id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 15699 Crash in garbage collection P.Yu@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-13.0.1-x86_64-i386-64bit ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Current thread 0x00007ff8489f34c0 (most recent call first): Garbage-collecting File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py"", line 2000 in save_state File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py"", line 219 in take_snapshot File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py"", line 1417 in take_snapshot File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py"", line 296 in process File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py"", line 273 in discovery File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py"", line 636 in save File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py"", line 912 in save File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core_formats/__init__.py"", line 95 in save File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/cmd.py"", line 101 in provider_save File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 2908 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/cmd.py"", line 86 in cmd_save File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 2908 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py"", line 49 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py"", line 62 in display File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py"", line 138 in show_save_file_dialog File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py"", line 127 in File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 275 in event_loop File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 918 in init File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1069 in File """", line 88 in _run_code File """", line 198 in _run_module_as_main Extension modules: 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""1953.1"" }, { ""source"" : ""P"", ""arch"" : ""x86_64"", ""base"" : 4830998528, ""size"" : 5259264, ""uuid"" : ""35b47b1c-6952-3d39-a5e7-711f3ca228f2"", ""path"" : ""\/Applications\/ChimeraX-1.7.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtCore.framework\/Versions\/A\/QtCore"", ""name"" : ""QtCore"" }, { ""source"" : ""P"", ""arch"" : ""x86_64"", ""base"" : 4888403968, ""size"" : 6979584, ""uuid"" : ""49d915f7-1c6d-3bbd-b96f-064260e7d998"", ""path"" : ""\/Applications\/ChimeraX-1.7.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtGui.framework\/Versions\/A\/QtGui"", ""name"" : ""QtGui"" } ], ""vmSummary"" : ""ReadOnly portion of Libraries: Total=1.1G resident=0K(0%) swapped_out_or_unallocated=1.1G(100%)\nWritable regions: Total=3.7G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=3.7G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 256K 2 \nActivity Tracing 256K 1 \nCG backing stores 3120K 8 \nCG image 256K 28 \nColorSync 248K 29 \nCoreAnimation 1932K 23 \nCoreGraphics 24K 4 \nCoreUI image data 4348K 44 \nFoundation 40K 2 \nImage IO 4K 1 \nKernel Alloc Once 8K 1 \nMALLOC 2.8G 735 \nMALLOC guard page 32K 8 \nMALLOC_LARGE (reserved) 256K 1 reserved VM address space (unallocated)\nMALLOC_NANO (reserved) 384.0M 1 reserved VM address space (unallocated)\nMach message 24K 4 \nOpenGL GLSL 384K 4 \nSTACK GUARD 100K 25 \nStack 140.7M 26 \nStack Guard 56.0M 1 \nVM_ALLOCATE 368.5M 315 \n__CTF 756 1 \n__DATA 48.7M 758 \n__DATA_CONST 41.1M 391 \n__DATA_DIRTY 1824K 226 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__LINKEDIT 214.5M 155 \n__OBJC_RO 65.1M 1 \n__OBJC_RW 1982K 1 \n__TEXT 907.0M 764 \ndyld private memory 416K 3 \nmapped file 558.0M 106 \nshared memory 3640K 33 \n=========== ======= ======= \nTOTAL 5.6G 3704 \nTOTAL, minus reserved VM space 5.2G 3704 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""60da5e84ab0ca017dace9abf"", ""factorPackIds"" : { }, ""deploymentId"" : 240000008 }, { ""rolloutId"" : ""60186475825c62000ccf5450"", ""factorPackIds"" : { }, ""deploymentId"" : 240000026 } ], ""experiments"" : [ ] }, ""reportNotes"" : [ ""dyld_process_snapshot_create_for_process failed with 5"" ] } ===== Log before crash start ===== Startup Messages --- warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle UCSF ChimeraX version: 1.7.1 (2024-01-23) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/peiyuyu/Documents/Goethe University/3. Homology > model/AcrEF/20240725_alphafold_AcrF_7ouk_5enr_docking.cxs"" format session opened ChimeraX session > hide #!3 models > show #!2 models > select #2/A:446 5 atoms, 4 bonds, 1 residue, 1 model selected > view #2/A:446 > view #2/A:450 > select add #2 23508 atoms, 23949 bonds, 2995 pseudobonds, 3102 residues, 2 models selected > select subtract #2 Nothing selected > hide #!2 models > show #!2 models > hide #!2 models > show #4 models > show #!3 models > show #!2 models > show #!1 models > close session > open ""/Users/peiyuyu/Documents/Goethe University/3. Homology > model/AcrEF/20240725_alphafold_AcrF_7ouk_5enr_docking.cxs"" format session opened ChimeraX session > hide #!3 models > show #!2 models > show #!3 models > select add #3 17713 atoms, 17209 bonds, 6 pseudobonds, 3018 residues, 2 models selected > hide sel atoms > show sel atoms > style sel stick Changed 17713 atom styles > hide sel cartoons > select subtract #3 1 model selected > select #3/C 4686 atoms, 4515 bonds, 2 pseudobonds, 828 residues, 2 models selected > hide sel cartoons > hide sel atoms > select #3/C:MBX 36 atoms, 39 bonds, 1 residue, 1 model selected > show sel atoms > select add #3 17713 atoms, 17209 bonds, 6 pseudobonds, 3018 residues, 3 models selected > select subtract #3 1 model selected > select #1 26894 atoms, 26994 bonds, 4364 pseudobonds, 3820 residues, 3 models selected > ~select #1 2 models selected > select #2 23508 atoms, 23949 bonds, 2995 pseudobonds, 3102 residues, 2 models selected > hide sel atoms > select subtract #2 Nothing selected > hide #!2 models > select #3 17713 atoms, 17209 bonds, 6 pseudobonds, 3018 residues, 2 models selected > hide sel atoms > select #3/C:MBX 36 atoms, 39 bonds, 1 residue, 1 model selected > show sel atoms > ~select #3/C:MBX 1 model selected > show #!2 models > select #2/C89-200 Nothing selected > select #2/C:89-200 859 atoms, 872 bonds, 65 pseudobonds, 112 residues, 2 models selected > show sel atoms > style sel stick Changed 859 atom styles > hide sel atoms > ~select #2/C:89-200 Nothing selected > ~select #2/C:89-130 Nothing selected > show #!2-3 atoms > undo > select #2/C:89-130 321 atoms, 324 bonds, 28 pseudobonds, 42 residues, 2 models selected > show sel atoms > ~select #2/C:89-130 Nothing selected > select #2/C:89-130 321 atoms, 324 bonds, 28 pseudobonds, 42 residues, 2 models selected > hbonds sel reveal true 257 hydrogen bonds found > hbonds sel reveal true 257 hydrogen bonds found > undo > ~hbonds > color bfactor #!2-3 41221 atoms, 6120 residues, 1 surfaces, atom bfactor range 5.45 to 131 > undo > coulombic #!2-3 Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for fold_2024_07_20_acrf_k12_homotrimer_model_0.cif_A SES surface #2.2: minimum, -28.85, mean -2.83, maximum 12.49 Coulombic values for fold_2024_07_20_acrf_k12_homotrimer_model_0.cif_B SES surface #2.3: minimum, -20.53, mean -2.83, maximum 13.33 Coulombic values for fold_2024_07_20_acrf_k12_homotrimer_model_0.cif_C SES surface #2.4: minimum, -19.38, mean -2.82, maximum 13.24 Coulombic values for 5enr_A SES surface #3.3: minimum, -21.78, mean -3.52, maximum 8.57 Coulombic values for 5enr_B SES surface #3.4: minimum, -23.07, mean -3.48, maximum 9.80 Coulombic values for 5enr_C SES surface #3.5: minimum, -21.01, mean -3.50, maximum 8.21 Coulombic values for 5enr_D SES surface #3.6: minimum, -18.23, mean -5.09, maximum 8.23 Coulombic values for 5enr_E SES surface #3.7: minimum, -18.81, mean -5.17, maximum 6.57 Coulombic values for 5enr_F SES surface #3.8: minimum, -18.17, mean -4.99, maximum 6.42 To also show corresponding color key, enter the above coulombic command and add key true > hide sel atoms > select #2 23508 atoms, 23949 bonds, 2995 pseudobonds, 3102 residues, 2 models selected > hide sel atoms > select #3 17713 atoms, 17209 bonds, 6 pseudobonds, 3018 residues, 2 models selected > hide sel atoms > show sel cartoons > select subtract #3 7 models selected > hide #!3 models > hide #!2 atoms > show #!2 cartoons > select add #2 23508 atoms, 23949 bonds, 2995 pseudobonds, 3102 residues, 2 models selected > hide sel atoms > show sel cartoons > style sel stick Changed 23508 atom styles > select subtract #2 3 models selected > hide #!2 models > show #!2 models > show #!3 models > hide #!2 models > nucleotides #!3 atoms > style nucleic & #!3 stick Changed 0 atom styles > nucleotides #!3 atoms > style nucleic & #!3 stick Changed 0 atom styles > nucleotides #!3 tube/slab shape box > nucleotides #!3 atoms > style nucleic & #!3 stick Changed 0 atom styles > style #!3 stick Changed 17713 atom styles > style #!3 sphere Changed 17713 atom styles > ui mousemode right ""map eraser"" Can only have one displayed volume when erasing > close session > open ""/Users/peiyuyu/Documents/Goethe University/3. Homology > model/AcrEF/20240725_alphafold_AcrF_7ouk_5enr_docking.cxs"" format session opened ChimeraX session > ui mousemode right ""map eraser"" > ui mousemode right ""translate selected models"" > hide #!3 models > show #!2 models > show #!3 models > select #3 17713 atoms, 17209 bonds, 6 pseudobonds, 3018 residues, 2 models selected > hide sel cartoons > ~select #3 1 model selected > select #2/C:616-630 106 atoms, 107 bonds, 1 pseudobond, 15 residues, 2 models selected > show sel atoms > style sel stick Changed 106 atom styles > select #2/C:616-630, 131-154, 271-291, 324-329 481 atoms, 487 bonds, 30 pseudobonds, 66 residues, 2 models selected > show sel atoms > style sel stick Changed 481 atom styles > ~select #2/C:616-630, 131-154, 271-291, 324-329 Nothing selected > select #2/C:616-630, 131-154, 271-291, 324-329 481 atoms, 487 bonds, 30 pseudobonds, 66 residues, 2 models selected > color sel byhetero > ~select #2/C:616-630, 131-154, 271-291, 324-329 Nothing selected > save ""/Users/peiyuyu/Documents/Goethe University/3. Homology > model/AcrEF/20240730_alphafold_AcrF_7ouk_docking.cxs"" ===== Log before crash end ===== Log: Startup Messages --- warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle UCSF ChimeraX version: 1.7.1 (2024-01-23) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 INTEL-20.2.44 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine OpenGL vendor: Intel Inc. Python: 3.11.2 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: MacBookPro16,2 Processor Name: Quad-Core Intel Core i5 Processor Speed: 2 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 512 KB L3 Cache: 6 MB Hyper-Threading Technology: Enabled Memory: 16 GB System Firmware Version: 1916.40.8.0.0 (iBridge: 20.16.420.0.0,0) OS Loader Version: 564.40.4~27 Software: System Software Overview: System Version: macOS 13.0.1 (22A400) Kernel Version: Darwin 22.1.0 Time since boot: 27天12小時11分鐘 Graphics/Displays: Intel Iris Plus Graphics: Chipset Model: Intel Iris Plus Graphics Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x8a53 Revision ID: 0x0007 Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Framebuffer Depth: 30-Bit Color (ARGB2101010) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal DELL U2722DE: Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition) UI Looks like: 2560 x 1440 @ 59.00Hz Framebuffer Depth: 30-Bit Color (ARGB2101010) Display Serial Number: BSQKDH3 Mirror: Off Online: Yes Rotation: Supported Connection Type: Thunderbolt/DisplayPort Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.4.1 Babel: 2.14.0 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 blosc2: 2.0.0 build: 0.10.0 certifi: 2022.12.7 cftime: 1.6.3 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.13 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.4.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.2 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.49.1 ChimeraX-AtomicLibrary: 12.1.5 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 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: 2.10.5 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: 1.3.2 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.3.2 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: 1.7.1 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.2 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 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: 1.1.8 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: 2.1.2 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.6.1 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.14 ChimeraX-ModelPanel: 1.4 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-NRRD: 1.1 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.1 ChimeraX-PDB: 2.7.3 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 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 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-SelInspector: 1.0 ChimeraX-SeqView: 2.11 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.2 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.12.4 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.2 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: 1.33.3 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: 0.2.1 contourpy: 1.2.0 cxservices: 1.2.2 cycler: 0.12.1 Cython: 0.29.33 debugpy: 1.8.0 decorator: 5.1.1 docutils: 0.19 executing: 2.0.1 filelock: 3.9.0 fonttools: 4.47.2 funcparserlib: 2.0.0a0 glfw: 2.6.4 grako: 3.16.5 h5py: 3.10.0 html2text: 2020.1.16 idna: 3.6 ihm: 0.38 imagecodecs: 2023.9.18 imagesize: 1.4.1 ipykernel: 6.23.2 ipython: 8.14.0 ipython-genutils: 0.2.0 ipywidgets: 8.1.1 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.2.0 jupyter-core: 5.7.1 jupyterlab-widgets: 3.0.9 kiwisolver: 1.4.5 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.4 matplotlib: 3.7.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.6.0 netCDF4: 1.6.2 networkx: 3.1 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.8 numpy: 1.25.1 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 10.2.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 4.1.0 prompt-toolkit: 3.0.43 psutil: 5.9.5 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.16.1 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.2801 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 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: 2023.3.post1 pyzmq: 25.1.2 qtconsole: 5.4.3 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.11.1 setuptools: 67.4.0 setuptools-scm: 7.0.5 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 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: 0.5.0 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2023.7.18 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.4 traitlets: 5.9.0 typing-extensions: 4.9.0 tzdata: 2023.4 urllib3: 2.1.0 wcwidth: 0.2.13 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.9 }}} " defect closed normal Core duplicate Tom Goddard all ChimeraX