0.62157,44.71,-0.72534,-0.39814,0.56157,169,-0.036534,0.83689,0.54615,136.84,#9,0.79558,0.33084,-0.50755,49.979,0.60106,-0.32581,0.72978,173.46,0.076068,-0.88566,-0.45806,141.13
    1392 
    1393 > fitmap #8 inMap #1
    1394 
    1395 Fit molecule
    1396 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
    1397 (#8) to map cryosparc_P122_J482_003_volume_map (1).mrc (#1) using 4737 atoms 
    1398 average map value = -0.0001557, steps = 220 
    1399 shifted from previous position = 34.4 
    1400 rotated from previous position = 13.7 degrees 
    1401 atoms outside contour = 4737, contour level = 0.10714 
    1402  
    1403 Position of
    1404 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
    1405 (#8) relative to cryosparc_P122_J482_003_volume_map (1).mrc (#1) coordinates: 
    1406 Matrix rotation and translation 
    1407 -0.59337904 0.39472638 -0.70149301 15.58357562 
    1408 -0.77494843 -0.51576627 0.36529460 153.90466178 
    1409 -0.21761501 0.76037905 0.61193748 126.40547452 
    1410 Axis 0.29794421 -0.36490591 -0.88208442 
    1411 Axis point 49.43314375 37.01777903 0.00000000 
    1412 Rotation angle (degrees) 138.46958829 
    1413 Shift along axis -163.01798392 
    1414  
    1415 
    1416 > fitmap #9 inMap #1
    1417 
    1418 Fit molecule
    1419 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
    1420 (#9) to map cryosparc_P122_J482_003_volume_map (1).mrc (#1) using 4737 atoms 
    1421 average map value = -0.0005607, steps = 188 
    1422 shifted from previous position = 28.5 
    1423 rotated from previous position = 23.5 degrees 
    1424 atoms outside contour = 4737, contour level = 0.10714 
    1425  
    1426 Position of
    1427 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
    1428 (#9) relative to cryosparc_P122_J482_003_volume_map (1).mrc (#1) coordinates: 
    1429 Matrix rotation and translation 
    1430 0.55684007 0.19458370 -0.80750626 31.45155338 
    1431 0.82481919 -0.24422806 0.50992742 150.98828914 
    1432 -0.09799213 -0.94999467 -0.29649234 147.12942730 
    1433 Axis -0.83842948 -0.40747214 0.36194262 
    1434 Axis point 0.00000000 123.41655057 32.72092284 
    1435 Rotation angle (degrees) 119.46818259 
    1436 Shift along axis -34.64102022 
    1437  
    1438 
    1439 > ui mousemode right "translate selected models"
    1440 
    1441 Drag select of 980 residues 
    1442 
    1443 > view matrix models
    1444 > #8,-0.59338,0.39473,-0.70149,135.36,-0.77495,-0.51577,0.36529,146.11,-0.21762,0.76038,0.61194,89.887,#9,0.55684,0.19458,-0.80751,151.23,0.82482,-0.24423,0.50993,143.19,-0.097992,-0.94999,-0.29649,110.61
    1445 
    1446 > fitmap #9 inMap #1
    1447 
    1448 Fit molecule
    1449 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
    1450 (#9) to map cryosparc_P122_J482_003_volume_map (1).mrc (#1) using 4737 atoms 
    1451 average map value = 0.1296, steps = 268 
    1452 shifted from previous position = 35.4 
    1453 rotated from previous position = 28.5 degrees 
    1454 atoms outside contour = 2247, contour level = 0.10714 
    1455  
    1456 Position of
    1457 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
    1458 (#9) relative to cryosparc_P122_J482_003_volume_map (1).mrc (#1) coordinates: 
    1459 Matrix rotation and translation 
    1460 0.21655754 0.37106564 -0.90300231 140.08778531 
    1461 0.94719644 0.14418810 0.28640655 135.91408502 
    1462 0.23647781 -0.91734406 -0.32024703 143.18623375 
    1463 Axis -0.68597216 -0.64934682 0.32831526 
    1464 Axis point 0.00000000 83.02464481 84.91999610 
    1465 Rotation angle (degrees) 118.66912068 
    1466 Shift along axis -137.34147382 
    1467  
    1468 
    1469 > fitmap #8 inMap #1
    1470 
    1471 Fit molecule
    1472 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
    1473 (#8) to map cryosparc_P122_J482_003_volume_map (1).mrc (#1) using 4737 atoms 
    1474 average map value = 0.05356, steps = 284 
    1475 shifted from previous position = 19.7 
    1476 rotated from previous position = 22.9 degrees 
    1477 atoms outside contour = 3710, contour level = 0.10714 
    1478  
    1479 Position of
    1480 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
    1481 (#8) relative to cryosparc_P122_J482_003_volume_map (1).mrc (#1) coordinates: 
    1482 Matrix rotation and translation 
    1483 -0.59328132 0.11780182 -0.79632912 140.10884055 
    1484 -0.78557228 -0.30071813 0.54078171 138.46098801 
    1485 -0.17576553 0.94640974 0.27095230 106.75620040 
    1486 Axis 0.34709426 -0.53101375 -0.77301356 
    1487 Axis point 111.00925700 -4.44760771 0.00000000 
    1488 Rotation angle (degrees) 144.24505627 
    1489 Shift along axis -107.41770462 
    1490  
    1491 
    1492 > ui mousemode right "rotate selected models"
    1493 
    1494 > ui mousemode right "translate selected models"
    1495 
    1496 > view matrix models
    1497 > #8,-0.59328,0.1178,-0.79633,138.1,-0.78557,-0.30072,0.54078,139.58,-0.17577,0.94641,0.27095,102.83,#9,0.21656,0.37107,-0.903,138.07,0.9472,0.14419,0.28641,137.03,0.23648,-0.91734,-0.32025,139.26
    1498 
    1499 Drag select of 12 residues 
    1500 
    1501 > view matrix models
    1502 > #8,-0.59328,0.1178,-0.79633,156.85,-0.78557,-0.30072,0.54078,137.86,-0.17577,0.94641,0.27095,136.96
    1503 
    1504 > fitmap #8 inMap #1
    1505 
    1506 Fit molecule
    1507 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
    1508 (#8) to map cryosparc_P122_J482_003_volume_map (1).mrc (#1) using 4737 atoms 
    1509 average map value = 0.1286, steps = 168 
    1510 shifted from previous position = 17.5 
    1511 rotated from previous position = 29.6 degrees 
    1512 atoms outside contour = 2258, contour level = 0.10714 
    1513  
    1514 Position of
    1515 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
    1516 (#8) relative to cryosparc_P122_J482_003_volume_map (1).mrc (#1) coordinates: 
    1517 Matrix rotation and translation 
    1518 -0.82721618 0.18944314 -0.52898462 140.58045518 
    1519 -0.50731220 -0.65654110 0.55820085 134.80884922 
    1520 -0.24155282 0.73011311 0.63920823 142.51790837 
    1521 Axis 0.22237576 -0.37180515 -0.90128239 
    1522 Axis point 96.80068636 18.67151445 0.00000000 
    1523 Rotation angle (degrees) 157.26089928 
    1524 Shift along axis -147.30982056 
    1525  
    1526 
    1527 > fitmap #9 inMap #1
    1528 
    1529 Fit molecule
    1530 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
    1531 (#9) to map cryosparc_P122_J482_003_volume_map (1).mrc (#1) using 4737 atoms 
    1532 average map value = 0.1296, steps = 68 
    1533 shifted from previous position = 4.56 
    1534 rotated from previous position = 0.0414 degrees 
    1535 atoms outside contour = 2247, contour level = 0.10714 
    1536  
    1537 Position of
    1538 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
    1539 (#9) relative to cryosparc_P122_J482_003_volume_map (1).mrc (#1) coordinates: 
    1540 Matrix rotation and translation 
    1541 0.21598263 0.37072598 -0.90327947 140.09571243 
    1542 0.94733734 0.14445566 0.28580509 135.91222227 
    1543 0.23643919 -0.91743929 -0.32000265 143.18785790 
    1544 Axis -0.68569713 -0.64949550 0.32859555 
    1545 Axis point 0.00000000 83.01705196 84.95176759 
    1546 Rotation angle (degrees) 118.67117648 
    1547 Shift along axis -137.28671147 
    1548  
    1549 
    1550 > select clear
    1551 
    1552 > hide #8 models
    1553 
    1554 > hide #9 models
    1555 
    1556 > show #9 models
    1557 
    1558 > hide #9 models
    1559 
    1560 > volume #2 level 0.5323
    1561 
    1562 > volume #7 color #aaaaff
    1563 
    1564 > volume #7 color #ff5500
    1565 
    1566 > hide #!7 models
    1567 
    1568 > show #!7 models
    1569 
    1570 > hide #!7 models
    1571 
    1572 > show #!6 models
    1573 
    1574 > hide #!6 models
    1575 
    1576 > hide #!2 models
    1577 
    1578 > show #!6 models
    1579 
    1580 > volume #6 level 0.00389
    1581 
    1582 > volume #6 level 0.0034
    1583 
    1584 > volume #7 level 0.004435
    1585 
    1586 > volume #4 level 0.004406
    1587 
    1588 > volume #6 level 0.004456
    1589 
    1590 > volume #5 level 0.003186
    1591 
    1592 > hide #!7 models
    1593 
    1594 > hide #!6 models
    1595 
    1596 > hide #5.1 models
    1597 
    1598 > hide #!4 models
    1599 
    1600 > show #!4 models
    1601 
    1602 > hide #!4 models
    1603 
    1604 > hide #!5 models
    1605 
    1606 > show #!5 models
    1607 
    1608 > hide #!5 models
    1609 
    1610 > show #5.1 models
    1611 
    1612 > show #!6 models
    1613 
    1614 > hide #5.1 models
    1615 
    1616 > volume level 0.00319
    1617 
    1618 > volume #1 level 0.08883
    1619 
    1620 > show #!7 models
    1621 
    1622 > hide #!7 models
    1623 
    1624 > show #!7 models
    1625 
    1626 > hide #!7 models
    1627 
    1628 > show #8 models
    1629 
    1630 > select #8/B:18
    1631 
    1632 9 atoms, 8 bonds, 1 residue, 1 model selected 
    1633 
    1634 > show sel atoms
    1635 
    1636 > hide sel atoms
    1637 
    1638 > select clear
    1639 
    1640 > show #9 models
    1641 
    1642 > hide #9 models
    1643 
    1644 > show #9 models
    1645 
    1646 > hide #9 models
    1647 
    1648 > show #9 models
    1649 
    1650 > hide #9 models
    1651 
    1652 > show #9 models
    1653 
    1654 > hide #9 models
    1655 
    1656 > hide #8 models
    1657 
    1658 > show #8 models
    1659 
    1660 > hide #8 models
    1661 
    1662 > show #!7 models
    1663 
    1664 > show #5.1 models
    1665 
    1666 > show #!4 models
    1667 
    1668 > save C:\Users\lilyh\Desktop\image117.png supersample 3
    1669 
    1670 > save C:\Users\lilyh\Desktop\image118.png supersample 3
    1671 
    1672 > hide #!4 models
    1673 
    1674 > show #!4 models
    1675 
    1676 > hide #!4 models
    1677 
    1678 > hide #!7 models
    1679 
    1680 > hide #!6 models
    1681 
    1682 > show #!6 models
    1683 
    1684 > hide #5.1 models
    1685 
    1686 > show #!2 models
    1687 
    1688 > hide #!2 models
    1689 
    1690 > show #!2 models
    1691 
    1692 > hide #!2 models
    1693 
    1694 > show #!2 models
    1695 
    1696 > volume #2 level 0.6781
    1697 
    1698 > hide #!6 models
    1699 
    1700 > volume #2 level 0.6509
    1701 
    1702 > volume #1 level 0.1349
    1703 
    1704 > show #!6 models
    1705 
    1706 > hide #!6 models
    1707 
    1708 > show #!6 models
    1709 
    1710 > hide #!6 models
    1711 
    1712 > volume #2 level 0.5094
    1713 
    1714 > save C:\Users\lilyh\Desktop\image119.png supersample 3
    1715 
    1716 > show #!6 models
    1717 
    1718 > hide #!6 models
    1719 
    1720 > show #!6 models
    1721 
    1722 > hide #!6 models
    1723 
    1724 > open C:/Users/lilyh/Downloads/cryosparc_P122_J507_004_volume_map_sharp.mrc
    1725 
    1726 Opened cryosparc_P122_J507_004_volume_map_sharp.mrc as #10, grid size
    1727 256,256,256, pixel 1.09, shown at level 0.0356, step 1, values float32 
    1728 
    1729 > volume #10 level 0.5011
    1730 
    1731 > volume #1 level 0.1412
    1732 
    1733 > volume #10 level 0.5574
    1734 
    1735 > volume #2 level 0.557
    1736 
    1737 > show #!6 models
    1738 
    1739 > volume #10 color #aaff7f
    1740 
    1741 > volume #10 color #ffaaff
    1742 
    1743 > volume #10 color #aa557f
    1744 
    1745 > open C:/Users/lilyh/Downloads/cryosparc_P122_J482_003_volume_map_sharp.mrc
    1746 
    1747 Opened cryosparc_P122_J482_003_volume_map_sharp.mrc as #11, grid size
    1748 256,256,256, pixel 1.09, shown at level 0.0359, step 1, values float32 
    1749 
    1750 > volume #11 level 0.2754
    1751 
    1752 > hide #!1 models
    1753 
    1754 > volume #11 level 0.2933
    1755 
    1756 > volume #10 level 0.5318
    1757 
    1758 > save C:\Users\lilyh\Desktop\image120.png supersample 3
    1759 
    1760 > show #!6 models
    1761 
    1762 > hide #!6 models
    1763 
    1764 > show #!6 models
    1765 
    1766 > save C:\Users\lilyh\Desktop\image121.png supersample 3
    1767 
    1768 > hide #!6 models
    1769 
    1770 > save C:\Users\lilyh\Desktop\image122.png supersample 3
    1771 
    1772 > open "C:/Users/lilyh/Downloads/cryosparc_P122_J506_003_volume_map_sharp
    1773 > (1).mrc"
    1774 
    1775 Opened cryosparc_P122_J506_003_volume_map_sharp (1).mrc as #12, grid size
    1776 256,256,256, pixel 1.09, shown at level 0.0511, step 1, values float32 
    1777 
    1778 > volume #12 level 0.421
    1779 
    1780 > volume #12 level 0.4848
    1781 
    1782 > close #12
    1783 
    1784 > open C:/Users/lilyh/Downloads/cryosparc_P122_J534_class_02_00031_volume.mrc
    1785 
    1786 Opened cryosparc_P122_J534_class_02_00031_volume.mrc as #12, grid size
    1787 100,100,100, pixel 2.78, shown at level 0.0675, step 1, values float32 
    1788 
    1789 > open C:/Users/lilyh/Downloads/cryosparc_P122_J534_class_01_00031_volume.mrc
    1790 
    1791 Opened cryosparc_P122_J534_class_01_00031_volume.mrc as #13, grid size
    1792 100,100,100, pixel 2.78, shown at level 0.0686, step 1, values float32 
    1793 
    1794 > open C:/Users/lilyh/Downloads/cryosparc_P122_J534_class_00_00031_volume.mrc
    1795 
    1796 Opened cryosparc_P122_J534_class_00_00031_volume.mrc as #14, grid size
    1797 100,100,100, pixel 2.78, shown at level 0.0664, step 1, values float32 
    1798 
    1799 > volume #12 level 0.2438
    1800 
    1801 > volume #13 level 0.2523
    1802 
    1803 > volume #14 level 0.2188
    1804 
    1805 > show #9 models
    1806 
    1807 > open C:/Users/lilyh/Downloads/cryosparc_P122_J535_class_02_00031_volume.mrc
    1808 
    1809 Opened cryosparc_P122_J535_class_02_00031_volume.mrc as #15, grid size
    1810 100,100,100, pixel 2.78, shown at level 0.057, step 1, values float32 
    1811 
    1812 > open C:/Users/lilyh/Downloads/cryosparc_P122_J535_class_01_00031_volume.mrc
    1813 
    1814 Opened cryosparc_P122_J535_class_01_00031_volume.mrc as #16, grid size
    1815 100,100,100, pixel 2.78, shown at level 0.0563, step 1, values float32 
    1816 
    1817 > open C:/Users/lilyh/Downloads/cryosparc_P122_J535_class_00_00031_volume.mrc
    1818 
    1819 Opened cryosparc_P122_J535_class_00_00031_volume.mrc as #17, grid size
    1820 100,100,100, pixel 2.78, shown at level 0.0561, step 1, values float32 
    1821 
    1822 > volume #17 level 0.1619
    1823 
    1824 > volume #16 level 0.1707
    1825 
    1826 > volume #15 level 0.1911
    1827 
    1828 > volume #17 level 0.1892
    1829 
    1830 > open C:/Users/lilyh/Downloads/cryosparc_P122_J513_class_01_00031_volume.mrc
    1831 
    1832 Opened cryosparc_P122_J513_class_01_00031_volume.mrc as #18, grid size
    1833 100,100,100, pixel 2.78, shown at level 0.0579, step 1, values float32 
    1834 
    1835 > open C:/Users/lilyh/Downloads/cryosparc_P122_J513_class_02_00031_volume.mrc
    1836 
    1837 Opened cryosparc_P122_J513_class_02_00031_volume.mrc as #19, grid size
    1838 100,100,100, pixel 2.78, shown at level 0.0563, step 1, values float32 
    1839 
    1840 > open C:/Users/lilyh/Downloads/cryosparc_P122_J513_class_00_00031_volume.mrc
    1841 
    1842 Opened cryosparc_P122_J513_class_00_00031_volume.mrc as #20, grid size
    1843 100,100,100, pixel 2.78, shown at level 0.0611, step 1, values float32 
    1844 
    1845 > hide #!15 models
    1846 
    1847 > hide #!16 models
    1848 
    1849 > hide #!17 models
    1850 
    1851 > volume #20 level 0.168
    1852 
    1853 > volume #19 level 0.1494
    1854 
    1855 > volume #18 level 0.1919
    1856 
    1857 > volume #20 level 0.1253
    1858 
    1859 > show #!17 models
    1860 
    1861 > hide #!17 models
    1862 
    1863 > show #!16 models
    1864 
    1865 > hide #!16 models
    1866 
    1867 > show #!15 models
    1868 
    1869 > hide #!15 models
    1870 
    1871 > hide #!11 models
    1872 
    1873 > hide #!10 models
    1874 
    1875 > hide #9 models
    1876 
    1877 > hide #!5 models
    1878 
    1879 > hide #!20 models
    1880 
    1881 > hide #!19 models
    1882 
    1883 > volume #18 level 0.1369
    1884 
    1885 > show #!19 models
    1886 
    1887 > volume #19 level 0.1315
    1888 
    1889 > volume #20 level 0.1502
    1890 
    1891 > hide #!19 models
    1892 
    1893 > show #!19 models
    1894 
    1895 > tile
    1896 
    1897 3 models tiled 
    1898 
    1899 > volume #!18-20 planes z style image imageMode "full region"
    1900 
    1901 > mousemode rightMode "move planes"
    1902 
    1903 > volume #!18-20 planes z style image imageMode "full region"
    1904 
    1905 > mousemode rightMode "move planes"
    1906 
    1907 > volume #!18-20 planes z style image imageMode "full region"
    1908 
    1909 > mousemode rightMode "move planes"
    1910 
    1911 > volume #18 region 0,0,0,99,99,99 step 1
    1912 
    1913 > volume #18 style surface region 0,0,0,99,99,99 step 1
    1914 
    1915 > volume #19 region 0,0,0,99,99,99 step 1
    1916 
    1917 > volume #19 style surface region 0,0,0,99,99,99 step 1
    1918 
    1919 > volume #20 level -0.03735,0 level 0.1826,0.8 level 1.122,1
    1920 
    1921 > volume #20 region 0,0,0,99,99,99 step 1
    1922 
    1923 > volume #20 style surface region 0,0,0,99,99,99 step 1
    1924 
    1925 > lighting flat
    1926 
    1927 > lighting soft
    1928 
    1929 > open "C:/Users/lilyh/Downloads/cryosparc_P122_J510_class_00_00031_volume
    1930 > (1).mrc"
    1931 
    1932 Opened cryosparc_P122_J510_class_00_00031_volume (1).mrc as #21, grid size
    1933 100,100,100, pixel 2.78, shown at level 0.0528, step 1, values float32 
    1934 
    1935 > open "C:/Users/lilyh/Downloads/cryosparc_P122_J510_class_02_00031_volume
    1936 > (1).mrc"
    1937 
    1938 Opened cryosparc_P122_J510_class_02_00031_volume (1).mrc as #22, grid size
    1939 100,100,100, pixel 2.78, shown at level 0.052, step 1, values float32 
    1940 
    1941 > open "C:/Users/lilyh/Downloads/cryosparc_P122_J510_class_01_00031_volume
    1942 > (1).mrc"
    1943 
    1944 Opened cryosparc_P122_J510_class_01_00031_volume (1).mrc as #23, grid size
    1945 100,100,100, pixel 2.78, shown at level 0.0559, step 1, values float32 
    1946 
    1947 > tile
    1948 
    1949 6 models tiled 
    1950 
    1951 > volume level 0.15
    1952 
    1953 Drag select of 21 cryosparc_P122_J510_class_00_00031_volume (1).mrc , 22
    1954 cryosparc_P122_J510_class_02_00031_volume (1).mrc , 23
    1955 cryosparc_P122_J510_class_01_00031_volume (1).mrc 
    1956 
    1957 > color #21.1#22.1#23.1 dark gray
    1958 
    1959 Drag select of 18 cryosparc_P122_J513_class_01_00031_volume.mrc , 19
    1960 cryosparc_P122_J513_class_02_00031_volume.mrc , 20
    1961 cryosparc_P122_J513_class_00_00031_volume.mrc 
    1962 
    1963 > color #18.1#19.1#20.1 cornflower blue
    1964 
    1965 Drag select of 18 cryosparc_P122_J513_class_01_00031_volume.mrc , 19
    1966 cryosparc_P122_J513_class_02_00031_volume.mrc , 20
    1967 cryosparc_P122_J513_class_00_00031_volume.mrc , 21
    1968 cryosparc_P122_J510_class_00_00031_volume (1).mrc , 22
    1969 cryosparc_P122_J510_class_02_00031_volume (1).mrc , 23
    1970 cryosparc_P122_J510_class_01_00031_volume (1).mrc 
    1971 
    1972 > lighting soft
    1973 
    1974 > lighting shadows true intensity 0.5
    1975 
    1976 > lighting soft
    1977 
    1978 Drag select of 21 cryosparc_P122_J510_class_00_00031_volume (1).mrc , 22
    1979 cryosparc_P122_J510_class_02_00031_volume (1).mrc , 23
    1980 cryosparc_P122_J510_class_01_00031_volume (1).mrc 
    1981 
    1982 > ui mousemode right "translate selected models"
    1983 
    1984 > view matrix models
    1985 > #21,1,0,0,29.909,0,1,0,140.61,0,0,1,2.181,#22,1,0,0,-28.528,0,1,0,167.93,0,0,1,-276.02,#23,1,0,0,-87.313,0,1,0,196.91,0,0,1,-554.6
    1986 
    1987 Drag select of 18 cryosparc_P122_J513_class_01_00031_volume.mrc , 21
    1988 cryosparc_P122_J510_class_00_00031_volume (1).mrc 
    1989 
    1990 > view matrix models
    1991 > #18,0.92111,0.38436,0.061799,-60.026,-0.3739,0.91767,-0.13443,96.536,-0.10838,0.10072,0.98899,-58.625,#21,1,0,0,17.422,0,1,0,152.14,0,0,1,-60.779
    1992 
    1993 Drag select of 20 cryosparc_P122_J513_class_00_00031_volume.mrc , 23
    1994 cryosparc_P122_J510_class_01_00031_volume (1).mrc 
    1995 
    1996 > view matrix models
    1997 > #20,0.92111,0.38436,0.061799,-141.34,-0.3739,0.91767,-0.13443,127.57,-0.10838,0.10072,0.98899,-444.33,#23,1,0,0,-64.293,0,1,0,184.44,0,0,1,-444.32
    1998 
    1999 Drag select of 18 cryosparc_P122_J513_class_01_00031_volume.mrc , 21
    2000 cryosparc_P122_J510_class_00_00031_volume (1).mrc 
    2001 
    2002 > view matrix models
    2003 > #18,0.92111,0.38436,0.061799,-65.853,-0.3739,0.91767,-0.13443,93.567,-0.10838,0.10072,0.98899,-82.506,#21,1,0,0,11.595,0,1,0,149.17,0,0,1,-84.66
    2004 
    2005 > select clear
    2006 
    2007 > hide #!19 models
    2008 
    2009 > show #!19 models
    2010 
    2011 > open C:/Users/lilyh/Downloads/cryosparc_P122_J514_class_01_00031_volume.mrc
    2012 
    2013 Opened cryosparc_P122_J514_class_01_00031_volume.mrc as #24, grid size
    2014 100,100,100, pixel 2.78, shown at level 0.0498, step 1, values float32 
    2015 
    2016 > open C:/Users/lilyh/Downloads/cryosparc_P122_J514_class_00_00031_volume.mrc
    2017 
    2018 Opened cryosparc_P122_J514_class_00_00031_volume.mrc as #25, grid size
    2019 100,100,100, pixel 2.78, shown at level 0.0491, step 1, values float32 
    2020 
    2021 > open C:/Users/lilyh/Downloads/cryosparc_P122_J514_class_02_00031_volume.mrc
    2022 
    2023 Opened cryosparc_P122_J514_class_02_00031_volume.mrc as #26, grid size
    2024 100,100,100, pixel 2.78, shown at level 0.0495, step 1, values float32 
    2025 
    2026 > volume level 0.15
    2027 
    2028 > tile
    2029 
    2030 9 models tiled 
    2031 Drag select of 24 cryosparc_P122_J514_class_01_00031_volume.mrc , 25
    2032 cryosparc_P122_J514_class_00_00031_volume.mrc , 26
    2033 cryosparc_P122_J514_class_02_00031_volume.mrc 
    2034 
    2035 > ui mousemode right "rotate selected models"
    2036 
    2037 > view matrix models
    2038 > #24,-0.96661,0.23993,-0.090029,218.35,0.22146,0.95886,0.17757,293.36,0.12893,0.15171,-0.97998,-126.14,#25,-0.96661,0.23993,-0.090029,265.93,0.22146,0.95886,0.17757,273.88,0.12893,0.15171,-0.97998,19.103,#26,-0.96661,0.23993,-0.090029,316.72,0.22146,0.95886,0.17757,255.13,0.12893,0.15171,-0.97998,164.38
    2039 
    2040 > select clear
    2041 
    2042 Drag select of 24 cryosparc_P122_J514_class_01_00031_volume.mrc , 25
    2043 cryosparc_P122_J514_class_00_00031_volume.mrc , 26
    2044 cryosparc_P122_J514_class_02_00031_volume.mrc 
    2045 
    2046 > ui mousemode right "rotate selected models"
    2047 
    2048 > view matrix models
    2049 > #24,-0.68697,0.72668,-0.0011518,87.673,0.70213,0.66335,-0.25882,336.47,-0.18732,-0.17861,-0.96592,-31.413,#25,-0.68697,0.72668,-0.0011518,148.68,0.70213,0.66335,-0.25882,306.7,-0.18732,-0.17861,-0.96592,106.83,#26,-0.68697,0.72668,-0.0011518,212.77,0.70213,0.66335,-0.25882,275.9,-0.18732,-0.17861,-0.96592,245.56
    2050 
    2051 > view matrix models
    2052 > #24,-0.84324,0.34721,0.41035,140.03,0.35169,0.93369,-0.067337,316.29,-0.40652,0.087531,-0.90944,-56.464,#25,-0.84324,0.34721,0.41035,163.14,0.35169,0.93369,-0.067337,293.46,-0.40652,0.087531,-0.90944,94.085,#26,-0.84324,0.34721,0.41035,189.14,0.35169,0.93369,-0.067337,271,-0.40652,0.087531,-0.90944,246.14
    2053 
    2054 > tile
    2055 
    2056 9 models tiled 
    2057 
    2058 > select #24
    2059 
    2060 2 models selected 
    2061 
    2062 > view matrix models
    2063 > #24,-0.9732,0.13667,-0.18492,325.59,0.13697,0.99051,0.011225,285.97,0.1847,-0.014405,-0.98269,186.63
    2064 
    2065 > select #25
    2066 
    2067 2 models selected 
    2068 
    2069 > view matrix models
    2070 > #25,-0.97124,0.20972,-0.11275,274.21,0.20827,0.97776,0.02458,290.19,0.1154,0.00038985,-0.99332,48.306
    2071 
    2072 > select clear
    2073 
    2074 > select #26
    2075 
    2076 2 models selected 
    2077 
    2078 > view matrix models
    2079 > #26,-0.95822,0.18981,-0.21398,261.28,0.18598,0.98182,0.038061,306.44,0.21731,-0.0033254,-0.9761,-116.46
    2080 
    2081 > select clear
    2082 
    2083 Drag select of 24 cryosparc_P122_J514_class_01_00031_volume.mrc , 25
    2084 cryosparc_P122_J514_class_00_00031_volume.mrc , 26
    2085 cryosparc_P122_J514_class_02_00031_volume.mrc 
    2086 
    2087 > color #24.1#25.1#26.1 gray
    2088 
    2089 > select clear
    2090 
    2091 > show #9 models
    2092 
    2093 > hide #9 models
    2094 
    2095 > ui mousemode right select
    2096 
    2097 > save C:\Users\lilyh\Desktop\image123.png supersample 3
    2098 
    2099 > ~tile
    2100 
    2101 > hide #!26 models
    2102 
    2103 > hide #!25 models
    2104 
    2105 > hide #!24 models
    2106 
    2107 > hide #!20 models
    2108 
    2109 > hide #!19 models
    2110 
    2111 > hide #!18 models
    2112 
    2113 > show #!17 models
    2114 
    2115 > hide #!17 models
    2116 
    2117 > show #!6 models
    2118 
    2119 > show #!10 models
    2120 
    2121 > show #!11 models
    2122 
    2123 > hide #!11 models
    2124 
    2125 > show #!11 models
    2126 
    2127 Drag select of 10 cryosparc_P122_J507_004_volume_map_sharp.mrc , 11
    2128 cryosparc_P122_J482_003_volume_map_sharp.mrc 
    2129 Drag select of 21 cryosparc_P122_J510_class_00_00031_volume (1).mrc , 22
    2130 cryosparc_P122_J510_class_02_00031_volume (1).mrc , 23
    2131 cryosparc_P122_J510_class_01_00031_volume (1).mrc 
    2132 
    2133 > ui mousemode right "rotate selected models"
    2134 
    2135 > view matrix models
    2136 > #21,0.97291,0.23052,-0.017584,-41.237,-0.23116,0.97119,-0.057973,54.578,0.0037132,0.060467,0.99816,-96.273,#22,0.97291,0.23052,-0.017584,-41.237,-0.23116,0.97119,-0.057973,54.578,0.0037132,0.060467,0.99816,-96.273,#23,0.97291,0.23052,-0.017584,-41.237,-0.23116,0.97119,-0.057973,54.578,0.0037132,0.060467,0.99816,-96.273
    2137 
    2138 > ui mousemode right "translate selected models"
    2139 
    2140 > view matrix models
    2141 > #21,0.97291,0.23052,-0.017584,-23.174,-0.23116,0.97119,-0.057973,41.586,0.0037132,0.060467,0.99816,-7.629,#22,0.97291,0.23052,-0.017584,-23.174,-0.23116,0.97119,-0.057973,41.586,0.0037132,0.060467,0.99816,-7.629,#23,0.97291,0.23052,-0.017584,-23.174,-0.23116,0.97119,-0.057973,41.586,0.0037132,0.060467,0.99816,-7.629
    2142 
    2143 > fitmap #21 inMap #11
    2144 
    2145 Fit map cryosparc_P122_J510_class_00_00031_volume (1).mrc in map
    2146 cryosparc_P122_J482_003_volume_map_sharp.mrc using 3844 points 
    2147 correlation = 0.8682, correlation about mean = 0.8339, overlap = 394.1 
    2148 steps = 84, shift = 3.79, angle = 13.9 degrees 
    2149  
    2150 Position of cryosparc_P122_J510_class_00_00031_volume (1).mrc (#21) relative
    2151 to cryosparc_P122_J482_003_volume_map_sharp.mrc (#11) coordinates: 
    2152 Matrix rotation and translation 
    2153 0.99999770 -0.00113062 0.00180339 -0.16379964 
    2154 0.00113007 0.99999924 0.00030748 -0.21275999 
    2155 -0.00180374 -0.00030544 0.99999829 0.30589603 
    2156 Axis -0.14250878 0.83869044 0.52563257 
    2157 Axis point 167.84735995 0.00000000 90.58973462 
    2158 Rotation angle (degrees) 0.12321195 
    2159 Shift along axis 0.00569203 
    2160  
    2161 
    2162 > fitmap #23 inMap #11
    2163 
    2164 Fit map cryosparc_P122_J510_class_01_00031_volume (1).mrc in map
    2165 cryosparc_P122_J482_003_volume_map_sharp.mrc using 3850 points 
    2166 correlation = 0.8692, correlation about mean = 0.8367, overlap = 395.1 
    2167 steps = 96, shift = 3.78, angle = 13.9 degrees 
    2168  
    2169 Position of cryosparc_P122_J510_class_01_00031_volume (1).mrc (#23) relative
    2170 to cryosparc_P122_J482_003_volume_map_sharp.mrc (#11) coordinates: 
    2171 Matrix rotation and translation 
    2172 0.99999724 -0.00120749 0.00200091 -0.16756740 
    2173 0.00120548 0.99999869 0.00100615 -0.33521827 
    2174 -0.00200212 -0.00100374 0.99999746 0.44164081 
    2175 Axis -0.39503510 0.78678090 0.47426056 
    2176 Axis point 217.66418739 0.00000000 81.69243662 
    2177 Rotation angle (degrees) 0.14575657 
    2178 Shift along axis 0.01190449 
    2179  
    2180 
    2181 > fitmap #22 inMap #11
    2182 
    2183 Fit map cryosparc_P122_J510_class_02_00031_volume (1).mrc in map
    2184 cryosparc_P122_J482_003_volume_map_sharp.mrc using 3885 points 
    2185 correlation = 0.868, correlation about mean = 0.8378, overlap = 394.7 
    2186 steps = 88, shift = 3.77, angle = 13.8 degrees 
    2187  
    2188 Position of cryosparc_P122_J510_class_02_00031_volume (1).mrc (#22) relative
    2189 to cryosparc_P122_J482_003_volume_map_sharp.mrc (#11) coordinates: 
    2190 Matrix rotation and translation 
    2191 0.99999742 -0.00044905 0.00221325 -0.29811604 
    2192 0.00044722 0.99999949 0.00082670 -0.19350796 
    2193 -0.00221362 -0.00082571 0.99999718 0.44077115 
    2194 Axis -0.34357548 0.92044951 0.18635610 
    2195 Axis point 198.40582146 0.00000000 133.92316790 
    2196 Rotation angle (degrees) 0.13778116 
    2197 Shift along axis 0.00645145 
    2198  
    2199 
    2200 > fitmap #24 inMap #11
    2201 
    2202 Fit map cryosparc_P122_J514_class_01_00031_volume.mrc in map
    2203 cryosparc_P122_J482_003_volume_map_sharp.mrc using 3837 points 
    2204 correlation = 0.3865, correlation about mean = 0.1375, overlap = 127.6 
    2205 steps = 488, shift = 48.7, angle = 50.9 degrees 
    2206  
    2207 Position of cryosparc_P122_J514_class_01_00031_volume.mrc (#24) relative to
    2208 cryosparc_P122_J482_003_volume_map_sharp.mrc (#11) coordinates: 
    2209 Matrix rotation and translation 
    2210 -0.87435716 -0.46943886 -0.12299046 342.58917502 
    2211 -0.47102628 0.75998173 0.44784138 46.36316524 
    2212 -0.11676365 0.44950505 -0.88561357 176.49363820 
    2213 Axis 0.25063484 -0.93807816 -0.23914755 
    2214 Axis point 177.33207737 0.00000000 82.64004135 
    2215 Rotation angle (degrees) 179.80983969 
    2216 Shift along axis 0.16449149 
    2217  
    2218 
    2219 > volume #6 level 0.002529
    2220 
    2221 > volume #10 level 0.4262
    2222 
    2223 > show #9 models
    2224 
    2225 > show #8 models
    2226 
    2227 > hide #!23 models
    2228 
    2229 > hide #!22 models
    2230 
    2231 > hide #!21 models
    2232 
    2233 > hide #!10 models
    2234 
    2235 > hide #!6 models
    2236 
    2237 > show #!23 models
    2238 
    2239 > volume #23 level 0.2683
    2240 
    2241 > volume #22 level 0.2389
    2242 
    2243 > volume #21 level 0.2202
    2244 
    2245 > show #!22 models
    2246 
    2247 > show #!23 models
    2248 
    2249 > hide #!11 models
    2250 
    2251 > volume #21 level 0.2266
    2252 
    2253 > volume #22 level 0.227
    2254 
    2255 > volume #23 level 0.227
    2256 
    2257 > save C:\Users\lilyh\Desktop\image124.png supersample 3
    2258 
    2259 > show #!17 models
    2260 
    2261 > hide #!17 models
    2262 
    2263 > show #!17 models
    2264 
    2265 > show #!16 models
    2266 
    2267 > show #!15 models
    2268 
    2269 > hide #!23 models
    2270 
    2271 > hide #!22 models
    2272 
    2273 > hide #!21 models
    2274 
    2275 > volume #15 level 0.1672
    2276 
    2277 > volume #15 level 0.227
    2278 
    2279 > volume #16 level 0.227
    2280 
    2281 > volume #17 level 0.227
    2282 
    2283 > hide #!17 models
    2284 
    2285 > hide #!16 models
    2286 
    2287 > hide #!15 models
    2288 
    2289 > open C:/Users/lilyh/Downloads/cryosparc_P122_J549_class_00_00031_volume.mrc
    2290 
    2291 Opened cryosparc_P122_J549_class_00_00031_volume.mrc as #27, grid size
    2292 100,100,100, pixel 2.78, shown at level 0.0661, step 1, values float32 
    2293 
    2294 > open C:/Users/lilyh/Downloads/cryosparc_P122_J549_class_02_00031_volume.mrc
    2295 
    2296 Opened cryosparc_P122_J549_class_02_00031_volume.mrc as #28, grid size
    2297 100,100,100, pixel 2.78, shown at level 0.0634, step 1, values float32 
    2298 
    2299 > open C:/Users/lilyh/Downloads/cryosparc_P122_J549_class_01_00031_volume.mrc
    2300 
    2301 Opened cryosparc_P122_J549_class_01_00031_volume.mrc as #29, grid size
    2302 100,100,100, pixel 2.78, shown at level 0.0648, step 1, values float32 
    2303 
    2304 > volume #27 level 0.1598
    2305 
    2306 > volume #27 level 0.227
    2307 
    2308 > volume #27 level 0.2062
    2309 
    2310 > volume #28 level 0.1752
    2311 
    2312 > volume #29 level 0.1892
    2313 
    2314 > volume #19 change image level -0.03572,0 level 0.1738,0.8 level 1.116,1
    2315 
    2316 > volume #18 change image level -0.03663,0 level 0.1745,0.8 level 1.134,1
    2317 
    2318 Drag select of 18 cryosparc_P122_J513_class_01_00031_volume.mrc , 19
    2319 cryosparc_P122_J513_class_02_00031_volume.mrc , 20
    2320 cryosparc_P122_J513_class_00_00031_volume.mrc 
    2321 
    2322 > ui mousemode right "rotate selected models"
    2323 
    2324 > view matrix models
    2325 > #18,0.98908,0.13745,0.053101,-42.594,-0.13165,0.98619,-0.10051,44.188,-0.066182,0.092418,0.99352,-91.271,#19,0.98908,0.13745,0.053101,-42.594,-0.13165,0.98619,-0.10051,44.188,-0.066182,0.092418,0.99352,-91.271,#20,0.98908,0.13745,0.053101,-42.594,-0.13165,0.98619,-0.10051,44.188,-0.066182,0.092418,0.99352,-91.271
    2326 
    2327 > ui mousemode right "translate selected models"
    2328 
    2329 > view matrix models
    2330 > #18,0.98908,0.13745,0.053101,-24.002,-0.13165,0.98619,-0.10051,31.413,-0.066182,0.092418,0.99352,-1.8236,#19,0.98908,0.13745,0.053101,-24.002,-0.13165,0.98619,-0.10051,31.413,-0.066182,0.092418,0.99352,-1.8236,#20,0.98908,0.13745,0.053101,-24.002,-0.13165,0.98619,-0.10051,31.413,-0.066182,0.092418,0.99352,-1.8236
    2331 
    2332 > fitmap #18 inMap #21
    2333 
    2334 Fit map cryosparc_P122_J513_class_01_00031_volume.mrc in map
    2335 cryosparc_P122_J510_class_00_00031_volume (1).mrc using 3531 points 
    2336 correlation = 0.9852, correlation about mean = 0.937, overlap = 818.5 
    2337 steps = 64, shift = 3.15, angle = 10.4 degrees 
    2338  
    2339 Position of cryosparc_P122_J513_class_01_00031_volume.mrc (#18) relative to
    2340 cryosparc_P122_J510_class_00_00031_volume (1).mrc (#21) coordinates: 
    2341 Matrix rotation and translation 
    2342 0.99998737 -0.00487273 -0.00123410 0.93607583 
    2343 0.00487290 0.99998812 0.00012815 -0.63986405 
    2344 0.00123346 -0.00013417 0.99999924 -0.25009704 
    2345 Axis -0.02608453 -0.24536670 0.96907935 
    2346 Axis point 137.30468320 191.16118119 0.00000000 
    2347 Rotation angle (degrees) 0.28810121 
    2348 Shift along axis -0.10977963 
    2349  
    2350 
    2351 > fitmap #19 inMap #21
    2352 
    2353 Fit map cryosparc_P122_J513_class_02_00031_volume.mrc in map
    2354 cryosparc_P122_J510_class_00_00031_volume (1).mrc using 3459 points 
    2355 correlation = 0.9911, correlation about mean = 0.9625, overlap = 817.8 
    2356 steps = 76, shift = 3.07, angle = 10.3 degrees 
    2357  
    2358 Position of cryosparc_P122_J513_class_02_00031_volume.mrc (#19) relative to
    2359 cryosparc_P122_J510_class_00_00031_volume (1).mrc (#21) coordinates: 
    2360 Matrix rotation and translation 
    2361 0.99999505 -0.00102057 -0.00297896 0.65883504 
    2362 0.00102279 0.99999920 0.00074681 -0.18621108 
    2363 0.00297820 -0.00074985 0.99999529 -0.36137254 
    2364 Axis -0.23120724 -0.92027206 0.31566209 
    2365 Axis point 111.60487742 0.00000000 213.60106474 
    2366 Rotation angle (degrees) 0.18544544 
    2367 Shift along axis -0.09503419 
    2368  
    2369 
    2370 > fitmap #20 inMap #21
    2371 
    2372 Fit map cryosparc_P122_J513_class_00_00031_volume.mrc in map
    2373 cryosparc_P122_J510_class_00_00031_volume (1).mrc using 3482 points 
    2374 correlation = 0.9896, correlation about mean = 0.9563, overlap = 820.3 
    2375 steps = 60, shift = 3.09, angle = 10.2 degrees 
    2376  
    2377 Position of cryosparc_P122_J513_class_00_00031_volume.mrc (#20) relative to
    2378 cryosparc_P122_J510_class_00_00031_volume (1).mrc (#21) coordinates: 
    2379 Matrix rotation and translation 
    2380 0.99999754 -0.00087826 -0.00204103 0.49941442 
    2381 0.00087765 0.99999957 -0.00030151 -0.06366800 
    2382 0.00204129 0.00029972 0.99999788 -0.41357419 
    2383 Axis 0.13407012 -0.91033414 0.39155708 
    2384 Axis point 195.76000615 0.00000000 246.88280533 
    2385 Rotation angle (degrees) 0.12846926 
    2386 Shift along axis -0.03702220 
    2387  
    2388 
    2389 > fitmap #22 inMap #21
    2390 
    2391 Fit map cryosparc_P122_J510_class_02_00031_volume (1).mrc in map
    2392 cryosparc_P122_J510_class_00_00031_volume (1).mrc using 2977 points 
    2393 correlation = 0.9922, correlation about mean = 0.955, overlap = 787.2 
    2394 steps = 40, shift = 0.0417, angle = 0.0138 degrees 
    2395  
    2396 Position of cryosparc_P122_J510_class_02_00031_volume (1).mrc (#22) relative
    2397 to cryosparc_P122_J510_class_00_00031_volume (1).mrc (#21) coordinates: 
    2398 Matrix rotation and translation 
    2399 0.99999958 0.00078079 0.00047614 -0.13384199 
    2400 -0.00078094 0.99999965 0.00030881 0.06917322 
    2401 -0.00047590 -0.00030918 0.99999984 0.14858538 
    2402 Axis -0.32009729 0.49312790 -0.80892682 
    2403 Axis point 115.79670913 189.20825354 0.00000000 
    2404 Rotation angle (degrees) 0.05530802 
    2405 Shift along axis -0.04324099 
    2406  
    2407 
    2408 > fitmap #23 inMap #21
    2409 
    2410 Fit map cryosparc_P122_J510_class_01_00031_volume (1).mrc in map
    2411 cryosparc_P122_J510_class_00_00031_volume (1).mrc using 2979 points 
    2412 correlation = 0.9944, correlation about mean = 0.9665, overlap = 789.7 
    2413 steps = 40, shift = 0.0122, angle = 0.199 degrees 
    2414  
    2415 Position of cryosparc_P122_J510_class_01_00031_volume (1).mrc (#23) relative
    2416 to cryosparc_P122_J510_class_00_00031_volume (1).mrc (#21) coordinates: 
    2417 Matrix rotation and translation 
    2418 0.99999393 -0.00327470 0.00118935 0.29050043 
    2419 0.00327499 0.99999461 -0.00024230 -0.43631200 
    2420 -0.00118855 0.00024619 0.99999926 0.14361836 
    2421 Axis 0.06993302 0.34042547 0.93766725 
    2422 Axis point 134.04127686 88.32435076 0.00000000 
    2423 Rotation angle (degrees) 0.20010857 
    2424 Shift along axis 0.00645009 
    2425  
    2426 
    2427 > fitmap #27 inMap #21
    2428 
    2429 Fit map cryosparc_P122_J549_class_00_00031_volume.mrc in map
    2430 cryosparc_P122_J510_class_00_00031_volume (1).mrc using 2861 points 
    2431 correlation = 0.9924, correlation about mean = 0.9594, overlap = 799.2 
    2432 steps = 44, shift = 0.098, angle = 0.0573 degrees 
    2433  
    2434 Position of cryosparc_P122_J549_class_00_00031_volume.mrc (#27) relative to
    2435 cryosparc_P122_J510_class_00_00031_volume (1).mrc (#21) coordinates: 
    2436 Matrix rotation and translation 
    2437 0.99999529 0.00150375 -0.00268668 0.27160752 
    2438 -0.00150382 0.99999894 -0.00002031 0.30438763 
    2439 0.00268665 0.00002436 0.99999642 -0.43536963 
    2440 Axis 0.00725437 -0.87258645 -0.48840583 
    2441 Axis point 171.45570900 0.00000000 100.92925358 
    2442 Rotation angle (degrees) 0.17641211 
    2443 Shift along axis -0.05099712 
    2444  
    2445 
    2446 > fitmap #278in #21
    2447 
    2448 Missing or invalid "atomsOrMap" argument: only initial part "#278" of atom
    2449 specifier valid 
    2450 
    2451 > fitmap #28 inMap #21
    2452 
    2453 Fit map cryosparc_P122_J549_class_02_00031_volume.mrc in map
    2454 cryosparc_P122_J510_class_00_00031_volume (1).mrc using 3187 points 
    2455 correlation = 0.9887, correlation about mean = 0.9458, overlap = 812.9 
    2456 steps = 40, shift = 0.0783, angle = 0.119 degrees 
    2457  
    2458 Position of cryosparc_P122_J549_class_02_00031_volume.mrc (#28) relative to
    2459 cryosparc_P122_J510_class_00_00031_volume (1).mrc (#21) coordinates: 
    2460 Matrix rotation and translation 
    2461 0.99999703 -0.00072491 -0.00233975 0.50430132 
    2462 0.00072235 0.99999921 -0.00109376 0.08179126 
    2463 0.00234054 0.00109207 0.99999670 -0.56387928 
    2464 Axis 0.40746574 -0.87246047 0.26978584 
    2465 Axis point 239.15502653 0.00000000 218.36493337 
    2466 Rotation angle (degrees) 0.15368079 
    2467 Shift along axis -0.01800077 
    2468  
    2469 
    2470 > fitmap #29 inMap #21
    2471 
    2472 Fit map cryosparc_P122_J549_class_01_00031_volume.mrc in map
    2473 cryosparc_P122_J510_class_00_00031_volume (1).mrc using 3060 points 
    2474 correlation = 0.9868, correlation about mean = 0.9335, overlap = 806.6 
    2475 steps = 44, shift = 0.105, angle = 0.245 degrees 
    2476  
    2477 Position of cryosparc_P122_J549_class_01_00031_volume.mrc (#29) relative to
    2478 cryosparc_P122_J510_class_00_00031_volume (1).mrc (#21) coordinates: 
    2479 Matrix rotation and translation 
    2480 0.99999317 -0.00282414 -0.00239730 0.78329290 
    2481 0.00282702 0.99999535 0.00120206 -0.48850983 
    2482 0.00239390 -0.00120882 0.99999644 -0.26422500 
    2483 Axis -0.30943374 -0.61494617 0.72532197 
    2484 Axis point 202.30267331 262.22460773 0.00000000 
    2485 Rotation angle (degrees) 0.22320350 
    2486 Shift along axis -0.13361820 
    2487  
    2488 
    2489 > select clear
    2490 
    2491 > hide #9 models
    2492 
    2493 > hide #8 models
    2494 
    2495 > tile
    2496 
    2497 9 models tiled 
    2498 Drag select of 27 cryosparc_P122_J549_class_00_00031_volume.mrc , 28
    2499 cryosparc_P122_J549_class_02_00031_volume.mrc , 29
    2500 cryosparc_P122_J549_class_01_00031_volume.mrc 
    2501 
    2502 > color #27.1#28.1#29.1 light gray
    2503 
    2504 > color #27.1#28.1#29.1 dim gray
    2505 
    2506 > select clear
    2507 
    2508 > lighting soft
    2509 
    2510 > lighting flat
    2511 
    2512 > lighting soft
    2513 
    2514 Drag select of 27 cryosparc_P122_J549_class_00_00031_volume.mrc , 28
    2515 cryosparc_P122_J549_class_02_00031_volume.mrc , 29
    2516 cryosparc_P122_J549_class_01_00031_volume.mrc 
    2517 Drag select of 21 cryosparc_P122_J510_class_00_00031_volume (1).mrc , 22
    2518 cryosparc_P122_J510_class_02_00031_volume (1).mrc , 23
    2519 cryosparc_P122_J510_class_01_00031_volume (1).mrc 
    2520 
    2521 > select clear
    2522 
    2523 > show #!26 models
    2524 
    2525 > show #!25 models
    2526 
    2527 > show #!24 models
    2528 
    2529 > tile
    2530 
    2531 12 models tiled 
    2532 
    2533 > select #24
    2534 
    2535 2 models selected 
    2536 
    2537 > ui mousemode right "rotate selected models"
    2538 
    2539 [Repeated 1 time(s)]
    2540 
    2541 > view matrix models
    2542 > #24,-0.84731,0.038394,-0.52972,337.66,-0.036697,0.99077,0.13051,152.88,0.52984,0.13002,-0.83807,-124.39
    2543 
    2544 > select clear
    2545 
    2546 > select #25
    2547 
    2548 2 models selected 
    2549 
    2550 > view matrix models
    2551 > #25,-0.82929,-0.025865,-0.55822,333.67,-0.068492,0.9961,0.055598,177.44,0.5546,0.08434,-0.82783,-271.33
    2552 
    2553 > select clear
    2554 
    2555 Drag select of 27 cryosparc_P122_J549_class_00_00031_volume.mrc , 28
    2556 cryosparc_P122_J549_class_02_00031_volume.mrc , 29
    2557 cryosparc_P122_J549_class_01_00031_volume.mrc 
    2558 No visible atoms or bonds selected 
    2559 
    2560 > color #27.1#28.1#29.1 lime
    2561 
    2562 > color #27.1#28.1#29.1 light gray
    2563 
    2564 > select clear
    2565 
    2566 > save C:\Users\lilyh\Desktop\image125.png supersample 3
    2567 
    2568 Drag select of 27 cryosparc_P122_J549_class_00_00031_volume.mrc , 28
    2569 cryosparc_P122_J549_class_02_00031_volume.mrc , 29
    2570 cryosparc_P122_J549_class_01_00031_volume.mrc 
    2571 
    2572 > color #27.1#28.1#29.1 medium blue
    2573 
    2574 > select clear
    2575 
    2576 Drag select of 27 cryosparc_P122_J549_class_00_00031_volume.mrc , 28
    2577 cryosparc_P122_J549_class_02_00031_volume.mrc , 29
    2578 cryosparc_P122_J549_class_01_00031_volume.mrc 
    2579 
    2580 > ui mousemode right "rotate selected models"
    2581 
    2582 > ui mousemode right "translate selected models"
    2583 
    2584 > view matrix models
    2585 > #27,-0.7941,0.56332,-0.22823,204.39,0.5355,0.82606,0.17569,-179.55,0.2875,0.017299,-0.95762,224.97,#28,-0.79276,0.56484,-0.22911,185.65,0.53727,0.82505,0.17499,-167.44,0.28787,0.015631,-0.95754,78.415,#29,-0.79158,0.56703,-0.22777,173.02,0.53902,0.82352,0.17685,-156.49,0.28785,0.017224,-0.95752,-70.598
    2586 
    2587 > select clear
    2588 
    2589 [Repeated 1 time(s)]
    2590 
    2591 > select #21
    2592 
    2593 2 models selected 
    2594 
    2595 > view matrix models
    2596 > #21,-0.79263,0.56451,-0.23035,215.1,0.53626,0.82525,0.17715,87.026,0.2901,0.016886,-0.95685,-53.236
    2597 
    2598 > select #24
    2599 
    2600 2 models selected 
    2601 Drag select of 21 cryosparc_P122_J510_class_00_00031_volume (1).mrc , 24
    2602 cryosparc_P122_J514_class_01_00031_volume.mrc , 25
    2603 cryosparc_P122_J514_class_00_00031_volume.mrc 
    2604 
    2605 > view matrix models
    2606 > #21,-0.79263,0.56451,-0.23035,256.41,0.53626,0.82525,0.17715,222.66,0.2901,0.016886,-0.95685,100.04,#24,-0.87796,0.44865,-0.16701,277.44,0.42107,0.88969,0.1765,229.98,0.22778,0.084635,-0.97003,96.802,#25,-0.88373,0.40867,-0.22804,278.05,0.39003,0.91245,0.12371,248.94,0.25864,0.020386,-0.96576,-47.626
    2607 
    2608 > select #21
    2609 
    2610 2 models selected 
    2611 
    2612 > view matrix models
    2613 > #21,-0.79263,0.56451,-0.23035,215.09,0.53626,0.82525,0.17715,89.159,0.2901,0.016886,-0.95685,-56.931
    2614 
    2615 Drag select of 26 cryosparc_P122_J514_class_02_00031_volume.mrc 
    2616 
    2617 > ui mousemode right "rotate selected models"
    2618 
    2619 > view matrix models
    2620 > #26,-0.90457,0.4177,-0.085275,292.05,0.36426,0.8612,0.35447,207.44,0.2215,0.28958,-0.93117,216.55
    2621 
    2622 > view matrix models
    2623 > #26,-0.90849,0.41789,-0.0040277,281.07,0.30314,0.66559,0.68198,195.83,0.28767,0.61835,-0.73136,135.05
    2624 
    2625 > view matrix models
    2626 > #26,-0.9081,0.41867,-0.0082793,281.52,0.30698,0.67903,0.66684,195.63,0.28481,0.60302,-0.74515,139.45
    2627 
    2628 > view matrix models
    2629 > #26,-0.94964,0.27299,0.15384,283.88,0.065522,-0.30712,0.94941,321.34,0.30643,0.91168,0.27377,-49.003
    2630 
    2631 > view matrix models
    2632 > #26,-0.99252,0.12202,0.0049363,331.23,0.12173,0.98534,0.11955,259.8,0.009723,0.11925,-0.99282,278.79
    2633 
    2634 Drag select of 21 cryosparc_P122_J510_class_00_00031_volume (1).mrc , 22
    2635 cryosparc_P122_J510_class_02_00031_volume (1).mrc , 23
    2636 cryosparc_P122_J510_class_01_00031_volume (1).mrc 
    2637 
    2638 > ui mousemode right "translate selected models"
    2639 
    2640 > view matrix models
    2641 > #21,-0.79263,0.56451,-0.23035,205.65,0.53626,0.82525,0.17715,39.617,0.2901,0.016886,-0.95685,-60.862,#22,-0.79296,0.56397,-0.23055,231.95,0.53554,0.82561,0.17766,21.22,0.29054,0.017409,-0.95671,236.97,#23,-0.7905,0.56705,-0.23143,221.61,0.53875,0.82353,0.17759,27.051,0.29129,0.015701,-0.95651,85.606
    2642 
    2643 Drag select of 24 cryosparc_P122_J514_class_01_00031_volume.mrc , 25
    2644 cryosparc_P122_J514_class_00_00031_volume.mrc , 26
    2645 cryosparc_P122_J514_class_02_00031_volume.mrc 
    2646 
    2647 > view matrix models
    2648 > #24,-0.87796,0.44865,-0.16701,260.59,0.42107,0.88969,0.1765,135.3,0.22778,0.084635,-0.97003,100.1,#25,-0.88373,0.40867,-0.22804,261.2,0.39003,0.91245,0.12371,154.26,0.25864,0.020386,-0.96576,-44.332,#26,-0.99252,0.12202,0.0049363,314.38,0.12173,0.98534,0.11955,165.12,0.009723,0.11925,-0.99282,282.08
    2649 
    2650 > select clear
    2651 
    2652 > save C:\Users\lilyh\Desktop\image126.png supersample 3
    2653 
    2654 > show #9 models
    2655 
    2656 > molmap #9 10
    2657 
    2658 Opened
    2659 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
    2660 map 10 as #30, grid size 40,51,41, pixel 3.33, shown at level 0.0534, step 1,
    2661 values float32 
    2662 
    2663 > select #30
    2664 
    2665 2 models selected 
    2666 
    2667 > ui mousemode right "rotate selected models"
    2668 
    2669 > view matrix models
    2670 > #30,0.16233,0.29077,-0.94292,140.16,0.95098,-0.301,0.070898,134.84,-0.26321,-0.90821,-0.32538,145.61
    2671 
    2672 > view matrix models
    2673 > #30,0.16168,0.40195,0.90128,144.21,0.96958,0.10535,-0.22092,134.68,-0.18375,0.90958,-0.37269,147.58
    2674 
    2675 > hide #9 models
    2676 
    2677 > hide #!30 models
    2678 
    2679 > close session
    2680 
    2681 > open C:/Users/lilyh/Downloads/Class3D_Job171/run_it025_class003.mrc
    2682 
    2683 Opened run_it025_class003.mrc as #1, grid size 256,256,256, pixel 1.09, shown
    2684 at level 0.000507, step 1, values float32 
    2685 
    2686 > open C:/Users/lilyh/Downloads/Class3D_Job171/run_it025_class002.mrc
    2687 
    2688 Opened run_it025_class002.mrc as #2, grid size 256,256,256, pixel 1.09, shown
    2689 at level 0.000511, step 1, values float32 
    2690 
    2691 > open C:/Users/lilyh/Downloads/Class3D_Job171/run_it025_class001.mrc
    2692 
    2693 Opened run_it025_class001.mrc as #3, grid size 256,256,256, pixel 1.09, shown
    2694 at level 0.000505, step 1, values float32 
    2695 
    2696 > open C:/Users/lilyh/Downloads/Class3D_Job171/run_it025_class004.mrc
    2697 
    2698 Opened run_it025_class004.mrc as #4, grid size 256,256,256, pixel 1.09, shown
    2699 at level 0.000511, step 1, values float32 
    2700 
    2701 > volume level 0.3
    2702 
    2703 > volume #1 level 0.006789
    2704 
    2705 > tile
    2706 
    2707 1 model tiled 
    2708 
    2709 > tile
    2710 
    2711 1 model tiled 
    2712 
    2713 > volume level 0.00679
    2714 
    2715 > tile
    2716 
    2717 4 models tiled 
    2718 
    2719 > volume #1 level 0.005695
    2720 
    2721 > volume level 0.00569
    2722 
    2723 > close session
    2724 
    2725 > open C:/Users/lilyh/Downloads/run_it016_class001.mrc
    2726 
    2727 Opened run_it016_class001.mrc as #1, grid size 256,256,256, pixel 1.09, shown
    2728 at level 0.00271, step 1, values float32 
    2729 
    2730 > open C:/Users/lilyh/Downloads/run_it016_class005.mrc
    2731 
    2732 Opened run_it016_class005.mrc as #2, grid size 256,256,256, pixel 1.09, shown
    2733 at level 0.00283, step 1, values float32 
    2734 
    2735 > open C:/Users/lilyh/Downloads/run_it016_class004.mrc
    2736 
    2737 Opened run_it016_class004.mrc as #3, grid size 256,256,256, pixel 1.09, shown
    2738 at level 0.00277, step 1, values float32 
    2739 
    2740 > open C:/Users/lilyh/Downloads/run_it016_class003.mrc
    2741 
    2742 Opened run_it016_class003.mrc as #4, grid size 256,256,256, pixel 1.09, shown
    2743 at level 0.00278, step 1, values float32 
    2744 
    2745 > open C:/Users/lilyh/Downloads/run_it016_class002.mrc
    2746 
    2747 Opened run_it016_class002.mrc as #5, grid size 256,256,256, pixel 1.09, shown
    2748 at level 0.00274, step 1, values float32 
    2749 
    2750 > volume level 0.00569
    2751 
    2752 > hide #!5 models
    2753 
    2754 > hide #!4 models
    2755 
    2756 > hide #!3 models
    2757 
    2758 > hide #!2 models
    2759 
    2760 > volume #1 level 0.008511
    2761 
    2762 > show #!2 models
    2763 
    2764 > hide #!1 models
    2765 
    2766 > volume #1 level 0.01015
    2767 
    2768 > hide #!1 models
    2769 
    2770 > volume #2 level 0.009196
    2771 
    2772 > hide #!2 models
    2773 
    2774 > show #!3 models
    2775 
    2776 > volume #3 level 0.009482
    2777 
    2778 > hide #!3 models
    2779 
    2780 > show #!4 models
    2781 
    2782 > volume #4 level 0.006495
    2783 
    2784 > hide #!4 models
    2785 
    2786 > show #!5 models
    2787 
    2788 > volume #5 level 0.006699
    2789 
    2790 > volume #5 level 0.00796
    2791 
    2792 > close session
    2793 
    2794 > open C:/Users/lilyh/Downloads/Class3D_Job172/run_it025_class002.mrc
    2795 
    2796 Opened run_it025_class002.mrc as #1, grid size 256,256,256, pixel 1.09, shown
    2797 at level 0.000511, step 1, values float32 
    2798 
    2799 > open C:/Users/lilyh/Downloads/Class3D_Job172/run_it025_class001.mrc
    2800 
    2801 Opened run_it025_class001.mrc as #2, grid size 256,256,256, pixel 1.09, shown
    2802 at level 0.000505, step 1, values float32 
    2803 
    2804 > open C:/Users/lilyh/Downloads/Class3D_Job172/run_it025_class004.mrc
    2805 
    2806 Opened run_it025_class004.mrc as #3, grid size 256,256,256, pixel 1.09, shown
    2807 at level 0.000511, step 1, values float32 
    2808 
    2809 > open C:/Users/lilyh/Downloads/Class3D_Job172/run_it025_class003.mrc
    2810 
    2811 Opened run_it025_class003.mrc as #4, grid size 256,256,256, pixel 1.09, shown
    2812 at level 0.000507, step 1, values float32 
    2813 
    2814 > volume level 0.00569
    2815 
    2816 > hide #!4 models
    2817 
    2818 > hide #!3 models
    2819 
    2820 > hide #!2 models
    2821 
    2822 > tile
    2823 
    2824 1 model tiled 
    2825 
    2826 > show #!3 models
    2827 
    2828 > show #!4 models
    2829 
    2830 > show #!2 models
    2831 
    2832 > tile
    2833 
    2834 4 models tiled 
    2835 
    2836 > volume #1 level 0.006258
    2837 
    2838 > close session
    2839 
    2840 > open
    2841 > C:/Users/lilyh/Desktop/output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
    2842 
    2843 Chain information for
    2844 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
    2845 #1 
    2846 --- 
    2847 Chain | Description 
    2848 B | No description available 
    2849 C | No description available 
    2850  
    2851 
    2852 > open
    2853 > C:/Users/lilyh/Desktop/output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
    2854 
    2855 Chain information for
    2856 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
    2857 #2 
    2858 --- 
    2859 Chain | Description 
    2860 B | No description available 
    2861 C | No description available 
    2862  
    2863 
    2864 > open C:/Users/lilyh/Downloads/cryosparc_P122_J482_003_volume_map_sharp.mrc
    2865 
    2866 Opened cryosparc_P122_J482_003_volume_map_sharp.mrc as #3, grid size
    2867 256,256,256, pixel 1.09, shown at level 0.0359, step 1, values float32 
    2868 
    2869 > ~tile
    2870 
    2871 > volume #3 level 0.1907
    2872 
    2873 > ui mousemode right "rotate selected models"
    2874 
    2875 > ui mousemode right "translate selected models"
    2876 
    2877 Drag select of 3 cryosparc_P122_J482_003_volume_map_sharp.mrc 
    2878 
    2879 > view matrix models #3,1,0,0,-166.29,0,1,0,-175.89,0,0,1,-100.88
    2880 
    2881 Drag select of 4 residues 
    2882 
    2883 > ui mousemode right "rotate selected models"
    2884 
    2885 > view matrix models
    2886 > #1,-0.97633,-0.14064,0.16431,-5.2566,0.021158,-0.81816,-0.5746,5.6834,0.21524,-0.55752,0.80177,2.3439
    2887 
    2888 Drag select of 3 cryosparc_P122_J482_003_volume_map_sharp.mrc 
    2889 
    2890 > ui mousemode right "translate selected models"
    2891 
    2892 > view matrix models #3,1,0,0,-134.31,0,1,0,-151.91,0,0,1,-130.5
    2893 
    2894 > ui mousemode right "rotate selected models"
    2895 
    2896 > view matrix models
    2897 > #3,0.87002,0.44753,0.20683,-208.17,0.2944,-0.13511,-0.94608,98.666,-0.39545,0.88401,-0.2493,-27.679
    2898 
    2899 > ui mousemode right "translate selected models"
    2900 
    2901 > view matrix models
    2902 > #3,0.87002,0.44753,0.20683,-212.56,0.2944,-0.13511,-0.94608,116.66,-0.39545,0.88401,-0.2493,-30.3
    2903 
    2904 > fitmap #1 inMap #3
    2905 
    2906 Fit molecule
    2907 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
    2908 (#1) to map cryosparc_P122_J482_003_volume_map_sharp.mrc (#3) using 4737 atoms 
    2909 average map value = 0.1856, steps = 156 
    2910 shifted from previous position = 7.64 
    2911 rotated from previous position = 26.9 degrees 
    2912 atoms outside contour = 2745, contour level = 0.19069 
    2913  
    2914 Position of
    2915 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
    2916 (#1) relative to cryosparc_P122_J482_003_volume_map_sharp.mrc (#3)
    2917 coordinates: 
    2918 Matrix rotation and translation 
    2919 -0.83214070 0.17998909 -0.52454334 140.52207659 
    2920 -0.49786038 -0.65912186 0.56364293 134.67261516 
    2921 -0.24428840 0.73017959 0.63809159 142.54394458 
    2922 Axis 0.22140877 -0.37259604 -0.90119384 
    2923 Axis point 96.40388725 19.11225562 0.00000000 
    2924 Rotation angle (degrees) 157.90866282 
    2925 Shift along axis -147.52538930 
    2926  
    2927 
    2928 > fitmap #2 inMap #3
    2929 
    2930 Fit molecule
    2931 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
    2932 (#2) to map cryosparc_P122_J482_003_volume_map_sharp.mrc (#3) using 4737 atoms 
    2933 average map value = 0.1868, steps = 232 
    2934 shifted from previous position = 4.35 
    2935 rotated from previous position = 48.8 degrees 
    2936 atoms outside contour = 2724, contour level = 0.19069 
    2937  
    2938 Position of
    2939 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
    2940 (#2) relative to cryosparc_P122_J482_003_volume_map_sharp.mrc (#3)
    2941 coordinates: 
    2942 Matrix rotation and translation 
    2943 0.22180925 0.37383074 -0.90058379 140.05335003 
    2944 0.94562907 0.14284690 0.29219918 135.77559386 
    2945 0.23787864 -0.91643073 -0.32182045 143.26005403 
    2946 Axis -0.68825231 -0.64829556 0.32560962 
    2947 Axis point 0.00000000 83.08323191 84.71542206 
    2948 Rotation angle (degrees) 118.59284157 
    2949 Shift along axis -137.76790527 
    2950  
    2951 
    2952 > hide #1 models
    2953 
    2954 > hide #2 models
    2955 
    2956 > hide #!3 models
    2957 
    2958 > show #1 models
    2959 
    2960 > molmap #1 10 onGrid #3
    2961 
    2962 Opened
    2963 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
    2964 map 10 as #4, grid size 256,256,256, pixel 1.09, shown at level 0.0546, step
    2965 1, values float32 
    2966 
    2967 > hide #1 models
    2968 
    2969 > show #2 models
    2970 
    2971 > hide #!4 models
    2972 
    2973 > molmap #2 10 onGrid #3
    2974 
    2975 Opened
    2976 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
    2977 map 10 as #5, grid size 256,256,256, pixel 1.09, shown at level 0.0528, step
    2978 1, values float32 
    2979 
    2980 > hide #2 models
    2981 
    2982 > show #2 models
    2983 
    2984 > hide #2 models
    2985 
    2986 > show #!4 models
    2987 
    2988 > hide #!5 models
    2989 
    2990 > show #!3 models
    2991 
    2992 > hide #!3 models
    2993 
    2994 > show #!3 models
    2995 
    2996 > hide #!4 models
    2997 
    2998 > show #!4 models
    2999 
    3000 > close #4
    3001 
    3002 > close #5
    3003 
    3004 > molmap #2 6 onGrid #3
    3005 
    3006 Opened
    3007 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
    3008 map 6 as #4, grid size 256,256,256, pixel 1.09, shown at level 0.0793, step 1,
    3009 values float32 
    3010 
    3011 > volume #4 level 0.3144
    3012 
    3013 > close #4
    3014 
    3015 > molmap #2 8 onGrid #3
    3016 
    3017 Opened
    3018 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
    3019 map 8 as #4, grid size 256,256,256, pixel 1.09, shown at level 0.0638, step 1,
    3020 values float32 
    3021 
    3022 > molmap #2 9 onGrid #3
    3023 
    3024 Opened
    3025 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
    3026 map 9 as #4, grid size 256,256,256, pixel 1.09, shown at level 0.0578, step 1,
    3027 values float32 
    3028 
    3029 > molmap #1 9 onGrid #3
    3030 
    3031 Opened
    3032 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
    3033 map 9 as #5, grid size 256,256,256, pixel 1.09, shown at level 0.0601, step 1,
    3034 values float32 
    3035 
    3036 > hide #!3 models
    3037 
    3038 > show #!3 models
    3039 
    3040 > hide #!3 models
    3041 
    3042 > hide #!4 models
    3043 
    3044 > show #!4 models
    3045 
    3046 > hide #!4 models
    3047 
    3048 > show #!4 models
    3049 
    3050 > save C:/Users/lilyh/Desktop/Mask_Generation_J65/rank2_molmap9A.mrc models #4
    3051 
    3052 > save C:/Users/lilyh/Desktop/Mask_Generation_J65/rank1_molmap9A.mrc models #5
    3053 
    3054 > hide #!5 models
    3055 
    3056 > hide #!4 models
    3057 
    3058 > show #2 models
    3059 
    3060 > combine #1 #2
    3061 
    3062 Remapping chain ID 'B' in
    3063 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
    3064 #2 to 'D' 
    3065 Remapping chain ID 'C' in
    3066 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
    3067 #2 to 'E' 
    3068 
    3069 > hide #2 models
    3070 
    3071 > hide #6 models
    3072 
    3073 > show #6 models
    3074 
    3075 > hide #6 models
    3076 
    3077 > show #2 models
    3078 
    3079 > show #1 models
    3080 
    3081 > hide #1 models
    3082 
    3083 > hide #2 models
    3084 
    3085 > show #6 models
    3086 
    3087 > hide #6 models
    3088 
    3089 > show #6 models
    3090 
    3091 > hide #6 models
    3092 
    3093 > show #!5 models
    3094 
    3095 > hide #5.1 models
    3096 
    3097 > hide #!5 models
    3098 
    3099 > show #6 models
    3100 
    3101 > select add #6
    3102 
    3103 9474 atoms, 9646 bonds, 1170 residues, 3 models selected 
    3104 
    3105 > select subtract #6
    3106 
    3107 2 models selected 
    3108 
    3109 > select add #6
    3110 
    3111 9474 atoms, 9646 bonds, 1170 residues, 3 models selected 
    3112 
    3113 > hide #6 models
    3114 
    3115 > show #6 models
    3116 
    3117 > hide #6 models
    3118 
    3119 > open C:/Users/lilyh/Downloads/cryosparc_P104_J3813_003_volume_map.mrc
    3120 
    3121 Opened cryosparc_P104_J3813_003_volume_map.mrc as #7, grid size 256,256,256,
    3122 pixel 1.09, shown at level 0.00684, step 1, values float32 
    3123 
    3124 > volume #7 level 0.1148
    3125 
    3126 > volume #7 level 0.1211
    3127 
    3128 > hide #!7 models
    3129 
    3130 > show #!7 models
    3131 
    3132 > hide #!7 models
    3133 
    3134 > show #!7 models
    3135 
    3136 > hide #!7 models
    3137 
    3138 > open C:/Users/lilyh/Downloads/Class3D_job201/run_it025_class001.mrc
    3139 
    3140 Opened run_it025_class001.mrc as #8, grid size 256,256,256, pixel 1.09, shown
    3141 at level 0.00129, step 1, values float32 
    3142 
    3143 > open C:/Users/lilyh/Downloads/Class3D_job201/run_it025_class005.mrc
    3144 
    3145 Opened run_it025_class005.mrc as #9, grid size 256,256,256, pixel 1.09, shown
    3146 at level 0.00106, step 1, values float32 
    3147 
    3148 > open C:/Users/lilyh/Downloads/Class3D_job201/run_it025_class004.mrc
    3149 
    3150 Opened run_it025_class004.mrc as #10, grid size 256,256,256, pixel 1.09, shown
    3151 at level 0.00094, step 1, values float32 
    3152 
    3153 > open C:/Users/lilyh/Downloads/Class3D_job201/run_it025_class003.mrc
    3154 
    3155 Opened run_it025_class003.mrc as #11, grid size 256,256,256, pixel 1.09, shown
    3156 at level 0.00107, step 1, values float32 
    3157 
    3158 > open C:/Users/lilyh/Downloads/Class3D_job201/run_it025_class002.mrc
    3159 
    3160 Opened run_it025_class002.mrc as #12, grid size 256,256,256, pixel 1.09, shown
    3161 at level 0.00137, step 1, values float32 
    3162 
    3163 > titile
    3164 
    3165 Unknown command: titile 
    3166 
    3167 > tile
    3168 
    3169 5 models tiled 
    3170 
    3171 > volume level 0.003
    3172 
    3173 > volume #12 level 0.005901
    3174 
    3175 > volume level 0.0059
    3176 
    3177 > volume #11 level 0.003133
    3178 
    3179 > volume #9 level 0.003281
    3180 
    3181 > volume level 0.00328
    3182 
    3183 > open C:/Users/lilyh/Downloads/Class3D_job201/run_it025_class006.mrc
    3184 
    3185 Opened run_it025_class006.mrc as #13, grid size 256,256,256, pixel 1.09, shown
    3186 at level 0.00103, step 1, values float32 
    3187 
    3188 > volume level 0.00328
    3189 
    3190 > tile
    3191 
    3192 6 models tiled 
    3193 
    3194 > select #13
    3195 
    3196 2 models selected 
    3197 
    3198 > select #13
    3199 
    3200 2 models selected 
    3201 
    3202 > ui mousemode right "rotate selected models"
    3203 
    3204 > view matrix models
    3205 > #13,-0.3926,0.33493,0.85656,-255.41,-0.81533,-0.55768,-0.15564,282.95,0.42556,-0.75948,0.49202,-170.95
    3206 
    3207 > view matrix models
    3208 > #13,-0.79801,-0.50365,0.33094,-10.132,0.46274,-0.86389,-0.1989,152.61,0.38608,-0.0055828,0.92245,-329.17
    3209 
    3210 > select clear
    3211 
    3212 > volume #12 level 0.004396
    3213 
    3214 > volume #11 level 0.006833
    3215 
    3216 > volume #13 level 0.002836
    3217 
    3218 > volume #10 level 0.003457
    3219 
    3220 > volume #9 level 0.002396
    3221 
    3222 > volume #8 level 0.003082
    3223 
    3224 > volume #13 level 0.007239
    3225 
    3226 > volume #13 level 0.007165
    3227 
    3228 > volume #13 level 0.005574
    3229 
    3230 > volume #11 level 0.004612
    3231 
    3232 > volume level 0.004
    3233 
    3234 > volume #8 level 0.002216
    3235 
    3236 > volume #8 level 0.005916
    3237 
    3238 > ~tile
    3239 
    3240 > hide #!8 models
    3241 
    3242 > hide #!9 models
    3243 
    3244 > hide #!10 models
    3245 
    3246 > hide #!12 models
    3247 
    3248 > fitmap #11 inMap #13
    3249 
    3250 Fit map run_it025_class003.mrc in map run_it025_class006.mrc using 43937
    3251 points 
    3252 correlation = 0.98, correlation about mean = 0.7752, overlap = 1.881 
    3253 steps = 68, shift = 0.168, angle = 3.81 degrees 
    3254  
    3255 Position of run_it025_class003.mrc (#11) relative to run_it025_class006.mrc
    3256 (#13) coordinates: 
    3257 Matrix rotation and translation 
    3258 0.99800934 -0.06302882 0.00217236 8.74105301 
    3259 0.06296948 0.99779424 0.02101206 -11.26954788 
    3260 -0.00349194 -0.02083345 0.99977686 3.50822058 
    3261 Axis -0.31489768 0.04262519 0.94816799 
    3262 Axis point 183.70273900 133.34854015 0.00000000 
    3263 Rotation angle (degrees) 3.80971165 
    3264 Shift along axis 0.09347853 
    3265  
    3266 
    3267 > volume #13 level 0.005221
    3268 
    3269 > volume #11 level 0.005572
    3270 
    3271 > volume #11 level 0.007348
    3272 
    3273 > volume #13 level 0.007441
    3274 
    3275 > tile
    3276 
    3277 2 models tiled 
    3278 
    3279 > hide #!11 models
    3280 
    3281 > hide #!13 models
    3282 
    3283 > show #!13 models
    3284 
    3285 > hide #!13 models
    3286 
    3287 > show #!9 models
    3288 
    3289 > volume #9 level 0.003558
    3290 
    3291 > volume #9 level 0.002741
    3292 
    3293 > show #1 models
    3294 
    3295 > hide #1 models
    3296 
    3297 > close session
    3298 
    3299 > open C:/Users/lilyh/Downloads/Class3D_job201/run_it025_class006.mrc
    3300 
    3301 Opened run_it025_class006.mrc as #1, grid size 256,256,256, pixel 1.09, shown
    3302 at level 0.00103, step 1, values float32 
    3303 
    3304 > open C:/Users/lilyh/Downloads/Class3D_job201/run_it025_class005.mrc
    3305 
    3306 Opened run_it025_class005.mrc as #2, grid size 256,256,256, pixel 1.09, shown
    3307 at level 0.00106, step 1, values float32 
    3308 
    3309 > open C:/Users/lilyh/Downloads/Class3D_job201/run_it025_class004.mrc
    3310 
    3311 Opened run_it025_class004.mrc as #3, grid size 256,256,256, pixel 1.09, shown
    3312 at level 0.00094, step 1, values float32 
    3313 
    3314 > open C:/Users/lilyh/Downloads/Class3D_job201/run_it025_class003.mrc
    3315 
    3316 Opened run_it025_class003.mrc as #4, grid size 256,256,256, pixel 1.09, shown
    3317 at level 0.00107, step 1, values float32 
    3318 
    3319 > open C:/Users/lilyh/Downloads/Class3D_job201/run_it025_class002.mrc
    3320 
    3321 Opened run_it025_class002.mrc as #5, grid size 256,256,256, pixel 1.09, shown
    3322 at level 0.00137, step 1, values float32 
    3323 
    3324 > open C:/Users/lilyh/Downloads/Class3D_job201/run_it025_class001.mrc
    3325 
    3326 Opened run_it025_class001.mrc as #6, grid size 256,256,256, pixel 1.09, shown
    3327 at level 0.00129, step 1, values float32 
    3328 
    3329 > open
    3330 > C:/Users/lilyh/Desktop/output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
    3331 
    3332 Chain information for
    3333 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
    3334 #7 
    3335 --- 
    3336 Chain | Description 
    3337 B | No description available 
    3338 C | No description available 
    3339  
    3340 
    3341 > open
    3342 > C:/Users/lilyh/Desktop/output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
    3343 
    3344 Chain information for
    3345 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
    3346 #8 
    3347 --- 
    3348 Chain | Description 
    3349 B | No description available 
    3350 C | No description available 
    3351  
    3352 
    3353 > ~tile
    3354 
    3355 > ui mousemode right "translate selected models"
    3356 
    3357 Drag select of 1153 residues 
    3358 
    3359 > ui mousemode right "translate selected models"
    3360 
    3361 > view matrix models
    3362 > #7,1,0,0,137.53,0,1,0,146,0,0,1,0,#8,1,0,0,137.53,0,1,0,146,0,0,1,0
    3363 
    3364 > view matrix models
    3365 > #7,1,0,0,114.21,0,1,0,131.39,0,0,1,140.78,#8,1,0,0,114.21,0,1,0,131.39,0,0,1,140.78
    3366 
    3367 > select up
    3368 
    3369 9403 atoms, 9574 bonds, 1162 residues, 2 models selected 
    3370 
    3371 > volume level 0.004
    3372 
    3373 > hide #!1 models
    3374 
    3375 > hide #!2 models
    3376 
    3377 > hide #!3 models
    3378 
    3379 > show #!2 models
    3380 
    3381 > hide #!4 models
    3382 
    3383 > hide #!5 models
    3384 
    3385 > hide #!6 models
    3386 
    3387 > volume #2 level 0.002844
    3388 
    3389 > select #2
    3390 
    3391 2 models selected 
    3392 
    3393 > select clear
    3394 
    3395 > ui mousemode right "rotate selected models"
    3396 
    3397 Drag select of 3 residues 
    3398 
    3399 > view matrix models
    3400 > #7,-0.26975,0.35466,-0.89524,106.01,-0.92422,-0.35631,0.13733,134.33,-0.27028,0.86444,0.4239,134.69
    3401 
    3402 Drag select of 5 residues 
    3403 
    3404 > view matrix models
    3405 > #8,-0.23883,0.13926,-0.96102,120.55,0.97103,0.042055,-0.23522,124.36,0.0076582,-0.98936,-0.14527,138.34
    3406 
    3407 > fitmap #7 inMap #2
    3408 
    3409 Fit molecule
    3410 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
    3411 (#7) to map run_it025_class005.mrc (#2) using 4737 atoms 
    3412 average map value = 0.003537, steps = 300 
    3413 shifted from previous position = 27.6 
    3414 rotated from previous position = 60 degrees 
    3415 atoms outside contour = 2044, contour level = 0.0028435 
    3416  
    3417 Position of
    3418 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
    3419 (#7) relative to run_it025_class005.mrc (#2) coordinates: 
    3420 Matrix rotation and translation 
    3421 0.67041123 0.22239462 -0.70787668 131.93155495 
    3422 -0.74176984 0.22410593 -0.63210285 137.33856533 
    3423 0.01806309 0.94885043 0.31520876 142.44349169 
    3424 Axis 0.79485896 -0.36498215 -0.48475484 
    3425 Axis point 0.00000000 4.25911866 203.78217280 
    3426 Rotation angle (degrees) 83.98072869 
    3427 Shift along axis -14.30931872 
    3428  
    3429 
    3430 > fitmap #8 inMap #2
    3431 
    3432 Fit molecule
    3433 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
    3434 (#8) to map run_it025_class005.mrc (#2) using 4737 atoms 
    3435 average map value = 0.004346, steps = 364 
    3436 shifted from previous position = 21.6 
    3437 rotated from previous position = 35.2 degrees 
    3438 atoms outside contour = 1606, contour level = 0.0028435 
    3439  
    3440 Position of
    3441 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
    3442 (#8) relative to run_it025_class005.mrc (#2) coordinates: 
    3443 Matrix rotation and translation 
    3444 0.26484965 0.37638631 -0.88779952 139.78430774 
    3445 0.93516327 0.12431824 0.33168451 136.13979180 
    3446 0.23521118 -0.91808404 -0.31905701 142.80814378 
    3447 Axis -0.70581293 -0.63422582 0.31557204 
    3448 Axis point 0.00000000 85.31235050 82.36563740 
    3449 Rotation angle (degrees) 117.70663459 
    3450 Shift along axis -139.93868660 
    3451  
    3452 Drag select of 7 residues 
    3453 
    3454 > ui mousemode right "rotate selected models"
    3455 
    3456 > view matrix models
    3457 > #7,-0.9098,0.34259,-0.23432,127.82,-0.39996,-0.5728,0.71549,145.72,0.1109,0.74467,0.65815,144.6
    3458 
    3459 > fitmap #7 inMap #2
    3460 
    3461 Fit molecule
    3462 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
    3463 (#7) to map run_it025_class005.mrc (#2) using 4737 atoms 
    3464 average map value = 0.004441, steps = 184 
    3465 shifted from previous position = 16.8 
    3466 rotated from previous position = 21.8 degrees 
    3467 atoms outside contour = 1577, contour level = 0.0028435 
    3468  
    3469 Position of
    3470 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
    3471 (#7) relative to run_it025_class005.mrc (#2) coordinates: 
    3472 Matrix rotation and translation 
    3473 -0.81810596 0.20765135 -0.53626815 140.57361684 
    3474 -0.52497845 -0.65032553 0.54906677 135.16355895 
    3475 -0.23473442 0.73072403 0.64104768 142.16276519 
    3476 Axis 0.22349149 -0.37097458 -0.90134867 
    3477 Axis point 97.41629186 17.89919390 0.00000000 
    3478 Rotation angle (degrees) 156.02063833 
    3479 Shift along axis -146.86345505 
    3480  
    3481 
    3482 > select clear
    3483 
    3484 > open C:/Users/lilyh/Downloads/cryosparc_P122_J505_mask.mrc
    3485 
    3486 Opened cryosparc_P122_J505_mask.mrc as #9, grid size 256,256,256, pixel 1.09,
    3487 shown at level 5e-05, step 1, values float32 
    3488 
    3489 > select #9
    3490 
    3491 2 models selected 
    3492 
    3493 > transparency #9.1 50
    3494 
    3495 > select clear
    3496 
    3497 > volume #2 level 0.004442
    3498 
    3499 > volume #2 level 0.005905
    3500 
    3501 > hide #7 models
    3502 
    3503 > show #7 models
    3504 
    3505 > hide #!9 models
    3506 
    3507 > volume #2 level 0.003388
    3508 
    3509 > volume #2 level 0.003864
    3510 
    3511 > hide #!2 models
    3512 
    3513 > show #!1 models
    3514 
    3515 > hide #!1 models
    3516 
    3517 > show #!3 models
    3518 
    3519 > hide #!3 models
    3520 
    3521 > show #!4 models
    3522 
    3523 > volume #4 level 0.003795
    3524 
    3525 > hide #!4 models
    3526 
    3527 > show #!5 models
    3528 
    3529 > volume #5 level 0.006975
    3530 
    3531 > volume #5 level 0.005339
    3532 
    3533 > volume #6 level 0.005784
    3534 
    3535 > open
    3536 > C:/Users/lilyh/Downloads/cryosparc_P104_J3423_class_02_00122_volume_sharp.mrc
    3537 
    3538 Opened cryosparc_P104_J3423_class_02_00122_volume_sharp.mrc as #10, grid size
    3539 128,128,128, pixel 2.17, shown at level 0.0672, step 1, values float32 
    3540 
    3541 > open
    3542 > C:/Users/lilyh/Downloads/cryosparc_P104_J3423_class_01_00122_volume_sharp.mrc
    3543 
    3544 Opened cryosparc_P104_J3423_class_01_00122_volume_sharp.mrc as #11, grid size
    3545 128,128,128, pixel 2.17, shown at level 0.0692, step 1, values float32 
    3546 
    3547 > volume #10 level 0.2801
    3548 
    3549 > hide #8 models
    3550 
    3551 > hide #7 models
    3552 
    3553 > volume #10 level 0.1828
    3554 
    3555 > volume #11 level 0.1865
    3556 
    3557 > select #10
    3558 
    3559 2 models selected 
    3560 
    3561 > ui mousemode right "move picked models"
    3562 
    3563 > ui mousemode right "rotate selected models"
    3564 
    3565 > view matrix models
    3566 > #10,-0.89307,-0.23379,0.38441,244.31,-0.23294,0.97123,0.049517,29.763,-0.38493,-0.045323,-0.92183,320.44
    3567 
    3568 > fitmap #10 inMap #11
    3569 
    3570 Fit map cryosparc_P104_J3423_class_02_00122_volume_sharp.mrc in map
    3571 cryosparc_P104_J3423_class_01_00122_volume_sharp.mrc using 8257 points 
    3572 correlation = 0.9071, correlation about mean = 0.5993, overlap = 1160 
    3573 steps = 196, shift = 2.97, angle = 62.1 degrees 
    3574  
    3575 Position of cryosparc_P104_J3423_class_02_00122_volume_sharp.mrc (#10)
    3576 relative to cryosparc_P104_J3423_class_01_00122_volume_sharp.mrc (#11)
    3577 coordinates: 
    3578 Matrix rotation and translation 
    3579 -0.71707819 0.69697322 0.00521346 140.85245041 
    3580 0.69697654 0.71709246 -0.00145090 -54.78773595 
    3581 -0.00474977 0.00259325 -0.99998535 273.87631528 
    3582 Axis 0.37610463 0.92657715 0.00030830 
    3583 Axis point 81.94288839 0.00000000 136.74420261 
    3584 Rotation angle (degrees) 179.69195567 
    3585 Shift along axis 2.29463106 
    3586  
    3587 
    3588 > select clear
    3589 
    3590 > show #8 models
    3591 
    3592 > hide #8 models
    3593 
    3594 > show #7 models
    3595 
    3596 > hide #7 models
    3597 
    3598 > show #8 models
    3599 
    3600 > show #7 models
    3601 
    3602 > fitmap #7 inMap #10
    3603 
    3604 Fit molecule
    3605 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
    3606 (#7) to map cryosparc_P104_J3423_class_02_00122_volume_sharp.mrc (#10) using
    3607 4737 atoms 
    3608 average map value = 0.2848, steps = 184 
    3609 shifted from previous position = 5.22 
    3610 rotated from previous position = 31.3 degrees 
    3611 atoms outside contour = 1714, contour level = 0.1828 
    3612  
    3613 Position of
    3614 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
    3615 (#7) relative to cryosparc_P104_J3423_class_02_00122_volume_sharp.mrc (#10)
    3616 coordinates: 
    3617 Matrix rotation and translation 
    3618 0.66845251 -0.31728464 0.67268246 136.65439192 
    3619 -0.70035335 -0.57296099 0.42570046 134.37842005 
    3620 0.25035259 -0.75567596 -0.60520857 131.31049403 
    3621 Axis -0.90059359 0.32195291 -0.29202312 
    3622 Axis point 0.00000000 111.70347316 7.72215948 
    3623 Rotation angle (degrees) 139.01301011 
    3624 Shift along axis -118.15224739 
    3625  
    3626 
    3627 > fitmap #8 inMap #10
    3628 
    3629 Fit molecule
    3630 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
    3631 (#8) to map cryosparc_P104_J3423_class_02_00122_volume_sharp.mrc (#10) using
    3632 4737 atoms 
    3633 average map value = 0.2896, steps = 196 
    3634 shifted from previous position = 3.65 
    3635 rotated from previous position = 29.1 degrees 
    3636 atoms outside contour = 1716, contour level = 0.1828 
    3637  
    3638 Position of
    3639 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
    3640 (#8) relative to cryosparc_P104_J3423_class_02_00122_volume_sharp.mrc (#10)
    3641 coordinates: 
    3642 Matrix rotation and translation 
    3643 0.00075152 -0.37212803 0.92818110 137.57900910 
    3644 0.97707992 0.19785664 0.07853393 135.30883867 
    3645 -0.21287147 0.90684810 0.36374751 130.60755963 
    3646 Axis 0.42444358 0.58469655 0.69135923 
    3647 Axis point 27.47524782 36.09958021 0.00000000 
    3648 Rotation angle (degrees) 102.63986242 
    3649 Shift along axis 227.80588093 
    3650  
    3651 
    3652 > hide #7 models
    3653 
    3654 > hide #8 models
    3655 
    3656 > show #8 models
    3657 
    3658 > show #7 models
    3659 
    3660 > hide #!11 models
    3661 
    3662 > show #!11 models
    3663 
    3664 > hide #!10 models
    3665 
    3666 > show #!10 models
    3667 
    3668 > hide #!10 models
    3669 
    3670 > select #11
    3671 
    3672 2 models selected 
    3673 
    3674 > transparency #11.1 40
    3675 
    3676 > select clear
    3677 
    3678 > show #!10 models
    3679 
    3680 > hide #!10 models
    3681 
    3682 > show #!10 models
    3683 
    3684 > hide #!10 models
    3685 
    3686 > show #!2 models
    3687 
    3688 > volume #2 level 0.003626
    3689 
    3690 > fitmap #2 inMap #11
    3691 
    3692 Fit map run_it025_class005.mrc in map
    3693 cryosparc_P104_J3423_class_01_00122_volume_sharp.mrc using 50478 points 
    3694 correlation = 0.9061, correlation about mean = 0.4069, overlap = 116.1 
    3695 steps = 104, shift = 2.12, angle = 26.6 degrees 
    3696  
    3697 Position of run_it025_class005.mrc (#2) relative to
    3698 cryosparc_P104_J3423_class_01_00122_volume_sharp.mrc (#11) coordinates: 
    3699 Matrix rotation and translation 
    3700 0.89449861 0.44705699 0.00350577 -49.12452265 
    3701 -0.44699715 0.89418161 0.02515531 74.93541992 
    3702 0.00811106 -0.02406845 0.99967741 1.93985496 
    3703 Axis -0.05497282 -0.00514317 -0.99847461 
    3704 Axis point 134.14963204 141.49583994 0.00000000 
    3705 Rotation angle (degrees) 26.59685498 
    3706 Shift along axis 0.37821183 
    3707  
    3708 
    3709 > hide #7 models
    3710 
    3711 > hide #8 models
    3712 
    3713 > volume #2 level 0.003898
    3714 
    3715 > volume #11 level 0.1809
    3716 
    3717 > volume #2 level 0.003388
    3718 
    3719 > open C:/Users/lilyh/Downloads/cryosparc_P104_J3410_class_00_final_volume.mrc
    3720 
    3721 Opened cryosparc_P104_J3410_class_00_final_volume.mrc as #12, grid size
    3722 128,128,128, pixel 2.17, shown at level 0.025, step 1, values float32 
    3723 
    3724 > volume #12 level 0.1722
    3725 
    3726 > volume #12 level 0.1402
    3727 
    3728 > hide #!12 models
    3729 
    3730 > hide #!11 models
    3731 
    3732 > volume #2 level 0.002912
    3733 
    3734 > show #!3 models
    3735 
    3736 > close session
    3737 
    3738 > open C:/Users/lilyh/Downloads/Class3D_job201/run_it025_class005.mrc
    3739 
    3740 Opened run_it025_class005.mrc as #1, grid size 256,256,256, pixel 1.09, shown
    3741 at level 0.00106, step 1, values float32 
    3742 
    3743 > open C:/Users/lilyh/Downloads/Class3D_job201/run_it025_class004.mrc
    3744 
    3745 Opened run_it025_class004.mrc as #2, grid size 256,256,256, pixel 1.09, shown
    3746 at level 0.00094, step 1, values float32 
    3747 
    3748 > open C:/Users/lilyh/Downloads/Class3D_job201/run_it025_class003.mrc
    3749 
    3750 Opened run_it025_class003.mrc as #3, grid size 256,256,256, pixel 1.09, shown
    3751 at level 0.00107, step 1, values float32 
    3752 
    3753 > open C:/Users/lilyh/Downloads/Class3D_job201/run_it025_class002.mrc
    3754 
    3755 Opened run_it025_class002.mrc as #4, grid size 256,256,256, pixel 1.09, shown
    3756 at level 0.00137, step 1, values float32 
    3757 
    3758 > open C:/Users/lilyh/Downloads/Class3D_job201/run_it025_class001.mrc
    3759 
    3760 Opened run_it025_class001.mrc as #5, grid size 256,256,256, pixel 1.09, shown
    3761 at level 0.00129, step 1, values float32 
    3762 
    3763 > open C:/Users/lilyh/Downloads/Class3D_job201/run_it025_class006.mrc
    3764 
    3765 Opened run_it025_class006.mrc as #6, grid size 256,256,256, pixel 1.09, shown
    3766 at level 0.00103, step 1, values float32 
    3767 
    3768 > volume level 0.003
    3769 
    3770 > tile
    3771 
    3772 6 models tiled 
    3773 
    3774 > hide #!6 models
    3775 
    3776 > hide #!5 models
    3777 
    3778 > close session
    3779 
    3780 > open C:/Users/lilyh/Downloads/Class3D_Job203/run_it025_class004.mrc
    3781 
    3782 Opened run_it025_class004.mrc as #1, grid size 256,256,256, pixel 1.09, shown
    3783 at level 0.00105, step 1, values float32 
    3784 
    3785 > open C:/Users/lilyh/Downloads/Class3D_Job203/run_it025_class003.mrc
    3786 
    3787 Opened run_it025_class003.mrc as #2, grid size 256,256,256, pixel 1.09, shown
    3788 at level 0.00126, step 1, values float32 
    3789 
    3790 > open C:/Users/lilyh/Downloads/Class3D_Job203/run_it025_class002.mrc
    3791 
    3792 Opened run_it025_class002.mrc as #3, grid size 256,256,256, pixel 1.09, shown
    3793 at level 0.00117, step 1, values float32 
    3794 
    3795 > open C:/Users/lilyh/Downloads/Class3D_Job203/run_it025_class001.mrc
    3796 
    3797 Opened run_it025_class001.mrc as #4, grid size 256,256,256, pixel 1.09, shown
    3798 at level 0.000995, step 1, values float32 
    3799 
    3800 > open C:/Users/lilyh/Downloads/Class3D_Job203/run_it025_class005.mrc
    3801 
    3802 Opened run_it025_class005.mrc as #5, grid size 256,256,256, pixel 1.09, shown
    3803 at level 0.000954, step 1, values float32 
    3804 
    3805 > volume level 0.003
    3806 
    3807 > tile
    3808 
    3809 5 models tiled 
    3810 
    3811 > volume #3 level 0.006424
    3812 
    3813 > hide #!1 models
    3814 
    3815 > hide #!2 models
    3816 
    3817 > hide #!3 models
    3818 
    3819 > hide #!4 models
    3820 
    3821 > hide #!5 models
    3822 
    3823 > open C:/Users/lilyh/Downloads/Class3D_Job204/run_it025_class003.mrc
    3824 
    3825 Opened run_it025_class003.mrc as #6, grid size 256,256,256, pixel 1.09, shown
    3826 at level 0.00128, step 1, values float32 
    3827 
    3828 > open C:/Users/lilyh/Downloads/Class3D_Job204/run_it025_class002.mrc
    3829 
    3830 Opened run_it025_class002.mrc as #7, grid size 256,256,256, pixel 1.09, shown
    3831 at level 0.000939, step 1, values float32 
    3832 
    3833 > open C:/Users/lilyh/Downloads/Class3D_Job204/run_it025_class001.mrc
    3834 
    3835 Opened run_it025_class001.mrc as #8, grid size 256,256,256, pixel 1.09, shown
    3836 at level 0.000951, step 1, values float32 
    3837 
    3838 > open C:/Users/lilyh/Downloads/Class3D_Job204/run_it025_class004.mrc
    3839 
    3840 Opened run_it025_class004.mrc as #9, grid size 256,256,256, pixel 1.09, shown
    3841 at level 0.00102, step 1, values float32 
    3842 
    3843 > volume level 0.003
    3844 
    3845 > tile
    3846 
    3847 4 models tiled 
    3848 
    3849 > volume #6 level 0.002824
    3850 
    3851 > volume #9 level 0.004489
    3852 
    3853 > volume #8 level 0.006079
    3854 
    3855 > volume #7 level 0.005781
    3856 
    3857 > close session
    3858 
    3859 > open C:/Users/lilyh/Downloads/Class3D_Job205/run_it025_class005.mrc
    3860 
    3861 Opened run_it025_class005.mrc as #1, grid size 256,256,256, pixel 1.09, shown
    3862 at level 0.0011, step 1, values float32 
    3863 
    3864 > open C:/Users/lilyh/Downloads/Class3D_Job205/run_it025_class004.mrc
    3865 
    3866 Opened run_it025_class004.mrc as #2, grid size 256,256,256, pixel 1.09, shown
    3867 at level 0.000697, step 1, values float32 
    3868 
    3869 > open C:/Users/lilyh/Downloads/Class3D_Job205/run_it025_class003.mrc
    3870 
    3871 Opened run_it025_class003.mrc as #3, grid size 256,256,256, pixel 1.09, shown
    3872 at level 0.000861, step 1, values float32 
    3873 
    3874 > open C:/Users/lilyh/Downloads/Class3D_Job205/run_it025_class002.mrc
    3875 
    3876 Opened run_it025_class002.mrc as #4, grid size 256,256,256, pixel 1.09, shown
    3877 at level 0.00113, step 1, values float32 
    3878 
    3879 > open C:/Users/lilyh/Downloads/Class3D_Job205/run_it025_class001.mrc
    3880 
    3881 Opened run_it025_class001.mrc as #5, grid size 256,256,256, pixel 1.09, shown
    3882 at level 0.000747, step 1, values float32 
    3883 
    3884 > open C:/Users/lilyh/Downloads/Class3D_Job205/run_it025_class006.mrc
    3885 
    3886 Opened run_it025_class006.mrc as #6, grid size 256,256,256, pixel 1.09, shown
    3887 at level 0.000788, step 1, values float32 
    3888 
    3889 > volume level 0.003
    3890 
    3891 > tile
    3892 
    3893 6 models tiled 
    3894 
    3895 > close session
    3896 
    3897 > open C:/Users/lilyh/Downloads/Class3D_Job204/run_it025_class004.mrc
    3898 
    3899 Opened run_it025_class004.mrc as #1, grid size 256,256,256, pixel 1.09, shown
    3900 at level 0.00102, step 1, values float32 
    3901 
    3902 > open C:/Users/lilyh/Downloads/Class3D_Job204/run_it025_class003.mrc
    3903 
    3904 Opened run_it025_class003.mrc as #2, grid size 256,256,256, pixel 1.09, shown
    3905 at level 0.00128, step 1, values float32 
    3906 
    3907 > open C:/Users/lilyh/Downloads/Class3D_Job204/run_it025_class002.mrc
    3908 
    3909 Opened run_it025_class002.mrc as #3, grid size 256,256,256, pixel 1.09, shown
    3910 at level 0.000939, step 1, values float32 
    3911 
    3912 > open C:/Users/lilyh/Downloads/Class3D_Job204/run_it025_class001.mrc
    3913 
    3914 Opened run_it025_class001.mrc as #4, grid size 256,256,256, pixel 1.09, shown
    3915 at level 0.000951, step 1, values float32 
    3916 
    3917 > volume level 0.003
    3918 
    3919 > tile
    3920 
    3921 4 models tiled 
    3922 
    3923 > hide #!2 models
    3924 
    3925 > show #!2 models
    3926 
    3927 > hide #!2 models
    3928 
    3929 > show #!2 models
    3930 
    3931 > volume #2 level 0.003843
    3932 
    3933 > volume #2 level 0.002895
    3934 
    3935 > volume #4 level 0.003456
    3936 
    3937 > volume #3 level 0.003193
    3938 
    3939 > volume #1 level 0.006309
    3940 
    3941 > volume #3 level 0.001957
    3942 
    3943 > volume #3 level 0.005626
    3944 
    3945 > volume #4 level 0.006535
    3946 
    3947 > hide #!3 models
    3948 
    3949 > hide #!4 models
    3950 
    3951 > hide #!1 models
    3952 
    3953 > show #!1 models
    3954 
    3955 > hide #!1 models
    3956 
    3957 > volume #2 level 0.003281
    3958 
    3959 > volume #2 level 0.003879
    3960 
    3961 > volume #2 level 0.003773
    3962 
    3963 > volume #2 level 0.003351
    3964 
    3965 > open C:/Users/lilyh/Downloads/cryosparc_P122_J505_mask.mrc
    3966 
    3967 Opened cryosparc_P122_J505_mask.mrc as #5, grid size 256,256,256, pixel 1.09,
    3968 shown at level 5e-05, step 1, values float32 
    3969 
    3970 > close session
    3971 
    3972 > t~ile
    3973 
    3974 Unknown command: t~ile 
    3975 
    3976 > ~tile
    3977 
    3978 No models found for tiling. 
    3979 
    3980 > open C:/Users/lilyh/Downloads/cryosparc_P122_J505_mask.mrc
    3981 
    3982 Opened cryosparc_P122_J505_mask.mrc as #1, grid size 256,256,256, pixel 1.09,
    3983 shown at level 5e-05, step 1, values float32 
    3984 
    3985 > open C:/Users/lilyh/Downloads/Class3D_Job204/run_it025_class003.mrc
    3986 
    3987 Opened run_it025_class003.mrc as #2, grid size 256,256,256, pixel 1.09, shown
    3988 at level 0.00128, step 1, values float32 
    3989 
    3990 > volume #2 level 0.004269
    3991 
    3992 > volume #2 level 0.005218
    3993 
    3994 > select add #1
    3995 
    3996 2 models selected 
    3997 
    3998 > transparency #1.1 40
    3999 
    4000 > volume #2 level 0.007081
    4001 
    4002 > volume #2 level 0.005886
    4003 
    4004 > hide #!2 models
    4005 
    4006 > hide #!1 models
    4007 
    4008 > show #!1 models
    4009 
    4010 > hide #!1 models
    4011 
    4012 > show #!2 models
    4013 
    4014 > close session
    4015 
    4016 > open C:/Users/lilyh/Downloads/Class3D_Job203/run_it025_class003.mrc
    4017 
    4018 Opened run_it025_class003.mrc as #1, grid size 256,256,256, pixel 1.09, shown
    4019 at level 0.00126, step 1, values float32 
    4020 
    4021 > open C:/Users/lilyh/Downloads/Class3D_Job203/run_it025_class002.mrc
    4022 
    4023 Opened run_it025_class002.mrc as #2, grid size 256,256,256, pixel 1.09, shown
    4024 at level 0.00117, step 1, values float32 
    4025 
    4026 > open C:/Users/lilyh/Downloads/Class3D_Job203/run_it025_class001.mrc
    4027 
    4028 Opened run_it025_class001.mrc as #3, grid size 256,256,256, pixel 1.09, shown
    4029 at level 0.000995, step 1, values float32 
    4030 
    4031 > open C:/Users/lilyh/Downloads/Class3D_Job203/run_it025_class005.mrc
    4032 
    4033 Opened run_it025_class005.mrc as #4, grid size 256,256,256, pixel 1.09, shown
    4034 at level 0.000954, step 1, values float32 
    4035 
    4036 > open C:/Users/lilyh/Downloads/Class3D_Job203/run_it025_class004.mrc
    4037 
    4038 Opened run_it025_class004.mrc as #5, grid size 256,256,256, pixel 1.09, shown
    4039 at level 0.00105, step 1, values float32 
    4040 
    4041 > tile
    4042 
    4043 5 models tiled 
    4044 
    4045 > volume level 0.003
    4046 
    4047 > hide #!1 models
    4048 
    4049 Traceback (most recent call last): 
    4050 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4051 packages\chimerax\core\history.py", line 109, in save 
    4052 json.dump(obj, f, ensure_ascii=False) 
    4053 File "C:\Program Files\ChimeraX1.6.1\bin\lib\json\\__init__.py", line 180, in
    4054 dump 
    4055 fp.write(chunk) 
    4056 OSError: [Errno 28] No space left on device 
    4057  
    4058 During handling of the above exception, another exception occurred: 
    4059  
    4060 OSError: [Errno 28] No space left on device 
    4061  
    4062 During handling of the above exception, another exception occurred: 
    4063  
    4064 Traceback (most recent call last): 
    4065 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4066 packages\chimerax\core\triggerset.py", line 138, in invoke 
    4067 return self._func(self._name, data) 
    4068 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4069 packages\chimerax\cmd_line\tool.py", line 351, in _command_started_cb 
    4070 self.history_dialog.add(self._just_typed_command or cmd_text, 
    4071 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4072 packages\chimerax\cmd_line\tool.py", line 456, in add 
    4073 self._history.enqueue((item, typed)) 
    4074 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4075 packages\chimerax\core\history.py", line 171, in enqueue 
    4076 self.save() 
    4077 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4078 packages\chimerax\core\history.py", line 201, in save 
    4079 self._history.save(self._queue) 
    4080 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4081 packages\chimerax\core\history.py", line 109, in save 
    4082 json.dump(obj, f, ensure_ascii=False) 
    4083 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4084 packages\chimerax\core\safesave.py", line 85, in __exit__ 
    4085 self._f.close() 
    4086 OSError: [Errno 28] No space left on device 
    4087  
    4088 Error processing trigger "command started": 
    4089 OSError: [Errno 28] No space left on device 
    4090  
    4091 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4092 packages\chimerax\core\safesave.py", line 85, in __exit__ 
    4093 self._f.close() 
    4094  
    4095 See log for complete Python traceback. 
    4096  
    4097 
    4098 > close session
    4099 
    4100 Traceback (most recent call last): 
    4101 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4102 packages\chimerax\core\history.py", line 109, in save 
    4103 json.dump(obj, f, ensure_ascii=False) 
    4104 File "C:\Program Files\ChimeraX1.6.1\bin\lib\json\\__init__.py", line 180, in
    4105 dump 
    4106 fp.write(chunk) 
    4107 OSError: [Errno 28] No space left on device 
    4108  
    4109 During handling of the above exception, another exception occurred: 
    4110  
    4111 OSError: [Errno 28] No space left on device 
    4112  
    4113 During handling of the above exception, another exception occurred: 
    4114  
    4115 Traceback (most recent call last): 
    4116 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4117 packages\chimerax\core\triggerset.py", line 138, in invoke 
    4118 return self._func(self._name, data) 
    4119 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4120 packages\chimerax\cmd_line\tool.py", line 351, in _command_started_cb 
    4121 self.history_dialog.add(self._just_typed_command or cmd_text, 
    4122 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4123 packages\chimerax\cmd_line\tool.py", line 456, in add 
    4124 self._history.enqueue((item, typed)) 
    4125 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4126 packages\chimerax\core\history.py", line 171, in enqueue 
    4127 self.save() 
    4128 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4129 packages\chimerax\core\history.py", line 201, in save 
    4130 self._history.save(self._queue) 
    4131 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4132 packages\chimerax\core\history.py", line 109, in save 
    4133 json.dump(obj, f, ensure_ascii=False) 
    4134 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4135 packages\chimerax\core\safesave.py", line 85, in __exit__ 
    4136 self._f.close() 
    4137 OSError: [Errno 28] No space left on device 
    4138  
    4139 Error processing trigger "command started": 
    4140 OSError: [Errno 28] No space left on device 
    4141  
    4142 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4143 packages\chimerax\core\safesave.py", line 85, in __exit__ 
    4144 self._f.close() 
    4145  
    4146 See log for complete Python traceback. 
    4147  
    4148 
    4149 > open C:/Users/lilyh/Downloads/Class3D_Job215/run_it025_class004.mrc
    4150 
    4151 Opened run_it025_class004.mrc as #1, grid size 256,256,256, pixel 1.09, shown
    4152 at level 0.00158, step 1, values float32 
    4153 
    4154 > open C:/Users/lilyh/Downloads/Class3D_Job215/run_it025_class003.mrc
    4155 
    4156 Opened run_it025_class003.mrc as #2, grid size 256,256,256, pixel 1.09, shown
    4157 at level 0.00159, step 1, values float32 
    4158 
    4159 > open C:/Users/lilyh/Downloads/Class3D_Job215/run_it025_class002.mrc
    4160 
    4161 Opened run_it025_class002.mrc as #3, grid size 256,256,256, pixel 1.09, shown
    4162 at level 0.0016, step 1, values float32 
    4163 
    4164 > open C:/Users/lilyh/Downloads/Class3D_Job215/run_it025_class001.mrc
    4165 
    4166 Opened run_it025_class001.mrc as #4, grid size 256,256,256, pixel 1.09, shown
    4167 at level 0.00158, step 1, values float32 
    4168 
    4169 > volume level 0.003
    4170 
    4171 > tile
    4172 
    4173 4 models tiled 
    4174 
    4175 > volume level 0.004
    4176 
    4177 > volume #1 level 0.004881
    4178 
    4179 > volume level 0.003
    4180 
    4181 > ~tile
    4182 
    4183 Traceback (most recent call last): 
    4184 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4185 packages\chimerax\core\history.py", line 109, in save 
    4186 json.dump(obj, f, ensure_ascii=False) 
    4187 File "C:\Program Files\ChimeraX1.6.1\bin\lib\json\\__init__.py", line 180, in
    4188 dump 
    4189 fp.write(chunk) 
    4190 OSError: [Errno 28] No space left on device 
    4191  
    4192 During handling of the above exception, another exception occurred: 
    4193  
    4194 OSError: [Errno 28] No space left on device 
    4195  
    4196 During handling of the above exception, another exception occurred: 
    4197  
    4198 Traceback (most recent call last): 
    4199 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4200 packages\chimerax\core\triggerset.py", line 138, in invoke 
    4201 return self._func(self._name, data) 
    4202 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4203 packages\chimerax\cmd_line\tool.py", line 351, in _command_started_cb 
    4204 self.history_dialog.add(self._just_typed_command or cmd_text, 
    4205 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4206 packages\chimerax\cmd_line\tool.py", line 456, in add 
    4207 self._history.enqueue((item, typed)) 
    4208 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4209 packages\chimerax\core\history.py", line 171, in enqueue 
    4210 self.save() 
    4211 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4212 packages\chimerax\core\history.py", line 201, in save 
    4213 self._history.save(self._queue) 
    4214 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4215 packages\chimerax\core\history.py", line 109, in save 
    4216 json.dump(obj, f, ensure_ascii=False) 
    4217 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4218 packages\chimerax\core\safesave.py", line 85, in __exit__ 
    4219 self._f.close() 
    4220 OSError: [Errno 28] No space left on device 
    4221  
    4222 Error processing trigger "command started": 
    4223 OSError: [Errno 28] No space left on device 
    4224  
    4225 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4226 packages\chimerax\core\safesave.py", line 85, in __exit__ 
    4227 self._f.close() 
    4228  
    4229 See log for complete Python traceback. 
    4230  
    4231 
    4232 > hide #!2 models
    4233 
    4234 Traceback (most recent call last): 
    4235 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4236 packages\chimerax\core\history.py", line 109, in save 
    4237 json.dump(obj, f, ensure_ascii=False) 
    4238 File "C:\Program Files\ChimeraX1.6.1\bin\lib\json\\__init__.py", line 180, in
    4239 dump 
    4240 fp.write(chunk) 
    4241 OSError: [Errno 28] No space left on device 
    4242  
    4243 During handling of the above exception, another exception occurred: 
    4244  
    4245 OSError: [Errno 28] No space left on device 
    4246  
    4247 During handling of the above exception, another exception occurred: 
    4248  
    4249 Traceback (most recent call last): 
    4250 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4251 packages\chimerax\core\triggerset.py", line 138, in invoke 
    4252 return self._func(self._name, data) 
    4253 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4254 packages\chimerax\cmd_line\tool.py", line 351, in _command_started_cb 
    4255 self.history_dialog.add(self._just_typed_command or cmd_text, 
    4256 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4257 packages\chimerax\cmd_line\tool.py", line 456, in add 
    4258 self._history.enqueue((item, typed)) 
    4259 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4260 packages\chimerax\core\history.py", line 171, in enqueue 
    4261 self.save() 
    4262 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4263 packages\chimerax\core\history.py", line 201, in save 
    4264 self._history.save(self._queue) 
    4265 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4266 packages\chimerax\core\history.py", line 109, in save 
    4267 json.dump(obj, f, ensure_ascii=False) 
    4268 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4269 packages\chimerax\core\safesave.py", line 85, in __exit__ 
    4270 self._f.close() 
    4271 OSError: [Errno 28] No space left on device 
    4272  
    4273 Error processing trigger "command started": 
    4274 OSError: [Errno 28] No space left on device 
    4275  
    4276 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4277 packages\chimerax\core\safesave.py", line 85, in __exit__ 
    4278 self._f.close() 
    4279  
    4280 See log for complete Python traceback. 
    4281  
    4282 
    4283 > show #!2 models
    4284 
    4285 Traceback (most recent call last): 
    4286 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4287 packages\chimerax\core\history.py", line 109, in save 
    4288 json.dump(obj, f, ensure_ascii=False) 
    4289 File "C:\Program Files\ChimeraX1.6.1\bin\lib\json\\__init__.py", line 180, in
    4290 dump 
    4291 fp.write(chunk) 
    4292 OSError: [Errno 28] No space left on device 
    4293  
    4294 During handling of the above exception, another exception occurred: 
    4295  
    4296 OSError: [Errno 28] No space left on device 
    4297  
    4298 During handling of the above exception, another exception occurred: 
    4299  
    4300 Traceback (most recent call last): 
    4301 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4302 packages\chimerax\core\triggerset.py", line 138, in invoke 
    4303 return self._func(self._name, data) 
    4304 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4305 packages\chimerax\cmd_line\tool.py", line 351, in _command_started_cb 
    4306 self.history_dialog.add(self._just_typed_command or cmd_text, 
    4307 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4308 packages\chimerax\cmd_line\tool.py", line 456, in add 
    4309 self._history.enqueue((item, typed)) 
    4310 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4311 packages\chimerax\core\history.py", line 171, in enqueue 
    4312 self.save() 
    4313 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4314 packages\chimerax\core\history.py", line 201, in save 
    4315 self._history.save(self._queue) 
    4316 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4317 packages\chimerax\core\history.py", line 109, in save 
    4318 json.dump(obj, f, ensure_ascii=False) 
    4319 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4320 packages\chimerax\core\safesave.py", line 85, in __exit__ 
    4321 self._f.close() 
    4322 OSError: [Errno 28] No space left on device 
    4323  
    4324 Error processing trigger "command started": 
    4325 OSError: [Errno 28] No space left on device 
    4326  
    4327 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4328 packages\chimerax\core\safesave.py", line 85, in __exit__ 
    4329 self._f.close() 
    4330  
    4331 See log for complete Python traceback. 
    4332  
    4333 
    4334 > close session
    4335 
    4336 Traceback (most recent call last): 
    4337 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4338 packages\chimerax\core\history.py", line 109, in save 
    4339 json.dump(obj, f, ensure_ascii=False) 
    4340 File "C:\Program Files\ChimeraX1.6.1\bin\lib\json\\__init__.py", line 180, in
    4341 dump 
    4342 fp.write(chunk) 
    4343 OSError: [Errno 28] No space left on device 
    4344  
    4345 During handling of the above exception, another exception occurred: 
    4346  
    4347 OSError: [Errno 28] No space left on device 
    4348  
    4349 During handling of the above exception, another exception occurred: 
    4350  
    4351 Traceback (most recent call last): 
    4352 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4353 packages\chimerax\core\triggerset.py", line 138, in invoke 
    4354 return self._func(self._name, data) 
    4355 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4356 packages\chimerax\cmd_line\tool.py", line 351, in _command_started_cb 
    4357 self.history_dialog.add(self._just_typed_command or cmd_text, 
    4358 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4359 packages\chimerax\cmd_line\tool.py", line 456, in add 
    4360 self._history.enqueue((item, typed)) 
    4361 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4362 packages\chimerax\core\history.py", line 171, in enqueue 
    4363 self.save() 
    4364 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4365 packages\chimerax\core\history.py", line 201, in save 
    4366 self._history.save(self._queue) 
    4367 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4368 packages\chimerax\core\history.py", line 109, in save 
    4369 json.dump(obj, f, ensure_ascii=False) 
    4370 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4371 packages\chimerax\core\safesave.py", line 85, in __exit__ 
    4372 self._f.close() 
    4373 OSError: [Errno 28] No space left on device 
    4374  
    4375 Error processing trigger "command started": 
    4376 OSError: [Errno 28] No space left on device 
    4377  
    4378 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4379 packages\chimerax\core\safesave.py", line 85, in __exit__ 
    4380 self._f.close() 
    4381  
    4382 See log for complete Python traceback. 
    4383  
    4384 
    4385 > open C:/Users/lilyh/Downloads/Class3D_Job204/run_it025_class003.mrc
    4386 
    4387 Traceback (most recent call last): 
    4388 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4389 packages\chimerax\core\history.py", line 109, in save 
    4390 json.dump(obj, f, ensure_ascii=False) 
    4391 File "C:\Program Files\ChimeraX1.6.1\bin\lib\json\\__init__.py", line 180, in
    4392 dump 
    4393 fp.write(chunk) 
    4394 OSError: [Errno 28] No space left on device 
    4395  
    4396 During handling of the above exception, another exception occurred: 
    4397  
    4398 OSError: [Errno 28] No space left on device 
    4399  
    4400 During handling of the above exception, another exception occurred: 
    4401  
    4402 Traceback (most recent call last): 
    4403 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4404 packages\chimerax\core\triggerset.py", line 138, in invoke 
    4405 return self._func(self._name, data) 
    4406 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4407 packages\chimerax\cmd_line\tool.py", line 351, in _command_started_cb 
    4408 self.history_dialog.add(self._just_typed_command or cmd_text, 
    4409 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4410 packages\chimerax\cmd_line\tool.py", line 456, in add 
    4411 self._history.enqueue((item, typed)) 
    4412 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4413 packages\chimerax\core\history.py", line 171, in enqueue 
    4414 self.save() 
    4415 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4416 packages\chimerax\core\history.py", line 201, in save 
    4417 self._history.save(self._queue) 
    4418 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4419 packages\chimerax\core\history.py", line 109, in save 
    4420 json.dump(obj, f, ensure_ascii=False) 
    4421 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4422 packages\chimerax\core\safesave.py", line 85, in __exit__ 
    4423 self._f.close() 
    4424 OSError: [Errno 28] No space left on device 
    4425  
    4426 Error processing trigger "command started": 
    4427 OSError: [Errno 28] No space left on device 
    4428  
    4429 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4430 packages\chimerax\core\safesave.py", line 85, in __exit__ 
    4431 self._f.close() 
    4432  
    4433 See log for complete Python traceback. 
    4434  
    4435 Opened run_it025_class003.mrc as #1, grid size 256,256,256, pixel 1.09, shown
    4436 at level 0.00128, step 1, values float32 
    4437 
    4438 > volume #1 level 0.003667
    4439 
    4440 Traceback (most recent call last): 
    4441 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4442 packages\chimerax\core\history.py", line 109, in save 
    4443 json.dump(obj, f, ensure_ascii=False) 
    4444 File "C:\Program Files\ChimeraX1.6.1\bin\lib\json\\__init__.py", line 180, in
    4445 dump 
    4446 fp.write(chunk) 
    4447 OSError: [Errno 28] No space left on device 
    4448  
    4449 During handling of the above exception, another exception occurred: 
    4450  
    4451 OSError: [Errno 28] No space left on device 
    4452  
    4453 During handling of the above exception, another exception occurred: 
    4454  
    4455 Traceback (most recent call last): 
    4456 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4457 packages\chimerax\core\triggerset.py", line 138, in invoke 
    4458 return self._func(self._name, data) 
    4459 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4460 packages\chimerax\cmd_line\tool.py", line 351, in _command_started_cb 
    4461 self.history_dialog.add(self._just_typed_command or cmd_text, 
    4462 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4463 packages\chimerax\cmd_line\tool.py", line 456, in add 
    4464 self._history.enqueue((item, typed)) 
    4465 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4466 packages\chimerax\core\history.py", line 171, in enqueue 
    4467 self.save() 
    4468 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4469 packages\chimerax\core\history.py", line 201, in save 
    4470 self._history.save(self._queue) 
    4471 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4472 packages\chimerax\core\history.py", line 109, in save 
    4473 json.dump(obj, f, ensure_ascii=False) 
    4474 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4475 packages\chimerax\core\safesave.py", line 85, in __exit__ 
    4476 self._f.close() 
    4477 OSError: [Errno 28] No space left on device 
    4478  
    4479 Error processing trigger "command started": 
    4480 OSError: [Errno 28] No space left on device 
    4481  
    4482 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4483 packages\chimerax\core\safesave.py", line 85, in __exit__ 
    4484 self._f.close() 
    4485  
    4486 See log for complete Python traceback. 
    4487  
    4488 
    4489 > close session
    4490 
    4491 Traceback (most recent call last): 
    4492 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4493 packages\chimerax\core\history.py", line 109, in save 
    4494 json.dump(obj, f, ensure_ascii=False) 
    4495 File "C:\Program Files\ChimeraX1.6.1\bin\lib\json\\__init__.py", line 180, in
    4496 dump 
    4497 fp.write(chunk) 
    4498 OSError: [Errno 28] No space left on device 
    4499  
    4500 During handling of the above exception, another exception occurred: 
    4501  
    4502 OSError: [Errno 28] No space left on device 
    4503  
    4504 During handling of the above exception, another exception occurred: 
    4505  
    4506 Traceback (most recent call last): 
    4507 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4508 packages\chimerax\core\triggerset.py", line 138, in invoke 
    4509 return self._func(self._name, data) 
    4510 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4511 packages\chimerax\cmd_line\tool.py", line 351, in _command_started_cb 
    4512 self.history_dialog.add(self._just_typed_command or cmd_text, 
    4513 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4514 packages\chimerax\cmd_line\tool.py", line 456, in add 
    4515 self._history.enqueue((item, typed)) 
    4516 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4517 packages\chimerax\core\history.py", line 171, in enqueue 
    4518 self.save() 
    4519 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4520 packages\chimerax\core\history.py", line 201, in save 
    4521 self._history.save(self._queue) 
    4522 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4523 packages\chimerax\core\history.py", line 109, in save 
    4524 json.dump(obj, f, ensure_ascii=False) 
    4525 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4526 packages\chimerax\core\safesave.py", line 85, in __exit__ 
    4527 self._f.close() 
    4528 OSError: [Errno 28] No space left on device 
    4529  
    4530 Error processing trigger "command started": 
    4531 OSError: [Errno 28] No space left on device 
    4532  
    4533 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4534 packages\chimerax\core\safesave.py", line 85, in __exit__ 
    4535 self._f.close() 
    4536  
    4537 See log for complete Python traceback. 
    4538  
    4539 
    4540 > open C:/Users/lilyh/Downloads/Class3D_Job214/run_it025_class001.mrc
    4541 
    4542 Traceback (most recent call last): 
    4543 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4544 packages\chimerax\core\history.py", line 109, in save 
    4545 json.dump(obj, f, ensure_ascii=False) 
    4546 File "C:\Program Files\ChimeraX1.6.1\bin\lib\json\\__init__.py", line 180, in
    4547 dump 
    4548 fp.write(chunk) 
    4549 OSError: [Errno 28] No space left on device 
    4550  
    4551 During handling of the above exception, another exception occurred: 
    4552  
    4553 OSError: [Errno 28] No space left on device 
    4554  
    4555 During handling of the above exception, another exception occurred: 
    4556  
    4557 Traceback (most recent call last): 
    4558 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4559 packages\chimerax\core\triggerset.py", line 138, in invoke 
    4560 return self._func(self._name, data) 
    4561 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4562 packages\chimerax\cmd_line\tool.py", line 351, in _command_started_cb 
    4563 self.history_dialog.add(self._just_typed_command or cmd_text, 
    4564 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4565 packages\chimerax\cmd_line\tool.py", line 456, in add 
    4566 self._history.enqueue((item, typed)) 
    4567 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4568 packages\chimerax\core\history.py", line 171, in enqueue 
    4569 self.save() 
    4570 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4571 packages\chimerax\core\history.py", line 201, in save 
    4572 self._history.save(self._queue) 
    4573 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4574 packages\chimerax\core\history.py", line 109, in save 
    4575 json.dump(obj, f, ensure_ascii=False) 
    4576 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4577 packages\chimerax\core\safesave.py", line 85, in __exit__ 
    4578 self._f.close() 
    4579 OSError: [Errno 28] No space left on device 
    4580  
    4581 Error processing trigger "command started": 
    4582 OSError: [Errno 28] No space left on device 
    4583  
    4584 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4585 packages\chimerax\core\safesave.py", line 85, in __exit__ 
    4586 self._f.close() 
    4587  
    4588 See log for complete Python traceback. 
    4589  
    4590 File size 42254336 too small for grid size (256,256,256) 
    4591 
    4592 > open C:/Users/lilyh/Downloads/Class3D_Job214/run_it025_class001.mrc
    4593 
    4594 Traceback (most recent call last): 
    4595 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4596 packages\chimerax\core\history.py", line 109, in save 
    4597 json.dump(obj, f, ensure_ascii=False) 
    4598 File "C:\Program Files\ChimeraX1.6.1\bin\lib\json\\__init__.py", line 180, in
    4599 dump 
    4600 fp.write(chunk) 
    4601 OSError: [Errno 28] No space left on device 
    4602  
    4603 During handling of the above exception, another exception occurred: 
    4604  
    4605 OSError: [Errno 28] No space left on device 
    4606  
    4607 During handling of the above exception, another exception occurred: 
    4608  
    4609 Traceback (most recent call last): 
    4610 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4611 packages\chimerax\core\triggerset.py", line 138, in invoke 
    4612 return self._func(self._name, data) 
    4613 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4614 packages\chimerax\cmd_line\tool.py", line 351, in _command_started_cb 
    4615 self.history_dialog.add(self._just_typed_command or cmd_text, 
    4616 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4617 packages\chimerax\cmd_line\tool.py", line 456, in add 
    4618 self._history.enqueue((item, typed)) 
    4619 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4620 packages\chimerax\core\history.py", line 171, in enqueue 
    4621 self.save() 
    4622 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4623 packages\chimerax\core\history.py", line 201, in save 
    4624 self._history.save(self._queue) 
    4625 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4626 packages\chimerax\core\history.py", line 109, in save 
    4627 json.dump(obj, f, ensure_ascii=False) 
    4628 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4629 packages\chimerax\core\safesave.py", line 85, in __exit__ 
    4630 self._f.close() 
    4631 OSError: [Errno 28] No space left on device 
    4632  
    4633 Error processing trigger "command started": 
    4634 OSError: [Errno 28] No space left on device 
    4635  
    4636 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4637 packages\chimerax\core\safesave.py", line 85, in __exit__ 
    4638 self._f.close() 
    4639  
    4640 See log for complete Python traceback. 
    4641  
    4642 File size 42254336 too small for grid size (256,256,256) 
    4643 
    4644 > open "C:\Users\lilyh\Downloads\cryodrgn training test
    4645 > J65\test_kmeans20\vol_001.mrc" format mrc
    4646 
    4647 Traceback (most recent call last): 
    4648 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4649 packages\chimerax\core\history.py", line 109, in save 
    4650 json.dump(obj, f, ensure_ascii=False) 
    4651 File "C:\Program Files\ChimeraX1.6.1\bin\lib\json\\__init__.py", line 180, in
    4652 dump 
    4653 fp.write(chunk) 
    4654 OSError: [Errno 28] No space left on device 
    4655  
    4656 During handling of the above exception, another exception occurred: 
    4657  
    4658 OSError: [Errno 28] No space left on device 
    4659  
    4660 During handling of the above exception, another exception occurred: 
    4661  
    4662 Traceback (most recent call last): 
    4663 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4664 packages\chimerax\core\triggerset.py", line 138, in invoke 
    4665 return self._func(self._name, data) 
    4666 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4667 packages\chimerax\cmd_line\tool.py", line 351, in _command_started_cb 
    4668 self.history_dialog.add(self._just_typed_command or cmd_text, 
    4669 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4670 packages\chimerax\cmd_line\tool.py", line 456, in add 
    4671 self._history.enqueue((item, typed)) 
    4672 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4673 packages\chimerax\core\history.py", line 171, in enqueue 
    4674 self.save() 
    4675 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4676 packages\chimerax\core\history.py", line 201, in save 
    4677 self._history.save(self._queue) 
    4678 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4679 packages\chimerax\core\history.py", line 109, in save 
    4680 json.dump(obj, f, ensure_ascii=False) 
    4681 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4682 packages\chimerax\core\safesave.py", line 85, in __exit__ 
    4683 self._f.close() 
    4684 OSError: [Errno 28] No space left on device 
    4685  
    4686 Error processing trigger "command started": 
    4687 OSError: [Errno 28] No space left on device 
    4688  
    4689 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4690 packages\chimerax\core\safesave.py", line 85, in __exit__ 
    4691 self._f.close() 
    4692  
    4693 See log for complete Python traceback. 
    4694  
    4695 Opened vol_001.mrc as #1, grid size 128,128,128, pixel 1.09, shown at level
    4696 0.011, step 1, values float32 
    4697 
    4698 > volume #1 level 0.05401
    4699 
    4700 Traceback (most recent call last): 
    4701 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4702 packages\chimerax\core\history.py", line 109, in save 
    4703 json.dump(obj, f, ensure_ascii=False) 
    4704 File "C:\Program Files\ChimeraX1.6.1\bin\lib\json\\__init__.py", line 180, in
    4705 dump 
    4706 fp.write(chunk) 
    4707 OSError: [Errno 28] No space left on device 
    4708  
    4709 During handling of the above exception, another exception occurred: 
    4710  
    4711 OSError: [Errno 28] No space left on device 
    4712  
    4713 During handling of the above exception, another exception occurred: 
    4714  
    4715 Traceback (most recent call last): 
    4716 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4717 packages\chimerax\core\triggerset.py", line 138, in invoke 
    4718 return self._func(self._name, data) 
    4719 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4720 packages\chimerax\cmd_line\tool.py", line 351, in _command_started_cb 
    4721 self.history_dialog.add(self._just_typed_command or cmd_text, 
    4722 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4723 packages\chimerax\cmd_line\tool.py", line 456, in add 
    4724 self._history.enqueue((item, typed)) 
    4725 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4726 packages\chimerax\core\history.py", line 171, in enqueue 
    4727 self.save() 
    4728 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4729 packages\chimerax\core\history.py", line 201, in save 
    4730 self._history.save(self._queue) 
    4731 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4732 packages\chimerax\core\history.py", line 109, in save 
    4733 json.dump(obj, f, ensure_ascii=False) 
    4734 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4735 packages\chimerax\core\safesave.py", line 85, in __exit__ 
    4736 self._f.close() 
    4737 OSError: [Errno 28] No space left on device 
    4738  
    4739 Error processing trigger "command started": 
    4740 OSError: [Errno 28] No space left on device 
    4741  
    4742 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4743 packages\chimerax\core\safesave.py", line 85, in __exit__ 
    4744 self._f.close() 
    4745  
    4746 See log for complete Python traceback. 
    4747  
    4748 
    4749 > volume #1 level 0.05062
    4750 
    4751 Traceback (most recent call last): 
    4752 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4753 packages\chimerax\core\history.py", line 109, in save 
    4754 json.dump(obj, f, ensure_ascii=False) 
    4755 File "C:\Program Files\ChimeraX1.6.1\bin\lib\json\\__init__.py", line 180, in
    4756 dump 
    4757 fp.write(chunk) 
    4758 OSError: [Errno 28] No space left on device 
    4759  
    4760 During handling of the above exception, another exception occurred: 
    4761  
    4762 OSError: [Errno 28] No space left on device 
    4763  
    4764 During handling of the above exception, another exception occurred: 
    4765  
    4766 Traceback (most recent call last): 
    4767 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4768 packages\chimerax\core\triggerset.py", line 138, in invoke 
    4769 return self._func(self._name, data) 
    4770 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4771 packages\chimerax\cmd_line\tool.py", line 351, in _command_started_cb 
    4772 self.history_dialog.add(self._just_typed_command or cmd_text, 
    4773 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4774 packages\chimerax\cmd_line\tool.py", line 456, in add 
    4775 self._history.enqueue((item, typed)) 
    4776 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4777 packages\chimerax\core\history.py", line 171, in enqueue 
    4778 self.save() 
    4779 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4780 packages\chimerax\core\history.py", line 201, in save 
    4781 self._history.save(self._queue) 
    4782 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4783 packages\chimerax\core\history.py", line 109, in save 
    4784 json.dump(obj, f, ensure_ascii=False) 
    4785 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4786 packages\chimerax\core\safesave.py", line 85, in __exit__ 
    4787 self._f.close() 
    4788 OSError: [Errno 28] No space left on device 
    4789  
    4790 Error processing trigger "command started": 
    4791 OSError: [Errno 28] No space left on device 
    4792  
    4793 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4794 packages\chimerax\core\safesave.py", line 85, in __exit__ 
    4795 self._f.close() 
    4796  
    4797 See log for complete Python traceback. 
    4798  
    4799 
    4800 > close session
    4801 
    4802 Traceback (most recent call last): 
    4803 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4804 packages\chimerax\core\history.py", line 109, in save 
    4805 json.dump(obj, f, ensure_ascii=False) 
    4806 File "C:\Program Files\ChimeraX1.6.1\bin\lib\json\\__init__.py", line 180, in
    4807 dump 
    4808 fp.write(chunk) 
    4809 OSError: [Errno 28] No space left on device 
    4810  
    4811 During handling of the above exception, another exception occurred: 
    4812  
    4813 OSError: [Errno 28] No space left on device 
    4814  
    4815 During handling of the above exception, another exception occurred: 
    4816  
    4817 Traceback (most recent call last): 
    4818 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4819 packages\chimerax\core\triggerset.py", line 138, in invoke 
    4820 return self._func(self._name, data) 
    4821 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4822 packages\chimerax\cmd_line\tool.py", line 351, in _command_started_cb 
    4823 self.history_dialog.add(self._just_typed_command or cmd_text, 
    4824 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4825 packages\chimerax\cmd_line\tool.py", line 456, in add 
    4826 self._history.enqueue((item, typed)) 
    4827 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4828 packages\chimerax\core\history.py", line 171, in enqueue 
    4829 self.save() 
    4830 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4831 packages\chimerax\core\history.py", line 201, in save 
    4832 self._history.save(self._queue) 
    4833 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4834 packages\chimerax\core\history.py", line 109, in save 
    4835 json.dump(obj, f, ensure_ascii=False) 
    4836 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4837 packages\chimerax\core\safesave.py", line 85, in __exit__ 
    4838 self._f.close() 
    4839 OSError: [Errno 28] No space left on device 
    4840  
    4841 Error processing trigger "command started": 
    4842 OSError: [Errno 28] No space left on device 
    4843  
    4844 File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
    4845 packages\chimerax\core\safesave.py", line 85, in __exit__ 
    4846 self._f.close() 
    4847  
    4848 See log for complete Python traceback. 
    4849  
    4850 
    4851 > open C:/Users/lilyh/Downloads/Refine3D_Job216/run_class001.mrc
    4852 
    4853 Opened run_class001.mrc as #1, grid size 256,256,256, pixel 1.09, shown at
    4854 level 0.00114, step 1, values float32 
    4855 
    4856 > volume #1 level 0.002668
    4857 
    4858 > volume #1 level 0.00279
    4859 
    4860 [Repeated 1 time(s)]
    4861 
    4862 > volume #1 level 0.002887
    4863 
    4864 > volume #1 level 0.004101
    4865 
    4866 > volume #1 level 0.002862
    4867 
    4868 > close session
    4869 
    4870 > open C:/Users/lilyh/Downloads/Class3D_Job215/run_it025_class003.mrc
    4871 
    4872 Opened run_it025_class003.mrc as #1, grid size 256,256,256, pixel 1.09, shown
    4873 at level 0.00159, step 1, values float32 
    4874 
    4875 > open C:/Users/lilyh/Downloads/Class3D_Job215/run_it025_class002.mrc
    4876 
    4877 Opened run_it025_class002.mrc as #2, grid size 256,256,256, pixel 1.09, shown
    4878 at level 0.0016, step 1, values float32 
    4879 
    4880 > open C:/Users/lilyh/Downloads/Class3D_Job215/run_it025_class001.mrc
    4881 
    4882 Opened run_it025_class001.mrc as #3, grid size 256,256,256, pixel 1.09, shown
    4883 at level 0.00158, step 1, values float32 
    4884 
    4885 > open C:/Users/lilyh/Downloads/Class3D_Job215/run_it025_class004.mrc
    4886 
    4887 Opened run_it025_class004.mrc as #4, grid size 256,256,256, pixel 1.09, shown
    4888 at level 0.00158, step 1, values float32 
    4889 
    4890 > tile
    4891 
    4892 4 models tiled 
    4893 
    4894 > volume level 0.34
    4895 
    4896 > volume level 0.035
    4897 
    4898 > volume level
    4899 
    4900 Missing "level" keyword's argument 
    4901 
    4902 > volume #1 level 0.0058
    4903 
    4904 > volume level 0.005
    4905 
    4906 > volume #3 level 0.00611
    4907 
    4908 > close session
    4909 
    4910 > open C:/Users/lilyh/Downloads/Class3D_Job204/run_it025_class003.mrc
    4911 
    4912 Opened run_it025_class003.mrc as #1, grid size 256,256,256, pixel 1.09, shown
    4913 at level 0.00128, step 1, values float32 
    4914 
    4915 > open C:/Users/lilyh/Downloads/Class3D_Job204/run_it025_class002.mrc
    4916 
    4917 Opened run_it025_class002.mrc as #2, grid size 256,256,256, pixel 1.09, shown
    4918 at level 0.000939, step 1, values float32 
    4919 
    4920 > open C:/Users/lilyh/Downloads/Class3D_Job204/run_it025_class001.mrc
    4921 
    4922 Opened run_it025_class001.mrc as #3, grid size 256,256,256, pixel 1.09, shown
    4923 at level 0.000951, step 1, values float32 
    4924 
    4925 > open C:/Users/lilyh/Downloads/Class3D_Job204/run_it025_class004.mrc
    4926 
    4927 Opened run_it025_class004.mrc as #4, grid size 256,256,256, pixel 1.09, shown
    4928 at level 0.00102, step 1, values float32 
    4929 
    4930 > volume level 0.005
    4931 
    4932 > tile
    4933 
    4934 4 models tiled 
    4935 
    4936 > close session
    4937 
    4938 > open C:/Users/lilyh/Downloads/Class3D_Job203/run_it025_class004.mrc
    4939 
    4940 Opened run_it025_class004.mrc as #1, grid size 256,256,256, pixel 1.09, shown
    4941 at level 0.00105, step 1, values float32 
    4942 
    4943 > open C:/Users/lilyh/Downloads/Class3D_Job203/run_it025_class003.mrc
    4944 
    4945 Opened run_it025_class003.mrc as #2, grid size 256,256,256, pixel 1.09, shown
    4946 at level 0.00126, step 1, values float32 
    4947 
    4948 > open C:/Users/lilyh/Downloads/Class3D_Job203/run_it025_class002.mrc
    4949 
    4950 Opened run_it025_class002.mrc as #3, grid size 256,256,256, pixel 1.09, shown
    4951 at level 0.00117, step 1, values float32 
    4952 
    4953 > open C:/Users/lilyh/Downloads/Class3D_Job203/run_it025_class001.mrc
    4954 
    4955 Opened run_it025_class001.mrc as #4, grid size 256,256,256, pixel 1.09, shown
    4956 at level 0.000995, step 1, values float32 
    4957 
    4958 > open C:/Users/lilyh/Downloads/Class3D_Job203/run_it025_class005.mrc
    4959 
    4960 Opened run_it025_class005.mrc as #5, grid size 256,256,256, pixel 1.09, shown
    4961 at level 0.000954, step 1, values float32 
    4962 
    4963 > tile
    4964 
    4965 5 models tiled 
    4966 
    4967 > volume level 0.005
    4968 
    4969 > volume level 0.003
    4970 
    4971 > hide #!3 models
    4972 
    4973 > show #!3 models
    4974 
    4975 > close session
    4976 
    4977 > open C:/Users/lilyh/Downloads/Class3D_job201/run_it025_class006.mrc
    4978 
    4979 Opened run_it025_class006.mrc as #1, grid size 256,256,256, pixel 1.09, shown
    4980 at level 0.00103, step 1, values float32 
    4981 
    4982 > open C:/Users/lilyh/Downloads/Class3D_job201/run_it025_class005.mrc
    4983 
    4984 Opened run_it025_class005.mrc as #2, grid size 256,256,256, pixel 1.09, shown
    4985 at level 0.00106, step 1, values float32 
    4986 
    4987 > open C:/Users/lilyh/Downloads/Class3D_job201/run_it025_class004.mrc
    4988 
    4989 Opened run_it025_class004.mrc as #3, grid size 256,256,256, pixel 1.09, shown
    4990 at level 0.00094, step 1, values float32 
    4991 
    4992 > open C:/Users/lilyh/Downloads/Class3D_job201/run_it025_class003.mrc
    4993 
    4994 Opened run_it025_class003.mrc as #4, grid size 256,256,256, pixel 1.09, shown
    4995 at level 0.00107, step 1, values float32 
    4996 
    4997 > open C:/Users/lilyh/Downloads/Class3D_job201/run_it025_class002.mrc
    4998 
    4999 Opened run_it025_class002.mrc as #5, grid size 256,256,256, pixel 1.09, shown
    5000 at level 0.00137, step 1, values float32 
    5001 
    5002 > open C:/Users/lilyh/Downloads/Class3D_job201/run_it025_class001.mrc
    5003 
    5004 Opened run_it025_class001.mrc as #6, grid size 256,256,256, pixel 1.09, shown
    5005 at level 0.00129, step 1, values float32 
    5006 
    5007 > volume level 0.003
    5008 
    5009 > tile
    5010 
    5011 6 models tiled 
    5012 
    5013 > close session
    5014 
    5015 > open C:/Users/lilyh/Downloads/Class3D_job201/run_it025_class006.mrc
    5016 
    5017 Opened run_it025_class006.mrc as #1, grid size 256,256,256, pixel 1.09, shown
    5018 at level 0.00103, step 1, values float32 
    5019 
    5020 > open C:/Users/lilyh/Downloads/Class3D_job201/run_it025_class005.mrc
    5021 
    5022 Opened run_it025_class005.mrc as #2, grid size 256,256,256, pixel 1.09, shown
    5023 at level 0.00106, step 1, values float32 
    5024 
    5025 > open C:/Users/lilyh/Downloads/Class3D_job201/run_it025_class004.mrc
    5026 
    5027 Opened run_it025_class004.mrc as #3, grid size 256,256,256, pixel 1.09, shown
    5028 at level 0.00094, step 1, values float32 
    5029 
    5030 > open C:/Users/lilyh/Downloads/Class3D_job201/run_it025_class003.mrc
    5031 
    5032 Opened run_it025_class003.mrc as #4, grid size 256,256,256, pixel 1.09, shown
    5033 at level 0.00107, step 1, values float32 
    5034 
    5035 > open C:/Users/lilyh/Downloads/Class3D_job201/run_it025_class002.mrc
    5036 
    5037 Opened run_it025_class002.mrc as #5, grid size 256,256,256, pixel 1.09, shown
    5038 at level 0.00137, step 1, values float32 
    5039 
    5040 > open C:/Users/lilyh/Downloads/Class3D_job201/run_it025_class001.mrc
    5041 
    5042 Opened run_it025_class001.mrc as #6, grid size 256,256,256, pixel 1.09, shown
    5043 at level 0.00129, step 1, values float32 
    5044 
    5045 > tile
    5046 
    5047 6 models tiled 
    5048 
    5049 > volume level 0.004
    5050 
    5051 > volume level 0.003
    5052 
    5053 > hide #!6 models
    5054 
    5055 > show #!6 models
    5056 
    5057 > hide #!6 models
    5058 
    5059 > show #!6 models
    5060 
    5061 > close session
    5062 
    5063 > open C:/Users/lilyh/Downloads/Class3D_job201/run_it025_class006.mrc
    5064 
    5065 Opened run_it025_class006.mrc as #1, grid size 256,256,256, pixel 1.09, shown
    5066 at level 0.00103, step 1, values float32 
    5067 
    5068 > open C:/Users/lilyh/Downloads/Class3D_job201/run_it025_class005.mrc
    5069 
    5070 Opened run_it025_class005.mrc as #2, grid size 256,256,256, pixel 1.09, shown
    5071 at level 0.00106, step 1, values float32 
    5072 
    5073 > open C:/Users/lilyh/Downloads/Class3D_job201/run_it025_class004.mrc
    5074 
    5075 Opened run_it025_class004.mrc as #3, grid size 256,256,256, pixel 1.09, shown
    5076 at level 0.00094, step 1, values float32 
    5077 
    5078 > open C:/Users/lilyh/Downloads/Class3D_job201/run_it025_class003.mrc
    5079 
    5080 Opened run_it025_class003.mrc as #4, grid size 256,256,256, pixel 1.09, shown
    5081 at level 0.00107, step 1, values float32 
    5082 
    5083 > open C:/Users/lilyh/Downloads/Class3D_job201/run_it025_class002.mrc
    5084 
    5085 Opened run_it025_class002.mrc as #5, grid size 256,256,256, pixel 1.09, shown
    5086 at level 0.00137, step 1, values float32 
    5087 
    5088 > open C:/Users/lilyh/Downloads/Class3D_job201/run_it025_class001.mrc
    5089 
    5090 Opened run_it025_class001.mrc as #6, grid size 256,256,256, pixel 1.09, shown
    5091 at level 0.00129, step 1, values float32 
    5092 
    5093 > volume level 0.003
    5094 
    5095 > tile
    5096 
    5097 6 models tiled 
    5098 
    5099 > hide #!6 models
    5100 
    5101 > show #!6 models
    5102 
    5103 > hide #!6 models
    5104 
    5105 > show #!6 models
    5106 
    5107 > hide #!5 models
    5108 
    5109 > hide #!6 models
    5110 
    5111 > ~tile
    5112 
    5113 > close session
    5114 
    5115 > open C:/Users/lilyh/Downloads/Class3D_Job203/run_it025_class005.mrc
    5116 
    5117 Opened run_it025_class005.mrc as #1, grid size 256,256,256, pixel 1.09, shown
    5118 at level 0.000954, step 1, values float32 
    5119 
    5120 > open C:/Users/lilyh/Downloads/Class3D_Job203/run_it025_class004.mrc
    5121 
    5122 Opened run_it025_class004.mrc as #2, grid size 256,256,256, pixel 1.09, shown
    5123 at level 0.00105, step 1, values float32 
    5124 
    5125 > open C:/Users/lilyh/Downloads/Class3D_Job203/run_it025_class003.mrc
    5126 
    5127 Opened run_it025_class003.mrc as #3, grid size 256,256,256, pixel 1.09, shown
    5128 at level 0.00126, step 1, values float32 
    5129 
    5130 > open C:/Users/lilyh/Downloads/Class3D_Job203/run_it025_class002.mrc
    5131 
    5132 Opened run_it025_class002.mrc as #4, grid size 256,256,256, pixel 1.09, shown
    5133 at level 0.00117, step 1, values float32 
    5134 
    5135 > open C:/Users/lilyh/Downloads/Class3D_Job203/run_it025_class001.mrc
    5136 
    5137 Opened run_it025_class001.mrc as #5, grid size 256,256,256, pixel 1.09, shown
    5138 at level 0.000995, step 1, values float32 
    5139 
    5140 > tile
    5141 
    5142 5 models tiled 
    5143 
    5144 > volume level 0.005
    5145 
    5146 Drag select of 1 run_it025_class005.mrc , 2 run_it025_class004.mrc , 3
    5147 run_it025_class003.mrc , 4 run_it025_class002.mrc , 5 run_it025_class001.mrc 
    5148 
    5149 > color #1.1#2.1#3.1#4.1#5.1 yellow
    5150 
    5151 > select clear
    5152 
    5153 > open C:/Users/lilyh/Downloads/Class3D_Job204/run_it025_class003.mrc
    5154 
    5155 Opened run_it025_class003.mrc as #6, grid size 256,256,256, pixel 1.09, shown
    5156 at level 0.00128, step 1, values float32 
    5157 
    5158 > open C:/Users/lilyh/Downloads/Class3D_Job204/run_it025_class002.mrc
    5159 
    5160 Opened run_it025_class002.mrc as #7, grid size 256,256,256, pixel 1.09, shown
    5161 at level 0.000939, step 1, values float32 
    5162 
    5163 > open C:/Users/lilyh/Downloads/Class3D_Job204/run_it025_class001.mrc
    5164 
    5165 Opened run_it025_class001.mrc as #8, grid size 256,256,256, pixel 1.09, shown
    5166 at level 0.000951, step 1, values float32 
    5167 
    5168 > open C:/Users/lilyh/Downloads/Class3D_Job204/run_it025_class004.mrc
    5169 
    5170 Opened run_it025_class004.mrc as #9, grid size 256,256,256, pixel 1.09, shown
    5171 at level 0.00102, step 1, values float32 
    5172 
    5173 > volume level 0.005
    5174 
    5175 > tile
    5176 
    5177 9 models tiled 
    5178 
    5179 > volume #1 level 0.008094
    5180 
    5181 > close session
    5182 
    5183 > open C:/Users/lilyh/Downloads/Class3D_Job204/run_it025_class001.mrc
    5184 
    5185 Opened run_it025_class001.mrc as #1, grid size 256,256,256, pixel 1.09, shown
    5186 at level 0.000951, step 1, values float32 
    5187 
    5188 > open C:/Users/lilyh/Downloads/Class3D_Job204/run_it025_class004.mrc
    5189 
    5190 Opened run_it025_class004.mrc as #2, grid size 256,256,256, pixel 1.09, shown
    5191 at level 0.00102, step 1, values float32 
    5192 
    5193 > open C:/Users/lilyh/Downloads/Class3D_Job204/run_it025_class003.mrc
    5194 
    5195 Opened run_it025_class003.mrc as #3, grid size 256,256,256, pixel 1.09, shown
    5196 at level 0.00128, step 1, values float32 
    5197 
    5198 > open C:/Users/lilyh/Downloads/Class3D_Job204/run_it025_class002.mrc
    5199 
    5200 Opened run_it025_class002.mrc as #4, grid size 256,256,256, pixel 1.09, shown
    5201 at level 0.000939, step 1, values float32 
    5202 
    5203 > color dark gray
    5204 
    5205 > open C:/Users/lilyh/Downloads/Class3D_Job203/run_it025_class005.mrc
    5206 
    5207 Opened run_it025_class005.mrc as #5, grid size 256,256,256, pixel 1.09, shown
    5208 at level 0.000954, step 1, values float32 
    5209 
    5210 > open C:/Users/lilyh/Downloads/Class3D_Job203/run_it025_class004.mrc
    5211 
    5212 Opened run_it025_class004.mrc as #6, grid size 256,256,256, pixel 1.09, shown
    5213 at level 0.00105, step 1, values float32 
    5214 
    5215 > open C:/Users/lilyh/Downloads/Class3D_Job203/run_it025_class003.mrc
    5216 
    5217 Opened run_it025_class003.mrc as #7, grid size 256,256,256, pixel 1.09, shown
    5218 at level 0.00126, step 1, values float32 
    5219 
    5220 > open C:/Users/lilyh/Downloads/Class3D_Job203/run_it025_class002.mrc
    5221 
    5222 Opened run_it025_class002.mrc as #8, grid size 256,256,256, pixel 1.09, shown
    5223 at level 0.00117, step 1, values float32 
    5224 
    5225 > open C:/Users/lilyh/Downloads/Class3D_Job203/run_it025_class001.mrc
    5226 
    5227 Opened run_it025_class001.mrc as #9, grid size 256,256,256, pixel 1.09, shown
    5228 at level 0.000995, step 1, values float32 
    5229 
    5230 > tile
    5231 
    5232 9 models tiled 
    5233 
    5234 > volume level 0.005
    5235 
    5236 > volume #1 level 0.003593
    5237 
    5238 > volume level 0.003
    5239 
    5240 > close session
    5241 
    5242 > open C:/Users/lilyh/Downloads/Class3D_Job215/run_it025_class003.mrc
    5243 
    5244 Opened run_it025_class003.mrc as #1, grid size 256,256,256, pixel 1.09, shown
    5245 at level 0.00159, step 1, values float32 
    5246 
    5247 > open C:/Users/lilyh/Downloads/Class3D_Job215/run_it025_class002.mrc
    5248 
    5249 Opened run_it025_class002.mrc as #2, grid size 256,256,256, pixel 1.09, shown
    5250 at level 0.0016, step 1, values float32 
    5251 
    5252 > open C:/Users/lilyh/Downloads/Class3D_Job215/run_it025_class001.mrc
    5253 
    5254 Opened run_it025_class001.mrc as #3, grid size 256,256,256, pixel 1.09, shown
    5255 at level 0.00158, step 1, values float32 
    5256 
    5257 > open C:/Users/lilyh/Downloads/Class3D_Job215/run_it025_class004.mrc
    5258 
    5259 Opened run_it025_class004.mrc as #4, grid size 256,256,256, pixel 1.09, shown
    5260 at level 0.00158, step 1, values float32 
    5261 
    5262 > volume level 0.003
    5263 
    5264 > tile
    5265 
    5266 4 models tiled 
    5267 
    5268 > ~tile
    5269 
    5270 > volume level 0.006
    5271 
    5272 > volume level 0.004
    5273 
    5274 > open C:/Users/lilyh/Downloads/Class3D_Job214/run_it025_class001.mrc
    5275 
    5276 File size 42254336 too small for grid size (256,256,256) 
    5277 
    5278 > open C:/Users/lilyh/Downloads/Class3D_Job214/run_it025_class002.mrc
    5279 
    5280 MRC file is truncated. Failed reading 1 values, type int32 
    5281 
    5282 > hide #!3 models
    5283 
    5284 > hide #!4 models
    5285 
    5286 > hide #!2 models
    5287 
    5288 > volume #1 level 0.007255
    5289 
    5290 > hide #!1 models
    5291 
    5292 > close session
    5293 
    5294 > open C:/Users/lilyh/Downloads/cryosparc_P122_J561_class_02_final_volume.mrc
    5295 
    5296 Opened cryosparc_P122_J561_class_02_final_volume.mrc as #1, grid size
    5297 128,128,128, pixel 2.17, shown at level 0.0361, step 1, values float32 
    5298 
    5299 > volume #1 level 0.2064
    5300 
    5301 > volume #1 level 0.1013
    5302 
    5303 > volume #1 level 0.3732
    5304 
    5305 > close #1
    5306 
    5307 > open
    5308 > C:/Users/lilyh/Downloads/cryosparc_P104_J3831_class_00_00064_volume_sharp.mrc
    5309 
    5310 Opened cryosparc_P104_J3831_class_00_00064_volume_sharp.mrc as #1, grid size
    5311 128,128,128, pixel 2.17, shown at level 0.069, step 1, values float32 
    5312 
    5313 > volume #1 level 0.3242
    5314 
    5315 > volume #1 level 0.5218
    5316 
    5317 > volume #1 level 0.2542
    5318 
    5319 > volume #1 level 0.1843
    5320 
    5321 > volume #1 level 0.2584
    5322 
    5323 > close session
    5324 
    5325 > open C:/Users/lilyh/Downloads/cryosparc_P104_J3840_class_00_00014_volume.mrc
    5326 
    5327 Opened cryosparc_P104_J3840_class_00_00014_volume.mrc as #1, grid size
    5328 100,100,100, pixel 2.78, shown at level 0.0938, step 1, values float32 
    5329 
    5330 > open C:/Users/lilyh/Downloads/cryosparc_P104_J3840_class_02_00014_volume.mrc
    5331 
    5332 Opened cryosparc_P104_J3840_class_02_00014_volume.mrc as #2, grid size
    5333 100,100,100, pixel 2.78, shown at level 0.0776, step 1, values float32 
    5334 
    5335 > volume level 0.3
    5336 
    5337 > volume level 0.01
    5338 
    5339 > volume level 0.2
    5340 
    5341 > select clear
    5342 
    5343 > hide #!2 models
    5344 
    5345 > volume #1 level 0.1793
    5346 
    5347 > show #!2 models
    5348 
    5349 > hide #!1 models
    5350 
    5351 > volume #2 level 0.1643
    5352 
    5353 > show #!1 models
    5354 
    5355 > open
    5356 > C:/Users/lilyh/Desktop/output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
    5357 
    5358 Chain information for
    5359 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
    5360 #3 
    5361 --- 
    5362 Chain | Description 
    5363 B | No description available 
    5364 C | No description available 
    5365  
    5366 
    5367 > open
    5368 > C:/Users/lilyh/Desktop/output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
    5369 
    5370 Chain information for
    5371 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
    5372 #4 
    5373 --- 
    5374 Chain | Description 
    5375 B | No description available 
    5376 C | No description available 
    5377  
    5378 Drag select of 664 residues 
    5379 
    5380 > ui mousemode right "translate selected models"
    5381 
    5382 [Repeated 1 time(s)]
    5383 
    5384 > view matrix models
    5385 > #3,1,0,0,-6.5711,0,1,0,148.71,0,0,1,146.56,#4,1,0,0,-6.5711,0,1,0,148.71,0,0,1,146.56
    5386 
    5387 > view matrix models
    5388 > #3,1,0,0,140.73,0,1,0,142.06,0,0,1,166.35,#4,1,0,0,140.73,0,1,0,142.06,0,0,1,166.35
    5389 
    5390 Drag select of 11 residues 
    5391 
    5392 > ui mousemode right "rotate selected models"
    5393 
    5394 > view matrix models
    5395 > #3,-0.57291,0.56028,-0.59821,131.63,-0.81897,-0.42042,0.39057,146.37,-0.03267,0.71368,0.69971,162.45
    5396 
    5397 > ui mousemode right "translate selected models"
    5398 
    5399 > view matrix models
    5400 > #3,-0.57291,0.56028,-0.59821,135.24,-0.81897,-0.42042,0.39057,134.9,-0.03267,0.71368,0.69971,142.91
    5401 
    5402 Drag select of 4 residues 
    5403 
    5404 > ui mousemode right "rotate selected models"
    5405 
    5406 > view matrix models
    5407 > #4,-0.84866,0.014175,-0.52876,151.09,0.50027,0.34616,-0.79366,137.46,0.17178,-0.93807,-0.30086,162.79
    5408 
    5409 > ui mousemode right "translate selected models"
    5410 
    5411 > view matrix models
    5412 > #4,-0.84866,0.014175,-0.52876,143.91,0.50027,0.34616,-0.79366,143.32,0.17178,-0.93807,-0.30086,140.56
    5413 
    5414 > fitmap #3 inMap #1
    5415 
    5416 Fit molecule
    5417 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
    5418 (#3) to map cryosparc_P104_J3840_class_00_00014_volume.mrc (#1) using 4737
    5419 atoms 
    5420 average map value = 0.2715, steps = 128 
    5421 shifted from previous position = 4.03 
    5422 rotated from previous position = 24.4 degrees 
    5423 atoms outside contour = 1635, contour level = 0.17928 
    5424  
    5425 Position of
    5426 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
    5427 (#3) relative to cryosparc_P104_J3840_class_00_00014_volume.mrc (#1)
    5428 coordinates: 
    5429 Matrix rotation and translation 
    5430 -0.80367765 0.20930131 -0.55704142 139.20195012 
    5431 -0.56151103 -0.57663386 0.59346331 137.70755920 
    5432 -0.19699630 0.78973812 0.58095276 140.63323724 
    5433 Axis 0.22480157 -0.41237440 -0.88284291 
    5434 Axis point 97.39666990 13.51352648 0.00000000 
    5435 Rotation angle (degrees) 154.11595677 
    5436 Shift along axis -149.65131159 
    5437  
    5438 
    5439 > fitmap #4 inMap #1
    5440 
    5441 Fit molecule
    5442 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
    5443 (#4) to map cryosparc_P104_J3840_class_00_00014_volume.mrc (#1) using 4737
    5444 atoms 
    5445 average map value = 0.2727, steps = 156 
    5446 shifted from previous position = 6.21 
    5447 rotated from previous position = 12.7 degrees 
    5448 atoms outside contour = 1648, contour level = 0.17928 
    5449  
    5450 Position of
    5451 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
    5452 (#4) relative to cryosparc_P104_J3840_class_00_00014_volume.mrc (#1)
    5453 coordinates: 
    5454 Matrix rotation and translation 
    5455 -0.72465165 0.11784257 -0.67896473 139.13357974 
    5456 0.67018689 0.34985529 -0.65456153 139.46728049 
    5457 0.16040419 -0.92936236 -0.33249977 140.25765476 
    5458 Axis -0.26380023 -0.80576799 0.53023333 
    5459 Axis point 15.37419665 -0.00000000 136.83963007 
    5460 Rotation angle (degrees) 148.61069825 
    5461 Shift along axis -74.71245831 
    5462  
    5463 
    5464 > select clear
    5465 
    5466 > select #4/C:1344
    5467 
    5468 8 atoms, 7 bonds, 1 residue, 1 model selected 
    5469 
    5470 > ui mousemode right "rotate selected models"
    5471 
    5472 > view matrix models
    5473 > #4,0.019792,0.61825,-0.78573,135.09,0.93872,0.259,0.22744,138.85,0.34412,-0.74208,-0.57524,139.06
    5474 
    5475 > fitmap #4 inMap #1
    5476 
    5477 Fit molecule
    5478 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
    5479 (#4) to map cryosparc_P104_J3840_class_00_00014_volume.mrc (#1) using 4737
    5480 atoms 
    5481 average map value = 0.274, steps = 364 
    5482 shifted from previous position = 5.89 
    5483 rotated from previous position = 22.2 degrees 
    5484 atoms outside contour = 1693, contour level = 0.17928 
    5485  
    5486 Position of
    5487 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
    5488 (#4) relative to cryosparc_P104_J3840_class_00_00014_volume.mrc (#1)
    5489 coordinates: 
    5490 Matrix rotation and translation 
    5491 -0.00403472 0.32547376 -0.94554246 139.28256451 
    5492 0.98794031 0.14765329 0.04660945 138.66762524 
    5493 0.15478261 -0.93395145 -0.32214439 141.81145818 
    5494 Axis -0.60682679 -0.68094366 0.40997193 
    5495 Axis point -63.57020772 0.00000000 137.27636390 
    5496 Rotation angle (degrees) 126.10471944 
    5497 Shift along axis -120.80651422 
    5498  
    5499 
    5500 > hide #!2 models
    5501 
    5502 > show #!2 models
    5503 
    5504 > hide #!1 models
    5505 
    5506 > show #!1 models
    5507 
    5508 > open C:/Users/lilyh/Downloads/cryosparc_P104_J3841_class_00_00015_volume.mrc
    5509 
    5510 Opened cryosparc_P104_J3841_class_00_00015_volume.mrc as #5, grid size
    5511 100,100,100, pixel 2.78, shown at level 0.0751, step 1, values float32 
    5512 
    5513 > open C:/Users/lilyh/Downloads/cryosparc_P104_J3841_class_02_00015_volume.mrc
    5514 
    5515 Opened cryosparc_P104_J3841_class_02_00015_volume.mrc as #6, grid size
    5516 100,100,100, pixel 2.78, shown at level 0.115, step 1, values float32 
    5517 
    5518 > open C:/Users/lilyh/Downloads/cryosparc_P104_J3841_class_01_00015_volume.mrc
    5519 
    5520 Opened cryosparc_P104_J3841_class_01_00015_volume.mrc as #7, grid size
    5521 100,100,100, pixel 2.78, shown at level 0.104, step 1, values float32 
    5522 
    5523 > volume level 0.1
    5524 
    5525 > volume level 0.15
    5526 
    5527 > hide #4 models
    5528 
    5529 > hide #3 models
    5530 
    5531 > hide #!2 models
    5532 
    5533 > hide #!1 models
    5534 
    5535 > hide #!7 models
    5536 
    5537 > hide #!6 models
    5538 
    5539 > volume #5 level 0.1727
    5540 
    5541 [Repeated 1 time(s)]
    5542 
    5543 > show #!2 models
    5544 
    5545 > hide #!2 models
    5546 
    5547 > show #!2 models
    5548 
    5549 > hide #!2 models
    5550 
    5551 > show #!2 models
    5552 
    5553 > hide #!2 models
    5554 
    5555 > show #3 models
    5556 
    5557 > show #4 models
    5558 
    5559 > hide #3 models
    5560 
    5561 > show #3 models
    5562 
    5563 > hide #4 models
    5564 
    5565 > hide #3 models
    5566 
    5567 > hide #!5 models
    5568 
    5569 > show #!7 models
    5570 
    5571 > show #!6 models
    5572 
    5573 > volume level 0.16
    5574 
    5575 > tile
    5576 
    5577 2 models tiled 
    5578 
    5579 > hide #!6 models
    5580 
    5581 > hide #!7 models
    5582 
    5583 > show #!5 models
    5584 
    5585 > show #4 models
    5586 
    5587 Drag select of 6 residues 
    5588 
    5589 > ui mousemode right "rotate selected models"
    5590 
    5591 > view matrix models
    5592 > #4,0.44181,0.28757,-0.84977,136.71,0.87872,-0.32953,0.34535,139.19,-0.18072,-0.89928,-0.39828,143.75
    5593 
    5594 > fitmap #4 inMap #5
    5595 
    5596 Fit molecule
    5597 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
    5598 (#4) to map cryosparc_P104_J3841_class_00_00015_volume.mrc (#5) using 4737
    5599 atoms 
    5600 average map value = 0.2677, steps = 108 
    5601 shifted from previous position = 4.19 
    5602 rotated from previous position = 29.2 degrees 
    5603 atoms outside contour = 1496, contour level = 0.16 
    5604  
    5605 Position of
    5606 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
    5607 (#4) relative to cryosparc_P104_J3841_class_00_00015_volume.mrc (#5)
    5608 coordinates: 
    5609 Matrix rotation and translation 
    5610 0.40458000 0.45199490 -0.79499420 137.51699231 
    5611 0.89851553 -0.03463048 0.43757376 139.00030117 
    5612 0.17025005 -0.89134812 -0.42013520 139.78403552 
    5613 Axis -0.78075886 -0.56709353 0.26233667 
    5614 Axis point 0.00000000 83.52968226 73.62359898 
    5615 Rotation angle (degrees) 121.67449137 
    5616 Shift along axis -149.52330366 
    5617  
    5618 
    5619 > show #3 models
    5620 
    5621 > fitmap #3 inMap #5
    5622 
    5623 Fit molecule
    5624 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
    5625 (#3) to map cryosparc_P104_J3841_class_00_00015_volume.mrc (#5) using 4737
    5626 atoms 
    5627 average map value = 0.2672, steps = 252 
    5628 shifted from previous position = 2.19 
    5629 rotated from previous position = 32.3 degrees 
    5630 atoms outside contour = 1568, contour level = 0.16 
    5631  
    5632 Position of
    5633 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
    5634 (#3) relative to cryosparc_P104_J3841_class_00_00015_volume.mrc (#5)
    5635 coordinates: 
    5636 Matrix rotation and translation 
    5637 -0.82334954 0.19085833 -0.53447977 139.38346698 
    5638 -0.53284129 -0.58418121 0.61221922 137.66377373 
    5639 -0.19538591 0.78886335 0.58268255 139.87094027 
    5640 Axis 0.21581660 -0.41429106 -0.88418670 
    5641 Axis point 95.86945170 15.26248499 0.00000000 
    5642 Rotation angle (degrees) 155.84252521 
    5643 Shift along axis -150.62362998 
    5644  
    5645 
    5646 > ~tile
    5647 
    5648 > hide #3 models
    5649 
    5650 > hide #4 models
    5651 
    5652 > show #!7 models
    5653 
    5654 > hide #!7 models
    5655 
    5656 > hide #!5 models
    5657 
    5658 > show #!5 models
    5659 
    5660 > hide #!5 models
    5661 
    5662 > show #!5 models
    5663 
    5664 > show #!7 models
    5665 
    5666 > tile
    5667 
    5668 2 models tiled 
    5669 
    5670 > select #7
    5671 
    5672 2 models selected 
    5673 
    5674 > ui mousemode right "rotate selected models"
    5675 
    5676 > view matrix models
    5677 > #7,-0.89191,0.41363,-0.18277,353.27,-0.08103,-0.54381,-0.83529,447.96,-0.44489,-0.73019,0.51855,-143.07
    5678 
    5679 > view matrix models
    5680 > #7,0.96609,0.1062,-0.23537,69.625,0.23741,-0.72375,0.64794,161.46,-0.10154,-0.68184,-0.72442,1.1122
    5681 
    5682 > select clear
    5683 
    5684 > ~tile
    5685 
    5686 > select #7
    5687 
    5688 2 models selected 
    5689 
    5690 > transparency #7.1 50
    5691 
    5692 > select clear
    5693 
    5694 > open C:/Users/lilyh/Downloads/cryosparc_P104_J2660_class_00_final_volume.mrc
    5695 
    5696 Opened cryosparc_P104_J2660_class_00_final_volume.mrc as #8, grid size
    5697 128,128,128, pixel 2.02, shown at level 0.0239, step 1, values float32 
    5698 
    5699 > ui mousemode right "rotate selected models"
    5700 
    5701 Drag select of 8 cryosparc_P104_J2660_class_00_final_volume.mrc 
    5702 
    5703 > ui mousemode right "translate selected models"
    5704 
    5705 > view matrix models #8,1,0,0,212.72,0,1,0,59.179,0,0,1,-71.919
    5706 
    5707 > volume #8 level 0.2662
    5708 
    5709 > ui mousemode right "rotate selected models"
    5710 
    5711 > view matrix models
    5712 > #8,-0.37423,-0.69971,0.60858,404.61,-0.029598,0.66494,0.74631,12.347,-0.92687,0.26128,-0.26955,174.28
    5713 
    5714 > ui mousemode right "translate selected models"
    5715 
    5716 > view matrix models
    5717 > #8,-0.37423,-0.69971,0.60858,432.15,-0.029598,0.66494,0.74631,-1.6278,-0.92687,0.26128,-0.26955,74.045
    5718 
    5719 > view matrix models
    5720 > #8,-0.37423,-0.69971,0.60858,380.54,-0.029598,0.66494,0.74631,-31.393,-0.92687,0.26128,-0.26955,52.549
    5721 
    5722 > ui mousemode right "rotate selected models"
    5723 
    5724 > view matrix models
    5725 > #8,0.1292,0.21741,-0.96749,395.59,0.26679,-0.94732,-0.17725,243.59,-0.95506,-0.23522,-0.1804,106.75
    5726 
    5727 > ui mousemode right "rotate selected models"
    5728 
    5729 > view matrix models
    5730 > #8,0.56913,-0.77999,0.2602,309.7,-0.76562,-0.6181,-0.17825,338.46,0.29986,-0.097772,-0.94896,19.951
    5731 
    5732 > fitmap #8 inMap #7
    5733 
    5734 Fit map cryosparc_P104_J2660_class_00_final_volume.mrc in map
    5735 cryosparc_P104_J3841_class_01_00015_volume.mrc using 3029 points 
    5736 correlation = 0.8162, correlation about mean = 0.204, overlap = 182.1 
    5737 steps = 108, shift = 23.8, angle = 36.1 degrees 
    5738  
    5739 Position of cryosparc_P104_J2660_class_00_final_volume.mrc (#8) relative to
    5740 cryosparc_P104_J3841_class_01_00015_volume.mrc (#7) coordinates: 
    5741 Matrix rotation and translation 
    5742 0.64857666 -0.61909464 0.44279798 88.24673902 
    5743 0.50645738 0.78528765 0.35612380 -96.79789458 
    5744 -0.56819814 -0.00671530 0.82286438 173.90885359 
    5745 Axis -0.23321133 0.64980798 0.72343768 
    5746 Axis point 251.99048310 15.44791935 0.00000000 
    5747 Rotation angle (degrees) 51.07044851 
    5748 Shift along axis 42.33203390 
    5749  
    5750 
    5751 > ui mousemode right "rotate selected models"
    5752 
    5753 [Repeated 1 time(s)]
    5754 
    5755 > view matrix models
    5756 > #8,0.75259,0.23069,0.61676,113.86,0.34933,-0.93383,-0.076973,227.32,0.55819,0.27338,-0.78338,-62.498
    5757 
    5758 > ui mousemode right "rotate selected models"
    5759 
    5760 > view matrix models
    5761 > #8,-0.61284,-0.71456,0.3374,444.76,-0.52427,0.68713,0.50299,69.501,-0.59125,0.13136,-0.79572,107.52
    5762 
    5763 > ui mousemode right "rotate selected models"
    5764 
    5765 > ui mousemode right "translate selected models"
    5766 
    5767 > view matrix models
    5768 > #8,-0.61284,-0.71456,0.3374,454.85,-0.52427,0.68713,0.50299,54.133,-0.59125,0.13136,-0.79572,102.79
    5769 
    5770 > fitmap #8 inMap #7
    5771 
    5772 Fit map cryosparc_P104_J2660_class_00_final_volume.mrc in map
    5773 cryosparc_P104_J3841_class_01_00015_volume.mrc using 3029 points 
    5774 correlation = 0.8442, correlation about mean = 0.1124, overlap = 211.3 
    5775 steps = 84, shift = 16.1, angle = 22.9 degrees 
    5776  
    5777 Position of cryosparc_P104_J2660_class_00_final_volume.mrc (#8) relative to
    5778 cryosparc_P104_J3841_class_01_00015_volume.mrc (#7) coordinates: 
    5779 Matrix rotation and translation 
    5780 -0.33843644 -0.90901010 0.24323095 279.54240726 
    5781 0.94031514 -0.33648246 0.05086088 38.54103562 
    5782 0.03560988 0.24592693 0.96863399 47.18137507 
    5783 Axis 0.10424990 0.11095973 0.98834199 
    5784 Axis point 126.90884054 111.48145220 0.00000000 
    5785 Rotation angle (degrees) 110.67964412 
    5786 Shift along axis 80.05010425 
    5787  
    5788 
    5789 > ui mousemode right "translate selected models"
    5790 
    5791 > view matrix models
    5792 > #8,-0.34366,-0.91896,0.19343,471.74,-0.59493,0.37242,0.71229,118.3,-0.7266,0.12971,-0.6747,52.323
    5793 
    5794 > volume #7 level 0.199
    5795 
    5796 > hide #!8 models
    5797 
    5798 > open
    5799 > C:/Users/lilyh/Desktop/output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
    5800 
    5801 Chain information for
    5802 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
    5803 #9 
    5804 --- 
    5805 Chain | Description 
    5806 B | No description available 
    5807 C | No description available 
    5808  
    5809 
    5810 > open
    5811 > C:/Users/lilyh/Desktop/output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
    5812 
    5813 Chain information for
    5814 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
    5815 #10 
    5816 --- 
    5817 Chain | Description 
    5818 B | No description available 
    5819 C | No description available 
    5820  
    5821 Drag select of 18 residues 
    5822 
    5823 > ui mousemode right "rotate selected models"
    5824 
    5825 > view matrix models
    5826 > #9,0.98433,0.022143,-0.17496,-0.66808,-0.059044,-0.89345,-0.44526,6.1219,-0.16618,0.44861,-0.87814,-8.0178
    5827 
    5828 > view matrix models
    5829 > #9,0.99895,-0.045366,-0.0066739,0.1599,0.04289,0.87293,0.48596,2.1187,-0.016221,-0.48574,0.87395,1.5313
    5830 
    5831 > view matrix models
    5832 > #9,0.66822,0.20542,-0.71504,-4.0514,0.50778,0.5765,0.64016,5.2699,0.54373,-0.79085,0.28092,2.7649
    5833 
    5834 > ui mousemode right "translate selected models"
    5835 
    5836 > view matrix models
    5837 > #9,0.66822,0.20542,-0.71504,-4.0081,0.50778,0.5765,0.64016,102.34,0.54373,-0.79085,0.28092,-7.2576
    5838 
    5839 Drag select of 7 residues 
    5840 
    5841 > view matrix models #10,1,0,0,0.99151,0,1,0,112.48,0,0,1,-1.2505
    5842 
    5843 > ui mousemode right "move picked models"
    5844 
    5845 > ui mousemode right "rotate selected models"
    5846 
    5847 > view matrix models
    5848 > #10,0.68788,0.55306,-0.47004,2.8404,-0.13975,-0.53456,-0.8335,110.73,-0.71224,0.63903,-0.29042,2.0665
    5849 
    5850 > ui mousemode right "translate selected models"
    5851 
    5852 Drag select of 203 residues 
    5853 
    5854 > view matrix models
    5855 > #9,0.66822,0.20542,-0.71504,30.898,0.50778,0.5765,0.64016,168.94,0.54373,-0.79085,0.28092,-30.565,#10,0.68788,0.55306,-0.47004,37.747,-0.13975,-0.53456,-0.8335,177.33,-0.71224,0.63903,-0.29042,-21.241
    5856 
    5857 > view matrix models
    5858 > #9,0.66822,0.20542,-0.71504,245.22,0.50778,0.5765,0.64016,222.28,0.54373,-0.79085,0.28092,-76.139,#10,0.68788,0.55306,-0.47004,252.07,-0.13975,-0.53456,-0.8335,230.68,-0.71224,0.63903,-0.29042,-66.815
    5859 
    5860 > view matrix models
    5861 > #9,0.66822,0.20542,-0.71504,246.23,0.50778,0.5765,0.64016,104.39,0.54373,-0.79085,0.28092,-32.852,#10,0.68788,0.55306,-0.47004,253.07,-0.13975,-0.53456,-0.8335,112.78,-0.71224,0.63903,-0.29042,-23.528
    5862 
    5863 > view matrix models
    5864 > #9,0.66822,0.20542,-0.71504,271.91,0.50778,0.5765,0.64016,119.63,0.54373,-0.79085,0.28092,-37.1,#10,0.68788,0.55306,-0.47004,278.75,-0.13975,-0.53456,-0.8335,128.02,-0.71224,0.63903,-0.29042,-27.776
    5865 
    5866 > view matrix models
    5867 > #9,0.66822,0.20542,-0.71504,288.57,0.50778,0.5765,0.64016,70.846,0.54373,-0.79085,0.28092,-26.604,#10,0.68788,0.55306,-0.47004,295.42,-0.13975,-0.53456,-0.8335,79.238,-0.71224,0.63903,-0.29042,-17.28
    5868 
    5869 > view matrix models
    5870 > #9,0.66822,0.20542,-0.71504,295.91,0.50778,0.5765,0.64016,80.527,0.54373,-0.79085,0.28092,-32.517,#10,0.68788,0.55306,-0.47004,302.75,-0.13975,-0.53456,-0.8335,88.919,-0.71224,0.63903,-0.29042,-23.193
    5871 
    5872 > fitmap #9 inMap #5
    5873 
    5874 Fit molecule
    5875 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
    5876 (#9) to map cryosparc_P104_J3841_class_00_00015_volume.mrc (#5) using 4737
    5877 atoms 
    5878 average map value = 0.2531, steps = 112 
    5879 shifted from previous position = 13 
    5880 rotated from previous position = 26.1 degrees 
    5881 atoms outside contour = 1672, contour level = 0.16 
    5882  
    5883 Position of
    5884 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
    5885 (#9) relative to cryosparc_P104_J3841_class_00_00015_volume.mrc (#5)
    5886 coordinates: 
    5887 Matrix rotation and translation 
    5888 0.78919791 0.48026688 -0.38276687 138.57310128 
    5889 -0.60009732 0.47054039 -0.64689642 140.90193819 
    5890 -0.13057568 0.74022663 0.65955632 142.30666846 
    5891 Axis 0.78094843 -0.14198330 -0.60824361 
    5892 Axis point 0.00000000 -67.75881031 273.63354210 
    5893 Rotation angle (degrees) 62.63564907 
    5894 Shift along axis 1.65560238 
    5895  
    5896 
    5897 > fitmap #10 inMap #5
    5898 
    5899 Fit molecule
    5900 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
    5901 (#10) to map cryosparc_P104_J3841_class_00_00015_volume.mrc (#5) using 4737
    5902 atoms 
    5903 average map value = 0.2677, steps = 116 
    5904 shifted from previous position = 13.7 
    5905 rotated from previous position = 25.9 degrees 
    5906 atoms outside contour = 1501, contour level = 0.16 
    5907  
    5908 Position of
    5909 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
    5910 (#10) relative to cryosparc_P104_J3841_class_00_00015_volume.mrc (#5)
    5911 coordinates: 
    5912 Matrix rotation and translation 
    5913 0.40431650 0.45195684 -0.79514980 137.52728504 
    5914 0.89853275 -0.03394204 0.43759211 138.96002973 
    5915 0.17078376 -0.89139384 -0.41982134 139.78924768 
    5916 Axis -0.78058761 -0.56734668 0.26229895 
    5917 Axis point 0.00000000 83.51913258 73.64363572 
    5918 Rotation angle (degrees) 121.64962689 
    5919 Shift along axis -149.52403183 
    5920  
    5921 
    5922 > select #9/B:44
    5923 
    5924 6 atoms, 5 bonds, 1 residue, 1 model selected 
    5925 
    5926 > ui mousemode right "rotate selected models"
    5927 
    5928 > view matrix models
    5929 > #9,0.52546,0.090663,-0.84598,306.7,0.64148,0.61097,0.46392,82.451,0.55893,-0.78644,0.26288,-36.561
    5930 
    5931 > fitmap #9 inMap #5
    5932 
    5933 Fit molecule
    5934 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
    5935 (#9) to map cryosparc_P104_J3841_class_00_00015_volume.mrc (#5) using 4737
    5936 atoms 
    5937 average map value = 0.2531, steps = 116 
    5938 shifted from previous position = 1.54 
    5939 rotated from previous position = 37.7 degrees 
    5940 atoms outside contour = 1675, contour level = 0.16 
    5941  
    5942 Position of
    5943 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
    5944 (#9) relative to cryosparc_P104_J3841_class_00_00015_volume.mrc (#5)
    5945 coordinates: 
    5946 Matrix rotation and translation 
    5947 0.78795938 0.48179115 -0.38340242 138.62887360 
    5948 -0.60153478 0.46942351 -0.64637258 140.89905027 
    5949 -0.13143850 0.73994518 0.65970075 142.30122984 
    5950 Axis 0.77999330 -0.14176416 -0.60951897 
    5951 Axis point -0.00000000 -67.57787002 273.76712820 
    5952 Rotation angle (degrees) 62.70694705 
    5953 Shift along axis 1.41985915 
    5954  
    5955 
    5956 > hide #!7 models
    5957 
    5958 > select #5
    5959 
    5960 2 models selected 
    5961 
    5962 > transparency #5.1 40
    5963 
    5964 > select clear
    5965 
    5966 Drag select of 3 residues 
    5967 
    5968 > ui mousemode right "rotate selected models"
    5969 
    5970 > view matrix models
    5971 > #10,-0.54115,0.39838,-0.74057,312.04,-0.59235,-0.80568,-0.0005531,84.935,-0.59688,0.43838,0.67198,-34.397
    5972 
    5973 > fitmap #10 inMap #5
    5974 
    5975 Fit molecule
    5976 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
    5977 (#10) to map cryosparc_P104_J3841_class_00_00015_volume.mrc (#5) using 4737
    5978 atoms 
    5979 average map value = 0.2695, steps = 164 
    5980 shifted from previous position = 3.51 
    5981 rotated from previous position = 15.2 degrees 
    5982 atoms outside contour = 1666, contour level = 0.16 
    5983  
    5984 Position of
    5985 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
    5986 (#10) relative to cryosparc_P104_J3841_class_00_00015_volume.mrc (#5)
    5987 coordinates: 
    5988 Matrix rotation and translation 
    5989 -0.63474801 0.13654917 -0.76055855 139.48720426 
    5990 0.75291691 0.33069089 -0.56899885 139.50146415 
    5991 0.17381348 -0.93380827 -0.31271557 139.92147679 
    5992 Axis -0.30986833 -0.79365358 0.52354142 
    5993 Axis point 5.15411940 0.00000000 139.45035548 
    5994 Rotation angle (degrees) 143.93856981 
    5995 Shift along axis -80.68381346 
    5996  
    5997 Drag select of 3 residues 
    5998 
    5999 > ui mousemode right "rotate selected models"
    6000 
    6001 > view matrix models
    6002 > #9,-0.87633,0.25645,-0.40777,302.94,0.30826,0.94904,-0.06562,78.421,0.37016,-0.1832,-0.91072,-43.145
    6003 
    6004 > ui mousemode right "translate selected models"
    6005 
    6006 > view matrix models
    6007 > #9,-0.87633,0.25645,-0.40777,303.84,0.30826,0.94904,-0.06562,81.783,0.37016,-0.1832,-0.91072,-32.446
    6008 
    6009 Drag select of 3 residues 
    6010 
    6011 > view matrix models
    6012 > #10,-0.64585,0.18251,-0.74133,308.6,-0.37901,-0.91955,0.1038,84.536,-0.66275,0.34801,0.66307,-35.641
    6013 
    6014 > ui mousemode right "rotate selected models"
    6015 
    6016 > view matrix models
    6017 > #10,-0.033075,0.54731,-0.83628,305.22,-0.54907,-0.70911,-0.44236,85.098,-0.83512,0.44454,0.32396,-34.93
    6018 
    6019 > fitmap #10 inMap #5
    6020 
    6021 Fit molecule
    6022 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
    6023 (#10) to map cryosparc_P104_J3841_class_00_00015_volume.mrc (#5) using 4737
    6024 atoms 
    6025 average map value = 0.2676, steps = 336 
    6026 shifted from previous position = 4.58 
    6027 rotated from previous position = 16 degrees 
    6028 atoms outside contour = 1629, contour level = 0.16 
    6029  
    6030 Position of
    6031 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
    6032 (#10) relative to cryosparc_P104_J3841_class_00_00015_volume.mrc (#5)
    6033 coordinates: 
    6034 Matrix rotation and translation 
    6035 -0.15805239 0.27883243 -0.94724439 139.68901397 
    6036 0.97228215 0.21133702 -0.10002054 138.86978828 
    6037 0.17229885 -0.93679729 -0.30450612 140.36999314 
    6038 Axis -0.53630226 -0.71753138 0.44444191 
    6039 Axis point -45.66636184 0.00000000 139.78927356 
    6040 Rotation angle (degrees) 128.72702769 
    6041 Shift along axis -112.17265703 
    6042  
    6043 
    6044 > fitmap #9 inMap #5
    6045 
    6046 Fit molecule
    6047 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
    6048 (#9) to map cryosparc_P104_J3841_class_00_00015_volume.mrc (#5) using 4737
    6049 atoms 
    6050 average map value = 0.2672, steps = 144 
    6051 shifted from previous position = 5.15 
    6052 rotated from previous position = 14.4 degrees 
    6053 atoms outside contour = 1567, contour level = 0.16 
    6054  
    6055 Position of
    6056 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
    6057 (#9) relative to cryosparc_P104_J3841_class_00_00015_volume.mrc (#5)
    6058 coordinates: 
    6059 Matrix rotation and translation 
    6060 -0.82457962 0.18916644 -0.53318343 139.37676089 
    6061 -0.53090671 -0.58434705 0.61373987 137.66693836 
    6062 -0.19546521 0.78914800 0.58227037 139.87069367 
    6063 Axis 0.21537034 -0.41465860 -0.88412322 
    6064 Axis point 95.77178000 15.34987923 0.00000000 
    6065 Rotation angle (degrees) 155.96940382 
    6066 Shift along axis -150.73008630 
    6067  
    6068 
    6069 > volume #5 level 0.1827
    6070 
    6071 > volume #5 level 0.2219
    6072 
    6073 > show #4 models
    6074 
    6075 > hide #4 models
    6076 
    6077 > hide #!5 models
    6078 
    6079 > show #!5 models
    6080 
    6081 > show #!8 models
    6082 
    6083 > hide #!8 models
    6084 
    6085 > show #!7 models
    6086 
    6087 > volume #7 level 0.2154
    6088 
    6089 > volume #7 level 0.2298
    6090 
    6091 > open C:/Users/lilyh/Downloads/Class3D_Job204/run_it025_class002.mrc
    6092 
    6093 Opened run_it025_class002.mrc as #11, grid size 256,256,256, pixel 1.09, shown
    6094 at level 0.000939, step 1, values float32 
    6095 
    6096 > volume #11 level 0.002252
    6097 
    6098 > close #11
    6099 
    6100 > open C:/Users/lilyh/Downloads/Class3D_Job204/run_it025_class003.mrc
    6101 
    6102 Opened run_it025_class003.mrc as #11, grid size 256,256,256, pixel 1.09, shown
    6103 at level 0.00128, step 1, values float32 
    6104 
    6105 > volume #11 level 0.002547
    6106 
    6107 > close #11
    6108 
    6109 > open C:/Users/lilyh/Downloads/Class3D_Job204/run_it025_class004.mrc
    6110 
    6111 Opened run_it025_class004.mrc as #11, grid size 256,256,256, pixel 1.09, shown
    6112 at level 0.00102, step 1, values float32 
    6113 
    6114 > open C:/Users/lilyh/Downloads/Class3D_Job204/run_it025_class001.mrc
    6115 
    6116 Opened run_it025_class001.mrc as #12, grid size 256,256,256, pixel 1.09, shown
    6117 at level 0.000951, step 1, values float32 
    6118 
    6119 > volume #12 level 0.001977
    6120 
    6121 > volume #11 level 0.001253
    6122 
    6123 > close #11
    6124 
    6125 > volume #12 level 0.002814
    6126 
    6127 > volume #12 level 0.002205
    6128 
    6129 > close #12
    6130 
    6131 > open C:/Users/lilyh/Downloads/Class3D_job201/run_it025_class005.mrc
    6132 
    6133 Opened run_it025_class005.mrc as #11, grid size 256,256,256, pixel 1.09, shown
    6134 at level 0.00106, step 1, values float32 
    6135 
    6136 > volume #11 level 0.006096
    6137 
    6138 > close #11
    6139 
    6140 > open C:/Users/lilyh/Downloads/Class3D_job201/run_it025_class002.mrc
    6141 
    6142 Opened run_it025_class002.mrc as #11, grid size 256,256,256, pixel 1.09, shown
    6143 at level 0.00137, step 1, values float32 
    6144 
    6145 > volume #11 level 0.003523
    6146 
    6147 > close #11
    6148 
    6149 > open C:/Users/lilyh/Downloads/Class3D_job201/run_it025_class001.mrc
    6150 
    6151 Opened run_it025_class001.mrc as #11, grid size 256,256,256, pixel 1.09, shown
    6152 at level 0.00129, step 1, values float32 
    6153 
    6154 > volume #11 level 0.002185
    6155 
    6156 > close #11
    6157 
    6158 > open C:/Users/lilyh/Downloads/Class3D_job201/run_it025_class006.mrc
    6159 
    6160 Opened run_it025_class006.mrc as #11, grid size 256,256,256, pixel 1.09, shown
    6161 at level 0.00103, step 1, values float32 
    6162 
    6163 > open C:/Users/lilyh/Downloads/Class3D_job201/run_it025_class002.mrc
    6164 
    6165 Opened run_it025_class002.mrc as #12, grid size 256,256,256, pixel 1.09, shown
    6166 at level 0.00137, step 1, values float32 
    6167 
    6168 > volume #11 level 0.001803
    6169 
    6170 > close #11
    6171 
    6172 > volume #12 level 0.005643
    6173 
    6174 > ui mousemode right "rotate selected models"
    6175 
    6176 > select #12
    6177 
    6178 2 models selected 
    6179 
    6180 > ui mousemode right "rotate selected models"
    6181 
    6182 > view matrix models
    6183 > #12,-0.82607,-0.47214,-0.30772,362.05,0.54116,-0.51209,-0.66702,240.73,0.15735,-0.71753,0.67852,128.53
    6184 
    6185 > close #12
    6186 
    6187 > open C:/Users/lilyh/Downloads/Refine3D_Job216/run_class001.mrc
    6188 
    6189 Opened run_class001.mrc as #11, grid size 256,256,256, pixel 1.09, shown at
    6190 level 0.00114, step 1, values float32 
    6191 
    6192 > volume #11 level 0.003242
    6193 
    6194 > close #11
    6195 
    6196 > open C:/Users/lilyh/Downloads/Class3D_Job215/run_it025_class004.mrc
    6197 
    6198 Opened run_it025_class004.mrc as #11, grid size 256,256,256, pixel 1.09, shown
    6199 at level 0.00158, step 1, values float32 
    6200 
    6201 > volume #11 level 0.00575
    6202 
    6203 > close #11
    6204 
    6205 > open C:/Users/lilyh/Downloads/Class3D_Job215/run_it025_class003.mrc
    6206 
    6207 Opened run_it025_class003.mrc as #11, grid size 256,256,256, pixel 1.09, shown
    6208 at level 0.00159, step 1, values float32 
    6209 
    6210 > open C:/Users/lilyh/Downloads/Class3D_Job215/run_it025_class002.mrc
    6211 
    6212 Opened run_it025_class002.mrc as #12, grid size 256,256,256, pixel 1.09, shown
    6213 at level 0.0016, step 1, values float32 
    6214 
    6215 > open C:/Users/lilyh/Downloads/Class3D_Job215/run_it025_class001.mrc
    6216 
    6217 Opened run_it025_class001.mrc as #13, grid size 256,256,256, pixel 1.09, shown
    6218 at level 0.00158, step 1, values float32 
    6219 
    6220 > volume #11 level 0.004518
    6221 
    6222 > ui mousemode right "rotate selected models"
    6223 
    6224 > select #11
    6225 
    6226 2 models selected 
    6227 
    6228 > view matrix models
    6229 > #11,0.8962,-0.41114,-0.16668,96.395,-0.18162,0.0027544,-0.98336,306.73,0.40476,0.91157,-0.072204,-32.187
    6230 
    6231 > view matrix models
    6232 > #11,-0.75473,-0.6337,-0.16971,370.42,0.2408,-0.026953,-0.9702,246.89,0.61024,-0.77311,0.17293,136.71
    6233 
    6234 > view matrix models
    6235 > #11,-0.92814,0.31919,-0.19149,266.49,0.029443,-0.44989,-0.8926,325.62,-0.37106,-0.8341,0.40816,255.61
    6236 
    6237 > view matrix models
    6238 > #11,-0.91741,-0.18544,-0.35209,358.19,0.35934,-0.7662,-0.53274,269.42,-0.17098,-0.61526,0.76956,143.83
    6239 
    6240 > ui mousemode right "rotate selected models"
    6241 
    6242 > ui mousemode right "translate selected models"
    6243 
    6244 > view matrix models
    6245 > #11,-0.91741,-0.18544,-0.35209,383.47,0.35934,-0.7662,-0.53274,275.23,-0.17098,-0.61526,0.76956,-50.42
    6246 
    6247 > ui mousemode right "rotate selected models"
    6248 
    6249 > view matrix models
    6250 > #11,0.99334,-0.11503,0.0063032,41.353,-0.096633,-0.80217,0.58923,186,-0.062724,-0.58591,-0.80794,156.3
    6251 
    6252 > ui mousemode right "translate selected models"
    6253 
    6254 > view matrix models
    6255 > #11,0.99334,-0.11503,0.0063032,167.63,-0.096633,-0.80217,0.58923,170.5,-0.062724,-0.58591,-0.80794,140.95
    6256 
    6257 > view matrix models
    6258 > #11,0.99334,-0.11503,0.0063032,148.87,-0.096633,-0.80217,0.58923,126.02,-0.062724,-0.58591,-0.80794,156.8
    6259 
    6260 > view matrix models
    6261 > #11,0.99334,-0.11503,0.0063032,182.21,-0.096633,-0.80217,0.58923,123.81,-0.062724,-0.58591,-0.80794,170.65
    6262 
    6263 > fitmap #11 inMap #5
    6264 
    6265 Fit map run_it025_class003.mrc in map
    6266 cryosparc_P104_J3841_class_00_00015_volume.mrc using 36877 points 
    6267 correlation = 0.951, correlation about mean = 0.4103, overlap = 96.2 
    6268 steps = 96, shift = 3.76, angle = 18.4 degrees 
    6269  
    6270 Position of run_it025_class003.mrc (#11) relative to
    6271 cryosparc_P104_J3841_class_00_00015_volume.mrc (#5) coordinates: 
    6272 Matrix rotation and translation 
    6273 0.92672300 -0.37387705 -0.03742304 66.38262387 
    6274 0.37568856 0.92370680 0.07499282 -49.74916531 
    6275 0.00652983 -0.08355696 0.99648165 7.70962580 
    6276 Axis -0.20660367 -0.05727428 0.97674694 
    6277 Axis point 162.15789928 143.92730321 0.00000000 
    6278 Rotation angle (degrees) 22.56337518 
    6279 Shift along axis -3.33519283 
    6280  
    6281 
    6282 > volume #11 level 0.004225
    6283 
    6284 > open C:/Users/lilyh/Downloads/cryosparc_P104_J3849_class_01_00019_volume.mrc
    6285 
    6286 Opened cryosparc_P104_J3849_class_01_00019_volume.mrc as #14, grid size
    6287 100,100,100, pixel 2.78, shown at level 0.077, step 1, values float32 
    6288 
    6289 > select #14
    6290 
    6291 2 models selected 
    6292 
    6293 > ui mousemode right "rotate selected models"
    6294 
    6295 > view matrix models
    6296 > #14,0.9718,0.22627,0.066405,-36.907,0.11593,-0.70364,0.70103,125.5,0.20535,-0.67356,-0.71003,301.76
    6297 
    6298 > ui mousemode right "translate selected models"
    6299 
    6300 > view matrix models
    6301 > #14,0.9718,0.22627,0.066405,-14.704,0.11593,-0.70364,0.70103,46.697,0.20535,-0.67356,-0.71003,124.38
    6302 
    6303 > view matrix models
    6304 > #14,0.9718,0.22627,0.066405,64.968,0.11593,-0.70364,0.70103,55.41,0.20535,-0.67356,-0.71003,144.69
    6305 
    6306 > view matrix models
    6307 > #14,0.9718,0.22627,0.066405,136.8,0.11593,-0.70364,0.70103,63.185,0.20535,-0.67356,-0.71003,135.07
    6308 
    6309 > volume #14 level 0.1526
    6310 
    6311 > fitmap #14 inMap #5
    6312 
    6313 Fit map cryosparc_P104_J3849_class_01_00019_volume.mrc in map
    6314 cryosparc_P104_J3841_class_00_00015_volume.mrc using 4897 points 
    6315 correlation = 0.9978, correlation about mean = 0.986, overlap = 599.5 
    6316 steps = 84, shift = 7.4, angle = 15.9 degrees 
    6317  
    6318 Position of cryosparc_P104_J3849_class_01_00019_volume.mrc (#14) relative to
    6319 cryosparc_P104_J3841_class_00_00015_volume.mrc (#5) coordinates: 
    6320 Matrix rotation and translation 
    6321 0.99999757 -0.00220530 -0.00028950 0.34498766 
    6322 0.00220542 0.99999752 0.00040847 -0.28661408 
    6323 0.00028860 -0.00040910 0.99999991 -0.16714422 
    6324 Axis -0.18076164 -0.12781697 0.97518616 
    6325 Axis point 141.05738771 140.80854643 0.00000000 
    6326 Rotation angle (degrees) 0.12957298 
    6327 Shift along axis -0.18872312 
    6328  
    6329 
    6330 > hide #!11 models
    6331 
    6332 > hide #10 models
    6333 
    6334 > hide #9 models
    6335 
    6336 > hide #!7 models
    6337 
    6338 > hide #!14 models
    6339 
    6340 > show #!14 models
    6341 
    6342 > select #14
    6343 
    6344 2 models selected 
    6345 
    6346 > transparency #14.1 50
    6347 
    6348 > select clear
    6349 
    6350 > select add #5
    6351 
    6352 2 models selected 
    6353 
    6354 > transparency #5.1 0
    6355 
    6356 > select clear
    6357 
    6358 [Repeated 1 time(s)]
    6359 
    6360 > hide #!5 models
    6361 
    6362 > show #!5 models
    6363 
    6364 > hide #!14 models
    6365 
    6366 > show #!14 models
    6367 
    6368 > show #!6 models
    6369 
    6370 > hide #!6 models
    6371 
    6372 > show #!8 models
    6373 
    6374 > hide #!8 models
    6375 
    6376 > show #!7 models
    6377 
    6378 > hide #!7 models
    6379 
    6380 > show #!7 models
    6381 
    6382 > volume #5 level 0.153
    6383 
    6384 > hide #!7 models
    6385 
    6386 > show #!7 models
    6387 
    6388 > volume #14 level 0.1545
    6389 
    6390 > hide #!7 models
    6391 
    6392 > hide #!5 models
    6393 
    6394 > volume #14 level 0.2075
    6395 
    6396 > volume #5 level 0.207
    6397 
    6398 > ~tile
    6399 
    6400 [Repeated 1 time(s)]
    6401 
    6402 > select #14
    6403 
    6404 2 models selected 
    6405 
    6406 > transparency #14.1 0
    6407 
    6408 > ui mousemode right "translate selected models"
    6409 
    6410 > view matrix models
    6411 > #14,0.9987,-0.0040992,-0.050866,147.89,0.036065,-0.64851,0.76035,149.04,-0.036104,-0.76119,-0.64752,88.288
    6412 
    6413 > select clear
    6414 
    6415 > show #!7 models
    6416 
    6417 > hide #!5 models
    6418 
    6419 > hide #!14 models
    6420 
    6421 > volume #7 level 0.1887
    6422 
    6423 > show #!8 models
    6424 
    6425 > select #7
    6426 
    6427 2 models selected 
    6428 
    6429 > transparency #7.1 0
    6430 
    6431 > select #8
    6432 
    6433 2 models selected 
    6434 
    6435 > ui mousemode right "translate selected models"
    6436 
    6437 > view matrix models
    6438 > #8,-0.34366,-0.91896,0.19343,514.32,-0.59493,0.37242,0.71229,45.093,-0.7266,0.12971,-0.6747,63.542
    6439 
    6440 > ui mousemode right "rotate selected models"
    6441 
    6442 > view matrix models
    6443 > #8,-0.5098,-0.7872,0.34702,500.82,-0.53663,0.60626,0.58692,23.959,-0.67241,0.11299,-0.73151,65.518
    6444 
    6445 > select clear
    6446 
    6447 > select #8
    6448 
    6449 2 models selected 
    6450 
    6451 > ui mousemode right "rotate selected models"
    6452 
    6453 > view matrix models
    6454 > #8,-0.21274,0.61919,0.75587,237.05,-0.88323,-0.45272,0.12227,258.09,0.4179,-0.6416,0.6432,-154.02
    6455 
    6456 > volume #8 level 0.2313
    6457 
    6458 > view matrix models
    6459 > #8,0.61822,-0.78599,0.004733,393.96,0.71276,0.56314,0.41815,-113.7,-0.33133,-0.25514,0.90836,-135.93
    6460 
    6461 > view matrix models
    6462 > #8,0.93832,0.34137,-0.05506,219.37,0.020064,-0.21272,-0.97691,243.93,-0.3452,0.91554,-0.20644,-143.17
    6463 
    6464 > view matrix models
    6465 > #8,0.43219,-0.49225,0.75558,290.24,0.80544,-0.16609,-0.56892,85.153,0.40555,0.85446,0.32469,-299.08
    6466 
    6467 > view matrix models
    6468 > #8,0.95951,-0.10645,0.26077,233.56,-0.27339,-0.12922,0.95318,36.366,-0.067772,-0.98589,-0.15309,49.749
    6469 
    6470 > ui mousemode right "translate selected models"
    6471 
    6472 > view matrix models
    6473 > #8,0.95951,-0.10645,0.26077,270.65,-0.27339,-0.12922,0.95318,67.45,-0.067772,-0.98589,-0.15309,101.38
    6474 
    6475 > ui mousemode right "translate selected models"
    6476 
    6477 > view matrix models
    6478 > #8,0.95951,-0.10645,0.26077,237.28,-0.27339,-0.12922,0.95318,41.515,-0.067772,-0.98589,-0.15309,55.27
    6479 
    6480 > view matrix models
    6481 > #8,0.95951,-0.10645,0.26077,168.92,-0.27339,-0.12922,0.95318,69.864,-0.067772,-0.98589,-0.15309,46.926
    6482 
    6483 > view matrix models
    6484 > #8,0.95951,-0.10645,0.26077,158.19,-0.27339,-0.12922,0.95318,75.927,-0.067772,-0.98589,-0.15309,79.931
    6485 
    6486 > ui mousemode right "rotate selected models"
    6487 
    6488 > view matrix models
    6489 > #8,-0.92751,0.11756,0.35483,366.78,0.32522,0.72177,0.61097,-66.466,-0.18428,0.68208,-0.70768,-43.935
    6490 
    6491 > fitmap #8 inMap #7
    6492 
    6493 Fit map cryosparc_P104_J2660_class_00_final_volume.mrc in map
    6494 cryosparc_P104_J3841_class_01_00015_volume.mrc using 3905 points 
    6495 correlation = 0.8418, correlation about mean = 0.1304, overlap = 246 
    6496 steps = 128, shift = 7.24, angle = 74.8 degrees 
    6497  
    6498 Position of cryosparc_P104_J2660_class_00_final_volume.mrc (#8) relative to
    6499 cryosparc_P104_J3841_class_01_00015_volume.mrc (#7) coordinates: 
    6500 Matrix rotation and translation 
    6501 -0.35794962 -0.89860469 0.25373505 279.32584170 
    6502 0.93341762 -0.35150982 0.07191796 38.28272836 
    6503 0.02456447 0.26258389 0.96459646 46.98423914 
    6504 Axis 0.10272289 0.12346760 0.98701761 
    6505 Axis point 127.47890854 109.07934950 0.00000000 
    6506 Rotation angle (degrees) 111.86565401 
    6507 Shift along axis 79.79410559 
    6508  
    6509 
    6510 > ui mousemode right "rotate selected models"
    6511 
    6512 [Repeated 1 time(s)]
    6513 
    6514 > view matrix models
    6515 > #8,-0.33649,-0.93498,0.11221,464.28,-0.65644,0.31833,0.68392,101.74,-0.67517,0.15648,-0.72087,93.401
    6516 
    6517 > ui mousemode right "rotate selected models"
    6518 
    6519 > view matrix models
    6520 > #8,-0.523,0.0458,0.8511,276.86,-0.67344,0.58987,-0.44557,208.25,-0.52245,-0.8062,-0.27766,138.62
    6521 
    6522 > view matrix models
    6523 > #8,0.41062,0.24389,0.87858,126.3,0.90783,-0.19927,-0.36897,89.083,0.085085,0.94911,-0.30324,-155.8
    6524 
    6525 > view matrix models
    6526 > #8,-0.33176,-0.93784,0.10194,465.27,-0.74618,0.327,0.5799,125.16,-0.57719,0.11632,-0.80828,96.19
    6527 
    6528 > ui mousemode right "translate selected models"
    6529 
    6530 > view matrix models
    6531 > #8,-0.33176,-0.93784,0.10194,432.23,-0.74618,0.327,0.5799,167.99,-0.57719,0.11632,-0.80828,83.083
    6532 
    6533 > show #9 models
    6534 
    6535 > close session
    6536 
    6537 > open C:/Users/lilyh/Downloads/cryosparc_P104_J3854_class_00_00019_volume.mrc
    6538 
    6539 Opened cryosparc_P104_J3854_class_00_00019_volume.mrc as #1, grid size
    6540 100,100,100, pixel 2.78, shown at level 0.0777, step 1, values float32 
    6541 
    6542 > open C:/Users/lilyh/Downloads/cryosparc_P104_J3854_class_01_00019_volume.mrc
    6543 
    6544 Opened cryosparc_P104_J3854_class_01_00019_volume.mrc as #2, grid size
    6545 100,100,100, pixel 2.78, shown at level 0.157, step 1, values float32 
    6546 
    6547 > volume level 0.06
    6548 
    6549 > volume level 0.1
    6550 
    6551 > volume level 0.3
    6552 
    6553 > volume #1 level 0.1684
    6554 
    6555 > volume level 0.168
    6556 
    6557 > select #2
    6558 
    6559 2 models selected 
    6560 
    6561 > transparency #2.1 50
    6562 
    6563 > select clear
    6564 
    6565 > volume #2 level 0.2507
    6566 
    6567 > volume level 0.251
    6568 
    6569 > open C:/Users/lilyh/Downloads/cryosparc_P104_J3849_class_01_00019_volume.mrc
    6570 
    6571 Opened cryosparc_P104_J3849_class_01_00019_volume.mrc as #3, grid size
    6572 100,100,100, pixel 2.78, shown at level 0.077, step 1, values float32 
    6573 
    6574 > volume #3 level 0.251
    6575 
    6576 > volume #3 level 0.2037
    6577 
    6578 > volume #2 level 0.204
    6579 
    6580 > volume #1 level 0.204
    6581 
    6582 > open C:/Users/lilyh/Downloads/cryosparc_P104_J3849_class_02_00019_volume.mrc
    6583 
    6584 Opened cryosparc_P104_J3849_class_02_00019_volume.mrc as #4, grid size
    6585 100,100,100, pixel 2.78, shown at level 0.155, step 1, values float32 
    6586 
    6587 > volume #4 level 0.251
    6588 
    6589 > volume #4 level 0.2322
    6590 
    6591 > open C:/Users/lilyh/Downloads/cryosparc_P122_J577_class_00_final_volume.mrc
    6592 
    6593 Opened cryosparc_P122_J577_class_00_final_volume.mrc as #5, grid size
    6594 128,128,128, pixel 2.17, shown at level 0.0161, step 1, values float32 
    6595 
    6596 > open C:/Users/lilyh/Downloads/cryosparc_P122_J578_class_02_final_volume.mrc
    6597 
    6598 Opened cryosparc_P122_J578_class_02_final_volume.mrc as #6, grid size
    6599 128,128,128, pixel 2.17, shown at level 0.0433, step 1, values float32 
    6600 
    6601 > open C:/Users/lilyh/Downloads/cryosparc_P122_J578_class_01_final_volume.mrc
    6602 
    6603 Opened cryosparc_P122_J578_class_01_final_volume.mrc as #7, grid size
    6604 128,128,128, pixel 2.17, shown at level 0.0228, step 1, values float32 
    6605 
    6606 > open C:/Users/lilyh/Downloads/cryosparc_P122_J578_class_00_final_volume.mrc
    6607 
    6608 Opened cryosparc_P122_J578_class_00_final_volume.mrc as #8, grid size
    6609 128,128,128, pixel 2.17, shown at level 0.0381, step 1, values float32 
    6610 
    6611 > open C:/Users/lilyh/Downloads/cryosparc_P122_J577_class_01_final_volume.mrc
    6612 
    6613 Opened cryosparc_P122_J577_class_01_final_volume.mrc as #9, grid size
    6614 128,128,128, pixel 2.17, shown at level 0.0243, step 1, values float32 
    6615 
    6616 > open C:/Users/lilyh/Downloads/cryosparc_P122_J577_class_02_final_volume.mrc
    6617 
    6618 Opened cryosparc_P122_J577_class_02_final_volume.mrc as #10, grid size
    6619 128,128,128, pixel 2.17, shown at level 0.0142, step 1, values float32 
    6620 
    6621 > volume level 0.251
    6622 
    6623 > hide #!10 models
    6624 
    6625 > hide #!9 models
    6626 
    6627 > hide #!8 models
    6628 
    6629 > hide #!7 models
    6630 
    6631 > hide #!6 models
    6632 
    6633 > close session
    6634 
    6635 > open C:/Users/lilyh/Downloads/cryosparc_P122_J577_class_00_final_volume.mrc
    6636 
    6637 Opened cryosparc_P122_J577_class_00_final_volume.mrc as #1, grid size
    6638 128,128,128, pixel 2.17, shown at level 0.0161, step 1, values float32 
    6639 
    6640 > open C:/Users/lilyh/Downloads/cryosparc_P122_J578_class_02_final_volume.mrc
    6641 
    6642 Opened cryosparc_P122_J578_class_02_final_volume.mrc as #2, grid size
    6643 128,128,128, pixel 2.17, shown at level 0.0433, step 1, values float32 
    6644 
    6645 > open C:/Users/lilyh/Downloads/cryosparc_P122_J578_class_01_final_volume.mrc
    6646 
    6647 Opened cryosparc_P122_J578_class_01_final_volume.mrc as #3, grid size
    6648 128,128,128, pixel 2.17, shown at level 0.0228, step 1, values float32 
    6649 
    6650 > open C:/Users/lilyh/Downloads/cryosparc_P122_J578_class_00_final_volume.mrc
    6651 
    6652 Opened cryosparc_P122_J578_class_00_final_volume.mrc as #4, grid size
    6653 128,128,128, pixel 2.17, shown at level 0.0381, step 1, values float32 
    6654 
    6655 > open C:/Users/lilyh/Downloads/cryosparc_P122_J577_class_01_final_volume.mrc
    6656 
    6657 Opened cryosparc_P122_J577_class_01_final_volume.mrc as #5, grid size
    6658 128,128,128, pixel 2.17, shown at level 0.0243, step 1, values float32 
    6659 
    6660 > open C:/Users/lilyh/Downloads/cryosparc_P122_J577_class_02_final_volume.mrc
    6661 
    6662 Opened cryosparc_P122_J577_class_02_final_volume.mrc as #6, grid size
    6663 128,128,128, pixel 2.17, shown at level 0.0142, step 1, values float32 
    6664 
    6665 > volume level 0.251
    6666 
    6667 > tile
    6668 
    6669 6 models tiled 
    6670 
    6671 > hide #!1 models
    6672 
    6673 > show #!1 models
    6674 
    6675 Drag select of 5 cryosparc_P122_J577_class_01_final_volume.mrc , 6
    6676 cryosparc_P122_J577_class_02_final_volume.mrc 
    6677 
    6678 > color #5.1#6.1 dark gray
    6679 
    6680 > select clear
    6681 
    6682 > volume #1 level 0.1001
    6683 
    6684 > ui mousemode right "rotate selected models"
    6685 
    6686 > select #1
    6687 
    6688 2 models selected 
    6689 
    6690 > view matrix models
    6691 > #1,-0.17616,-0.39778,-0.90041,347.09,0.78554,-0.60804,0.11494,117.04,-0.59321,-0.68706,0.41959,254.94
    6692 
    6693 > view matrix models
    6694 > #1,-0.82247,-0.18641,-0.53739,351.91,0.23322,-0.97222,-0.019702,263.76,-0.51879,-0.14153,0.8431,105.23
    6695 
    6696 > view matrix models
    6697 > #1,0.0079879,-0.026827,0.99961,6.0704,0.21935,-0.97525,-0.027926,267.19,0.97561,0.21949,-0.0019056,-32.258
    6698 
    6699 > volume #1 level 0.3873
    6700 
    6701 > ui mousemode right "rotate selected models"
    6702 
    6703 > view matrix models
    6704 > #1,-0.84596,-0.27576,0.4564,238.86,0.019045,-0.87098,-0.49094,344.59,0.5329,-0.40663,0.74207,18.775
    6705 
    6706 Drag select of 2 cryosparc_P122_J578_class_02_final_volume.mrc 
    6707 
    6708 > select #2
    6709 
    6710 2 models selected 
    6711 
    6712 > ui mousemode right "rotate selected models"
    6713 
    6714 > view matrix models
    6715 > #2,-0.08381,-0.71697,0.69204,250.28,0.95236,0.14672,0.26734,-39.145,-0.29322,0.68148,0.67052,-17.307
    6716 
    6717 > volume #2 level 0.1605
    6718 
    6719 > volume #2 level 0.1242
    6720 
    6721 > view matrix models
    6722 > #2,-0.22735,0.96053,0.16029,97.974,0.44963,-0.042463,0.89221,-31.5,0.8638,0.27491,-0.42223,40.225
    6723 
    6724 > select #3
    6725 
    6726 2 models selected 
    6727 
    6728 > ui mousemode right "rotate selected models"
    6729 
    6730 > view matrix models
    6731 > #3,-0.20471,0.71567,-0.66777,342.66,-0.11569,0.65974,0.74253,-34.841,0.97196,0.22926,-0.052255,-24.902
    6732 
    6733 > volume #3 level 0.1706
    6734 
    6735 > view matrix models
    6736 > #3,0.86882,-0.4906,-0.066818,274.59,-0.15688,-0.40077,0.90265,101.41,-0.46962,-0.77376,-0.42516,383.2
    6737 
    6738 > select #4
    6739 
    6740 2 models selected 
    6741 
    6742 > ui mousemode right "rotate selected models"
    6743 
    6744 > view matrix models
    6745 > #4,-0.25412,0.18404,0.9495,20.74,-0.0049442,-0.98196,0.18901,175.51,0.96716,0.043337,0.25045,-33.074
    6746 
    6747 > volume #4 level 0.3193
    6748 
    6749 > view matrix models
    6750 > #4,-0.42473,-0.35812,0.83148,138.34,-0.54636,-0.63093,-0.55084,296.66,0.72187,-0.68824,0.07231,130.18
    6751 
    6752 > view matrix models
    6753 > #4,-0.12584,-0.25431,0.9589,65.83,-0.28566,-0.91636,-0.28051,266.73,0.95003,-0.30922,0.042668,48.259
    6754 
    6755 > ui mousemode right "rotate selected models"
    6756 
    6757 > ui mousemode right "translate selected models"
    6758 
    6759 > view matrix models
    6760 > #4,-0.12584,-0.25431,0.9589,35.333,-0.28566,-0.91636,-0.28051,259.39,0.95003,-0.30922,0.042668,48.259
    6761 
    6762 > ui mousemode right "rotate selected models"
    6763 
    6764 > view matrix models
    6765 > #4,0.0045928,-0.22442,0.97448,11.285,-0.4067,-0.89067,-0.2032,261.67,0.91355,-0.39539,-0.095363,84.178
    6766 
    6767 > volume #4 level 0.2805
    6768 
    6769 > view matrix models
    6770 > #4,-0.2976,0.70521,-0.64352,133.16,-0.83644,-0.51754,-0.18033,262.37,-0.46022,0.4846,0.74388,29.503
    6771 
    6772 > volume #5 level 0.2636
    6773 
    6774 > ui mousemode right "rotate selected models"
    6775 
    6776 > view matrix models
    6777 > #4,-0.31726,0.82371,-0.46994,95.28,-0.90368,-0.11231,0.41322,132.85,0.28759,0.55577,0.78001,-87.059
    6778 
    6779 > select #5
    6780 
    6781 2 models selected 
    6782 
    6783 > view matrix models
    6784 > #5,-0.13106,0.13096,-0.98269,363.95,0.38525,0.92006,0.071229,-133.3,0.91346,-0.36924,-0.17104,87.836
    6785 
    6786 > volume #6 level 0.397
    6787 
    6788 > select #6
    6789 
    6790 2 models selected 
    6791 
    6792 > view matrix models
    6793 > #6,-0.45924,-0.38566,0.80023,333.1,-0.83047,-0.13334,-0.54086,261.91,0.31529,-0.91296,-0.25905,255.17
    6794 
    6795 > select clear
    6796 
    6797 > hide #!4 models
    6798 
    6799 > show #!4 models
    6800 
    6801 > close session
    6802 
    6803 > open C:/Users/lilyh/Downloads/cryosparc_P104_J2660_class_00_final_volume.mrc
    6804 
    6805 Opened cryosparc_P104_J2660_class_00_final_volume.mrc as #1, grid size
    6806 128,128,128, pixel 2.02, shown at level 0.0239, step 1, values float32 
    6807 
    6808 > volume #1 level 0.09419
    6809 
    6810 > volume #1 level 0.232
    6811 
    6812 > volume #1 level 0.1167
    6813 
    6814 > volume #1 level 0.1012
    6815 
    6816 > close session
    6817 
    6818 > open C:/Users/lilyh/Downloads/Class3D_Job205/run_it025_class005.mrc
    6819 
    6820 Opened run_it025_class005.mrc as #1, grid size 256,256,256, pixel 1.09, shown
    6821 at level 0.0011, step 1, values float32 
    6822 
    6823 > open C:/Users/lilyh/Downloads/Class3D_Job205/run_it025_class004.mrc
    6824 
    6825 Opened run_it025_class004.mrc as #2, grid size 256,256,256, pixel 1.09, shown
    6826 at level 0.000697, step 1, values float32 
    6827 
    6828 > open C:/Users/lilyh/Downloads/Class3D_Job205/run_it025_class003.mrc
    6829 
    6830 Opened run_it025_class003.mrc as #3, grid size 256,256,256, pixel 1.09, shown
    6831 at level 0.000861, step 1, values float32 
    6832 
    6833 > open C:/Users/lilyh/Downloads/Class3D_Job205/run_it025_class002.mrc
    6834 
    6835 Opened run_it025_class002.mrc as #4, grid size 256,256,256, pixel 1.09, shown
    6836 at level 0.00113, step 1, values float32 
    6837 
    6838 > open C:/Users/lilyh/Downloads/Class3D_Job205/run_it025_class001.mrc
    6839 
    6840 Opened run_it025_class001.mrc as #5, grid size 256,256,256, pixel 1.09, shown
    6841 at level 0.000747, step 1, values float32 
    6842 
    6843 > open C:/Users/lilyh/Downloads/Class3D_Job205/run_it025_class006.mrc
    6844 
    6845 Opened run_it025_class006.mrc as #6, grid size 256,256,256, pixel 1.09, shown
    6846 at level 0.000788, step 1, values float32 
    6847 
    6848 > tile
    6849 
    6850 6 models tiled 
    6851 
    6852 > volume 0.004
    6853 
    6854 Expected a density maps specifier or a keyword 
    6855 
    6856 > volume level0.004
    6857 
    6858 Expected a density maps specifier or a keyword 
    6859 
    6860 > volume level 0.004
    6861 
    6862 > volume level 0.003
    6863 
    6864 > volume level 0.002
    6865 
    6866 > hide #!4 models
    6867 
    6868 > show #!4 models
    6869 
    6870 > close session
    6871 
    6872 > ~tile
    6873 
    6874 No models found for tiling. 
    6875 
    6876 > open C:/Users/lilyh/Downloads/Class3D_Job205/run_it025_class002.mrc
    6877 
    6878 Opened run_it025_class002.mrc as #1, grid size 256,256,256, pixel 1.09, shown
    6879 at level 0.00113, step 1, values float32 
    6880 
    6881 > open
    6882 > C:/Users/lilyh/Desktop/output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
    6883 
    6884 Chain information for
    6885 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
    6886 #2 
    6887 --- 
    6888 Chain | Description 
    6889 B | No description available 
    6890 C | No description available 
    6891  
    6892 
    6893 > open
    6894 > C:/Users/lilyh/Desktop/output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
    6895 
    6896 Chain information for
    6897 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
    6898 #3 
    6899 --- 
    6900 Chain | Description 
    6901 B | No description available 
    6902 C | No description available 
    6903  
    6904 Drag select of 496 residues 
    6905 
    6906 > ui mousemode right "translate selected models"
    6907 
    6908 > view matrix models
    6909 > #2,1,0,0,116.83,0,1,0,136.92,0,0,1,0,#3,1,0,0,116.83,0,1,0,136.92,0,0,1,0
    6910 
    6911 > view matrix models
    6912 > #2,1,0,0,175.39,0,1,0,151.12,0,0,1,143.42,#3,1,0,0,175.39,0,1,0,151.12,0,0,1,143.42
    6913 
    6914 > view matrix models
    6915 > #2,1,0,0,169.46,0,1,0,151.58,0,0,1,154.07,#3,1,0,0,169.46,0,1,0,151.58,0,0,1,154.07
    6916 
    6917 > volume #1 level 0.002369
    6918 
    6919 Drag select of 3 residues 
    6920 
    6921 > ui mousemode right "rotate selected models"
    6922 
    6923 > view matrix models
    6924 > #2,-0.87121,0.48795,-0.053756,161.34,-0.24368,-0.33479,0.91024,158.95,0.42616,0.80611,0.41058,150.4
    6925 
    6926 > ui mousemode right "translate selected models"
    6927 
    6928 > view matrix models
    6929 > #2,-0.87121,0.48795,-0.053756,155.75,-0.24368,-0.33479,0.91024,134.02,0.42616,0.80611,0.41058,146.12
    6930 
    6931 Drag select of 1 run_it025_class002.mrc , 13 residues 
    6932 Drag select of 4 residues 
    6933 
    6934 > view matrix models #3,1,0,0,161.41,0,1,0,120.33,0,0,1,140.77
    6935 
    6936 > ui mousemode right "rotate selected models"
    6937 
    6938 > view matrix models
    6939 > #3,-0.30497,0.41351,-0.85791,168.55,0.95236,0.13377,-0.27407,113.45,0.0014333,-0.90062,-0.4346,138.1
    6940 
    6941 > ui mousemode right "translate selected models"
    6942 
    6943 Drag select of 9 residues 
    6944 
    6945 > view matrix models
    6946 > #3,-0.30497,0.41351,-0.85791,133.95,0.95236,0.13377,-0.27407,135.36,0.0014333,-0.90062,-0.4346,144.65
    6947 
    6948 Drag select of 8 residues 
    6949 
    6950 > ui mousemode right "rotate selected models"
    6951 
    6952 > view matrix models
    6953 > #2,-0.83018,0.13244,-0.54154,155.84,-0.50626,-0.58589,0.6328,133.36,-0.23348,0.79949,0.55344,144.46
    6954 
    6955 > ui mousemode right "translate selected models"
    6956 
    6957 > view matrix models
    6958 > #2,-0.83018,0.13244,-0.54154,138.53,-0.50626,-0.58589,0.6328,140.66,-0.23348,0.79949,0.55344,148.39
    6959 
    6960 > fitmap #2 inMap #1
    6961 
    6962 Fit molecule
    6963 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
    6964 (#2) to map run_it025_class002.mrc (#1) using 4737 atoms 
    6965 average map value = 0.003807, steps = 168 
    6966 shifted from previous position = 8.75 
    6967 rotated from previous position = 11.1 degrees 
    6968 atoms outside contour = 1494, contour level = 0.0023689 
    6969  
    6970 Position of
    6971 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
    6972 (#2) relative to run_it025_class002.mrc (#1) coordinates: 
    6973 Matrix rotation and translation 
    6974 -0.75937635 0.28001334 -0.58731599 140.81258219 
    6975 -0.60889975 -0.62397495 0.48979213 135.34798763 
    6976 -0.22932214 0.72955314 0.64433187 142.34319149 
    6977 Axis 0.24271444 -0.36240369 -0.89986292 
    6978 Axis point 101.86610532 13.24621529 0.00000000 
    6979 Rotation angle (degrees) 150.40171516 
    6980 Shift along axis -142.96272337 
    6981  
    6982 
    6983 > fitmap #3 inMap #1
    6984 
    6985 Fit molecule
    6986 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
    6987 (#3) to map run_it025_class002.mrc (#1) using 4737 atoms 
    6988 average map value = 0.003757, steps = 216 
    6989 shifted from previous position = 6.57 
    6990 rotated from previous position = 31 degrees 
    6991 atoms outside contour = 1469, contour level = 0.0023689 
    6992  
    6993 Position of
    6994 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
    6995 (#3) relative to run_it025_class002.mrc (#1) coordinates: 
    6996 Matrix rotation and translation 
    6997 0.16861729 0.36118350 -0.91712308 139.70264159 
    6998 0.95540655 0.16894469 0.24219006 136.18049483 
    6999 0.24241813 -0.91706281 -0.31659005 142.84727065 
    7000 Axis -0.66471271 -0.66487803 0.34072601 
    7001 Axis point -81.32086041 0.00000000 128.39297460 
    7002 Rotation angle (degrees) 119.30864552 
    7003 Shift along axis -134.73375957 
    7004  
    7005 
    7006 > select clear
    7007 
    7008 > select #1
    7009 
    7010 2 models selected 
    7011 
    7012 > transparency #1.1 50
    7013 
    7014 > select clear
    7015 
    7016 > volume #1 level 0.003368
    7017 
    7018 > close session
    7019 
    7020 > open C:/Users/lilyh/Downloads/Class3D_Job205/run_it025_class006.mrc
    7021 
    7022 Opened run_it025_class006.mrc as #1, grid size 256,256,256, pixel 1.09, shown
    7023 at level 0.000788, step 1, values float32 
    7024 
    7025 > open C:/Users/lilyh/Downloads/Class3D_Job205/run_it025_class005.mrc
    7026 
    7027 Opened run_it025_class005.mrc as #2, grid size 256,256,256, pixel 1.09, shown
    7028 at level 0.0011, step 1, values float32 
    7029 
    7030 > open C:/Users/lilyh/Downloads/Class3D_Job205/run_it025_class004.mrc
    7031 
    7032 Opened run_it025_class004.mrc as #3, grid size 256,256,256, pixel 1.09, shown
    7033 at level 0.000697, step 1, values float32 
    7034 
    7035 > open C:/Users/lilyh/Downloads/Class3D_Job205/run_it025_class003.mrc
    7036 
    7037 Opened run_it025_class003.mrc as #4, grid size 256,256,256, pixel 1.09, shown
    7038 at level 0.000861, step 1, values float32 
    7039 
    7040 > open C:/Users/lilyh/Downloads/Class3D_Job205/run_it025_class002.mrc
    7041 
    7042 Opened run_it025_class002.mrc as #5, grid size 256,256,256, pixel 1.09, shown
    7043 at level 0.00113, step 1, values float32 
    7044 
    7045 > open C:/Users/lilyh/Downloads/Class3D_Job205/run_it025_class001.mrc
    7046 
    7047 Opened run_it025_class001.mrc as #6, grid size 256,256,256, pixel 1.09, shown
    7048 at level 0.000747, step 1, values float32 
    7049 
    7050 > tile
    7051 
    7052 6 models tiled 
    7053 
    7054 > volume level 0.003
    7055 
    7056 > close session
    7057 
    7058 > open C:/Users/lilyh/Downloads/Class3D_Job204/run_it025_class003.mrc
    7059 
    7060 Opened run_it025_class003.mrc as #1, grid size 256,256,256, pixel 1.09, shown
    7061 at level 0.00128, step 1, values float32 
    7062 
    7063 > open C:/Users/lilyh/Downloads/Class3D_Job204/run_it025_class002.mrc
    7064 
    7065 Opened run_it025_class002.mrc as #2, grid size 256,256,256, pixel 1.09, shown
    7066 at level 0.000939, step 1, values float32 
    7067 
    7068 > open C:/Users/lilyh/Downloads/Class3D_Job204/run_it025_class001.mrc
    7069 
    7070 Opened run_it025_class001.mrc as #3, grid size 256,256,256, pixel 1.09, shown
    7071 at level 0.000951, step 1, values float32 
    7072 
    7073 > open C:/Users/lilyh/Downloads/Class3D_Job204/run_it025_class004.mrc
    7074 
    7075 Opened run_it025_class004.mrc as #4, grid size 256,256,256, pixel 1.09, shown
    7076 at level 0.00102, step 1, values float32 
    7077 
    7078 > volume level 0.003
    7079 
    7080 > tile
    7081 
    7082 4 models tiled 
    7083 Drag select of 1 run_it025_class003.mrc , 2 run_it025_class002.mrc , 3
    7084 run_it025_class001.mrc , 4 run_it025_class004.mrc 
    7085 
    7086 > color #1.1#2.1#3.1#4.1 orange
    7087 
    7088 > select clear
    7089 
    7090 > open C:/Users/lilyh/Downloads/Class3D_Job203/run_it025_class001.mrc
    7091 
    7092 Opened run_it025_class001.mrc as #5, grid size 256,256,256, pixel 1.09, shown
    7093 at level 0.000995, step 1, values float32 
    7094 
    7095 > open C:/Users/lilyh/Downloads/Class3D_Job203/run_it025_class005.mrc
    7096 
    7097 Opened run_it025_class005.mrc as #6, grid size 256,256,256, pixel 1.09, shown
    7098 at level 0.000954, step 1, values float32 
    7099 
    7100 > open C:/Users/lilyh/Downloads/Class3D_Job203/run_it025_class004.mrc
    7101 
    7102 Opened run_it025_class004.mrc as #7, grid size 256,256,256, pixel 1.09, shown
    7103 at level 0.00105, step 1, values float32 
    7104 
    7105 > open C:/Users/lilyh/Downloads/Class3D_Job203/run_it025_class003.mrc
    7106 
    7107 Opened run_it025_class003.mrc as #8, grid size 256,256,256, pixel 1.09, shown
    7108 at level 0.00126, step 1, values float32 
    7109 
    7110 > open C:/Users/lilyh/Downloads/Class3D_Job203/run_it025_class002.mrc
    7111 
    7112 Opened run_it025_class002.mrc as #9, grid size 256,256,256, pixel 1.09, shown
    7113 at level 0.00117, step 1, values float32 
    7114 
    7115 > tile
    7116 
    7117 9 models tiled 
    7118 
    7119 > volume level 0.003
    7120 
    7121 Drag select of 5 run_it025_class001.mrc , 6 run_it025_class005.mrc , 8
    7122 run_it025_class003.mrc , 9 run_it025_class002.mrc 
    7123 
    7124 > select clear
    7125 
    7126 > select #7
    7127 
    7128 2 models selected 
    7129 Drag select of 7 run_it025_class004.mrc , 8 run_it025_class003.mrc , 9
    7130 run_it025_class002.mrc 
    7131 
    7132 > ui mousemode right "rotate selected models"
    7133 
    7134 > view matrix models
    7135 > #7,0.92803,0.075234,0.36484,-33.016,0.24446,-0.862,-0.44407,-124.01,0.28108,0.5013,-0.81835,100.71,#8,0.92803,0.075234,0.36484,135.73,0.24446,-0.862,-0.44407,-79.793,0.28108,0.5013,-0.81835,152.68,#9,0.92803,0.075234,0.36484,304.3,0.24446,-0.862,-0.44407,-35.115,0.28108,0.5013,-0.81835,205.29
    7136 
    7137 Drag select of 5 run_it025_class001.mrc , 6 run_it025_class005.mrc 
    7138 Drag select of 5 run_it025_class001.mrc 
    7139 
    7140 > ui mousemode right "rotate selected models"
    7141 
    7142 > view matrix models
    7143 > #5,0.11241,0.020331,-0.99345,439.78,0.051347,-0.99857,-0.014626,83.128,-0.99233,-0.049367,-0.11329,302.1
    7144 
    7145 > select #6
    7146 
    7147 2 models selected 
    7148 
    7149 > view matrix models
    7150 > #6,0.14293,-0.1056,-0.98408,645.1,-0.26054,-0.96324,0.06552,122.73,-0.95482,0.24703,-0.16519,273.18
    7151 
    7152 Drag select of 7 run_it025_class004.mrc 
    7153 
    7154 > view matrix models
    7155 > #7,0.068303,-0.088093,-0.99377,292.88,-0.47246,-0.88017,0.04555,-95.731,-0.8787,0.46641,-0.10174,157.79
    7156 
    7157 > select #8
    7158 
    7159 2 models selected 
    7160 
    7161 > view matrix models
    7162 > #8,-0.091781,-0.043884,-0.99481,485.95,-0.23436,-0.97001,0.064412,-68.059,-0.96781,0.23905,0.078744,240.43
    7163 
    7164 > select #9
    7165 
    7166 2 models selected 
    7167 
    7168 > view matrix models
    7169 > #9,0.074899,0.055928,-0.99562,621.2,-0.21459,-0.97413,-0.070864,-5.7458,-0.97383,0.21896,-0.06096,319.14
    7170 
    7171 Drag select of 7 run_it025_class004.mrc 
    7172 
    7173 > ui mousemode right "translate selected models"
    7174 
    7175 > view matrix models
    7176 > #7,0.068303,-0.088093,-0.99377,284.63,-0.47246,-0.88017,0.04555,-5.874,-0.8787,0.46641,-0.10174,157.79
    7177 
    7178 Drag select of 8 run_it025_class003.mrc 
    7179 
    7180 > view matrix models
    7181 > #8,-0.091781,-0.043884,-0.99481,484.98,-0.23436,-0.97001,0.064412,-30.174,-0.96781,0.23905,0.078744,240.43
    7182 
    7183 > select clear
    7184 
    7185 > close session
    7186 
    7187 > open C:/Users/lilyh/Downloads/Class3D_Job205/run_it025_class005.mrc
    7188 
    7189 Opened run_it025_class005.mrc as #1, grid size 256,256,256, pixel 1.09, shown
    7190 at level 0.0011, step 1, values float32 
    7191 
    7192 > open C:/Users/lilyh/Downloads/Class3D_Job205/run_it025_class004.mrc
    7193 
    7194 Opened run_it025_class004.mrc as #2, grid size 256,256,256, pixel 1.09, shown
    7195 at level 0.000697, step 1, values float32 
    7196 
    7197 > open C:/Users/lilyh/Downloads/Class3D_Job205/run_it025_class003.mrc
    7198 
    7199 Opened run_it025_class003.mrc as #3, grid size 256,256,256, pixel 1.09, shown
    7200 at level 0.000861, step 1, values float32 
    7201 
    7202 > open C:/Users/lilyh/Downloads/Class3D_Job205/run_it025_class002.mrc
    7203 
    7204 Opened run_it025_class002.mrc as #4, grid size 256,256,256, pixel 1.09, shown
    7205 at level 0.00113, step 1, values float32 
    7206 
    7207 > open C:/Users/lilyh/Downloads/Class3D_Job205/run_it025_class001.mrc
    7208 
    7209 Opened run_it025_class001.mrc as #5, grid size 256,256,256, pixel 1.09, shown
    7210 at level 0.000747, step 1, values float32 
    7211 
    7212 > open C:/Users/lilyh/Downloads/Class3D_Job205/run_it025_class006.mrc
    7213 
    7214 Opened run_it025_class006.mrc as #6, grid size 256,256,256, pixel 1.09, shown
    7215 at level 0.000788, step 1, values float32 
    7216 
    7217 > volume level 0.003
    7218 
    7219 > tile
    7220 
    7221 6 models tiled 
    7222 
    7223 > close session
    7224 
    7225 > open C:/Users/lilyh/Downloads/Class3D_Job215/run_it025_class003.mrc
    7226 
    7227 Opened run_it025_class003.mrc as #1, grid size 256,256,256, pixel 1.09, shown
    7228 at level 0.00159, step 1, values float32 
    7229 
    7230 > open C:/Users/lilyh/Downloads/Class3D_Job215/run_it025_class002.mrc
    7231 
    7232 Opened run_it025_class002.mrc as #2, grid size 256,256,256, pixel 1.09, shown
    7233 at level 0.0016, step 1, values float32 
    7234 
    7235 > open C:/Users/lilyh/Downloads/Class3D_Job215/run_it025_class001.mrc
    7236 
    7237 Opened run_it025_class001.mrc as #3, grid size 256,256,256, pixel 1.09, shown
    7238 at level 0.00158, step 1, values float32 
    7239 
    7240 > open C:/Users/lilyh/Downloads/Class3D_Job215/run_it025_class004.mrc
    7241 
    7242 Opened run_it025_class004.mrc as #4, grid size 256,256,256, pixel 1.09, shown
    7243 at level 0.00158, step 1, values float32 
    7244 
    7245 > tile
    7246 
    7247 4 models tiled 
    7248 
    7249 > volume level 0.003
    7250 
    7251 > open C:/Users/lilyh/Downloads/Refine3D_Job216/run_class001.mrc
    7252 
    7253 Opened run_class001.mrc as #5, grid size 256,256,256, pixel 1.09, shown at
    7254 level 0.00114, step 1, values float32 
    7255 
    7256 > close session
    7257 
    7258 > open C:/Users/lilyh/Downloads/Class3D_Job204/run_it025_class003.mrc
    7259 
    7260 Opened run_it025_class003.mrc as #1, grid size 256,256,256, pixel 1.09, shown
    7261 at level 0.00128, step 1, values float32 
    7262 
    7263 > open C:/Users/lilyh/Downloads/Class3D_Job204/run_it025_class002.mrc
    7264 
    7265 Opened run_it025_class002.mrc as #2, grid size 256,256,256, pixel 1.09, shown
    7266 at level 0.000939, step 1, values float32 
    7267 
    7268 > open C:/Users/lilyh/Downloads/Class3D_Job204/run_it025_class001.mrc
    7269 
    7270 Opened run_it025_class001.mrc as #3, grid size 256,256,256, pixel 1.09, shown
    7271 at level 0.000951, step 1, values float32 
    7272 
    7273 > open C:/Users/lilyh/Downloads/Class3D_Job204/run_it025_class004.mrc
    7274 
    7275 Opened run_it025_class004.mrc as #4, grid size 256,256,256, pixel 1.09, shown
    7276 at level 0.00102, step 1, values float32 
    7277 
    7278 > volume level 0.003
    7279 
    7280 > tile
    7281 
    7282 4 models tiled 
    7283 
    7284 > close session
    7285 
    7286 > open C:/Users/lilyh/Downloads/Class3D_job201/run_it025_class005.mrc
    7287 
    7288 Opened run_it025_class005.mrc as #1, grid size 256,256,256, pixel 1.09, shown
    7289 at level 0.00106, step 1, values float32 
    7290 
    7291 > open C:/Users/lilyh/Downloads/Class3D_job201/run_it025_class004.mrc
    7292 
    7293 Opened run_it025_class004.mrc as #2, grid size 256,256,256, pixel 1.09, shown
    7294 at level 0.00094, step 1, values float32 
    7295 
    7296 > open C:/Users/lilyh/Downloads/Class3D_job201/run_it025_class003.mrc
    7297 
    7298 Opened run_it025_class003.mrc as #3, grid size 256,256,256, pixel 1.09, shown
    7299 at level 0.00107, step 1, values float32 
    7300 
    7301 > open C:/Users/lilyh/Downloads/Class3D_job201/run_it025_class002.mrc
    7302 
    7303 Opened run_it025_class002.mrc as #4, grid size 256,256,256, pixel 1.09, shown
    7304 at level 0.00137, step 1, values float32 
    7305 
    7306 > open C:/Users/lilyh/Downloads/Class3D_job201/run_it025_class001.mrc
    7307 
    7308 Opened run_it025_class001.mrc as #5, grid size 256,256,256, pixel 1.09, shown
    7309 at level 0.00129, step 1, values float32 
    7310 
    7311 > open C:/Users/lilyh/Downloads/Class3D_job201/run_it025_class006.mrc
    7312 
    7313 Opened run_it025_class006.mrc as #6, grid size 256,256,256, pixel 1.09, shown
    7314 at level 0.00103, step 1, values float32 
    7315 
    7316 > tile
    7317 
    7318 6 models tiled 
    7319 
    7320 > volume level 0.003
    7321 
    7322 > close session
    7323 
    7324 > open C:/Users/lilyh/Downloads/Class3D_Job203/run_it025_class004.mrc
    7325 
    7326 Opened run_it025_class004.mrc as #1, grid size 256,256,256, pixel 1.09, shown
    7327 at level 0.00105, step 1, values float32 
    7328 
    7329 > open C:/Users/lilyh/Downloads/Class3D_Job203/run_it025_class003.mrc
    7330 
    7331 Opened run_it025_class003.mrc as #2, grid size 256,256,256, pixel 1.09, shown
    7332 at level 0.00126, step 1, values float32 
    7333 
    7334 > open C:/Users/lilyh/Downloads/Class3D_Job203/run_it025_class002.mrc
    7335 
    7336 Opened run_it025_class002.mrc as #3, grid size 256,256,256, pixel 1.09, shown
    7337 at level 0.00117, step 1, values float32 
    7338 
    7339 > open C:/Users/lilyh/Downloads/Class3D_Job203/run_it025_class001.mrc
    7340 
    7341 Opened run_it025_class001.mrc as #4, grid size 256,256,256, pixel 1.09, shown
    7342 at level 0.000995, step 1, values float32 
    7343 
    7344 > open C:/Users/lilyh/Downloads/Class3D_Job203/run_it025_class005.mrc
    7345 
    7346 Opened run_it025_class005.mrc as #5, grid size 256,256,256, pixel 1.09, shown
    7347 at level 0.000954, step 1, values float32 
    7348 
    7349 > volume level 0.003
    7350 
    7351 > tile
    7352 
    7353 5 models tiled 
    7354 
    7355 > open C:/Users/lilyh/Downloads/Class3D_job201/run_it025_class005.mrc
    7356 
    7357 Opened run_it025_class005.mrc as #6, grid size 256,256,256, pixel 1.09, shown
    7358 at level 0.00106, step 1, values float32 
    7359 
    7360 > volume level 0.003
    7361 
    7362 > close session
    7363 
    7364 > open C:/Users/lilyh/Downloads/Class3D_Job203/run_it025_class004.mrc
    7365 
    7366 Opened run_it025_class004.mrc as #1, grid size 256,256,256, pixel 1.09, shown
    7367 at level 0.00105, step 1, values float32 
    7368 
    7369 > open C:/Users/lilyh/Downloads/Class3D_Job203/run_it025_class003.mrc
    7370 
    7371 Opened run_it025_class003.mrc as #2, grid size 256,256,256, pixel 1.09, shown
    7372 at level 0.00126, step 1, values float32 
    7373 
    7374 > open C:/Users/lilyh/Downloads/Class3D_Job203/run_it025_class002.mrc
    7375 
    7376 Opened run_it025_class002.mrc as #3, grid size 256,256,256, pixel 1.09, shown
    7377 at level 0.00117, step 1, values float32 
    7378 
    7379 > open C:/Users/lilyh/Downloads/Class3D_Job203/run_it025_class001.mrc
    7380 
    7381 Opened run_it025_class001.mrc as #4, grid size 256,256,256, pixel 1.09, shown
    7382 at level 0.000995, step 1, values float32 
    7383 
    7384 > open C:/Users/lilyh/Downloads/Class3D_Job203/run_it025_class005.mrc
    7385 
    7386 Opened run_it025_class005.mrc as #5, grid size 256,256,256, pixel 1.09, shown
    7387 at level 0.000954, step 1, values float32 
    7388 
    7389 > volume level 0.003
    7390 
    7391 > tile
    7392 
    7393 5 models tiled 
    7394 
    7395 > open C:/Users/lilyh/Downloads/Class3D_Job204/run_it025_class004.mrc
    7396 
    7397 Opened run_it025_class004.mrc as #6, grid size 256,256,256, pixel 1.09, shown
    7398 at level 0.00102, step 1, values float32 
    7399 
    7400 > open C:/Users/lilyh/Downloads/Class3D_Job204/run_it025_class003.mrc
    7401 
    7402 Opened run_it025_class003.mrc as #7, grid size 256,256,256, pixel 1.09, shown
    7403 at level 0.00128, step 1, values float32 
    7404 
    7405 > open C:/Users/lilyh/Downloads/Class3D_Job204/run_it025_class002.mrc
    7406 
    7407 Opened run_it025_class002.mrc as #8, grid size 256,256,256, pixel 1.09, shown
    7408 at level 0.000939, step 1, values float32 
    7409 
    7410 > open C:/Users/lilyh/Downloads/Class3D_Job204/run_it025_class001.mrc
    7411 
    7412 Opened run_it025_class001.mrc as #9, grid size 256,256,256, pixel 1.09, shown
    7413 at level 0.000951, step 1, values float32 
    7414 
    7415 > tile
    7416 
    7417 9 models tiled 
    7418 
    7419 > volume level 0.003
    7420 
    7421 > close session
    7422 
    7423 > open C:/Users/lilyh/Downloads/Class3D_Job205/run_it025_class005.mrc
    7424 
    7425 Opened run_it025_class005.mrc as #1, grid size 256,256,256, pixel 1.09, shown
    7426 at level 0.0011, step 1, values float32 
    7427 
    7428 > open C:/Users/lilyh/Downloads/Class3D_Job205/run_it025_class004.mrc
    7429 
    7430 Opened run_it025_class004.mrc as #2, grid size 256,256,256, pixel 1.09, shown
    7431 at level 0.000697, step 1, values float32 
    7432 
    7433 > open C:/Users/lilyh/Downloads/Class3D_Job205/run_it025_class003.mrc
    7434 
    7435 Opened run_it025_class003.mrc as #3, grid size 256,256,256, pixel 1.09, shown
    7436 at level 0.000861, step 1, values float32 
    7437 
    7438 > open C:/Users/lilyh/Downloads/Class3D_Job205/run_it025_class002.mrc
    7439 
    7440 Opened run_it025_class002.mrc as #4, grid size 256,256,256, pixel 1.09, shown
    7441 at level 0.00113, step 1, values float32 
    7442 
    7443 > open C:/Users/lilyh/Downloads/Class3D_Job205/run_it025_class001.mrc
    7444 
    7445 Opened run_it025_class001.mrc as #5, grid size 256,256,256, pixel 1.09, shown
    7446 at level 0.000747, step 1, values float32 
    7447 
    7448 > open C:/Users/lilyh/Downloads/Class3D_Job205/run_it025_class006.mrc
    7449 
    7450 Opened run_it025_class006.mrc as #6, grid size 256,256,256, pixel 1.09, shown
    7451 at level 0.000788, step 1, values float32 
    7452 
    7453 > volume level 0.003
    7454 
    7455 > tile
    7456 
    7457 6 models tiled 
    7458 Drag select of 1 run_it025_class005.mrc , 2 run_it025_class004.mrc , 3
    7459 run_it025_class003.mrc , 4 run_it025_class002.mrc , 5 run_it025_class001.mrc ,
    7460 6 run_it025_class006.mrc 
    7461 
    7462 > color #1.1#2.1#3.1#4.1#5.1#6.1 dark gray
    7463 
    7464 > select clear
    7465 
    7466 > open C:/Users/lilyh/Downloads/Class3D_job201/run_it025_class001.mrc
    7467 
    7468 Opened run_it025_class001.mrc as #7, grid size 256,256,256, pixel 1.09, shown
    7469 at level 0.00129, step 1, values float32 
    7470 
    7471 > open C:/Users/lilyh/Downloads/Class3D_job201/run_it025_class006.mrc
    7472 
    7473 Opened run_it025_class006.mrc as #8, grid size 256,256,256, pixel 1.09, shown
    7474 at level 0.00103, step 1, values float32 
    7475 
    7476 > open C:/Users/lilyh/Downloads/Class3D_job201/run_it025_class005.mrc
    7477 
    7478 Opened run_it025_class005.mrc as #9, grid size 256,256,256, pixel 1.09, shown
    7479 at level 0.00106, step 1, values float32 
    7480 
    7481 > open C:/Users/lilyh/Downloads/Class3D_job201/run_it025_class004.mrc
    7482 
    7483 Opened run_it025_class004.mrc as #10, grid size 256,256,256, pixel 1.09, shown
    7484 at level 0.00094, step 1, values float32 
    7485 
    7486 > open C:/Users/lilyh/Downloads/Class3D_job201/run_it025_class003.mrc
    7487 
    7488 Opened run_it025_class003.mrc as #11, grid size 256,256,256, pixel 1.09, shown
    7489 at level 0.00107, step 1, values float32 
    7490 
    7491 > open C:/Users/lilyh/Downloads/Class3D_job201/run_it025_class002.mrc
    7492 
    7493 Opened run_it025_class002.mrc as #12, grid size 256,256,256, pixel 1.09, shown
    7494 at level 0.00137, step 1, values float32 
    7495 
    7496 > tile
    7497 
    7498 12 models tiled 
    7499 
    7500 > volume level 0.003
    7501 
    7502 > volume level 0.002
    7503 
    7504 > volume level 0.0015
    7505 
    7506 > close session
    7507 
    7508 > open C:/Users/lilyh/Downloads/Class3D_Job203/run_it025_class005.mrc
    7509 
    7510 Opened run_it025_class005.mrc as #1, grid size 256,256,256, pixel 1.09, shown
    7511 at level 0.000954, step 1, values float32 
    7512 
    7513 > open C:/Users/lilyh/Downloads/Class3D_Job203/run_it025_class004.mrc
    7514 
    7515 Opened run_it025_class004.mrc as #2, grid size 256,256,256, pixel 1.09, shown
    7516 at level 0.00105, step 1, values float32 
    7517 
    7518 > open C:/Users/lilyh/Downloads/Class3D_Job203/run_it025_class003.mrc
    7519 
    7520 Opened run_it025_class003.mrc as #3, grid size 256,256,256, pixel 1.09, shown
    7521 at level 0.00126, step 1, values float32 
    7522 
    7523 > open C:/Users/lilyh/Downloads/Class3D_Job203/run_it025_class002.mrc
    7524 
    7525 Opened run_it025_class002.mrc as #4, grid size 256,256,256, pixel 1.09, shown
    7526 at level 0.00117, step 1, values float32 
    7527 
    7528 > open C:/Users/lilyh/Downloads/Class3D_Job203/run_it025_class001.mrc
    7529 
    7530 Opened run_it025_class001.mrc as #5, grid size 256,256,256, pixel 1.09, shown
    7531 at level 0.000995, step 1, values float32 
    7532 
    7533 > volume level 0.0015
    7534 
    7535 > tile
    7536 
    7537 5 models tiled 
    7538 
    7539 > volume level 0.002
    7540 
    7541 > close session
    7542 
    7543 > open
    7544 > C:/Users/lilyh/Downloads/cryosparc_P122_J579_class_00_00124_volume_sharp.mrc
    7545 
    7546 Opened cryosparc_P122_J579_class_00_00124_volume_sharp.mrc as #1, grid size
    7547 128,128,128, pixel 2.17, shown at level 0.0717, step 1, values float32 
    7548 
    7549 > open
    7550 > C:/Users/lilyh/Downloads/cryosparc_P122_J579_class_02_00124_volume_sharp.mrc
    7551 
    7552 Opened cryosparc_P122_J579_class_02_00124_volume_sharp.mrc as #2, grid size
    7553 128,128,128, pixel 2.17, shown at level 0.0743, step 1, values float32 
    7554 
    7555 > volume level 0.02
    7556 
    7557 > volume level 0.2
    7558 
    7559 > tile
    7560 
    7561 2 models tiled 
    7562 
    7563 > ~tile
    7564 
    7565 > ui mousemode right "rotate selected models"
    7566 
    7567 > select #2
    7568 
    7569 2 models selected 
    7570 
    7571 > view matrix models
    7572 > #2,-0.82076,0.49498,-0.28521,213.75,-0.49668,-0.86496,-0.071823,349.79,-0.28224,0.082706,0.95577,28.08
    7573 
    7574 > ui mousemode right "translate selected models"
    7575 
    7576 > view matrix models
    7577 > #2,-0.82076,0.49498,-0.28521,242.1,-0.49668,-0.86496,-0.071823,287.56,-0.28224,0.082706,0.95577,21.525
    7578 
    7579 > ui mousemode right "rotate selected models"
    7580 
    7581 > view matrix models
    7582 > #2,-0.60426,0.76104,-0.23599,166.93,-0.78805,-0.61457,0.035887,275.03,-0.11772,0.20766,0.97109,-21.167
    7583 
    7584 > select #1
    7585 
    7586 2 models selected 
    7587 
    7588 > ui mousemode right "translate selected models"
    7589 
    7590 > view matrix models
    7591 > #1,-0.81076,0.33009,0.48343,108.17,-0.10199,0.73356,-0.67193,181.79,-0.57642,-0.59408,-0.56108,386.98
    7592 
    7593 > select clear
    7594 
    7595 > close session
    7596 
    7597 > open
    7598 > C:/Users/lilyh/Downloads/cryosparc_P122_J579_class_00_00124_volume_sharp.mrc
    7599 
    7600 Opened cryosparc_P122_J579_class_00_00124_volume_sharp.mrc as #1, grid size
    7601 128,128,128, pixel 2.17, shown at level 0.0717, step 1, values float32 
    7602 
    7603 > open
    7604 > C:/Users/lilyh/Downloads/cryosparc_P122_J579_class_02_00124_volume_sharp.mrc
    7605 
    7606 Opened cryosparc_P122_J579_class_02_00124_volume_sharp.mrc as #2, grid size
    7607 128,128,128, pixel 2.17, shown at level 0.0743, step 1, values float32 
    7608 
    7609 > open
    7610 > C:/Users/lilyh/Desktop/output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
    7611 
    7612 Chain information for
    7613 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
    7614 #3 
    7615 --- 
    7616 Chain | Description 
    7617 B | No description available 
    7618 C | No description available 
    7619  
    7620 
    7621 > open
    7622 > C:/Users/lilyh/Desktop/output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
    7623 
    7624 Chain information for
    7625 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
    7626 #4 
    7627 --- 
    7628 Chain | Description 
    7629 B | No description available 
    7630 C | No description available 
    7631  
    7632 Drag select of 260 residues 
    7633 
    7634 > ui mousemode right "translate selected models"
    7635 
    7636 [Repeated 1 time(s)]
    7637 
    7638 > view matrix models
    7639 > #3,1,0,0,121.01,0,1,0,116.62,0,0,1,0,#4,1,0,0,121.01,0,1,0,116.62,0,0,1,0
    7640 
    7641 > view matrix models
    7642 > #3,1,0,0,118.88,0,1,0,140.35,0,0,1,131.07,#4,1,0,0,118.88,0,1,0,140.35,0,0,1,131.07
    7643 
    7644 > volume level 0.2
    7645 
    7646 > ui mousemode right "rotate selected models"
    7647 
    7648 > view matrix models
    7649 > #3,0.99439,-0.01493,0.10467,119.11,0.051869,0.93155,-0.35989,139.49,-0.092133,0.3633,0.9271,131.09,#4,0.99439,-0.01493,0.10467,119.11,0.051869,0.93155,-0.35989,139.49,-0.092133,0.3633,0.9271,131.09
    7650 
    7651 > ui mousemode right "rotate selected models"
    7652 
    7653 Drag select of 6 residues 
    7654 
    7655 > view matrix models
    7656 > #4,-0.38032,-0.18041,0.90709,128.09,-0.73751,-0.53266,-0.41516,142.61,0.55807,-0.82688,0.069528,124.96
    7657 
    7658 > select #1
    7659 
    7660 2 models selected 
    7661 
    7662 > fitmap #3 inMap #1
    7663 
    7664 Fit molecule
    7665 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
    7666 (#3) to map cryosparc_P122_J579_class_00_00124_volume_sharp.mrc (#1) using
    7667 4737 atoms 
    7668 average map value = 0.2555, steps = 136 
    7669 shifted from previous position = 15.6 
    7670 rotated from previous position = 35.2 degrees 
    7671 atoms outside contour = 1739, contour level = 0.2 
    7672  
    7673 Position of
    7674 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
    7675 (#3) relative to cryosparc_P122_J579_class_00_00124_volume_sharp.mrc (#1)
    7676 coordinates: 
    7677 Matrix rotation and translation 
    7678 0.98556459 0.00194738 -0.16928863 133.30506575 
    7679 -0.13601960 0.60447552 -0.78492548 139.94249861 
    7680 0.10080228 0.79662133 0.59601455 123.84832233 
    7681 Axis 0.98210478 -0.16772034 -0.08567437 
    7682 Axis point 0.00000000 -51.75014692 225.05652621 
    7683 Rotation angle (degrees) 53.62786733 
    7684 Shift along axis 96.83771109 
    7685  
    7686 
    7687 > hide #!2 models
    7688 
    7689 Drag select of 6 residues 
    7690 
    7691 > ui mousemode right "rotate selected models"
    7692 
    7693 > view matrix models
    7694 > #4,0.031318,0.76274,-0.64594,124.72,0.99934,-0.035783,0.006198,133.31,-0.018386,-0.64571,-0.76336,127.56
    7695 
    7696 > fitmap #4 inMap #1
    7697 
    7698 Fit molecule
    7699 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
    7700 (#4) to map cryosparc_P122_J579_class_00_00124_volume_sharp.mrc (#1) using
    7701 4737 atoms 
    7702 average map value = 0.2742, steps = 104 
    7703 shifted from previous position = 17 
    7704 rotated from previous position = 24 degrees 
    7705 atoms outside contour = 1545, contour level = 0.2 
    7706  
    7707 Position of
    7708 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
    7709 (#4) relative to cryosparc_P122_J579_class_00_00124_volume_sharp.mrc (#1)
    7710 coordinates: 
    7711 Matrix rotation and translation 
    7712 0.13533655 0.44155599 -0.88696805 137.99152580 
    7713 0.99063175 -0.07678487 0.11292838 141.93198995 
    7714 -0.01824152 -0.89394206 -0.44781117 128.33340948 
    7715 Axis -0.69983042 -0.60381280 0.38163790 
    7716 Axis point 0.00000000 65.78654861 83.15596640 
    7717 Rotation angle (degrees) 133.99771996 
    7718 Shift along axis -133.29412642 
    7719  
    7720 
    7721 > fitmap #3 inMap #1
    7722 
    7723 Fit molecule
    7724 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
    7725 (#3) to map cryosparc_P122_J579_class_00_00124_volume_sharp.mrc (#1) using
    7726 4737 atoms 
    7727 average map value = 0.2555, steps = 40 
    7728 shifted from previous position = 0.00486 
    7729 rotated from previous position = 0.0199 degrees 
    7730 atoms outside contour = 1740, contour level = 0.2 
    7731  
    7732 Position of
    7733 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
    7734 (#3) relative to cryosparc_P122_J579_class_00_00124_volume_sharp.mrc (#1)
    7735 coordinates: 
    7736 Matrix rotation and translation 
    7737 0.98552600 0.00208071 -0.16951152 133.30889725 
    7738 -0.13629950 0.60429427 -0.78501648 139.94459415 
    7739 0.10080144 0.79675850 0.59583132 123.84874121 
    7740 Axis 0.98206547 -0.16782730 -0.08591515 
    7741 Axis point 0.00000000 -51.72488393 225.03554041 
    7742 Rotation angle (degrees) 53.64220726 
    7743 Shift along axis 96.79105807 
    7744  
    7745 Drag select of 2 residues 
    7746 
    7747 > ui mousemode right "rotate selected models"
    7748 
    7749 > view matrix models
    7750 > #3,-0.62373,0.018902,-0.78141,126.25,-0.77429,-0.15166,0.61439,145.19,-0.1069,0.98825,0.10923,120.94
    7751 
    7752 > fitmap #3 inMap #1
    7753 
    7754 Fit molecule
    7755 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
    7756 (#3) to map cryosparc_P122_J579_class_00_00124_volume_sharp.mrc (#1) using
    7757 4737 atoms 
    7758 average map value = 0.2689, steps = 116 
    7759 shifted from previous position = 15.4 
    7760 rotated from previous position = 12.3 degrees 
    7761 atoms outside contour = 1605, contour level = 0.2 
    7762  
    7763 Position of
    7764 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
    7765 (#3) relative to cryosparc_P122_J579_class_00_00124_volume_sharp.mrc (#1)
    7766 coordinates: 
    7767 Matrix rotation and translation 
    7768 -0.71040150 0.15495235 -0.68652708 138.47625368 
    7769 -0.69954593 -0.26250889 0.66462361 142.65718785 
    7770 -0.07723447 0.95240686 0.29488300 129.84315872 
    7771 Axis 0.26445305 -0.55989809 -0.78522526 
    7772 Axis point 102.66199128 -8.28660745 0.00000000 
    7773 Rotation angle (degrees) 147.03611534 
    7774 Shift along axis -145.20914845 
    7775  
    7776 
    7777 > select #1
    7778 
    7779 2 models selected 
    7780 
    7781 > transparency #1.1 40
    7782 
    7783 > select clear
    7784 
    7785 > volume #1 level 0.1836
    7786 
    7787 Drag select of 5 residues 
    7788 
    7789 > ui mousemode right "rotate selected models"
    7790 
    7791 > view matrix models
    7792 > #3,-0.83225,0.065146,-0.55057,137.99,-0.53869,-0.3298,0.77527,142.68,-0.13107,0.9418,0.30957,128.36,#4,0.3305,0.44933,-0.82998,137.43,0.94315,-0.12452,0.30815,142.13,0.035113,-0.88464,-0.46494,126.8
    7793 
    7794 > fitmap #3 inMap #1
    7795 
    7796 Fit molecule
    7797 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
    7798 (#3) to map cryosparc_P122_J579_class_00_00124_volume_sharp.mrc (#1) using
    7799 4737 atoms 
    7800 average map value = 0.2688, steps = 64 
    7801 shifted from previous position = 1.78 
    7802 rotated from previous position = 11.4 degrees 
    7803 atoms outside contour = 1465, contour level = 0.18355 
    7804  
    7805 Position of
    7806 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
    7807 (#3) relative to cryosparc_P122_J579_class_00_00124_volume_sharp.mrc (#1)
    7808 coordinates: 
    7809 Matrix rotation and translation 
    7810 -0.71708570 0.14797209 -0.68109641 138.44697916 
    7811 -0.69213214 -0.26629377 0.67085073 142.61883019 
    7812 -0.08210455 0.95246620 0.29337169 129.79896388 
    7813 Axis 0.26331008 -0.56005657 -0.78549630 
    7814 Axis point 102.26986916 -7.56904057 0.00000000 
    7815 Rotation angle (degrees) 147.67235336 
    7816 Shift along axis -145.37673364 
    7817  
    7818 
    7819 > fitmap #4 inMap #1
    7820 
    7821 Fit molecule
    7822 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
    7823 (#4) to map cryosparc_P122_J579_class_00_00124_volume_sharp.mrc (#1) using
    7824 4737 atoms 
    7825 average map value = 0.2742, steps = 60 
    7826 shifted from previous position = 1.68 
    7827 rotated from previous position = 11.8 degrees 
    7828 atoms outside contour = 1444, contour level = 0.18355 
    7829  
    7830 Position of
    7831 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
    7832 (#4) relative to cryosparc_P122_J579_class_00_00124_volume_sharp.mrc (#1)
    7833 coordinates: 
    7834 Matrix rotation and translation 
    7835 0.13846539 0.44187094 -0.88632805 137.99583077 
    7836 0.99021338 -0.07754580 0.11603496 141.92403457 
    7837 -0.01745854 -0.89372073 -0.44828392 128.33220276 
    7838 Axis -0.70094544 -0.60314602 0.38064468 
    7839 Axis point 0.00000000 65.93479466 83.00386969 
    7840 Rotation angle (degrees) 133.92229560 
    7841 Shift along axis -133.47949403 
    7842  
    7843 
    7844 > hide #3 models
    7845 
    7846 > hide #4 models
    7847 
    7848 > show #!2 models
    7849 
    7850 > hide #!1 models
    7851 
    7852 > select #2
    7853 
    7854 2 models selected 
    7855 
    7856 > transparency #2.1 30
    7857 
    7858 > show #3 models
    7859 
    7860 > show #4 models
    7861 
    7862 Drag select of 19 residues 
    7863 
    7864 > ui mousemode right "rotate selected models"
    7865 
    7866 > view matrix models
    7867 > #3,-0.50701,0.052533,-0.86034,137.09,0.30081,0.94617,-0.1195,147.58,0.80775,-0.31938,-0.49552,140.25,#4,-0.10252,0.58529,-0.80432,137.06,-0.54894,-0.7076,-0.44494,146.72,-0.82955,0.3959,0.39383,141.7
    7868 
    7869 > fitmap #4 inMap #2
    7870 
    7871 Fit molecule
    7872 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
    7873 (#4) to map cryosparc_P122_J579_class_02_00124_volume_sharp.mrc (#2) using
    7874 4737 atoms 
    7875 average map value = 0.2256, steps = 96 
    7876 shifted from previous position = 16 
    7877 rotated from previous position = 11.4 degrees 
    7878 atoms outside contour = 2119, contour level = 0.2 
    7879  
    7880 Position of
    7881 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
    7882 (#4) relative to cryosparc_P122_J579_class_02_00124_volume_sharp.mrc (#2)
    7883 coordinates: 
    7884 Matrix rotation and translation 
    7885 -0.26691230 0.49881238 -0.82458724 135.25686697 
    7886 -0.57463650 -0.76926112 -0.27933905 145.17926819 
    7887 -0.77366065 0.39927888 0.49196104 157.75433495 
    7888 Axis 0.53392982 -0.04006853 -0.84457887 
    7889 Axis point 147.74647439 32.55639145 0.00000000 
    7890 Rotation angle (degrees) 140.54339965 
    7891 Shift along axis -66.83542338 
    7892  
    7893 
    7894 > fitmap #3 inMap #2
    7895 
    7896 Fit molecule
    7897 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
    7898 (#3) to map cryosparc_P122_J579_class_02_00124_volume_sharp.mrc (#2) using
    7899 4737 atoms 
    7900 average map value = 0.2187, steps = 76 
    7901 shifted from previous position = 13.2 
    7902 rotated from previous position = 11.5 degrees 
    7903 atoms outside contour = 2261, contour level = 0.2 
    7904  
    7905 Position of
    7906 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
    7907 (#3) relative to cryosparc_P122_J579_class_02_00124_volume_sharp.mrc (#2)
    7908 coordinates: 
    7909 Matrix rotation and translation 
    7910 -0.47059802 0.13194765 -0.87242614 133.11498143 
    7911 0.48403457 0.86530475 -0.13022396 145.00370756 
    7912 0.73773172 -0.48356754 -0.47107791 153.13314678 
    7913 Axis -0.20961825 -0.95521326 0.20887275 
    7914 Axis point -1.32659429 0.00000000 122.51744697 
    7915 Rotation angle (degrees) 122.56020872 
    7916 Shift along axis -134.42745161 
    7917  
    7918 
    7919 > hide #4 models
    7920 
    7921 > hide #3 models
    7922 
    7923 > show #!1 models
    7924 
    7925 > hide #!2 models
    7926 
    7927 > open C:/Users/lilyh/Downloads/cryosparc_P104_J3849_class_01_00019_volume.mrc
    7928 
    7929 Opened cryosparc_P104_J3849_class_01_00019_volume.mrc as #5, grid size
    7930 100,100,100, pixel 2.78, shown at level 0.077, step 1, values float32 
    7931 
    7932 > volume #5 level 0.1687
    7933 
    7934 > fitmap #1 inMap #5
    7935 
    7936 Fit map cryosparc_P122_J579_class_00_00124_volume_sharp.mrc in map
    7937 cryosparc_P104_J3849_class_01_00019_volume.mrc using 10424 points 
    7938 correlation = 0.8079, correlation about mean = 0.2155, overlap = 958.6 
    7939 steps = 236, shift = 15.7, angle = 41.6 degrees 
    7940  
    7941 Position of cryosparc_P122_J579_class_00_00124_volume_sharp.mrc (#1) relative
    7942 to cryosparc_P104_J3849_class_01_00019_volume.mrc (#5) coordinates: 
    7943 Matrix rotation and translation 
    7944 0.76523195 -0.59437069 0.24727220 87.70900441 
    7945 0.63192762 0.76683867 -0.11236516 -42.62192586 
    7946 -0.12283133 0.24224355 0.96240871 2.21063063 
    7947 Axis 0.26680177 0.27845982 0.92264671 
    7948 Axis point 109.64767691 98.16464158 0.00000000 
    7949 Rotation angle (degrees) 41.64816803 
    7950 Shift along axis 13.57205455 
    7951  
    7952 
    7953 > volume #5 level 0.2035
    7954 
    7955 > hide #!5 models
    7956 
    7957 > volume #1 level 0.1653
    7958 
    7959 > show #!5 models
    7960 
    7961 > hide #!5 models
    7962 
    7963 > show #4 models
    7964 
    7965 Drag select of 23 residues 
    7966 
    7967 > ui mousemode right "rotate selected models"
    7968 
    7969 > view matrix models
    7970 > #4,0.09026,0.5094,-0.85579,133.11,0.99122,0.037447,0.12683,137.19,0.096655,-0.85972,-0.50154,150.09
    7971 
    7972 > fitmap #4 inMap #1
    7973 
    7974 Fit molecule
    7975 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
    7976 (#4) to map cryosparc_P122_J579_class_00_00124_volume_sharp.mrc (#1) using
    7977 4737 atoms 
    7978 average map value = 0.2742, steps = 140 
    7979 shifted from previous position = 11.4 
    7980 rotated from previous position = 39.6 degrees 
    7981 atoms outside contour = 1320, contour level = 0.16533 
    7982  
    7983 Position of
    7984 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
    7985 (#4) relative to cryosparc_P122_J579_class_00_00124_volume_sharp.mrc (#1)
    7986 coordinates: 
    7987 Matrix rotation and translation 
    7988 0.13637045 0.44207814 -0.88654955 138.00552132 
    7989 0.99049224 -0.07721288 0.11385685 141.92033464 
    7990 -0.01811942 -0.89364713 -0.44840450 128.33544356 
    7991 Axis -0.70026483 -0.60360166 0.38117478 
    7992 Axis point -0.00000000 65.79183148 83.11487984 
    7993 Rotation angle (degrees) 133.99721845 
    7994 Shift along axis -133.38552807 
    7995  
    7996 
    7997 > volume #1 level 0.1858
    7998 
    7999 > show #3 models
    8000 
    8001 Drag select of 9 residues 
    8002 
    8003 > ui mousemode right "rotate selected models"
    8004 
    8005 > view matrix models
    8006 > #3,-0.32184,0.3742,-0.86971,132.62,-0.93442,-0.27357,0.22808,146.15,-0.15258,0.88608,0.43771,147.49
    8007 
    8008 > fitmap #3 inMap #1
    8009 
    8010 Fit molecule
    8011 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
    8012 (#3) to map cryosparc_P122_J579_class_00_00124_volume_sharp.mrc (#1) using
    8013 4737 atoms 
    8014 average map value = 0.2688, steps = 92 
    8015 shifted from previous position = 11.2 
    8016 rotated from previous position = 12.4 degrees 
    8017 atoms outside contour = 1491, contour level = 0.18583 
    8018  
    8019 Position of
    8020 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
    8021 (#3) relative to cryosparc_P122_J579_class_00_00124_volume_sharp.mrc (#1)
    8022 coordinates: 
    8023 Matrix rotation and translation 
    8024 -0.71613368 0.14940334 -0.68178534 138.45919970 
    8025 -0.69325450 -0.26553269 0.66999303 142.61665337 
    8026 -0.08093709 0.95245530 0.29373143 129.80825196 
    8027 Axis 0.26329719 -0.56008065 -0.78548345 
    8028 Axis point 102.31616735 -7.69697547 0.00000000 
    8029 Rotation angle (degrees) 147.56147530 
    8030 Shift along axis -145.38314455 
    8031  
    8032 
    8033 > volume #1 level 0.1767
    8034 
    8035 Drag select of 9 residues 
    8036 
    8037 > ui mousemode right "rotate selected models"
    8038 
    8039 > view matrix models
    8040 > #3,-0.50674,0.34267,-0.79107,139.7,-0.82603,-0.45562,0.33177,138.69,-0.24674,0.82158,0.51394,142.36,#4,-0.13956,0.32165,-0.93652,139.26,0.95264,0.30167,-0.038355,138.32,0.27019,-0.89752,-0.34852,140.77
    8041 
    8042 > fitmap #3 inMap #1
    8043 
    8044 Fit molecule
    8045 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
    8046 (#3) to map cryosparc_P122_J579_class_00_00124_volume_sharp.mrc (#1) using
    8047 4737 atoms 
    8048 average map value = 0.2688, steps = 108 
    8049 shifted from previous position = 3.66 
    8050 rotated from previous position = 23.1 degrees 
    8051 atoms outside contour = 1421, contour level = 0.17672 
    8052  
    8053 Position of
    8054 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
    8055 (#3) relative to cryosparc_P122_J579_class_00_00124_volume_sharp.mrc (#1)
    8056 coordinates: 
    8057 Matrix rotation and translation 
    8058 -0.71574780 0.14957956 -0.68215180 138.43929202 
    8059 -0.69369701 -0.26495699 0.66976289 142.65725088 
    8060 -0.08055805 0.95258796 0.29340527 129.79726519 
    8061 Axis 0.26339007 -0.56025381 -0.78532881 
    8062 Axis point 102.33277642 -7.73811179 0.00000000 
    8063 Rotation angle (degrees) 147.52755502 
    8064 Shift along axis -145.39426500 
    8065  
    8066 
    8067 > hide #4 models
    8068 
    8069 > hide #3 models
    8070 
    8071 > show #!2 models
    8072 
    8073 > hide #!2 models
    8074 
    8075 > open "C:/Users/lilyh/Downloads/cryosparc_P104_J3854_class_00_00019_volume
    8076 > (1).mrc"
    8077 
    8078 Opened cryosparc_P104_J3854_class_00_00019_volume (1).mrc as #6, grid size
    8079 100,100,100, pixel 2.78, shown at level 0.0777, step 1, values float32 
    8080 
    8081 > open "C:/Users/lilyh/Downloads/cryosparc_P104_J3849_class_01_00019_volume
    8082 > (1).mrc"
    8083 
    8084 Opened cryosparc_P104_J3849_class_01_00019_volume (1).mrc as #7, grid size
    8085 100,100,100, pixel 2.78, shown at level 0.077, step 1, values float32 
    8086 
    8087 > volume #7 level 0.09781
    8088 
    8089 > volume #6 level 0.1267
    8090 
    8091 > volume #6 level 0.123
    8092 
    8093 > volume #6 level 0.1475
    8094 
    8095 > volume #7 level 0.1337
    8096 
    8097 > volume #7 level 0.1489
    8098 
    8099 > volume #6 level 0.149
    8100 
    8101 > close #7
    8102 
    8103 > fitmap #6 inMap #1
    8104 
    8105 Fit map cryosparc_P104_J3854_class_00_00019_volume (1).mrc in map
    8106 cryosparc_P122_J579_class_00_00124_volume_sharp.mrc using 5052 points 
    8107 correlation = 0.8841, correlation about mean = 0.5569, overlap = 458.8 
    8108 steps = 92, shift = 0.816, angle = 5.08 degrees 
    8109  
    8110 Position of cryosparc_P104_J3854_class_00_00019_volume (1).mrc (#6) relative
    8111 to cryosparc_P122_J579_class_00_00124_volume_sharp.mrc (#1) coordinates: 
    8112 Matrix rotation and translation 
    8113 0.81555363 0.56673568 -0.11697413 -38.24119429 
    8114 -0.52459142 0.80939265 0.26398366 66.21842924 
    8115 0.24428696 -0.15392921 0.95740779 -21.22450642 
    8116 Axis -0.34166254 -0.29534717 -0.89220892 
    8117 Axis point 99.65908914 92.40817847 0.00000000 
    8118 Rotation angle (degrees) 37.70435627 
    8119 Shift along axis 12.44485188 
    8120  
    8121 
    8122 > fitmap #6 inMap #5
    8123 
    8124 Fit map cryosparc_P104_J3854_class_00_00019_volume (1).mrc in map
    8125 cryosparc_P104_J3849_class_01_00019_volume.mrc using 5052 points 
    8126 correlation = 1, correlation about mean = 0.9999, overlap = 601.7 
    8127 steps = 60, shift = 0.818, angle = 5.12 degrees 
    8128  
    8129 Position of cryosparc_P104_J3854_class_00_00019_volume (1).mrc (#6) relative
    8130 to cryosparc_P104_J3849_class_01_00019_volume.mrc (#5) coordinates: 
    8131 Matrix rotation and translation 
    8132 0.99999969 0.00070324 0.00036556 -0.15984070 
    8133 -0.00070335 0.99999971 0.00030313 0.07555488 
    8134 -0.00036535 -0.00030338 0.99999989 0.07006065 
    8135 Axis -0.35735128 0.43064975 -0.82875862 
    8136 Axis point 87.98866178 211.27603754 0.00000000 
    8137 Rotation angle (degrees) 0.04862214 
    8138 Shift along axis 0.03159360 
    8139  
    8140 
    8141 > fitmap #5 inMap #1
    8142 
    8143 Fit map cryosparc_P104_J3849_class_01_00019_volume.mrc in map
    8144 cryosparc_P122_J579_class_00_00124_volume_sharp.mrc using 3734 points 
    8145 correlation = 0.9083, correlation about mean = 0.4662, overlap = 430.2 
    8146 steps = 52, shift = 0.983, angle = 2.62 degrees 
    8147  
    8148 Position of cryosparc_P104_J3849_class_01_00019_volume.mrc (#5) relative to
    8149 cryosparc_P122_J579_class_00_00124_volume_sharp.mrc (#1) coordinates: 
    8150 Matrix rotation and translation 
    8151 0.78154503 0.61086849 -0.12659800 -38.46538511 
    8152 -0.56423810 0.77872567 0.27426573 74.83696355 
    8153 0.26612541 -0.14291960 0.95328446 -25.00206973 
    8154 Axis -0.31910885 -0.30039770 -0.89884969 
    8155 Axis point 102.59521868 93.24976900 0.00000000 
    8156 Rotation angle (degrees) 40.81906577 
    8157 Shift along axis 12.26689573 
    8158  
    8159 
    8160 > volume #5 level 0.149
    8161 
    8162 > close #6
    8163 
    8164 > fitmap #5 inMap #1
    8165 
    8166 Fit map cryosparc_P104_J3849_class_01_00019_volume.mrc in map
    8167 cryosparc_P122_J579_class_00_00124_volume_sharp.mrc using 5016 points 
    8168 correlation = 0.8849, correlation about mean = 0.5542, overlap = 458.2 
    8169 steps = 80, shift = 0.341, angle = 3.19 degrees 
    8170  
    8171 Position of cryosparc_P104_J3849_class_01_00019_volume.mrc (#5) relative to
    8172 cryosparc_P122_J579_class_00_00124_volume_sharp.mrc (#1) coordinates: 
    8173 Matrix rotation and translation 
    8174 0.81494805 0.56731495 -0.11837831 -38.08192224 
    8175 -0.52490148 0.80913880 0.26414548 66.31218937 
    8176 0.24563816 -0.15312790 0.95719055 -21.48783322 
    8177 Axis -0.34075206 -0.29726162 -0.89192127 
    8178 Axis point 99.83712720 92.22649630 0.00000000 
    8179 Rotation angle (degrees) 37.75476089 
    8180 Shift along axis 12.42988002 
    8181  
    8182 
    8183 > show #3 models
    8184 
    8185 > ui mousemode right "rotate selected models"
    8186 
    8187 > view matrix models
    8188 > #3,-0.96937,0.21384,-0.1208,141.73,-0.22179,-0.5509,0.80456,145.72,0.10549,0.80671,0.58145,145.79,#4,0.87271,0.14575,-0.46597,138.86,0.48676,-0.18553,0.85361,146.78,0.03796,-0.97177,-0.23286,142.53
    8189 
    8190 > ui mousemode right "translate selected models"
    8191 
    8192 > view matrix models
    8193 > #3,-0.96937,0.21384,-0.1208,140.12,-0.22179,-0.5509,0.80456,136.76,0.10549,0.80671,0.58145,143.16,#4,0.87271,0.14575,-0.46597,137.25,0.48676,-0.18553,0.85361,137.82,0.03796,-0.97177,-0.23286,139.9
    8194 
    8195 > fitmap #3 inMap #5
    8196 
    8197 Fit molecule
    8198 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
    8199 (#3) to map cryosparc_P104_J3849_class_01_00019_volume.mrc (#5) using 4737
    8200 atoms 
    8201 average map value = 0.2668, steps = 208 
    8202 shifted from previous position = 2.92 
    8203 rotated from previous position = 31.4 degrees 
    8204 atoms outside contour = 1519, contour level = 0.149 
    8205  
    8206 Position of
    8207 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
    8208 (#3) relative to cryosparc_P104_J3849_class_01_00019_volume.mrc (#5)
    8209 coordinates: 
    8210 Matrix rotation and translation 
    8211 -0.81080467 0.20616304 -0.54780710 139.35960081 
    8212 -0.55233221 -0.57923773 0.59951051 137.59557427 
    8213 -0.19371363 0.78865741 0.58351913 140.28578361 
    8214 Axis 0.22040457 -0.41260955 -0.88384115 
    8215 Axis point 96.82418453 14.06069474 0.00000000 
    8216 Rotation angle (degrees) 154.59016123 
    8217 Shift along axis -150.04810474 
    8218  
    8219 
    8220 > show #4 models
    8221 
    8222 Drag select of 2 residues 
    8223 
    8224 > ui mousemode right "rotate selected models"
    8225 
    8226 > view matrix models
    8227 > #4,0.14863,0.80296,-0.57721,142.09,0.984,-0.06209,0.167,134.15,0.098258,-0.5928,-0.79934,139.24
    8228 
    8229 > ui mousemode right "translate selected models"
    8230 
    8231 > view matrix models
    8232 > #4,0.14863,0.80296,-0.57721,142.69,0.984,-0.06209,0.167,140.01,0.098258,-0.5928,-0.79934,141.56
    8233 
    8234 > fitmap #4 inMap #5
    8235 
    8236 Fit molecule
    8237 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
    8238 (#4) to map cryosparc_P104_J3849_class_01_00019_volume.mrc (#5) using 4737
    8239 atoms 
    8240 average map value = 0.2681, steps = 128 
    8241 shifted from previous position = 3.92 
    8242 rotated from previous position = 28.2 degrees 
    8243 atoms outside contour = 1432, contour level = 0.149 
    8244  
    8245 Position of
    8246 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
    8247 (#4) relative to cryosparc_P104_J3849_class_01_00019_volume.mrc (#5)
    8248 coordinates: 
    8249 Matrix rotation and translation 
    8250 0.39950150 0.44819153 -0.79970181 137.49352972 
    8251 0.90099617 -0.03102539 0.43271628 138.90692727 
    8252 0.16912871 -0.89339905 -0.41621353 140.30829554 
    8253 Axis -0.77842029 -0.56869664 0.26579311 
    8254 Axis point 0.00000000 83.79869954 74.12315287 
    8255 Rotation angle (degrees) 121.59211575 
    8256 Shift along axis -148.73067764 
    8257  
    8258 
    8259 > hide #4 models
    8260 
    8261 > hide #3 models
    8262 
    8263 > show #4 models
    8264 
    8265 > show #3 models
    8266 
    8267 > hide #!1 models
    8268 
    8269 > select #5
    8270 
    8271 2 models selected 
    8272 
    8273 > transparency #5.1 40
    8274 
    8275 > select clear
    8276 
    8277 Drag select of 31 residues 
    8278 
    8279 > ui mousemode right "rotate selected models"
    8280 
    8281 > view matrix models
    8282 > #3,0.78315,-0.20016,0.58874,148.18,0.51615,0.73727,-0.43593,135.95,-0.3468,0.64527,0.6807,140.6,#4,-0.36052,-0.47912,0.80029,150.09,-0.84976,-0.18509,-0.49361,134.73,0.38463,-0.85801,-0.3404,140.84
    8283 
    8284 > fitmap #4 inMap #5
    8285 
    8286 Fit molecule
    8287 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
    8288 (#4) to map cryosparc_P104_J3849_class_01_00019_volume.mrc (#5) using 4737
    8289 atoms 
    8290 average map value = 0.2593, steps = 152 
    8291 shifted from previous position = 11.1 
    8292 rotated from previous position = 24.1 degrees 
    8293 atoms outside contour = 1623, contour level = 0.149 
    8294  
    8295 Position of
    8296 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_2_model_5-coot-0.pdb
    8297 (#4) relative to cryosparc_P104_J3849_class_01_00019_volume.mrc (#5)
    8298 coordinates: 
    8299 Matrix rotation and translation 
    8300 -0.71780569 -0.39253813 0.57503815 138.86001325 
    8301 -0.68092381 0.22348703 -0.69742122 136.90328824 
    8302 0.14525085 -0.89217008 -0.42770881 140.57539436 
    8303 Axis -0.35216703 0.77719026 -0.52149178 
    8304 Axis point 112.45114541 0.00000000 104.12749990 
    8305 Rotation angle (degrees) 163.94853420 
    8306 Shift along axis -15.81092807 
    8307  
    8308 
    8309 > fitmap #3 inMap #5
    8310 
    8311 Fit molecule
    8312 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
    8313 (#3) to map cryosparc_P104_J3849_class_01_00019_volume.mrc (#5) using 4737
    8314 atoms 
    8315 average map value = 0.2558, steps = 84 
    8316 shifted from previous position = 9.18 
    8317 rotated from previous position = 23.6 degrees 
    8318 atoms outside contour = 1692, contour level = 0.149 
    8319  
    8320 Position of
    8321 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
    8322 (#3) relative to cryosparc_P104_J3849_class_01_00019_volume.mrc (#5)
    8323 coordinates: 
    8324 Matrix rotation and translation 
    8325 0.82601767 -0.11849555 0.55104777 138.85065549 
    8326 0.54580427 0.41218081 -0.72952364 135.66491262 
    8327 -0.14068601 0.90336362 0.40514400 140.95811018 
    8328 Axis 0.86227214 0.36528105 0.35079411 
    8329 Axis point 0.00000000 -13.56525628 87.37325479 
    8330 Rotation angle (degrees) 71.23597585 
    8331 Shift along axis 218.73014810 
    8332  
    8333 
    8334 > hide #3 models
    8335 
    8336 > hide #4 models
    8337 
    8338 > show #!1 models
    8339 
    8340 > volume #1 level 0.4159
    8341 
    8342 > volume #5 level 0.1343
    8343 
    8344 > volume #2 level 0.2038
    8345 
    8346 > hide #!2 models
    8347 
    8348 > show #!1 models
    8349 
    8350 > volume #1 level 0.1904
    8351 
    8352 > hide #!1 models
    8353 
    8354 > open
    8355 > C:/Users/lilyh/Downloads/cryosparc_P122_J586_class_01_00144_volume_sharp.mrc
    8356 
    8357 Opened cryosparc_P122_J586_class_01_00144_volume_sharp.mrc as #6, grid size
    8358 128,128,128, pixel 2.17, shown at level 0.0602, step 1, values float32 
    8359 
    8360 > volume #6 level 0.2555
    8361 
    8362 > volume #6 level 0.2117
    8363 
    8364 > show #3 models
    8365 
    8366 Drag select of 5 residues 
    8367 
    8368 > select #6
    8369 
    8370 2 models selected 
    8371 
    8372 > transparency #6.1 50
    8373 
    8374 Drag select of 6 residues 
    8375 
    8376 > ui mousemode right "rotate selected models"
    8377 
    8378 > view matrix models
    8379 > #3,-0.67813,0.33882,-0.65218,128.67,-0.69902,-0.57138,0.42999,139.5,-0.22696,0.74748,0.62431,142.53
    8380 
    8381 > ui mousemode right "translate selected models"
    8382 
    8383 > view matrix models
    8384 > #3,-0.67813,0.33882,-0.65218,128.31,-0.69902,-0.57138,0.42999,134.3,-0.22696,0.74748,0.62431,144.29
    8385 
    8386 > view matrix models
    8387 > #3,-0.67813,0.33882,-0.65218,136.6,-0.69902,-0.57138,0.42999,129.07,-0.22696,0.74748,0.62431,145.24
    8388 
    8389 > fitmap #3 inMap #6
    8390 
    8391 Fit molecule
    8392 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
    8393 (#3) to map cryosparc_P122_J586_class_01_00144_volume_sharp.mrc (#6) using
    8394 4737 atoms 
    8395 average map value = 0.354, steps = 84 
    8396 shifted from previous position = 6.63 
    8397 rotated from previous position = 12.8 degrees 
    8398 atoms outside contour = 1827, contour level = 0.21168 
    8399  
    8400 Position of
    8401 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
    8402 (#3) relative to cryosparc_P122_J586_class_01_00144_volume_sharp.mrc (#6)
    8403 coordinates: 
    8404 Matrix rotation and translation 
    8405 -0.81462726 0.20404364 -0.54290759 140.14001245 
    8406 -0.52658410 -0.65253920 0.54488699 135.03225157 
    8407 -0.24308776 0.72976629 0.63902234 143.44609953 
    8408 Axis 0.22793547 -0.36964427 -0.90078218 
    8409 Axis point 97.70125556 17.65667045 0.00000000 
    8410 Rotation angle (degrees) 156.07428711 
    8411 Shift along axis -147.18470905 
    8412  
    8413 
    8414 > volume #6 level 0.2595
    8415 
    8416 > volume #6 level 0.2077
    8417 
    8418 > open
    8419 > C:/Users/lilyh/Downloads/cryosparc_P122_J586_class_00_00144_volume_sharp.mrc
    8420 
    8421 Opened cryosparc_P122_J586_class_00_00144_volume_sharp.mrc as #7, grid size
    8422 128,128,128, pixel 2.17, shown at level 0.0711, step 1, values float32 
    8423 
    8424 > volume #7 level 0.05556
    8425 
    8426 > volume #7 level 0.1917
    8427 
    8428 > select #7
    8429 
    8430 2 models selected 
    8431 
    8432 > ui mousemode right "rotate selected models"
    8433 
    8434 > view matrix models
    8435 > #7,0.60037,-0.77149,0.2106,129.13,-0.79701,-0.59888,0.07824,312.5,0.065759,-0.21482,-0.97444,290.71
    8436 
    8437 > ui mousemode right "translate selected models"
    8438 
    8439 > view matrix models
    8440 > #7,0.60037,-0.77149,0.2106,130.29,-0.79701,-0.59888,0.07824,320.1,0.065759,-0.21482,-0.97444,293.03
    8441 
    8442 > fitmap #3 inMap #7
    8443 
    8444 Fit molecule
    8445 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
    8446 (#3) to map cryosparc_P122_J586_class_00_00144_volume_sharp.mrc (#7) using
    8447 4737 atoms 
    8448 average map value = 0.2552, steps = 164 
    8449 shifted from previous position = 6.96 
    8450 rotated from previous position = 14.9 degrees 
    8451 atoms outside contour = 2257, contour level = 0.1917 
    8452  
    8453 Position of
    8454 output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
    8455 (#3) relative to cryosparc_P122_J586_class_00_00144_volume_sharp.mrc (#7)
    8456 coordinates: 
    8457 Matrix rotation and translation 
    8458 -0.24813858 0.56820600 -0.78458221 140.40470068 
    8459 0.95029673 0.29999978 -0.08328460 140.54712847 
    8460 0.18805168 -0.76625201 -0.61440581 132.39978626 
    8461 Axis -0.54708262 -0.77911638 0.30606907 
    8462 Axis point -18.95166982 0.00000000 107.44407402 
    8463 Rotation angle (degrees) 141.37721299 
    8464 Shift along axis -145.79206219 
    8465  
    8466 
    8467 > hide #!6 models
    8468 
    8469 > select #7
    8470 
    8471 2 models selected 
     550
     551[deleted a bunch to fit within ticket limits]
    8472552
    8473553> transparency #7.1 50