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Opened 5 years ago
Last modified 3 years ago
#3712 closed defect
ChimeraX bug report submission — at Initial Version
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Volume Data | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: Linux-4.15.0-96-generic-x86_64-with-debian-buster-sid ChimeraX Version: 1.0 (2020-06-04 23:15:07 UTC) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 1.0 (2020-06-04) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /misc/biophysik/lad58072/exosome_project/EM/CtExo10_RNA_cryo_20200130/J384/cryosparc_P1_J384_011_volume_map_filtered.mrc > format mrc Opened cryosparc_P1_J384_011_volume_map_filtered.mrc, grid size 384,384,384, pixel 1.06, shown at level 7.68e-05, step 2, values float32 > open > /misc/biophysik/lad58072/exosome_project/EM/CtExo10_RNA_cryo_20200130/phenix_divergent/Autosharpen_39/J384_sharpened_res_5.ccp4 Opened J384_sharpened_res_5.ccp4, grid size 384,384,384, pixel 1.06, shown at level 1.33, step 2, values float32 > open > /misc/biophysik/lad58072/exosome_project/EM/CtExo10_RNA_cryo_20200130/phenix_divergent/RealSpaceRefine_59/refine_59_minimized_isolde_001.pdb Chain information for refine_59_minimized_isolde_001.pdb #3 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available J | No description available R | No description available > ui tool show ISOLDE > set selectionWidth 4 Chain information for refine_59_minimized_isolde_001.pdb --- Chain | Description 3.2/A | No description available 3.2/B | No description available 3.2/C | No description available 3.2/D | No description available 3.2/E | No description available 3.2/F | No description available 3.2/G | No description available 3.2/H | No description available 3.2/I | No description available 3.2/J | No description available 3.2/R | No description available Done loading forcefield > volume #3.1.1.2 color #1d1c8d > select #3/a 4353 atoms, 4394 bonds, 1 model selected Alignment identifier is 3.2.A > select #3/b 3528 atoms, 3551 bonds, 2 pseudobonds, 2 models selected Alignment identifier is 3.2.B > select #3/c 4305 atoms, 4349 bonds, 6 pseudobonds, 2 models selected Alignment identifier is 3.2.C > select #3/d 3142 atoms, 3171 bonds, 2 pseudobonds, 2 models selected Alignment identifier is 3.2.D > select #3/e 4348 atoms, 4391 bonds, 4 pseudobonds, 2 models selected Alignment identifier is 3.2.E > select #3/f 4247 atoms, 4284 bonds, 1 model selected Alignment identifier is 3.2.F > select #3/g 3917 atoms, 3957 bonds, 1 model selected Alignment identifier is 3.2.G > select #3/h 4455 atoms, 4488 bonds, 2 pseudobonds, 2 models selected Alignment identifier is 3.2.H > save > /biophysik/lad58072/exosome_project/EM/CtExo10_RNA_cryo_20200130/phenix_divergent/RealSpaceRefine_59/refine_59_minimized_isolde_002.pdb > #3.2 > volume #3.1.1.1 level 0.6141 > select clear > volume #3.1.1.1 level 0.9801 > volume #3.1.1.1 level 0.1311 > select clear > volume #3.1.1.1 level 0.5117 > select clear > select clear > select clear > select clear > select clear > volume #3.1.1.1 level 0.3799 > volume #3.1.1.1 level 0.863 > select clear > save > /biophysik/lad58072/exosome_project/EM/CtExo10_RNA_cryo_20200130/phenix_divergent/RealSpaceRefine_59/refine_59_minimized_isolde_002.pdb > #3.2 > select #3/i 2770 atoms, 2793 bonds, 2 pseudobonds, 2 models selected Alignment identifier is 3.2.I > select clear > select clear > select clear > save > /biophysik/lad58072/exosome_project/EM/CtExo10_RNA_cryo_20200130/phenix_divergent/RealSpaceRefine_59/refine_59_minimized_isolde_002.pdb > #3.2 > select #3/a 4353 atoms, 4394 bonds, 1 model selected > select #3/b 3528 atoms, 3551 bonds, 2 pseudobonds, 2 models selected > save > /biophysik/lad58072/exosome_project/EM/CtExo10_RNA_cryo_20200130/phenix_divergent/RealSpaceRefine_59/refine_59_minimized_isolde_002.pdb > #3.2 > select #3/b 3528 atoms, 3551 bonds, 2 pseudobonds, 2 models selected reverting to start > save > /misc/biophysik/lad58072/exosome_project/EM/CtExo10_RNA_cryo_20200130/phenix_divergent/RealSpaceRefine_59/isolde.cxs > includeMaps true Taking snapshot of stepper: refine_59_minimized_isolde_001.pdb > select #3/j 14778 atoms, 14921 bonds, 6 pseudobonds, 2 models selected Alignment identifier is 3.2.J > select clear > open > /misc/biophysik/lad58072/exosome_project/EM/CtExo10_homology_models/CtExo10_hs_6d6q_model_reviewed- > coot-1.pdb Chain information for CtExo10_hs_6d6q_model_reviewed-coot-1.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available J | No description available > mmaker #1/j:1-245 to #3.2/j:1-245 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker refine_59_minimized_isolde_001.pdb, chain J (#3.2) with CtExo10_hs_6d6q_model_reviewed-coot-1.pdb, chain J (#1), sequence alignment score = 993.6 RMSD between 84 pruned atom pairs is 1.208 angstroms; (across all 219 pairs: 7.039) > select #1 48833 atoms, 49281 bonds, 30 pseudobonds, 2 models selected > hide sel atoms > show sel cartoons > select #1/j 14327 atoms, 14466 bonds, 6 pseudobonds, 2 models selected Alignment identifier is 1.J > style sel stick Changed 33 atom styles > select #1 48833 atoms, 49281 bonds, 30 pseudobonds, 2 models selected > rainbow sel > hide #!1 models > select clear > select clear > select clear > select clear > select clear > save > /biophysik/lad58072/exosome_project/EM/CtExo10_RNA_cryo_20200130/phenix_divergent/RealSpaceRefine_59/refine_59_minimized_isolde_002.pdb > #3.2 > save > /biophysik/lad58072/exosome_project/EM/CtExo10_RNA_cryo_20200130/phenix_divergent/RealSpaceRefine_59/refine_59_minimized_isolde_002.pdb > #3.2 > save > /biophysik/lad58072/exosome_project/EM/CtExo10_RNA_cryo_20200130/phenix_divergent/RealSpaceRefine_59/refine_59_minimized_isolde_002.pdb > #3.2 > volume #3.1.1.1 level 1.298 > volume #3.1.1.1 level 1.019 > select clear > select clear > volume #3.1.1.1 level 0.8163 > save > /biophysik/lad58072/exosome_project/EM/CtExo10_RNA_cryo_20200130/phenix_divergent/RealSpaceRefine_59/refine_59_minimized_isolde_002.pdb > #3.2 No rotamer preview selected! Ignoring command. No rotamer preview selected! Ignoring command. > save > /biophysik/lad58072/exosome_project/EM/CtExo10_RNA_cryo_20200130/phenix_divergent/RealSpaceRefine_59/refine_59_minimized_isolde_002.pdb > #3.2 > volume #3.1.1.1 level 1.457 > volume #3.1.1.1 level 0.8746 > volume #3.1.1.1 level 1.355 > volume #3.1.1.1 level 0.86 > volume #3.1.1.1 level 1.297 > volume #3.1.1.1 level 0.758 > volume #3.1.1.1 level 1.224 > volume #3.1.1.1 level 0.5686 > volume #3.1.1.1 level 0.9329 > volume #3.1.1.1 level 0.6123 > volume #3.1.1.1 level 0.2043 > volume #3.1.1.1 level 0.5395 > volume #3.1.1.1 level 0.86 > volume #3.1.1.1 level 0.5249 > volume #3.1.1.1 level 1.02 > select clear > select clear > select clear > select clear > volume #3.1.1.1 level 0.6998 > volume #3.1.1.1 level 1.224 > select clear > select clear > volume #3.1.1.1 level 1.035 > select clear > volume #3.1.1.1 level 0.5832 > volume #3.1.1.1 level 0.7289 > select clear > select clear > volume #3.1.1.1 level 1.239 > volume #3.1.1.1 level 0.6123 > volume #3.1.1.1 level 2.026 > volume #3.1.1.1 level 1.21 /biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/geometry/bounds.py:51: RuntimeWarning: overflow encountered in subtract size = self.xyz_max - self.xyz_min /biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/geometry/bounds.py:53: RuntimeWarning: overflow encountered in multiply r = 0.5*sqrt((size*size).sum()) Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. Traceback (most recent call last): File "/biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 289, in _coord_update_cb self.set_surface_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 303, in set_surface_mask indices = numpy.where(self.mgr.get_vertex_mask(v))[0] File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 178, in get_vertex_mask self._update_mask() File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 171, in _update_mask step=self.grid_step, pad=self.pad) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 248, in generate_mask self.replace_data(self._generate_data_array(coords, step, radius, pad=pad)) File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) ValueError: negative dimensions are not allowed Error processing trigger "atom coords updated": ValueError: negative dimensions are not allowed File "/home/lad58072/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py", line 236, in _generate_data_array data = numpy.zeros(dim, numpy.uint8) See log for complete Python traceback. /biophysik/soft/linux/chimerax-1.0/lib/python3.7/site- packages/chimerax/atomic/ribbon.py:763: RuntimeWarning: invalid value encountered in greater tethered = norm(offsets, axis=1) > min_tether_offset OpenGL version: 3.3.0 NVIDIA 440.33.01 OpenGL renderer: GeForce RTX 2080 Ti/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: System manufacturer Model: System Product Name OS: Ubuntu 18.04 bionic Architecture: 64bit ELF CPU: 28 Intel(R) Core(TM) i9-9940X CPU @ 3.30GHz Cache Size: 19712 KB Memory: total used free shared buff/cache available Mem: 125G 11G 104G 427M 9.7G 112G Swap: 93G 0B 93G Graphics: 19:00.0 VGA compatible controller [0300]: NVIDIA Corporation Device [10de:1e04] (rev a1) Subsystem: Gigabyte Technology Co., Ltd Device [1458:37c4] Kernel driver in use: nvidia PyQt version: 5.12.3 Compiled Qt version: 5.12.4 Runtime Qt version: 5.12.8
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