Opened 8 months ago
Closed 8 months ago
#17043 closed defect (can't reproduce)
Crash in atom-spec parsing with matchmaker, not a long atomspec.
Reported by: | Owned by: | Eric Pettersen | |
---|---|---|---|
Priority: | normal | Milestone: | |
Component: | Core | Version: | |
Keywords: | Cc: | ||
Blocked By: | Blocking: | ||
Notify when closed: | Platform: | all | |
Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: Linux-6.8.0-48-generic-x86_64-with-glibc2.39 ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Thread 0x00007ead2f4006c0 (most recent call first): File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 316 in wait File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 574 in wait File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 1297 in run File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap Current thread 0x00007eadfa146b80 (most recent call first): File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/atomic/molarray.py", line 150 in File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/atomic/molarray.py", line 150 in __iter__ File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/atomic/structure.py", line 891 in atomspec_atoms File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/atomspec.py", line 616 in _add_model_parts File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/atomspec.py", line 465 in _check File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/atomspec.py", line 479 in _check File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/atomspec.py", line 459 in find_matches File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/atomspec.py", line 601 in find_matches File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/atomspec.py", line 444 in find_matches File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/atomspec.py", line 983 in find_matches File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/atomspec.py", line 980 in evaluate File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/atomspec.py", line 1070 in evaluate File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/atomic/args.py", line 25 in parse File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/atomic/args.py", line 60 in parse File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2488 in _parse_arg File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2629 in _process_positional_arguments File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2853 in run File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 3457 in __call__ File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2918 in run File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/cmd_line/tool.py", line 319 in execute File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/cmd_line/tool.py", line 146 in keyPressEvent File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py", line 275 in event_loop File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/__main__.py", line 892 in init File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1043 in File "/usr/lib/ucsf-chimerax/lib/python3.9/runpy.py", line 87 in _run_code File "/usr/lib/ucsf-chimerax/lib/python3.9/runpy.py", line 197 in _run_module_as_main ===== 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: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > close > cd /home/sebols/projects/rsv/ Current working directory is: /home/sebols/projects/rsv > open ./2025_epitopeAnalyzer/scrubbed/250226_LOR24_PreF_1Fab.pdb Chain information for 250226_LOR24_PreF_1Fab.pdb #1 --- Chain | Description A B C | No description available H | No description available L | No description available > open ./2025_epitopeAnalyzer/scrubbed/250304_MPE8_PreF_1Fab.pdb Chain information for 250304_MPE8_PreF_1Fab.pdb #2 --- Chain | Description A B C | No description available H | No description available L | No description available > open ./2025_epitopeAnalyzer/scrubbed/250304_LOR69_PreF_1Fab.pdb Chain information for 250304_LOR69_PreF_1Fab.pdb #3 --- Chain | Description A B C | No description available H | No description available L | No description available > graphics bgColor white > graphics silhouettes true width 2.5 > lighting gentle > delete H > color all byhetero > view matrix camera > -0.88749,0.029198,-0.45986,6.6496,-0.46047,-0.018822,0.88748,426.58,0.017253,0.99941,0.030162,156.84 > hide all atoms > show all cartoons > mmaker #2-3/A:307-315,42-45 to #1/A:307-315,42-45 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 250226_LOR24_PreF_1Fab.pdb, chain A (#1) with 250304_MPE8_PreF_1Fab.pdb, chain A (#2), sequence alignment score = 47.9 RMSD between 13 pruned atom pairs is 0.344 angstroms; (across all 13 pairs: 0.344) Matchmaker 250226_LOR24_PreF_1Fab.pdb, chain A (#1) with 250304_LOR69_PreF_1Fab.pdb, chain A (#3), sequence alignment score = 68.7 RMSD between 13 pruned atom pairs is 0.315 angstroms; (across all 13 pairs: 0.315) > delete /B,C > color /A light gray > color #1/H #6C96C4 > color #1/L #A5BCD6 > color #2/H #6EC25F > color #2/L #A6D79D > color #3/H #B25D56 > color #3/L #D69B96 > rename #1 LOR24-Fab > rename #2 MPE8_5u68 > rename #3 LOR69-Fab > hide #1.1 models > hide #2.1 models > hide #3.1 models > select clear > ui tool show "Show Sequence Viewer" > sequence chain #2/H Alignment identifier is 2/H > sequence chain #2/L Alignment identifier is 2/L Drag select of 421 residues > select clear > hide #!1 models > hide #!3 models > ui tool show "Show Sequence Viewer" > sequence chain #2/A Alignment identifier is 2/A > select #2/A:509 6 atoms, 5 bonds, 1 residue, 1 model selected > select #2/A:474-509 293 atoms, 299 bonds, 36 residues, 1 model selected > select #2/A:61 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:61-75 112 atoms, 111 bonds, 15 residues, 1 model selected > select #2/A:50 7 atoms, 6 bonds, 1 residue, 1 model selected > select #2/A:50 7 atoms, 6 bonds, 1 residue, 1 model selected > select > #2/A:29-33,38-49,51-60,176-180,186-194,286-293,296-305,312-318,333-336,340-344,348-352,359-361,364-368,373-376,395-398,404-407,411-416,422-426,430-434,438-443,449-452,455-458,465-469 1052 atoms, 1054 bonds, 135 residues, 1 model selected > select #2/A:51 4 atoms, 3 bonds, 1 residue, 1 model selected > select #2/A:51-148 475 atoms, 479 bonds, 1 pseudobond, 61 residues, 2 models selected > select #2/A:51 4 atoms, 3 bonds, 1 residue, 1 model selected > select #2/A:51-217 990 atoms, 998 bonds, 1 pseudobond, 130 residues, 2 models selected > select #2/A:51 4 atoms, 3 bonds, 1 residue, 1 model selected > select #2/A:51-253 1279 atoms, 1291 bonds, 1 pseudobond, 166 residues, 2 models selected > select #2/A:277 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:277-283 59 atoms, 58 bonds, 7 residues, 1 model selected > select #2/A:278 7 atoms, 6 bonds, 1 residue, 1 model selected > select #2/A:278-279 16 atoms, 15 bonds, 2 residues, 1 model selected > select #2/A:278 7 atoms, 6 bonds, 1 residue, 1 model selected > select #2/A:278-339 492 atoms, 500 bonds, 62 residues, 1 model selected > select #2/A:278 7 atoms, 6 bonds, 1 residue, 1 model selected > select #2/A:278-293 131 atoms, 131 bonds, 16 residues, 1 model selected > select #2/A:278 7 atoms, 6 bonds, 1 residue, 1 model selected > select #2/A:278-306 239 atoms, 242 bonds, 29 residues, 1 model selected > select #2/A:278 7 atoms, 6 bonds, 1 residue, 1 model selected > select #2/A:278-299 181 atoms, 182 bonds, 22 residues, 1 model selected > select #2/A:302 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/A:302 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/A:304 7 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:304 7 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:315-316 17 atoms, 16 bonds, 2 residues, 1 model selected > select #2/A:315-321 55 atoms, 56 bonds, 7 residues, 1 model selected > select #2/A:333 6 atoms, 5 bonds, 1 residue, 1 model selected > select #2/A:333-341 76 atoms, 77 bonds, 9 residues, 1 model selected > select #2/A:323 7 atoms, 6 bonds, 1 residue, 1 model selected > select #2/A:323-327 38 atoms, 37 bonds, 5 residues, 1 model selected > select #2/A:319 6 atoms, 5 bonds, 1 residue, 1 model selected > select #2/A:319-321 21 atoms, 21 bonds, 3 residues, 1 model selected > select #2/A:322 6 atoms, 5 bonds, 1 residue, 1 model selected > select #2/A:322-344 181 atoms, 183 bonds, 23 residues, 1 model selected > select #2/A:335 7 atoms, 6 bonds, 1 residue, 1 model selected > select #2/A:335-337 25 atoms, 24 bonds, 3 residues, 1 model selected > select #2/A:353 7 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:353-358 43 atoms, 43 bonds, 6 residues, 1 model selected > select #2/A:353 7 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:353-382 228 atoms, 230 bonds, 30 residues, 1 model selected > select #2/A:392 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:392 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:392-407 116 atoms, 115 bonds, 16 residues, 1 model selected > select #2/A:392 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:392-437 335 atoms, 336 bonds, 46 residues, 1 model selected > select #2/A:465 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/A:465-469 42 atoms, 42 bonds, 5 residues, 1 model selected > select #2/A:462 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/A:462 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/A:461 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/A:461-462 18 atoms, 17 bonds, 2 residues, 1 model selected > select #2/A:461-462 18 atoms, 17 bonds, 2 residues, 1 model selected > select #2/A:461-462 18 atoms, 17 bonds, 2 residues, 1 model selected > select #2/A:461 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/A:461 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/A:462-463 18 atoms, 17 bonds, 2 residues, 1 model selected > select #2/A:462-463 18 atoms, 17 bonds, 2 residues, 1 model selected > select /A:51-253,278-304,322-339,353-376,392-463,474-530 7939 atoms, 8010 bonds, 3 pseudobonds, 1049 residues, 6 models selected > select #2/A:190 11 atoms, 11 bonds, 1 residue, 1 model selected > select #2/A:176 9 atoms, 8 bonds, 1 residue, 1 model selected > close > cd /home/sebols/projects/rsv/ Current working directory is: /home/sebols/projects/rsv > open ./2025_epitopeAnalyzer/scrubbed/250226_LOR24_PreF_1Fab.pdb Chain information for 250226_LOR24_PreF_1Fab.pdb #1 --- Chain | Description A B C | No description available H | No description available L | No description available > open ./2025_epitopeAnalyzer/scrubbed/250304_MPE8_PreF_1Fab.pdb Chain information for 250304_MPE8_PreF_1Fab.pdb #2 --- Chain | Description A B C | No description available H | No description available L | No description available > open ./2025_epitopeAnalyzer/scrubbed/250304_LOR69_PreF_1Fab.pdb Chain information for 250304_LOR69_PreF_1Fab.pdb #3 --- Chain | Description A B C | No description available H | No description available L | No description available > graphics bgColor white > graphics silhouettes true width 2.5 > lighting gentle > delete H > color all byhetero > view matrix camera > -0.88749,0.029198,-0.45986,6.6496,-0.46047,-0.018822,0.88748,426.58,0.017253,0.99941,0.030162,156.84 > hide all atoms > show all cartoons > mmaker #2-3/A:307-315,42-45 to #1/A:307-315,42-45 ===== 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: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.6 (Core Profile) Mesa 24.0.9-0ubuntu0.3 OpenGL renderer: Mesa Intel(R) UHD Graphics 770 (ADL-S GT1) OpenGL vendor: Intel Python: 3.9.11 Locale: en_US.UTF-8 Qt version: PyQt6 6.4.2, Qt 6.4.2 Qt runtime version: 6.4.3 Qt platform: xcb XDG_SESSION_TYPE=wayland DESKTOP_SESSION=ubuntu XDG_SESSION_DESKTOP=ubuntu XDG_CURRENT_DESKTOP=ubuntu:GNOME GNOME_SETUP_DISPLAY=:1 DISPLAY=:0 WAYLAND_DISPLAY=wayland-0 Manufacturer: Shuttle Inc. Model: DH670 OS: Ubuntu 24.04 Noble Numbat Architecture: 64bit ELF Virtual Machine: none CPU: 20 13th Gen Intel(R) Core(TM) i5-13500 Cache Size: 24576 KB Memory: total used free shared buff/cache available Mem: 30Gi 12Gi 4.4Gi 2.6Gi 16Gi 18Gi Swap: 0B 0B 0B Graphics: 00:02.0 VGA compatible controller [0300]: Intel Corporation AlderLake-S GT1 [8086:4680] (rev 0c) DeviceName: Onboard - Video Subsystem: Holco Enterprise Co, Ltd/Shuttle Computer AlderLake-S GT1 [1297:4132] Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 asttokens: 2.2.1 Babel: 2.12.1 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 build: 0.10.0 certifi: 2023.5.7 cftime: 1.6.2 charset-normalizer: 3.1.0 ChimeraX-AddCharge: 1.5.9.1 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.3.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.9.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.43.10 ChimeraX-AtomicLibrary: 10.0.6 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: 2.0.1 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.8 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: 1.0.2 ChimeraX-CheckWaters: 1.3.1 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.3 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.6.1 ChimeraX-CoreFormats: 1.1 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: 1.1.1 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: 1.2.1 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-Label: 1.1.7 ChimeraX-LinuxSupport: 1.0.1 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.2 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: 2.0.12 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.9 ChimeraX-ModelPanel: 1.3.7 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.0 ChimeraX-NRRD: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.10.1 ChimeraX-PDB: 2.7.2 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 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: 1.1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 3.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.1 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.8.3 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.1 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.10.3 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: 2.2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Topography: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.28.4 ChimeraX-uniprot: 2.2.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.1 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.1.3 contourpy: 1.0.7 cxservices: 1.2.2 cycler: 0.11.0 Cython: 0.29.33 debugpy: 1.6.7 decorator: 5.1.1 distro: 1.7.0 docutils: 0.19 executing: 1.2.0 filelock: 3.9.0 fonttools: 4.39.3 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.8.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.35 imagecodecs: 2022.9.26 imagesize: 1.4.1 importlib-metadata: 6.6.0 ipykernel: 6.21.1 ipython: 8.10.0 ipython-genutils: 0.2.0 ipywidgets: 8.0.6 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.0.2 jupyter-core: 5.3.0 jupyterlab-widgets: 3.0.7 kiwisolver: 1.4.4 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.2 matplotlib: 3.6.3 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.2 networkx: 2.8.8 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.4 numpy: 1.23.5 openvr: 1.23.701 packaging: 23.1 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.3.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 3.5.0 prompt-toolkit: 3.0.38 psutil: 5.9.4 ptyprocess: 0.7.0 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.14.0 pynrrd: 1.0.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.4.2 PyQt6-Qt6: 6.4.3 PyQt6-sip: 13.4.1 PyQt6-WebEngine-commercial: 6.4.0 PyQt6-WebEngine-Qt6: 6.4.3 python-dateutil: 2.8.2 pytz: 2023.3 pyzmq: 25.0.2 qtconsole: 5.4.0 QtPy: 2.3.1 RandomWords: 0.4.0 requests: 2.28.2 scipy: 1.9.3 setuptools: 67.4.0 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.4.1 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.4 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.1 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 stack-data: 0.6.2 tables: 3.7.0 tcia-utils: 1.2.0 tifffile: 2022.10.10 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.3.1 traitlets: 5.9.0 typing-extensions: 4.5.0 tzdata: 2023.3 urllib3: 1.26.15 wcwidth: 0.2.6 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.7 zipp: 3.15.0
Change History (2)
comment:1 by , 8 months ago
Component: | Unassigned → Core |
---|---|
Owner: | set to |
Platform: | → all |
Project: | → ChimeraX |
Status: | new → assigned |
Summary: | ChimeraX bug report submission → Crash in atom-spec parsing with matchmaker, not a long atomspec. |
comment:2 by , 8 months ago
Resolution: | → can't reproduce |
---|---|
Status: | assigned → closed |
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