id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 14987 Crash in garbage collection chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-12.7.4-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 0x000000010a6b3600 (most recent call first): Garbage-collecting File ""/private/var/folders/2d/_cyz5n8x4kx8h1216fjhp2c00000gn/T/AppTranslocation/A6584A2B-2D56-4B54-B05F-A2C8AD2E851A/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/ctypes/__init__.py"", line 512 in cast File ""/private/var/folders/2d/_cyz5n8x4kx8h1216fjhp2c00000gn/T/AppTranslocation/A6584A2B-2D56-4B54-B05F-A2C8AD2E851A/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/numpy/core/_internal.py"", line 282 in data_as File ""/private/var/folders/2d/_cyz5n8x4kx8h1216fjhp2c00000gn/T/AppTranslocation/A6584A2B-2D56-4B54-B05F-A2C8AD2E851A/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py"", line 333 in pointer File ""/private/var/folders/2d/_cyz5n8x4kx8h1216fjhp2c00000gn/T/AppTranslocation/A6584A2B-2D56-4B54-B05F-A2C8AD2E851A/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py"", line 208 in get_prop File ""/private/var/folders/2d/_cyz5n8x4kx8h1216fjhp2c00000gn/T/AppTranslocation/A6584A2B-2D56-4B54-B05F-A2C8AD2E851A/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py"", line 1887 in _update_graphics_if_needed File ""/private/var/folders/2d/_cyz5n8x4kx8h1216fjhp2c00000gn/T/AppTranslocation/A6584A2B-2D56-4B54-B05F-A2C8AD2E851A/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 149 in invoke File ""/private/var/folders/2d/_cyz5n8x4kx8h1216fjhp2c00000gn/T/AppTranslocation/A6584A2B-2D56-4B54-B05F-A2C8AD2E851A/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 248 in _activate File ""/private/var/folders/2d/_cyz5n8x4kx8h1216fjhp2c00000gn/T/AppTranslocation/A6584A2B-2D56-4B54-B05F-A2C8AD2E851A/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 217 in activate File ""/private/var/folders/2d/_cyz5n8x4kx8h1216fjhp2c00000gn/T/AppTranslocation/A6584A2B-2D56-4B54-B05F-A2C8AD2E851A/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 393 in activate_trigger File ""/private/var/folders/2d/_cyz5n8x4kx8h1216fjhp2c00000gn/T/AppTranslocation/A6584A2B-2D56-4B54-B05F-A2C8AD2E851A/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py"", line 294 in check_for_drawing_change File ""/private/var/folders/2d/_cyz5n8x4kx8h1216fjhp2c00000gn/T/AppTranslocation/A6584A2B-2D56-4B54-B05F-A2C8AD2E851A/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py"", line 76 in draw_new_frame File ""/private/var/folders/2d/_cyz5n8x4kx8h1216fjhp2c00000gn/T/AppTranslocation/A6584A2B-2D56-4B54-B05F-A2C8AD2E851A/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py"", line 150 in _redraw_timer_callback File ""/private/var/folders/2d/_cyz5n8x4kx8h1216fjhp2c00000gn/T/AppTranslocation/A6584A2B-2D56-4B54-B05F-A2C8AD2E851A/d/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 ""/private/var/folders/2d/_cyz5n8x4kx8h1216fjhp2c00000gn/T/AppTranslocation/A6584A2B-2D56-4B54-B05F-A2C8AD2E851A/d/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 ""/private/var/folders/2d/_cyz5n8x4kx8h1216fjhp2c00000gn/T/AppTranslocation/A6584A2B-2D56-4B54-B05F-A2C8AD2E851A/d/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: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, 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REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 384K 3 \nActivity Tracing 256K 1 \nCG backing stores 3840K 4 \nCG image 6260K 52 \nCG raster data 300K 1 \nColorSync 232K 28 \nCoreAnimation 14.3M 50 \nCoreGraphics 12K 2 \nCoreUI image data 3228K 24 \nFoundation 16K 1 \nKernel Alloc Once 8K 1 \nMALLOC 374.7M 177 \nMALLOC guard page 48K 10 \nMALLOC_MEDIUM (reserved) 400.0M 4 reserved VM address space (unallocated)\nMALLOC_NANO (reserved) 384.0M 1 reserved VM address space (unallocated)\nMach message 16K 2 \nOpenGL GLSL 384K 4 \nSTACK GUARD 100K 25 \nStack 155.7M 26 \nStack Guard 56.0M 1 \nVM_ALLOCATE 182.1M 238 \nVM_ALLOCATE (reserved) 32.0M 1 reserved VM address space (unallocated)\n__CTF 756 1 \n__DATA 58.9M 671 \n__DATA_CONST 31.0M 340 \n__DATA_DIRTY 1641K 213 \n__FONT_DATA 4K 1 \n__GLSLBUILTINS 5176K 1 \n__LINKEDIT 677.4M 151 \n__OBJC_RO 82.9M 1 \n__OBJC_RW 3200K 2 \n__TEXT 809.0M 675 \n__UNICODE 592K 1 \ndyld private memory 1184K 3 \nmapped file 182.2M 45 \nshared memory 3124K 30 \n=========== ======= ======= \nTOTAL 3.4G 2791 \nTOTAL, minus reserved VM space 2.6G 2791 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""6112dda2fc54bc3389840642"", ""factorPackIds"" : { ""SIRI_DICTATION_ASSETS"" : ""620aec83b02b354d3afd2f50"" }, ""deploymentId"" : 240000145 }, { ""rolloutId"" : ""60f8ddccefea4203d95cbeef"", ""factorPackIds"" : { }, ""deploymentId"" : 240000025 } ], ""experiments"" : [ ] } } ===== 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 5F1B format mmcif fromDatabase pdb 5f1b title: Structural basis of Ebola virus entry: viral glycoprotein bound to its endosomal receptor Niemann-Pick C1 [more info...] Chain information for 5f1b #1 --- Chain | Description | UniProt A | GP1 | VGP_EBOZ5 32-188 B | GP2 | VGP_EBOZ5 509-632 C | Niemann-Pick C1 protein | NPC1_HUMAN 2-248 Non-standard residues in 5f1b #1 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) > select /A 1271 atoms, 1225 bonds, 235 residues, 1 model selected > ui tool show ""Show Sequence Viewer"" > sequence chain /B Alignment identifier is 1/B > select add #1 3828 atoms, 3763 bonds, 1 pseudobond, 633 residues, 2 models selected > select subtract #1 Nothing selected > split Split 5f1b (#1) into 4 models Chain information for 5f1b A #1.1 --- Chain | Description A | No description available Chain information for 5f1b B #1.2 --- Chain | Description B | No description available Chain information for 5f1b C #1.3 --- Chain | Description C | No description available > select add #1.1 1271 atoms, 1225 bonds, 235 residues, 1 model selected > select subtract #1.1 Nothing selected > select add #1.2 718 atoms, 703 bonds, 1 pseudobond, 118 residues, 2 models selected > select subtract #1.2 Nothing selected > select add #1.3 1811 atoms, 1805 bonds, 278 residues, 1 model selected > select subtract #1.3 Nothing selected > select add #1.4 28 atoms, 29 bonds, 2 residues, 1 model selected > ui tool show ""Show Sequence Viewer"" > sequence chain #1.2/B Alignment identifier is 1.2/B > select subtract #1.4 Nothing selected > select add #1.2 718 atoms, 703 bonds, 1 pseudobond, 118 residues, 2 models selected > hide #!1.2 target m > select subtract #1.2 Nothing selected > select add #1.2 718 atoms, 703 bonds, 1 pseudobond, 118 residues, 2 models selected > show #!1.2 models > hide #!1 models > hide #1.1 models > hide #1.3 models > hide #1.4 models > close #1.2 > undo > show #!1 models > show #1.1 models > show #1.3 models > ui tool show ""Show Sequence Viewer"" > sequence chain #1.1/A Alignment identifier is 1.1/A > select > #1.1/A:35-38,43-46,63-69,86-89,96-98,101-103,105-114,135-144,151-154,159-161,165-167,177-185 500 atoms, 501 bonds, 64 residues, 1 model selected > select #1.1/A:111 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1.1/A:111-114 34 atoms, 33 bonds, 4 residues, 1 model selected > show sel target ab > label sel text ""{0.name} {0.number}{0.insertion_code}"" > select #1.1/A:79 7 atoms, 6 bonds, 1 residue, 1 model selected > select #1.1/A:79-80 14 atoms, 14 bonds, 2 residues, 1 model selected > show sel target ab > label sel text ""{0.name} {0.number}{0.insertion_code}"" > style sel ball Changed 14 atom styles > style sel ball Changed 14 atom styles > style sel ball Changed 14 atom styles > style sel ball Changed 14 atom styles > select #1.1/A:82 5 atoms, 4 bonds, 1 residue, 1 model selected > select #1.1/A:82 5 atoms, 4 bonds, 1 residue, 1 model selected > select #1.1/A:82 5 atoms, 4 bonds, 1 residue, 1 model selected > select #1.1/A:82,86 19 atoms, 19 bonds, 2 residues, 1 model selected > select #1.1/A:82,86-87 23 atoms, 23 bonds, 3 residues, 1 model selected > select #1.1/A:82,86-88 34 atoms, 35 bonds, 4 residues, 1 model selected > select #1.1/A:82,86-88,111-114 68 atoms, 68 bonds, 8 residues, 1 model selected > select #1.1/A:82,86-88,111-114,118 72 atoms, 71 bonds, 9 residues, 1 model selected > select #1.1/A:82,86-88,111-114,118,141-146 107 atoms, 106 bonds, 15 residues, 1 model selected > select #1.1/A:82,86-88,111-114,118,141-147 113 atoms, 112 bonds, 16 residues, 1 model selected > select #1.1/A:82,86-88,111-114,118,141-147,152 118 atoms, 116 bonds, 17 residues, 1 model selected > select #1.1/A:82,86-88,111-114,118,141-147,152,170 126 atoms, 123 bonds, 18 residues, 1 model selected > show sel target ab > label sel text ""{0.name} {0.number}{0.insertion_code}"" > set bgColor white > select #1.1/A 1271 atoms, 1225 bonds, 235 residues, 1 model selected > ui tool show ""Color Actions"" ===== 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 ATI-4.8.101 OpenGL renderer: AMD Radeon R9 M380 OpenGL Engine OpenGL vendor: ATI Technologies 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: iMac Model Identifier: iMac17,1 Processor Name: Quad-Core Intel Core i5 Processor Speed: 3.2 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 256 KB L3 Cache: 6 MB Memory: 32 GB System Firmware Version: 526.0.0.0.0 OS Loader Version: 540.120.3~37 SMC Version (system): 2.33f12 Software: System Software Overview: System Version: macOS 12.7.4 (21H1123) Kernel Version: Darwin 21.6.0 Time since boot: 1 day 23:50 Graphics/Displays: AMD Radeon R9 M380: Chipset Model: AMD Radeon R9 M380 Type: GPU Bus: PCIe PCIe Lane Width: x16 VRAM (Total): 2 GB Vendor: AMD (0x1002) Device ID: 0x6640 Revision ID: 0x0080 ROM Revision: 113-C6005R-800 VBIOS Version: 113-C6005T-009 EFI Driver Version: 01.00.800 Metal Family: Supported, Metal GPUFamily macOS 2 Displays: iMac: Display Type: Built-In Retina LCD Resolution: Retina 5K (5120 x 2880) Framebuffer Depth: 30-Bit Color (ARGB2101010) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal 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