id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 14924 Crash in python_instances_of_class chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-13.0-arm64-arm-64bit ChimeraX Version: 1.8.dev202403271703 (2024-03-27 17:03:08 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Thread 0x000000017a56f000 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 324 in wait File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 622 in wait File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1392 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Current thread 0x00000001ffaba500 (most recent call first): File 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""deploymentId"" : 400000001 } ] }, ""reportNotes"" : [ ""dyld_process_snapshot_create_for_process failed with 5"" ] } ===== Log before crash start ===== UCSF ChimeraX version: 1.8.dev202403271703 (2024-03-27) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > runscript /Users/diyamathai/Desktop/BIOL694/Group3_Project/Q5FAG7.py > open > /Users/diyamathai/Desktop/BIOL694/Group3_Project/AF-Q5FAG7-F1-model_v4.pdb AF-Q5FAG7-F1-model_v4.pdb title: Alphafold monomer V2.0 prediction for pilus assembly protein (Q5FAG7) [more info...] Chain information for AF-Q5FAG7-F1-model_v4.pdb #1 --- Chain | Description | UniProt A | pilus assembly protein | Q5FAG7_NEIG1 1-1004 > movie record > turn x 2 180 > wait 180 > mlp Map values for surface ""AF-Q5FAG7-F1-model_v4.pdb_A SES surface"": minimum -28.43, mean -6.816, maximum 22.22 > turn x 2 180 > wait 180 > coulombic Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for AF-Q5FAG7-F1-model_v4.pdb_A SES surface #1.1: minimum, -18.90, mean 0.94, maximum 17.46 > turn x 2 180 > wait 180 > hide surfaces > /Users/diyamathai/Desktop/BIOL694/Group3_Project/SWISSMODEL_Q5FAG7.pdb Traceback (most recent call last): File ""/Users/diyamathai/Desktop/BIOL694/Group3_Project/Q5FAG7.py"", line 37, in run(session, ""/Users/diyamathai/Desktop/BIOL694/Group3_Project/SWISSMODEL_Q5FAG7.pdb"") File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/run.py"", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 2853, in run raise UserError(self._error) chimerax.core.errors.UserError: Unknown command: /Users/diyamathai/Desktop/BIOL694/Group3_Project/SWISSMODEL_Q5FAG7.pdb Error opening python file /Users/diyamathai/Desktop/BIOL694/Group3_Project/Q5FAG7.py > close session > runscript /Users/diyamathai/Desktop/BIOL694/Group3_Project/Q5FAG7.py > open > /Users/diyamathai/Desktop/BIOL694/Group3_Project/AF-Q5FAG7-F1-model_v4.pdb AF-Q5FAG7-F1-model_v4.pdb title: Alphafold monomer V2.0 prediction for pilus assembly protein (Q5FAG7) [more info...] Chain information for AF-Q5FAG7-F1-model_v4.pdb #1 --- Chain | Description | UniProt A | pilus assembly protein | Q5FAG7_NEIG1 1-1004 > movie record Traceback (most recent call last): File ""/Users/diyamathai/Desktop/BIOL694/Group3_Project/Q5FAG7.py"", line 7, in run(session, ""movie record"") File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/run.py"", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 2904, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/movie/moviecmd.py"", line 147, in movie_record raise CommandError(""Already recording a movie"") chimerax.core.errors.UserError: Already recording a movie Error opening python file /Users/diyamathai/Desktop/BIOL694/Group3_Project/Q5FAG7.py > runscript /Users/diyamathai/Desktop/BIOL694/Group3_Project/Q5FAG7.py > open > /Users/diyamathai/Desktop/BIOL694/Group3_Project/AF-Q5FAG7-F1-model_v4.pdb AF-Q5FAG7-F1-model_v4.pdb title: Alphafold monomer V2.0 prediction for pilus assembly protein (Q5FAG7) [more info...] Chain information for AF-Q5FAG7-F1-model_v4.pdb #2 --- Chain | Description | UniProt A | pilus assembly protein | Q5FAG7_NEIG1 1-1004 > turn x 2 180 > wait 180 > mlp Map values for surface ""AF-Q5FAG7-F1-model_v4.pdb_A SES surface"": minimum -28.43, mean -6.816, maximum 22.22 > turn x 2 180 > wait 180 > coulombic Using Amber 20 recommended default charges and atom types for standard residues Traceback (most recent call last): File ""/Users/diyamathai/Desktop/BIOL694/Group3_Project/Q5FAG7.py"", line 25, in run(session, ""coulombic"") File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/run.py"", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 2904, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/coulombic/cmd.py"", line 102, in cmd_coulombic assign_charges(session, needs_assignment, his_scheme, charge_method, File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/coulombic/coulombic.py"", line 73, in assign_charges charged_struct = struct.copy(name=""copy of "" + struct.name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/atomic/structure.py"", line 162, in copy m._copy_custom_attrs(self) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/atomic/structure.py"", line 176, in _copy_custom_attrs py_objs = [py_obj for py_obj in python_instances_of_class(class_obj) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/atomic/molobject.py"", line 61, in python_instances_of_class return [x for x in instances if filt(x)] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/atomic/molobject.py"", line 61, in return [x for x in instances if filt(x)] ^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/atomic/molobject.py"", line 52, in filt = lambda x: open_structure(x.structure) ^^^^^^^^^^^ File ""atomic_cpp/cymol.pyx"", line 536, in chimerax.atomic.cymol.CyAtom.structure.__get__ RuntimeError: Atom already deleted Error opening python file /Users/diyamathai/Desktop/BIOL694/Group3_Project/Q5FAG7.py > close session > runscript /Users/diyamathai/Desktop/BIOL694/Group3_Project/Q5FAG7.py > open > /Users/diyamathai/Desktop/BIOL694/Group3_Project/AF-Q5FAG7-F1-model_v4.pdb AF-Q5FAG7-F1-model_v4.pdb title: Alphafold monomer V2.0 prediction for pilus assembly protein (Q5FAG7) [more info...] Chain information for AF-Q5FAG7-F1-model_v4.pdb #1 --- Chain | Description | UniProt A | pilus assembly protein | Q5FAG7_NEIG1 1-1004 > turn x 2 180 > wait 180 > mlp Map values for surface ""AF-Q5FAG7-F1-model_v4.pdb_A SES surface"": minimum -28.43, mean -6.816, maximum 22.22 > turn x 2 180 > wait 180 > coulombic Traceback (most recent call last): File ""/Users/diyamathai/Desktop/BIOL694/Group3_Project/Q5FAG7.py"", line 25, in run(session, ""coulombic"") File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/run.py"", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 2904, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/coulombic/cmd.py"", line 102, in cmd_coulombic assign_charges(session, needs_assignment, his_scheme, charge_method, File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/coulombic/coulombic.py"", line 73, in assign_charges charged_struct = struct.copy(name=""copy of "" + struct.name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/atomic/structure.py"", line 162, in copy m._copy_custom_attrs(self) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/atomic/structure.py"", line 176, in _copy_custom_attrs py_objs = [py_obj for py_obj in python_instances_of_class(class_obj) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/atomic/molobject.py"", line 61, in python_instances_of_class return [x for x in instances if filt(x)] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/atomic/molobject.py"", line 61, in return [x for x in instances if filt(x)] ^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/atomic/molobject.py"", line 52, in filt = lambda x: open_structure(x.structure) ^^^^^^^^^^^ File ""atomic_cpp/cymol.pyx"", line 536, in chimerax.atomic.cymol.CyAtom.structure.__get__ RuntimeError: Atom already deleted Error opening python file /Users/diyamathai/Desktop/BIOL694/Group3_Project/Q5FAG7.py > coulombic Traceback (most recent call last): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/toolbar/tool.py"", line 205, in callback bundle_info.run_provider(session, name, session.toolbar, display_name=display_name) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/toolshed/info.py"", line 397, in run_provider return api._api_caller.run_provider(api, session, name, mgr, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/toolshed/__init__.py"", line 1302, in run_provider return cls._get_func(api, ""run_provider"")(session, name, mgr, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/shortcuts/__init__.py"", line 66, in run_provider shortcuts.run_provider(session, name) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/shortcuts/shortcuts.py"", line 1387, in run_provider keyboard_shortcuts(session).try_shortcut(name) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/shortcuts/shortcuts.py"", line 402, in try_shortcut self.run_shortcut(keys) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/shortcuts/shortcuts.py"", line 420, in run_shortcut sc.run(self.session, status = self._enabled) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/shortcuts/shortcuts.py"", line 339, in run f(s) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/shortcuts/shortcuts.py"", line 72, in func_plus_tip func(cmd + "" %s"")(session) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/shortcuts/shortcuts.py"", line 593, in run_expanded_command run(session, cmd) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/shortcuts/shortcuts.py"", line 536, in run run_command(session, command, **kw) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/run.py"", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 2904, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/coulombic/cmd.py"", line 102, in cmd_coulombic assign_charges(session, needs_assignment, his_scheme, charge_method, File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/coulombic/coulombic.py"", line 73, in assign_charges charged_struct = struct.copy(name=""copy of "" + struct.name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/atomic/structure.py"", line 162, in copy m._copy_custom_attrs(self) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/atomic/structure.py"", line 176, in _copy_custom_attrs py_objs = [py_obj for py_obj in python_instances_of_class(class_obj) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/atomic/molobject.py"", line 61, in python_instances_of_class return [x for x in instances if filt(x)] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/atomic/molobject.py"", line 61, in return [x for x in instances if filt(x)] ^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/atomic/molobject.py"", line 52, in filt = lambda x: open_structure(x.structure) ^^^^^^^^^^^ File ""atomic_cpp/cymol.pyx"", line 536, in chimerax.atomic.cymol.CyAtom.structure.__get__ RuntimeError: Atom already deleted RuntimeError: Atom already deleted File ""atomic_cpp/cymol.pyx"", line 536, in chimerax.atomic.cymol.CyAtom.structure.__get__ See log for complete Python traceback. > close session > open /Users/diyamathai/Desktop/1iep_receptorH.pdb format pdb No such file/path: /Users/diyamathai/Desktop/1iep_receptorH.pdb > open > /Users/diyamathai/Desktop/BIOL694/Group3_Project/AF-Q5FAG7-F1-model_v4.pdb AF-Q5FAG7-F1-model_v4.pdb title: Alphafold monomer V2.0 prediction for pilus assembly protein (Q5FAG7) [more info...] Chain information for AF-Q5FAG7-F1-model_v4.pdb #1 --- Chain | Description | UniProt A | pilus assembly protein | Q5FAG7_NEIG1 1-1004 > coulombic Traceback (most recent call last): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/toolbar/tool.py"", line 205, in callback bundle_info.run_provider(session, name, session.toolbar, display_name=display_name) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/toolshed/info.py"", line 397, in run_provider return api._api_caller.run_provider(api, session, name, mgr, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/toolshed/__init__.py"", line 1302, in run_provider return cls._get_func(api, ""run_provider"")(session, name, mgr, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/shortcuts/__init__.py"", line 66, in run_provider shortcuts.run_provider(session, name) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/shortcuts/shortcuts.py"", line 1387, in run_provider keyboard_shortcuts(session).try_shortcut(name) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/shortcuts/shortcuts.py"", line 402, in try_shortcut self.run_shortcut(keys) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/shortcuts/shortcuts.py"", line 420, in run_shortcut sc.run(self.session, status = self._enabled) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/shortcuts/shortcuts.py"", line 339, in run f(s) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/shortcuts/shortcuts.py"", line 72, in func_plus_tip func(cmd + "" %s"")(session) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/shortcuts/shortcuts.py"", line 593, in run_expanded_command run(session, cmd) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/shortcuts/shortcuts.py"", line 536, in run run_command(session, command, **kw) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/run.py"", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 2904, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/coulombic/cmd.py"", line 102, in cmd_coulombic assign_charges(session, needs_assignment, his_scheme, charge_method, File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/coulombic/coulombic.py"", line 73, in assign_charges charged_struct = struct.copy(name=""copy of "" + struct.name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/atomic/structure.py"", line 162, in copy m._copy_custom_attrs(self) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/atomic/structure.py"", line 176, in _copy_custom_attrs py_objs = [py_obj for py_obj in python_instances_of_class(class_obj) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/atomic/molobject.py"", line 61, in python_instances_of_class return [x for x in instances if filt(x)] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/atomic/molobject.py"", line 61, in return [x for x in instances if filt(x)] ^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/atomic/molobject.py"", line 52, in filt = lambda x: open_structure(x.structure) ^^^^^^^^^^^ File ""atomic_cpp/cymol.pyx"", line 536, in chimerax.atomic.cymol.CyAtom.structure.__get__ RuntimeError: Atom already deleted RuntimeError: Atom already deleted File ""atomic_cpp/cymol.pyx"", line 536, in chimerax.atomic.cymol.CyAtom.structure.__get__ See log for complete Python traceback. > show atoms > hide atoms > show surfaces > coulombic Traceback (most recent call last): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/toolbar/tool.py"", line 205, in callback bundle_info.run_provider(session, name, session.toolbar, display_name=display_name) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/toolshed/info.py"", line 397, in run_provider return api._api_caller.run_provider(api, session, name, mgr, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/toolshed/__init__.py"", line 1302, in run_provider return cls._get_func(api, ""run_provider"")(session, name, mgr, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/shortcuts/__init__.py"", line 66, in run_provider shortcuts.run_provider(session, name) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/shortcuts/shortcuts.py"", line 1387, in run_provider keyboard_shortcuts(session).try_shortcut(name) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/shortcuts/shortcuts.py"", line 402, in try_shortcut self.run_shortcut(keys) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/shortcuts/shortcuts.py"", line 420, in run_shortcut sc.run(self.session, status = self._enabled) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/shortcuts/shortcuts.py"", line 339, in run f(s) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/shortcuts/shortcuts.py"", line 72, in func_plus_tip func(cmd + "" %s"")(session) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/shortcuts/shortcuts.py"", line 593, in run_expanded_command run(session, cmd) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/shortcuts/shortcuts.py"", line 536, in run run_command(session, command, **kw) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/run.py"", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 2904, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/coulombic/cmd.py"", line 102, in cmd_coulombic assign_charges(session, needs_assignment, his_scheme, charge_method, File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/coulombic/coulombic.py"", line 73, in assign_charges charged_struct = struct.copy(name=""copy of "" + struct.name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/atomic/structure.py"", line 162, in copy m._copy_custom_attrs(self) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/atomic/structure.py"", line 176, in _copy_custom_attrs py_objs = [py_obj for py_obj in python_instances_of_class(class_obj) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/atomic/molobject.py"", line 61, in python_instances_of_class return [x for x in instances if filt(x)] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/atomic/molobject.py"", line 61, in return [x for x in instances if filt(x)] ^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/atomic/molobject.py"", line 52, in filt = lambda x: open_structure(x.structure) ^^^^^^^^^^^ File ""atomic_cpp/cymol.pyx"", line 536, in chimerax.atomic.cymol.CyAtom.structure.__get__ RuntimeError: Atom already deleted RuntimeError: Atom already deleted File ""atomic_cpp/cymol.pyx"", line 536, in chimerax.atomic.cymol.CyAtom.structure.__get__ See log for complete Python traceback. > mlp Map values for surface ""AF-Q5FAG7-F1-model_v4.pdb_A SES surface"": minimum -28.43, mean -6.816, maximum 22.22 To also show corresponding color key, enter the above mlp command and add key true > color bfactor 7776 atoms, 1004 residues, 1 surfaces, atom bfactor range 32 to 98.3 > coulombic Traceback (most recent call last): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/toolbar/tool.py"", line 205, in callback bundle_info.run_provider(session, name, session.toolbar, display_name=display_name) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/toolshed/info.py"", line 397, in run_provider return api._api_caller.run_provider(api, session, name, mgr, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/toolshed/__init__.py"", line 1302, in run_provider return cls._get_func(api, ""run_provider"")(session, name, mgr, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/shortcuts/__init__.py"", line 66, in run_provider shortcuts.run_provider(session, name) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/shortcuts/shortcuts.py"", line 1387, in run_provider keyboard_shortcuts(session).try_shortcut(name) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/shortcuts/shortcuts.py"", line 402, in try_shortcut self.run_shortcut(keys) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/shortcuts/shortcuts.py"", line 420, in run_shortcut sc.run(self.session, status = self._enabled) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/shortcuts/shortcuts.py"", line 339, in run f(s) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/shortcuts/shortcuts.py"", line 72, in func_plus_tip func(cmd + "" %s"")(session) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/shortcuts/shortcuts.py"", line 593, in run_expanded_command run(session, cmd) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/shortcuts/shortcuts.py"", line 536, in run run_command(session, command, **kw) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/run.py"", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 2904, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/coulombic/cmd.py"", line 102, in cmd_coulombic assign_charges(session, needs_assignment, his_scheme, charge_method, File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/coulombic/coulombic.py"", line 73, in assign_charges charged_struct = struct.copy(name=""copy of "" + struct.name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/atomic/structure.py"", line 162, in copy m._copy_custom_attrs(self) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/atomic/structure.py"", line 176, in _copy_custom_attrs py_objs = [py_obj for py_obj in python_instances_of_class(class_obj) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/atomic/molobject.py"", line 61, in python_instances_of_class return [x for x in instances if filt(x)] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/atomic/molobject.py"", line 61, in return [x for x in instances if filt(x)] ^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/atomic/molobject.py"", line 52, in filt = lambda x: open_structure(x.structure) ^^^^^^^^^^^ File ""atomic_cpp/cymol.pyx"", line 536, in chimerax.atomic.cymol.CyAtom.structure.__get__ RuntimeError: Atom already deleted RuntimeError: Atom already deleted File ""atomic_cpp/cymol.pyx"", line 536, in chimerax.atomic.cymol.CyAtom.structure.__get__ See log for complete Python traceback. > close session > runscript /Users/diyamathai/Desktop/BIOL694/Group3_Project/Q5FAG7.py > open > /Users/diyamathai/Desktop/BIOL694/Group3_Project/AF-Q5FAG7-F1-model_v4.pdb AF-Q5FAG7-F1-model_v4.pdb title: Alphafold monomer V2.0 prediction for pilus assembly protein (Q5FAG7) [more info...] Chain information for AF-Q5FAG7-F1-model_v4.pdb #1 --- Chain | Description | UniProt A | pilus assembly protein | Q5FAG7_NEIG1 1-1004 > turn x 2 180 > wait 180 > mlp Map values for surface ""AF-Q5FAG7-F1-model_v4.pdb_A SES surface"": minimum -28.43, mean -6.816, maximum 22.22 > turn x 2 180 > wait 180 > coulombic Traceback (most recent call last): File ""/Users/diyamathai/Desktop/BIOL694/Group3_Project/Q5FAG7.py"", line 25, in run(session, ""coulombic"") File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/run.py"", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 2904, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/coulombic/cmd.py"", line 102, in cmd_coulombic assign_charges(session, needs_assignment, his_scheme, charge_method, File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/coulombic/coulombic.py"", line 73, in assign_charges charged_struct = struct.copy(name=""copy of "" + struct.name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/atomic/structure.py"", line 162, in copy m._copy_custom_attrs(self) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/atomic/structure.py"", line 176, in _copy_custom_attrs py_objs = [py_obj for py_obj in python_instances_of_class(class_obj) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/atomic/molobject.py"", line 61, in python_instances_of_class return [x for x in instances if filt(x)] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/atomic/molobject.py"", line 61, in return [x for x in instances if filt(x)] ^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/atomic/molobject.py"", line 52, in filt = lambda x: open_structure(x.structure) ^^^^^^^^^^^ File ""atomic_cpp/cymol.pyx"", line 536, in chimerax.atomic.cymol.CyAtom.structure.__get__ RuntimeError: Atom already deleted Error opening python file /Users/diyamathai/Desktop/BIOL694/Group3_Project/Q5FAG7.py > close session > runscript /Users/diyamathai/Desktop/BIOL694/Group3_Project/Q5FAG7.py > open > /Users/diyamathai/Desktop/BIOL694/Group3_Project/AF-Q5FAG7-F1-model_v4.pdb AF-Q5FAG7-F1-model_v4.pdb title: Alphafold monomer V2.0 prediction for pilus assembly protein (Q5FAG7) [more info...] Chain information for AF-Q5FAG7-F1-model_v4.pdb #1 --- Chain | Description | UniProt A | pilus assembly protein | Q5FAG7_NEIG1 1-1004 > movie record Traceback (most recent call last): File ""/Users/diyamathai/Desktop/BIOL694/Group3_Project/Q5FAG7.py"", line 7, in run(session, ""movie record"") File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/run.py"", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 2904, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/movie/moviecmd.py"", line 147, in movie_record raise CommandError(""Already recording a movie"") chimerax.core.errors.UserError: Already recording a movie Error opening python file /Users/diyamathai/Desktop/BIOL694/Group3_Project/Q5FAG7.py > close session > runscript /Users/diyamathai/Desktop/BIOL694/Group3_Project/Q5FAG7.py > open > /Users/diyamathai/Desktop/BIOL694/Group3_Project/AF-Q5FAG7-F1-model_v4.pdb AF-Q5FAG7-F1-model_v4.pdb title: Alphafold monomer V2.0 prediction for pilus assembly protein (Q5FAG7) [more info...] Chain information for AF-Q5FAG7-F1-model_v4.pdb #1 --- Chain | Description | UniProt A | pilus assembly protein | Q5FAG7_NEIG1 1-1004 > turn x 2 180 > wait 180 > mlp Map values for surface ""AF-Q5FAG7-F1-model_v4.pdb_A SES surface"": minimum -28.43, mean -6.816, maximum 22.22 > turn x 2 180 > wait 180 > hide surfaces > open /Users/diyamathai/Desktop/BIOL694/Group3_Project/SWISSMODEL_Q5FAG7.pdb SWISSMODEL_Q5FAG7.pdb title: SWISS-MODEL SERVER (https://swissmodel.expasy.org) Q5FAG7_NEIG1 Q5FAG7 Pilus assembly protein [more info...] Chain information for SWISSMODEL_Q5FAG7.pdb #2 --- Chain | Description A | No description available B | No description available > matchmaker #1 to #2 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 SWISSMODEL_Q5FAG7.pdb, chain A (#2) with AF-Q5FAG7-F1-model_v4.pdb, chain A (#1), sequence alignment score = 1816.9 RMSD between 215 pruned atom pairs is 1.067 angstroms; (across all 404 pairs: 5.635) > view clip false > turn x 2 180 > wait 180 > delete #1 > mlp Map values for surface ""SWISSMODEL_Q5FAG7.pdb_A SES surface"": minimum -30.39, mean -5.692, maximum 23.85 Map values for surface ""SWISSMODEL_Q5FAG7.pdb_B SES surface"": minimum -31.25, mean -5.754, maximum 22.28 > turn x 2 180 > wait 180 > coulombic ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.8.dev202403271703 (2024-03-27) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 83 OpenGL renderer: Apple M1 OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.6.1, Qt 6.6.1 Qt runtime version: 6.6.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro17,1 Model Number: MYD82LL/A Chip: Apple M1 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 8 GB System Firmware Version: 8419.41.10 OS Loader Version: 8419.41.10 Software: System Software Overview: System Version: macOS 13.0 (22A380) Kernel Version: Darwin 22.1.0 Time since boot: 38 days, 15 hours, 45 minutes Graphics/Displays: Apple M1: Chipset Model: Apple M1 Type: GPU Bus: Built-In Total Number of Cores: 8 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 2.4.1 Babel: 2.14.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 2.0.0 build: 1.1.1 certifi: 2023.11.17 cftime: 1.6.3 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.16 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.4.3 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.5 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.56 ChimeraX-AtomicLibrary: 14.0.3 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.12.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.5 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.8.dev202403271703 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.3 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.9 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.1.4 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.3 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.15 ChimeraX-ModelPanel: 1.5 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.1 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.1 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.3 ChimeraX-PDB: 2.7.5 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.3 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.16.3 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.37.1 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.3.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.3 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.2.0 cxservices: 1.2.2 cycler: 0.12.1 Cython: 3.0.9 debugpy: 1.8.1 decorator: 5.1.1 docutils: 0.20.1 executing: 2.0.1 filelock: 3.13.1 fonttools: 4.50.0 funcparserlib: 2.0.0a0 glfw: 2.7.0 grako: 3.16.5 h5py: 3.10.0 html2text: 2024.2.26 idna: 3.6 ihm: 0.43 imagecodecs: 2024.1.1 imagesize: 1.4.1 ipykernel: 6.29.2 ipython: 8.21.0 ipywidgets: 8.1.2 jedi: 0.19.1 Jinja2: 3.1.3 jupyter-client: 8.6.0 jupyter-core: 5.7.2 jupyterlab-widgets: 3.0.10 kiwisolver: 1.4.5 line-profiler: 4.1.2 lxml: 5.1.0 lz4: 4.3.3 MarkupSafe: 2.1.5 matplotlib: 3.8.3 matplotlib-inline: 0.1.6 msgpack: 1.0.8 ndindex: 1.8 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.2.1 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.9.0 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.3 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.2.0 pip: 24.0 pkginfo: 1.10.0 platformdirs: 4.2.0 prompt-toolkit: 3.0.43 psutil: 5.9.8 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.3.0 pygments: 2.17.2 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3302 pyparsing: 3.1.2 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.6.1 PyQt6-Qt6: 6.6.2 PyQt6-sip: 13.6.0 PyQt6-WebEngine-commercial: 6.6.0 PyQt6-WebEngine-Qt6: 6.6.2 python-dateutil: 2.9.0.post0 pytz: 2024.1 pyzmq: 25.1.2 qtconsole: 5.5.1 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.12.0 setuptools: 69.2.0 setuptools-scm: 8.0.4 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 7.2.6 sphinx-autodoc-typehints: 2.0.0 sphinxcontrib-applehelp: 1.0.8 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.6 sphinxcontrib-htmlhelp: 2.0.5 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.7 sphinxcontrib-serializinghtml: 1.1.10 stack-data: 0.6.3 superqt: 0.6.1 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2024.1.30 tinyarray: 1.2.4 tornado: 6.4 traitlets: 5.14.1 typing-extensions: 4.10.0 tzdata: 2024.1 urllib3: 2.2.1 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.10 }}} " defect closed normal Core duplicate Tom Goddard all ChimeraX