id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 8544 ISOLDE: after session restore 'mgr' is None chimerax-bug-report@… Tristan Croll "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 1.5 (2022-11-24) © 2016-2022 Regents of the University of California. All rights reserved. > open /Users/tahashahid/Documents/Work/Modelling/LTAg_ADP- > CGfork/MacBookPro/LTAg_ADP-CGfork_ISOLDE-3.cxs Opened P21_J80_009_volume_map_deepEMhanced-highRes.mrc as #1.1.1.1, grid size 384,384,384, pixel 0.835, shown at level 0.0292, step 1, values float32 Opened P21_J80_009_volume_map_deepEMhanced.mrc as #3, grid size 384,384,384, pixel 0.835, shown at level 0.0514, step 1, values float32 Restoring stepper: LTAg_ADP-CGfork_ISOLDE-2-6ADP.pdb Log from Tue Feb 21 19:02:33 2023UCSF ChimeraX version: 1.5 (2022-11-24) © 2016-2022 Regents of the University of California. All rights reserved. > open /Users/ts387/Documents/Work/Modelling/LTAg_ADP-CGfork/LTAg_ADP- > CGfork_ISOLDE-3.cxs Opened P21_J80_009_volume_map_deepEMhanced-highRes.mrc as #1.1.1.1, grid size 384,384,384, pixel 0.835, shown at level 0.0128, step 1, values float32 Opened P21_J80_009_volume_map_deepEMhanced.mrc as #3, grid size 384,384,384, pixel 0.835, shown at level 0.0674, step 1, values float32 Restoring stepper: LTAg_ADP-CGfork_ISOLDE-2-6ADP.pdb Log from Mon Feb 20 20:35:10 2023 > ui tool show ""Hide Dust"" UCSF ChimeraX version: 1.5 (2022-11-24) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > isolde start > set selectionWidth 4 Populating font family aliases took 329 ms. Replace uses of missing font family ""Carlito"" with one that exists to avoid this cost. > open /Users/tahashahid/Documents/Work/Modelling/LTAg_ADP- > CGfork/ISOLDE-2_Rsr/LTAg_ADP-CGfork_ISOLDE-2-6ADP.pdb format pdb Chain information for LTAg_ADP-CGfork_ISOLDE-2-6ADP.pdb #1 --- Chain | Description A D | No description available B C E F | No description available M | No description available > style stick Changed 36010 atom styles > color bychain > color byhetero > hide atoms > show cartoons > select ::name=""ADP"" 234 atoms, 246 bonds, 6 residues, 1 model selected > show sel target ab > open /Users/tahashahid/Documents/Work/Modelling/LTAg_ADP- > CGfork/P21_J80_009_volume_map_deepEMhanced-highRes.mrc format mrc Opened P21_J80_009_volume_map_deepEMhanced-highRes.mrc as #2, grid size 384,384,384, pixel 0.835, shown at level 0.00113, step 2, values float32 > surface dust #2 size 10.02 > color #2 #b2b2b23d models > color #2 #b2b2b240 models > volume #2 level 0.03954 > volume #2 level 0.05235 > volume #2 step 1 > volume #2 level 0.06303 > volume #2 style mesh > volume #2 color #b2b2b2 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... Chain information for LTAg_ADP-CGfork_ISOLDE-2-6ADP.pdb --- Chain | Description 1.2/A 1.2/D | No description available 1.2/B 1.2/C 1.2/E 1.2/F | No description available 1.2/M | No description available > clipper associate #2 toModel #1 Opened P21_J80_009_volume_map_deepEMhanced-highRes.mrc as #1.1.1.1, grid size 384,384,384, pixel 0.835, shown at step 1, values float32 Loading residue template for ADP from internal database > save /Users/tahashahid/Documents/Work/Modelling/LTAg_ADP- > CGfork/MacBookPro/LTAg_ADP-CGfork_ISOLDE-3.cxs includeMaps true > ui tool show ""Ramachandran Plot"" > isolde restrain ligands #1 > save /Users/tahashahid/Documents/Work/Modelling/LTAg_ADP- > CGfork/MacBookPro/LTAg_ADP-CGfork_ISOLDE-3.cxs includeMaps true > view #1.2/B:431 > volume #1.1.1.1 level 0.05647 > volume #1.1.1.1 level 0.0151 > view #1.2/A:431 > view #1.2/F:431 > save /Users/tahashahid/Documents/Work/Modelling/LTAg_ADP- > CGfork/MacBookPro/LTAg_ADP-CGfork_ISOLDE-3.cxs includeMaps true > select #1 36010 atoms, 36389 bonds, 2187 residues, 15 models selected > open /Users/tahashahid/Documents/Work/Modelling/LTAg_ADP- > CGfork/ModelAngelo/deepEMhanced-highRes/model.cif Summary of feedback from opening /Users/tahashahid/Documents/Work/Modelling/LTAg_ADP- CGfork/ModelAngelo/deepEMhanced-highRes/model.cif --- warnings | Missing entity information. Treating each chain as a separate entity. Missing or incomplete entity_poly_seq table. Inferred polymer connectivity. Chain information for model.cif #2 --- Chain | Description Aa | No description available Ab | No description available Ac | No description available Ad | No description available Ae | No description available Af | No description available Ag | No description available Ah | No description available Ai | No description available > select add #1 36010 atoms, 36389 bonds, 2187 residues, 15 models selected > select add #1 36010 atoms, 36389 bonds, 2187 residues, 15 models selected > select clear > select add #2 14777 atoms, 15066 bonds, 14 pseudobonds, 1820 residues, 2 models selected > style sel stick Changed 14777 atom styles > color sel bychain > color sel byhetero > select subtract #2 Nothing selected > open /Users/tahashahid/Documents/Work/Modelling/LTAg_ADP- > CGfork/P21_J80_009_volume_map_deepEMhanced.mrc Opened P21_J80_009_volume_map_deepEMhanced.mrc as #3, grid size 384,384,384, pixel 0.835, shown at level 9.44e-05, step 2, values float32 > surface dust #3 size 5.01 > volume #3 level 0.03222 > hide #!2 models > show #!3 models > volume #3 level 0.03936 > volume #3 step 1 > volume #3 color #ffffb245 > volume #3 color #ffffb240 > volume #3 level 0.07938 > volume #3 level 0.04736 > volume #3 style mesh > volume #3 color #ffffb2 > hide #!3 models > save /Users/tahashahid/Documents/Work/Modelling/LTAg_ADP- > CGfork/MacBookPro/LTAg_ADP-CGfork_ISOLDE-3.cxs includeMaps true > select #1 36010 atoms, 36389 bonds, 2187 residues, 15 models selected > isolde sim start sel ISOLDE: started sim > select clear > isolde sim pause > isolde sim resume > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > isolde sim pause > isolde sim resume > select clear [Repeated 1 time(s)] > isolde sim pause > isolde sim stop ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 11 residues in model #1.2 to IUPAC-IUB standards. ISOLDE: stopped sim > hide #!2 models > save /Users/tahashahid/Documents/Work/Modelling/LTAg_ADP- > CGfork/MacBookPro/LTAg_ADP-CGfork_ISOLDE-3.cxs includeMaps true Taking snapshot of stepper: LTAg_ADP-CGfork_ISOLDE-2-6ADP.pdb > show #!2 models > isolde sim start sel ISOLDE: started sim > select clear > isolde sim stop ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > hide #!2 models > show #!2 models > isolde sim start sel ISOLDE: started sim > select clear > isolde pepflip sel Flipping the peptide bond for 1 residues > select clear > isolde pepflip sel Flipping the peptide bond for 1 residues > isolde pepflip sel Flipping the peptide bond for 1 residues > select clear > isolde pepflip sel Flipping the peptide bond for 1 residues > select clear > isolde pepflip sel Flipping the peptide bond for 1 residues > isolde pepflip sel Flipping the peptide bond for 1 residues > select clear [Repeated 1 time(s)] > isolde pepflip sel Flipping the peptide bond for 1 residues > select clear [Repeated 1 time(s)] > isolde pepflip sel Flipping the peptide bond for 1 residues > isolde sim stop ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start sel ISOLDE: started sim > select clear > isolde pepflip sel Flipping the peptide bond for 1 residues > isolde pepflip sel Flipping the peptide bond for 1 residues > volume #1.1.1.1 level 0.02228 > volume #3 level 0.02735 > isolde pepflip sel Flipping the peptide bond for 1 residues > volume #3 level 0.03535 > isolde pepflip sel Flipping the peptide bond for 1 residues > select clear > isolde pepflip sel Flipping the peptide bond for 1 residues > isolde pepflip sel Flipping the peptide bond for 1 residues > select clear > volume #3 level 0.03936 > isolde sim stop discardTo start reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start sel ISOLDE: started sim > select clear > isolde sim stop ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB standards. ISOLDE: stopped sim > select clear > isolde sim start sel ISOLDE: started sim > select clear > isolde pepflip sel Flipping the peptide bond for 1 residues > select clear > isolde sim stop ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > save /Users/tahashahid/Documents/Work/Modelling/LTAg_ADP- > CGfork/MacBookPro/LTAg_ADP-CGfork_ISOLDE-3.cxs includeMaps true Taking snapshot of stepper: LTAg_ADP-CGfork_ISOLDE-2-6ADP.pdb > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > volume #1.1.1.1 level 0.002486 > hide #!2 models > volume #3 level 0.02735 > isolde sim start sel ISOLDE: started sim > isolde sim stop discardTo start reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > volume #3 level 0.007337 > volume #1.1.1.1 level 0.009084 > select clear > isolde sim start sel ISOLDE: started sim > show #!2 models > volume #1.1.1.1 level 0.009084 > hide #!2 models > volume #1.1.1.1 level 0.05527 > volume #3 level 0.06737 > isolde sim stop ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start sel ISOLDE: started sim > select clear > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > select clear > isolde pepflip sel Flipping the peptide bond for 1 residues > isolde pepflip sel Flipping the peptide bond for 1 residues > isolde sim stop ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start sel ISOLDE: started sim > select clear [Repeated 1 time(s)] > isolde sim stop ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start sel ISOLDE: started sim > select clear > isolde pepflip sel Flipping the peptide bond for 1 residues > isolde sim stop discardTo start reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start sel ISOLDE: started sim > select clear > volume #1.1.1.1 level -0.0008131 > volume #1.1.1.1 level 0.04208 > isolde sim stop discardTo start reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start sel ISOLDE: started sim > select clear > isolde sim stop ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > volume #1.1.1.1 level 0.01285 > hide #!2 models > isolde sim start sel ISOLDE: started sim > show #!2 models > hide #!2 models > show #!2 models > isolde sim stop discardTo start reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > save /Users/tahashahid/Documents/Work/Modelling/LTAg_ADP- > CGfork/MacBookPro/LTAg_ADP-CGfork_ISOLDE-3.cxs includeMaps true Taking snapshot of stepper: LTAg_ADP-CGfork_ISOLDE-2-6ADP.pdb > save /Users/tahashahid/Documents/Work/Modelling/LTAg_ADP- > CGfork/MacBookPro/LTAg_ADP-CGfork_ISOLDE-3.cxs includeMaps true Taking snapshot of stepper: LTAg_ADP-CGfork_ISOLDE-2-6ADP.pdb ——— End of log from Mon Feb 20 20:35:10 2023 ——— opened ChimeraX session > isolde start > set selectionWidth 4 Populating font family aliases took 273 ms. Replace uses of missing font family ""Carlito"" with one that exists to avoid this cost. > ui tool show ""Ramachandran Plot"" > isolde sim start sel ISOLDE: started sim > isolde sim stop discardTo start reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start sel Loading residue template for ADP from internal database ISOLDE: started sim > isolde sim stop discardTo start reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start sel ISOLDE: started sim > volume #1.1.1.1 level 0.06233 > isolde sim stop ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start sel ISOLDE: started sim > select clear > isolde sim stop ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > hide #!2 models > isolde sim start sel ISOLDE: started sim > volume #1.1.1.1 level 0.02274 > volume #1.1.1.1 level 0.1052 > select clear [Repeated 3 time(s)] > isolde sim stop ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > save /Users/ts387/Documents/Work/Modelling/LTAg_ADP-CGfork/LTAg_ADP- > CGfork_ISOLDE-3.cxs includeMaps true Taking snapshot of stepper: LTAg_ADP-CGfork_ISOLDE-2-6ADP.pdb > open /Users/ts387/Documents/Work/Modelling/LTAg_ADP- > CGfork/ModelAngelo/deepEMhanced/model.cif Summary of feedback from opening /Users/ts387/Documents/Work/Modelling/LTAg_ADP- CGfork/ModelAngelo/deepEMhanced/model.cif --- warnings | Missing entity information. Treating each chain as a separate entity. Missing or incomplete entity_poly_seq table. Inferred polymer connectivity. Chain information for model.cif #4 --- Chain | Description Aa | No description available Ab | No description available Ac | No description available Ad | No description available Ae | No description available Af | No description available Ag | No description available Ah | No description available > select clear > select add #4 14434 atoms, 14710 bonds, 18 pseudobonds, 1779 residues, 2 models selected > style sel stick Changed 14434 atom styles > color sel bychain > color sel byhetero > select subtract #4 Nothing selected > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > hide #!4 models > show #!2 models > show #!4 models > hide #!4 models > hide #!2 models > select clear > isolde sim start sel ISOLDE: started sim > select clear > volume #1.1.1.1 level 0.06563 > select clear > volume #1.1.1.1 level 0.02274 > volume #1.1.1.1 level 0.02604 > volume #1.1.1.1 level 0.04584 > isolde sim pause > isolde sim resume > show #!2 models > hide #!2 models > show #!4 models > hide #!4 models > show #!2 models > hide #!2 models > show #!4 models > select clear > hide #!4 models > volume #1.1.1.1 level 0.01944 > volume #3 level 0.03535 > select clear > isolde sim stop discardTo start reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > show #!2 models > isolde sim start sel ISOLDE: started sim > select clear > isolde sim stop ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > show #!4 models > isolde sim start sel ISOLDE: started sim > isolde sim stop ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start sel ISOLDE: started sim > select clear > isolde sim stop ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde sim start sel ISOLDE: started sim > select clear > isolde sim stop ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start sel ISOLDE: started sim > select clear [Repeated 2 time(s)] > hide #!4 models > hide #!2 models > show #!2 models > hide #!2 models > volume #1.1.1.1 level 0.09937 > volume #1.1.1.1 level 0.05633 > isolde sim stop discardTo start reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > show #!2 models > isolde sim start sel ISOLDE: started sim > select clear > isolde sim stop ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB standards. ISOLDE: stopped sim > hide #!2 models > show #!4 models > hide #!4 models > isolde sim start sel ISOLDE: started sim > select clear > volume #1.1.1.1 level 0.02252 > isolde sim stop discardTo start reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start sel ISOLDE: started sim > select clear > show #!2 models > select clear > isolde sim pause > isolde sim resume > isolde sim stop discardTo start reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start sel ISOLDE: started sim > show #!4 models > isolde sim stop ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde sim start sel ISOLDE: started sim > select clear > isolde sim stop ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB standards. ISOLDE: stopped sim > hide #!4 models > hide #!2 models > isolde sim start sel ISOLDE: started sim > show #!2 models > hide #!2 models > show #!2 models > show #!4 models > hide #!4 models > hide #!2 models > show #!2 models > isolde sim stop ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start sel ISOLDE: started sim > isolde sim stop ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde sim start sel ISOLDE: started sim > hide #!2 models > isolde sim stop ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > show #!2 models > isolde sim start sel ISOLDE: started sim > show #!4 models > hide #!4 models > hide #!2 models > isolde sim stop ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start sel ISOLDE: started sim > isolde sim stop ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > show #!2 models > hide #!2 models > show #!4 models > hide #!4 models > isolde sim start sel ISOLDE: started sim > select clear [Repeated 1 time(s)] > isolde pepflip sel Flipping the peptide bond for 1 residues > volume #1.1.1.1 level 0.07785 > isolde sim stop discardTo start reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start sel ISOLDE: started sim > select clear > show #!2 models > isolde sim stop ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start sel ISOLDE: started sim > volume #1.1.1.1 level 0.01022 > volume #3 level 0.1154 > isolde pepflip sel Flipping the peptide bond for 1 residues > volume #3 level 0.05136 > volume #1.1.1.1 level 0.05941 > isolde sim stop ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start sel ISOLDE: started sim > select clear > isolde sim stop discardTo start reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > volume #1.1.1.1 level 0.02924 > isolde sim start sel ISOLDE: started sim > hide #!2 models > show #!2 models > show #!4 models > hide #!4 models > hide #!2 models > show #!2 models > show #!4 models > hide #!4 models > hide #!2 models > show #!2 models > show #!4 models > hide #!4 models > isolde sim stop discardTo start reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > save /Users/ts387/Documents/Work/Modelling/LTAg_ADP-CGfork/LTAg_ADP- > CGfork_ISOLDE-3.cxs includeMaps true Taking snapshot of stepper: LTAg_ADP-CGfork_ISOLDE-2-6ADP.pdb > isolde sim start sel ISOLDE: started sim > isolde sim stop discardTo start reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start sel ISOLDE: started sim > select clear > isolde sim stop ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > select clear > hide #!2 models > isolde sim start sel ISOLDE: started sim > select clear > show #!2 models > show #!4 models > hide #!4 models > isolde sim stop ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB standards. ISOLDE: stopped sim > save /Users/ts387/Documents/Work/Modelling/LTAg_ADP-CGfork/LTAg_ADP- > CGfork_ISOLDE-3.cxs includeMaps true Taking snapshot of stepper: LTAg_ADP-CGfork_ISOLDE-2-6ADP.pdb ——— End of log from Tue Feb 21 19:02:33 2023 ——— opened ChimeraX session Traceback (most recent call last): File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/triggerset.py"", line 134, in invoke return self._func(self._name, data) File ""/Users/tahashahid/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/molobject.py"", line 1790, in _get_and_process_changes return self._process_changes(changes) File ""/Users/tahashahid/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/molobject.py"", line 1778, in _process_changes mgr.triggers.activate_trigger('changes', (mgr, processed_changeds)) AttributeError: 'NoneType' object has no attribute 'triggers' Error processing trigger ""new frame"": AttributeError: 'NoneType' object has no attribute 'triggers' File ""/Users/tahashahid/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/molobject.py"", line 1778, in _process_changes mgr.triggers.activate_trigger('changes', (mgr, processed_changeds)) See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/triggerset.py"", line 134, in invoke return self._func(self._name, data) File ""/Users/tahashahid/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/clipper/symmetry.py"", line 1252, in _set_default_cartoon_cb set_to_default_cartoon(self.session, model = self.structure) File ""/Users/tahashahid/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/clipper/util.py"", line 80, in set_to_default_cartoon cartoon.cartoon(session, atoms = atoms, suppress_backbone_display=False) File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/std_commands/cartoon.py"", line 70, in cartoon residues = all_residues(session) File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/structure.py"", line 2389, in all_residues structures = all_structures(session, atomic_only=atomic_only) File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/structure.py"", line 2365, in all_structures return Structures([m for m in session.models.list() if isinstance(m,class_obj)]) AttributeError: 'NoneType' object has no attribute 'models' Error processing trigger ""frame drawn"": AttributeError: 'NoneType' object has no attribute 'models' File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/structure.py"", line 2365, in all_structures return Structures([m for m in session.models.list() if isinstance(m,class_obj)]) See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/triggerset.py"", line 134, in invoke return self._func(self._name, data) File ""/Users/tahashahid/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/clipper/symmetry.py"", line 1905, in rebuild _copy_ribbon_drawing(self.master_ribbon, self, self.dim_factor) File ""/Users/tahashahid/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/clipper/symmetry.py"", line 1883, in master_ribbon return self.structure._ribbons_drawing AttributeError: 'NoneType' object has no attribute '_ribbons_drawing' Error processing trigger ""frame drawn"": AttributeError: 'NoneType' object has no attribute '_ribbons_drawing' File ""/Users/tahashahid/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/clipper/symmetry.py"", line 1883, in master_ribbon return self.structure._ribbons_drawing See log for complete Python traceback. OpenGL version: 4.1 ATI-4.9.51 OpenGL renderer: AMD Radeon Pro 555 OpenGL Engine OpenGL vendor: ATI Technologies Inc. Python: 3.9.11 Locale: UTF-8 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro14,3 Processor Name: Quad-Core Intel Core i7 Processor Speed: 2.8 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 256 KB L3 Cache: 6 MB Hyper-Threading Technology: Enabled Memory: 16 GB System Firmware Version: 499.40.2.0.0 OS Loader Version: 564.40.4~66 SMC Version (system): 2.45f5 Software: System Software Overview: System Version: macOS 13.2.1 (22D68) Kernel Version: Darwin 22.3.0 Time since boot: 4 days, 18 hours, 2 minutes Graphics/Displays: Intel HD Graphics 630: Chipset Model: Intel HD Graphics 630 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x591b Revision ID: 0x0004 Automatic Graphics Switching: Supported gMux Version: 4.0.29 [3.2.8] Metal Support: Metal 3 Radeon Pro 555: Chipset Model: Radeon Pro 555 Type: GPU Bus: PCIe PCIe Lane Width: x8 VRAM (Total): 2 GB Vendor: AMD (0x1002) Device ID: 0x67ef Revision ID: 0x00c7 ROM Revision: 113-C980AJ-927 VBIOS Version: 113-C9801AP-A02 EFI Driver Version: 01.A0.927 Automatic Graphics Switching: Supported gMux Version: 4.0.29 [3.2.8] Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2880 x 1800 Retina Framebuffer Depth: 24-Bit Color (ARGB8888) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.1.0 Babel: 2.11.0 backcall: 0.2.0 blockdiag: 3.0.0 build: 0.8.0 certifi: 2021.10.8 cftime: 1.6.2 charset-normalizer: 2.1.1 ChimeraX-AddCharge: 1.4 ChimeraX-AddH: 2.2.1 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2.1 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.6 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.41.5 ChimeraX-AtomicLibrary: 8.0.3 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.1 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.7.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.1 ChimeraX-ChangeChains: 1.0.2 ChimeraX-CheckWaters: 1.3 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.4 ChimeraX-Clipper: 0.19.0 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.2 ChimeraX-CommandLine: 1.2.4 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.5 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.1 ChimeraX-DistMonitor: 1.3 ChimeraX-DockPrep: 1.0 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.2 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ISOLDE: 1.5 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-Label: 1.1.7 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.2 ChimeraX-Map: 1.1.2 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.1 ChimeraX-MatchMaker: 2.0.9 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.8 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.6 ChimeraX-ModelPanel: 1.3.6 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.1 ChimeraX-MouseModes: 1.1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.9.1 ChimeraX-PDB: 2.6.8 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0.1 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.7.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.1 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.10 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.1.3 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.24.3 ChimeraX-uniprot: 2.2.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.1.4 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.1 ChimeraX-WebServices: 1.1.0 ChimeraX-Zone: 1.0.1 colorama: 0.4.5 cxservices: 1.2 cycler: 0.11.0 Cython: 0.29.32 debugpy: 1.6.4 decorator: 5.1.1 docutils: 0.19 entrypoints: 0.4 executing: 1.2.0 filelock: 3.7.1 fonttools: 4.38.0 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.7.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.33 imagecodecs: 2022.7.31 imagesize: 1.4.1 importlib-metadata: 5.1.0 ipykernel: 6.15.3 ipython: 8.4.0 ipython-genutils: 0.2.0 jedi: 0.18.1 Jinja2: 3.1.2 jupyter-client: 7.3.4 jupyter-core: 5.1.0 kiwisolver: 1.4.4 line-profiler: 3.5.1 lxml: 4.9.1 lz4: 4.0.2 MarkupSafe: 2.1.1 matplotlib: 3.5.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.0 networkx: 2.8.5 numexpr: 2.8.4 numpy: 1.23.1 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.2.0 pip: 22.3.1 pkginfo: 1.8.3 platformdirs: 2.5.4 prompt-toolkit: 3.0.33 psutil: 5.9.1 ptyprocess: 0.7.0 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.12.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 PyQt6-commercial: 6.3.1 PyQt6-Qt6: 6.3.2 PyQt6-sip: 13.4.0 PyQt6-WebEngine-commercial: 6.3.1 PyQt6-WebEngine-Qt6: 6.3.2 python-dateutil: 2.8.2 pytz: 2022.6 pyzmq: 24.0.1 qtconsole: 5.3.1 QtPy: 2.3.0 RandomWords: 0.4.0 requests: 2.28.1 scipy: 1.9.0 setuptools: 65.1.1 setuptools-scm: 7.0.5 sfftk-rw: 0.7.2 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 5.1.1 sphinx-autodoc-typehints: 1.19.1 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 stack-data: 0.6.2 tables: 3.7.0 tifffile: 2022.7.31 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.2 traitlets: 5.3.0 typing-extensions: 4.4.0 urllib3: 1.26.13 wcwidth: 0.2.5 webcolors: 1.12 wheel: 0.37.1 wheel-filename: 1.4.1 zipp: 3.11.0 }}} " defect assigned normal Third Party all ChimeraX