id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 15643 Crash in garbage collection chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-14.4.1-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 0x00007ff8527ac100 (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 1613 in remove_deleted_pointers File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py"", line 134 in __init__ File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py"", line 391 in __init__ File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py"", line 2226 in process_changes File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py"", line 2231 in changes File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/changes.py"", line 36 in check_for_changes File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py"", line 69 in draw_new_frame File ""/Applications/ChimeraX-1.7.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 ""/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 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2196K 2 \n__TEXT 1.0G 807 \ndyld private memory 420K 4 \nmapped file 565.7M 91 \nshared memory 3512K 29 \n=========== ======= ======= \nTOTAL 5.8G 3133 \nTOTAL, minus reserved VM space 5.6G 3133 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""cf0c682c1b5297a78f6da00f4ac9cb4f5dc5c1a8"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""645c2d2f9e69a025b0a37e29"", ""factorPackIds"" : { }, ""deploymentId"" : 240000003 }, { ""rolloutId"" : ""65a8173205d942272410674b"", ""factorPackIds"" : { ""SIRI_HOME_AUTOMATION_SERVER_FLOW_DEPRECATION"" : ""65d39fa4cb0e2417d11ce5f6"" }, ""deploymentId"" : 240000001 } ], ""experiments"" : [ { ""treatmentId"" : ""c47ab4cc-c9c3-4b5d-a87c-e2433ce02597"", ""experimentId"" : ""6639bc6ba73d460582162323"", ""deploymentId"" : 400000006 } ] } } ===== 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 (2023-12-19) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/will/Downloads/tetramermodelsaturday.pdb format pdb Summary of feedback from opening /Users/will/Downloads/tetramermodelsaturday.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 ASP A 241 VAL A 255 1 15 Start residue of secondary structure not found: HELIX 2 2 SER A 290 THR A 298 1 9 Start residue of secondary structure not found: HELIX 3 3 ASP A 301 ILE A 321 1 21 Start residue of secondary structure not found: HELIX 4 4 LYS A 338 LYS A 340 1 3 Start residue of secondary structure not found: HELIX 5 5 THR A 378 MET A 382 1 5 37 messages similar to the above omitted Chain information for tetramermodelsaturday.pdb --- Chain | Description 1.1/A | No description available 1.2/A | No description available 1.3/A | No description available 1.4/B | No description available > hide #1.1 models > show #1.1 models > hide #1.1 models > show #1.1 models > hide #1.1 models > show #1.1 models > hide #1.2 models > show #1.2 models > hide #1.1 models > show #1.1 models > hide #1.2 models > show #1.2 models > hide #1.3 models > show #1.3 models > hide #!1.4 models > hide #1.3 models > close #1.3 > close #1.4 > save /Users/will/Downloads/selenA.pdb > close #1 > open /Users/will/Downloads/x1226/sculpt_tetramermodelsaturday.pdb format pdb No such file/path: /Users/will/Downloads/x1226/sculpt_tetramermodelsaturday.pdb > open /Users/will/Downloads/tetramermodelsaturday.pdb format pdb Summary of feedback from opening /Users/will/Downloads/tetramermodelsaturday.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 ASP A 241 VAL A 255 1 15 Start residue of secondary structure not found: HELIX 2 2 SER A 290 THR A 298 1 9 Start residue of secondary structure not found: HELIX 3 3 ASP A 301 ILE A 321 1 21 Start residue of secondary structure not found: HELIX 4 4 LYS A 338 LYS A 340 1 3 Start residue of secondary structure not found: HELIX 5 5 THR A 378 MET A 382 1 5 37 messages similar to the above omitted Chain information for tetramermodelsaturday.pdb --- Chain | Description 1.1/A | No description available 1.2/A | No description available 1.3/A | No description available 1.4/B | No description available > hide #1.3 models > hide #!1.4 models > open /Users/will/Downloads/selenA.pdb Chain information for selenA.pdb --- Chain | Description 2.1/A | No description available 2.2/A | No description available > hide #!2 models > show #!2 models > close #2 > show #1.3 models > show #!1.4 models > save /Users/will/Downloads/selenA.pdb models #1.1-2 > save /Users/will/Downloads/SelenB.pdb models #1.3-4 > save /Users/will/Downloads/selenA.pdb models #1.1 > save /Users/will/Downloads/SelenB.pdb models #1.2 > save /Users/will/Downloads/selenC.pdb models #1.3 > save /Users/will/Downloads/SelenD.pdb models #1.4 > hide #1.2 models > hide #1.3 models > show #1.3 models > hide #1.3 models > show #1.2 models > show #1.3 models > open /Users/will/Downloads/x1226/AutoBuild_run_159_/working_best_placed.pdb Summary of feedback from opening /Users/will/Downloads/x1226/AutoBuild_run_159_/working_best_placed.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK THIS IS AutoBuild_run_159_/working_best.pdb Ignored bad PDB record found on line 2 REMARK WITH UNPLACED RESIDUES REMOVED Ignored bad PDB record found on line 3 Sat Jul 20 16:19:27 2024 Chain information for working_best_placed.pdb #2 --- Chain | Description U | No description available > ui mousemode right ""translate selected models"" > select clear > select #2/U:715 4 atoms, 3 bonds, 1 residue, 1 model selected > view matrix models #2,1,0,0,-2.991,0,1,0,-11.588,0,0,1,-23.305 > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.74386,-0.58338,0.3261,-12.329,0.071743,-0.41541,-0.9068,71.561,0.66447,0.69793,-0.26715,42.516 > view matrix models > #2,0.78767,-0.5741,0.22358,-6.1158,0.14997,-0.17332,-0.97338,71.152,0.59757,0.80023,-0.050424,27.085 > view matrix models > #2,0.82085,-0.54974,0.15488,-2.2933,0.19189,0.010049,-0.98136,68.198,0.53794,0.83528,0.11374,16.196 > view matrix models > #2,0.81932,-0.55116,0.15789,-2.4542,0.19026,0.0015985,-0.98173,68.38,0.54084,0.8344,0.10618,16.684 > view matrix models > #2,0.76902,-0.58151,0.26544,-8.5843,0.12013,-0.27638,-0.95351,71.854,0.62783,0.76516,-0.14268,33.495 > ui mousemode right ""translate selected models"" > view matrix models > #2,0.76902,-0.58151,0.26544,-3.3891,0.12013,-0.27638,-0.95351,40.697,0.62783,0.76516,-0.14268,4.676 > view matrix models > #2,0.76902,-0.58151,0.26544,-15.088,0.12013,-0.27638,-0.95351,39.611,0.62783,0.76516,-0.14268,19.178 > close #2 > open /Users/will/Downloads/x1226/AutoBuild_run_158_/overall_best.pdb Chain information for overall_best.pdb #2 --- Chain | Description A | No description available U | No description available > ui tool show Matchmaker > matchmaker #!2 to #1.1 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 tetramermodelsaturday.pdb, chain A (#1.1) with overall_best.pdb, chain A (#2), sequence alignment score = 1018 RMSD between 110 pruned atom pairs is 1.386 angstroms; (across all 286 pairs: 3.127) > hide #!1.4 models > show #!1.4 models > hide #1.3 models > show #1.3 models > hide #1.3 models > hide #1.2 models > show #1.2 models > hide #1.2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > open /Users/will/Downloads/x1226/AutoBuild_run_159_/working_best.pdb Chain information for working_best.pdb #3 --- Chain | Description U | No description available Drag select of 2 residues Drag select of 3 residues > view matrix models #3,1,0,0,-40.017,0,1,0,-28.346,0,0,1,-56.695 > view matrix models #3,1,0,0,-31.43,0,1,0,-38.699,0,0,1,-63.463 > view matrix models #3,1,0,0,-27.277,0,1,0,-113.88,0,0,1,-80.336 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.60863,-0.75532,-0.24301,15.761,0.019834,0.32066,-0.94699,-32.854,0.7932,0.57155,0.21014,-56.335 > view matrix models > #3,-0.86697,0.13725,-0.47909,86.333,-0.30623,-0.90514,0.29485,-105.3,-0.39318,0.40234,0.82676,-54.462 > ui mousemode right ""translate selected models"" > view matrix models > #3,-0.86697,0.13725,-0.47909,84.021,-0.30623,-0.90514,0.29485,-40.727,-0.39318,0.40234,0.82676,-39.514 > ui tool show ""Show Sequence Viewer"" > sequence chain #1.1/A Alignment identifier is 1.1/A > sequence chain #1.2/A Alignment identifier is 1.2/A > sequence chain #1.3/A Alignment identifier is 1.3/A > sequence chain #1.4/B Alignment identifier is 1.4/B > close #1.2-3 > close #2 > select #1.4/B:191-192 15 atoms, 15 bonds, 2 residues, 1 model selected > select #1.4/B 2295 atoms, 2346 bonds, 289 residues, 1 model selected > colour sel lime > view matrix models #1.4,1,0,0,31.652,0,1,0,-6.2748,0,0,1,-3.733 > undo > view matrix models #1.4,1,0,0,0.36801,0,1,0,0.72714,0,0,1,-0.28754 > undo > select clear Drag select of 7 residues > view matrix models > #1.1,1,0,0,-10.196,0,1,0,-1.8448,0,0,1,12.212,#3,-0.86697,0.13725,-0.47909,73.825,-0.30623,-0.90514,0.29485,-42.572,-0.39318,0.40234,0.82676,-27.302 > undo > select add #1 4612 atoms, 4683 bonds, 580 residues, 4 models selected > select subtract #1.1 2327 atoms, 2346 bonds, 294 residues, 3 models selected > select add #1 4612 atoms, 4683 bonds, 580 residues, 4 models selected > select subtract #1.4 2317 atoms, 2337 bonds, 291 residues, 3 models selected > select add #3 3750 atoms, 3780 bonds, 504 residues, 3 models selected > select add #1 6045 atoms, 6126 bonds, 793 residues, 4 models selected > select subtract #1 1465 atoms, 1443 bonds, 218 residues, 1 model selected > view matrix models > #3,-0.86697,0.13725,-0.47909,74.037,-0.30623,-0.90514,0.29485,-44.226,-0.39318,0.40234,0.82676,-27.8 > view matrix models > #3,-0.86697,0.13725,-0.47909,78.994,-0.30623,-0.90514,0.29485,-44.207,-0.39318,0.40234,0.82676,-34.393 ===== 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 (2023-12-19) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/will/Downloads/tetramermodelsaturday.pdb Summary of feedback from opening /Users/will/Downloads/tetramermodelsaturday.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 ASP A 241 VAL A 255 1 15 Start residue of secondary structure not found: HELIX 2 2 SER A 290 THR A 298 1 9 Start residue of secondary structure not found: HELIX 3 3 ASP A 301 ILE A 321 1 21 Start residue of secondary structure not found: HELIX 4 4 LYS A 338 LYS A 340 1 3 Start residue of secondary structure not found: HELIX 5 5 THR A 378 MET A 382 1 5 37 messages similar to the above omitted Chain information for tetramermodelsaturday.pdb --- Chain | Description 1.1/A | No description available 1.2/A | No description available 1.3/A | No description available 1.4/B | No description available OpenGL version: 4.1 ATI-5.5.17 OpenGL renderer: AMD Radeon Pro 5500 XT 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: iMac20,1 Processor Name: 8-Core Intel Core i7 Processor Speed: 3.8 GHz Number of Processors: 1 Total Number of Cores: 8 L2 Cache (per Core): 256 KB L3 Cache: 16 MB Hyper-Threading Technology: Enabled Memory: 32 GB System Firmware Version: 2022.100.22.0.0 (iBridge: 21.16.4222.0.0,0) OS Loader Version: 580~1678 Software: System Software Overview: System Version: macOS 14.4.1 (23E224) Kernel Version: Darwin 23.4.0 Time since boot: 1 day, 7 hours, 50 minutes Graphics/Displays: AMD Radeon Pro 5500 XT: Chipset Model: AMD Radeon Pro 5500 XT Type: GPU Bus: PCIe PCIe Lane Width: x16 VRAM (Total): 8 GB Vendor: AMD (0x1002) Device ID: 0x7340 Revision ID: 0x0041 ROM Revision: 113-D3220I-231 VBIOS Version: 113-D322A1XT-011 Option ROM Version: 113-D322A1XT-011 EFI Driver Version: 01.01.231 Metal Support: Metal 3 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: No Connection Type: Internal 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 duplicate Tom Goddard all ChimeraX