id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 14449 Crash in garbage collection chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-14.0-x86_64-i386-64bit ChimeraX Version: 1.7 (2023-12-19 08:36:03 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 0x000000020260f240 (most recent call first): Garbage-collecting File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py"", line 161 in File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py"", line 161 in __iter__ File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/mmcif/__init__.py"", line 123 in save File ""/Applications/ChimeraX-1.7.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.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.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.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.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.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.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.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.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.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.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: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, 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: 21474836480, ""uuid"" : ""fb8ba21b-013a-3f11-b51e-5d5b4271240d"" }, ""vmSummary"" : ""ReadOnly portion of Libraries: Total=1.2G resident=0K(0%) swapped_out_or_unallocated=1.2G(100%)\nWritable regions: Total=4.5G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=4.5G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 256K 2 \nActivity Tracing 256K 1 \nCG image 508K 57 \nColorSync 240K 30 \nCoreAnimation 1180K 132 \nCoreGraphics 32K 5 \nCoreUI image data 5332K 43 \nFoundation 36K 2 \nKernel Alloc Once 8K 1 \nMALLOC 3.5G 129 \nMALLOC guard page 384K 24 \nMach message 24K 6 \nOpenGL GLSL 384K 4 \nRosetta Arena 4096K 2 \nRosetta Generic 1692K 420 \nRosetta IndirectBranch 2048K 1 \nRosetta JIT 128.0M 1 \nRosetta Return Stack 800K 80 \nRosetta Thread Context 800K 80 \nSTACK GUARD 44K 11 \nStack 171.1M 42 \nStack Guard 56.1M 31 \nVM_ALLOCATE 216.9M 431 \nVM_ALLOCATE (reserved) 160.1M 11 reserved VM address space (unallocated)\n__CTF 824 1 \n__DATA 56.3M 830 \n__DATA_CONST 48.2M 452 \n__DATA_DIRTY 1863K 237 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 183.1M 156 \n__OBJC_RO 70.5M 1 \n__OBJC_RW 2151K 2 \n__TEXT 1.0G 834 \ndyld private memory 680K 6 \nmapped file 7.2G 1557 \nshared memory 3016K 25 \nunshared pmap 14.9M 9 \n=========== ======= ======= \nTOTAL 12.9G 5659 \nTOTAL, minus reserved VM space 12.8G 5659 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""f8dba78ebfe5f96a5b508b16520584c66dda7b6c"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""60356660bbe37970735c5624"", ""factorPackIds"" : { }, ""deploymentId"" : 240000027 }, { ""rolloutId"" : ""64b21a7351cbb02ce3442e4e"", ""factorPackIds"" : { ""REMINDERS_GROCERY"" : ""64fbafa16ec4a304c6ba89f9"" }, ""deploymentId"" : 240000032 } ], ""experiments"" : [ ] }, ""reportNotes"" : [ ""PC register does not match crashing frame (0x0 vs 0x7FF8A3E2EA78)"" ] } ===== Log before crash start ===== UCSF ChimeraX version: 1.7 (2023-12-19) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/yiyingli/Library/CloudStorage/OneDrive- > UCSanDiego/FtsH_1D/CryoEM_1D/CryoEM > final/Aged_C2_class/helix_aged_class2_refined.pdb"" format pdb Summary of feedback from opening /Users/yiyingli/Library/CloudStorage/OneDrive- UCSanDiego/FtsH_1D/CryoEM_1D/CryoEM final/Aged_C2_class/helix_aged_class2_refined.pdb --- warnings | Ignored bad PDB record found on line 20 Ignored bad PDB record found on line 21 GEOMETRY RESTRAINTS LIBRARY: CDL v1.2 Ignored bad PDB record found on line 22 DEVIATIONS FROM IDEAL VALUES. Ignored bad PDB record found on line 23 BOND : 0.005 0.040 64360 Ignored bad PDB record found on line 24 ANGLE : 0.775 8.973 87080 18 messages similar to the above omitted Chain information for helix_aged_class2_refined.pdb #1 --- Chain | Description A C E G I K M O Q S U W Y a c e g i k m | No description available > close > open ""/Users/yiyingli/Library/CloudStorage/OneDrive- > UCSanDiego/FtsH_1D/CryoEM_1D/CryoEM > final/ATP_C2_class2/FtsH_ATP_class2_refined.pdb"" format pdb Summary of feedback from opening /Users/yiyingli/Library/CloudStorage/OneDrive- UCSanDiego/FtsH_1D/CryoEM_1D/CryoEM final/ATP_C2_class2/FtsH_ATP_class2_refined.pdb --- warnings | Ignored bad PDB record found on line 20 Ignored bad PDB record found on line 21 GEOMETRY RESTRAINTS LIBRARY: CDL v1.2 Ignored bad PDB record found on line 22 DEVIATIONS FROM IDEAL VALUES. Ignored bad PDB record found on line 23 BOND : 0.005 0.031 3218 Ignored bad PDB record found on line 24 ANGLE : 0.753 8.833 4354 18 messages similar to the above omitted Chain information for FtsH_ATP_class2_refined.pdb #1 --- Chain | Description A | No description available > windowsize 900 900 > sym H,9.1,157.5,5,-2 Missing or invalid ""structures"" argument: only initial part ""H"" of atom specifier valid > sym c1*h,9.1,157.5,5,-2 Missing or invalid ""structures"" argument: invalid atomic structures specifier > sym #1 c1*h,9.1,157.5,5,-2 Made 5 copies for FtsH_ATP_class2_refined.pdb symmetry c1*h,9.1,157.5,5,-2 > sym #1 shift,5,10 Made 5 copies for FtsH_ATP_class2_refined.pdb symmetry shift,5,10 > sym #1 c1*h,9.1,157.5,5,-2 axis 10,10,10 Made 5 copies for FtsH_ATP_class2_refined.pdb symmetry c1*h,9.1,157.5,5,-2 > open ""/Users/yiyingli/Library/CloudStorage/OneDrive- > UCSanDiego/FtsH_1D/CryoEM_1D/TO SAVE DATA > W3/cryosparc_P3_J171_006_volume_map_sym_sharp.mrc"" format mrc Opened cryosparc_P3_J171_006_volume_map_sym_sharp.mrc as #5, grid size 448,448,448, pixel 0.86, shown at level 0.894, step 2, values float32 > ui tool show Log > volume #5 step 1 > ui tool show ""Map Coordinates"" > view orient > close #2 > close #3 > close #4 > view orient > log metadata #1 No models had metadata > log chains #1 Chain information for FtsH_ATP_class2_refined.pdb #1 --- Chain | Description A | No description available > ui tool show ""Map Statistics"" > measure mapstats Map cryosparc_P3_J171_006_volume_map_sym_sharp.mrc #5, minimum -2.2, maximum 6.847, mean 0.01989, SD 0.2062, RMS 0.2072 > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > view > view orient > ui tool show ""Side View"" > toolshed show > coordinates Unknown command: coordinates > mapcoor Unknown command: mapcoor > info 4 models #1, FtsH_ATP_class2_refined.pdb, hidden 3176 atoms, 3218 bonds, 406 residues, 1 chains (A) 0 missing structure #1.1, missing structure, shown, 0 pseudobonds #5, cryosparc_P3_J171_006_volume_map_sym_sharp.mrc, shown size 448,448,448, step 1, voxel size 0.86, level 0.894, value range -2.2001 - 6.8468, value type float32, 0 symmetry operators #5.1, surface, shown, 3666688 triangles > ui tool show ""Map Statistics"" > measure mapstats Map cryosparc_P3_J171_006_volume_map_sym_sharp.mrc #5, minimum -2.2, maximum 6.847, mean 0.01989, SD 0.2062, RMS 0.2072 > ui tool show ""Map Coordinates"" > volume #5 origin Missing ""origin"" keyword's argument > volume #5 origin 0,0,0 > volume #5 originIndex0,0,0 Expected a keyword > volume #5 originIndex 0,0,0 > view orient > show #!1 models > hide #!5 models > sym #1 c1*h,9.1,157.5,5 Made 5 copies for FtsH_ATP_class2_refined.pdb symmetry c1*h,9.1,157.5,5 > show #!1 models > hide #!1 models > hide #!2 models > show #!2 models > sym #1 c1*h,9.1,157.5,5,-223.5 Made 5 copies for FtsH_ATP_class2_refined.pdb symmetry c1*h,9.1,157.5,5,-223.5 > view > ui tool show ""Side View"" > sym #1 c1*h,9.1,157.5,5,-2 Made 5 copies for FtsH_ATP_class2_refined.pdb symmetry c1*h,9.1,157.5,5,-2 > hide #!2 models > close #2 > close #3 > close #4 > show #!1 models > view > sym #1 c1*h,9.1,157.5,5,-2 axis 0,0,1 Made 5 copies for FtsH_ATP_class2_refined.pdb symmetry c1*h,9.1,157.5,5,-2 > view > close #2 > show #!1 models > show #!5 models > hide #!5 models > view > sym #1 c1*h,9.1,157.5,5,-2 coordinateSystem #5 Made 5 copies for FtsH_ATP_class2_refined.pdb symmetry c1*h,9.1,157.5,5,-2 > view > select add #2 15880 atoms, 16090 bonds, 2030 residues, 6 models selected > close #2 > show #!1 models > sym #1 c1*h,9.1,157.5,5,-2 coordinateSystem #5 biomtSet true Expected a keyword > sym #1 c1*h,9.1,157.5,5,-2 coordinateSystem #5 biomtSet True Expected a keyword > sym #1 c1*h,9.1,157.5,5,-2 coordinateSystem #5 biomtSet true Expected a keyword > sym #1 c1*h,9.1,157.5,5,-2 biomtSet true coordinateSystem #5 Expected a keyword > sym #1 c1*h,9.1,157.5,5,-2 axis 0,0,1 biomtSet Expected a keyword > sym #1 c1*h,9.1,157.5,5,-2 axis 0,0,1 biomt true Expected a keyword > sym #1 c1*h,9.1,157.5,5,-2 axis 0,0,1 BIOMT Expected a keyword > sym #1 c1*h,9.1,157.5,5,-2 axis 0,0,1 bioMT Expected a keyword > sym #1 c1*h,9.1,157.5,5,-2 axis 0,0,1 bio Expected a keyword > sym #1 c1*h,9.1,157.5,5,-2 axis 0,0,1 biomt Expected a keyword > sym #1 c1*h,9.1,157.5,5,-2 axis 0,0,1 Made 5 copies for FtsH_ATP_class2_refined.pdb symmetry c1*h,9.1,157.5,5,-2 No model chosen to save relative to > save /Users/yiyingli/Desktop/5subunit.cif relModel #5 Not saving entity_poly_seq for non-authoritative sequences > biomt Unknown command: biomt > help help:user > sym #1 biomt c1*h,9.1,157.5,5,-2 axis 0,0,1 Expected a keyword > sym #1 biomt true c1*h,9.1,157.5,5,-2 axis 0,0,1 Expected a keyword > sym #1 biomt Molecule FtsH_ATP_class2_refined.pdb has no biological unit info > sym #1 biomt matri Expected a keyword > sym #1 biomt1 Unknown symmetry group ""biomt1"" > sym #1 biomtSet Unknown symmetry group ""biomtSet"" > sym #1 biomtSet true Expected a keyword > sym #1 c1*h,9.1,157.5,5 biomtSet true Expected a keyword > toolshed show > sym #1 c1*h,9.1,157.5,5 addMmcifAssembly true Made 5 copies for FtsH_ATP_class2_refined.pdb symmetry c1*h,9.1,157.5,5 No model chosen to save relative to > save /Users/yiyingli/Desktop/5subunit2.cif relModel #5 Not saving entity_poly_seq for non-authoritative sequences > open /Users/yiyingli/Desktop/ATP_group1.pdb Summary of feedback from opening /Users/yiyingli/Desktop/ATP_group1.pdb --- warning | Ignored bad PDB record found on line 3180 Chain information for ATP_group1.pdb #4 --- Chain | Description A | No description available > open /Users/yiyingli/Desktop/ATP_group1.pdb Summary of feedback from opening /Users/yiyingli/Desktop/ATP_group1.pdb --- warning | Ignored bad PDB record found on line 3180 Chain information for ATP_group1.pdb #6 --- Chain | Description A | No description available > hide #!2 models > show #!1 models > hide #!2.1 models > close #2 > close #3 > close #6 > show #!5 models > hide #!4 models > hide #!1 models > show #!4 models > hide #!5 models > show #!5 models > view orient > show #!1 models > close #1 > hide #!5 models > show #!5 models > volume #5 level 1 > volume #5 level 1.5 > view > view orient > hide #!5 models > sym #4 c1*h,9.1,157.5,5 addMmcifAssembly true Made 5 copies for ATP_group1.pdb symmetry c1*h,9.1,157.5,5 > view > save /Users/yiyingli/Desktop/5subunit.cif relModel #5 Not saving entity_poly_seq for non-authoritative sequences > sym #4 c1*h,9.1,157.5,5 biomt Expected a keyword > sym #4 biomt Molecule ATP_group1.pdb has no biological unit info > sym #4 c1*h,9.1,157.5,5 addMmcifAssembly true copies true Made 5 copies for ATP_group1.pdb symmetry c1*h,9.1,157.5,5 > hide #!1 models > show #!1 models > close #1 > combine #2 Remapping chain ID 'A' in ATP_group1.pdb #2.2 to 'B' Remapping chain ID 'A' in ATP_group1.pdb #2.3 to 'C' Remapping chain ID 'A' in ATP_group1.pdb #2.4 to 'D' Remapping chain ID 'A' in ATP_group1.pdb #2.5 to 'E' > save /Users/yiyingli/Desktop/5subunit.cif relModel #5 Not saving entity_poly_seq for non-authoritative sequences > sym #4 c1*h,9.1,157.5,5 addMmcifAssembly true copies true Made 5 copies for ATP_group1.pdb symmetry c1*h,9.1,157.5,5 > sym #4 c1*h,9.1,157.5,5 addMmcifAssembly false copies true Made 5 copies for ATP_group1.pdb symmetry c1*h,9.1,157.5,5 > close #4 > close #3 > close #2 > close #6 > hide #!1 models > show #!1 models > sym #1 c1*h,9.1,157.5,5 addMmcifAssembly false copies true Made 5 copies for combination symmetry c1*h,9.1,157.5,5 > hide #!2 models > show #!2 models > save /Users/yiyingli/Desktop/5subunit_noaddMmcif.cif models #2 relModel #5 Not saving entity_poly_seq for non-authoritative sequences ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.7 (2023-12-19) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 86 OpenGL renderer: Apple M2 OpenGL vendor: Apple 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: Mac Model Identifier: Mac14,2 Model Number: FLY13LL/A Chip: Unknown Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 8 GB System Firmware Version: 10151.1.1 OS Loader Version: 10151.1.1 Software: System Software Overview: System Version: macOS 14.0 (23A344) Kernel Version: Darwin 23.0.0 Time since boot: 3 days, 7 hours, 40 minutes Graphics/Displays: Apple M2: Chipset Model: Apple M2 Type: GPU Bus: Built-In Total Number of Cores: 8 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina Display Resolution: 2560 x 1664 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal DELL U2414H: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 50.00Hz Mirror: Off Online: Yes Installed Packages: alabaster: 0.7.13 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: 2.12.1 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.49.1 ChimeraX-AtomicLibrary: 12.1.3 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 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 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: 1.5.13 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: 1.0.3 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: 1.12.3 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: 1.33.2 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: 0.2.0 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: 4.47.0 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: 5.5.1 jupyterlab-widgets: 3.0.9 kiwisolver: 1.4.5 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.3 matplotlib: 3.7.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.8 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: 10.0.1 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: 1.0.7 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.5 sphinxcontrib-htmlhelp: 2.0.4 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.6 sphinxcontrib-serializinghtml: 1.1.9 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: 2023.3 urllib3: 2.1.0 wcwidth: 0.2.12 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.9 }}} " defect closed normal Core fixed Tom Goddard all ChimeraX