Opened 8 months ago

Closed 8 months ago

Last modified 8 months ago

#16856 closed defect (can't reproduce)

Crash after "alphafold predict"

Reported by: chimerax-bug-report@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Structure Prediction Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.19045
ChimeraX Version: 1.10.dev202502131920 (2025-02-13 19:20:23 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Windows fatal exception: code 0x8001010d

Thread 0x0000161c (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\threading.py", line 324 in wait
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\threading.py", line 622 in wait
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\threading.py", line 1392 in run
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\threading.py", line 995 in _bootstrap

Current thread 0x00006700 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\site-packages\chimerax\ui\gui.py", line 2710 in shown
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\site-packages\chimerax\ui\gui.py", line 2430 in _mw_set_shown
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\site-packages\chimerax\ui\gui.py", line 2092 in _tool_window_request_shown
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\site-packages\chimerax\ui\gui.py", line 2320 in shown
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\site-packages\chimerax\ui\gui.py", line 973 in set_tool_shown
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\site-packages\chimerax\ui\gui.py", line 429 in set_tool_shown
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\site-packages\chimerax\core\tools.py", line 194 in 
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\site-packages\chimerax\ui\gui.py", line 447 in thread_safe
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\site-packages\chimerax\core\tools.py", line 193 in display
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\site-packages\chimerax\core\toolshed\info.py", line 573 in start_tool
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\site-packages\chimerax\core\tools.py", line 421 in start_tools
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\site-packages\chimerax\ui\gui.py", line 278 in build
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\site-packages\chimerax\core\__main__.py", line 825 in init
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\site-packages\chimerax\core\__main__.py", line 1217 in 
  File "", line 88 in _run_code
  File "", line 198 in _run_module_as_main
Windows fatal exception: access violation

Thread 0x00006268 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\multiprocessing\pool.py", line 579 in _handle_results
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x000066fc (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\multiprocessing\pool.py", line 531 in _handle_tasks
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00005dfc (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\multiprocessing\connection.py", line 810 in _exhaustive_wait
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\multiprocessing\connection.py", line 878 in wait
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\multiprocessing\pool.py", line 502 in _wait_for_updates
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\multiprocessing\pool.py", line 522 in _handle_workers
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00000fe8 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00005a9c (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00002a08 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00006520 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00005190 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x0000615c (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00001318 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00005ea8 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x0000618c (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00003744 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x0000426c (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00005720 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x000025f0 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00006610 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x000060e0 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x000038ac (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\threading.py", line 995 in _bootstrap

Current thread 0x00006700 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\site-packages\chimerax\ui\gui.py", line 339 in event_loop
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\site-packages\chimerax\core\__main__.py", line 1054 in init
  File "C:\Program Files\ChimeraX 1.10.dev202502131920\bin\Lib\site-packages\chimerax\core\__main__.py", line 1217 in 
  File "", line 88 in _run_code
  File "", line 198 in _run_module_as_main
===== Log before crash start =====
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.10.dev202502131920 (2025-02-13)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> ui tool show AlphaFold

> alphafold predict
> LYNSYKYTQRELCIYYALASLRSLPEYLATHKITLDALHCPVPLEQINDNRLLIVLPDEITFIYEEVQLETIH,MTDFQKRVFRTVVALTCKKGSCSVLDLRRTYFQYYSSSLIENTLKVLVRDGAVKSKAGKYSAVAEVNGSQATPEDLE

Please cite ColabFold: Making protein folding accessible to all. Nature
Methods (2022) if you use these predictions.  


===== Log before crash end =====

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.10.dev202502131920 (2025-02-13)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 - Build 32.0.101.5768
OpenGL renderer: Intel(R) UHD Graphics 750
OpenGL vendor: Intel

Python: 3.11.4
Locale: en_US.cp1252
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: windows

Manufacturer: Dell Inc.
Model: OptiPlex 7090
OS: Microsoft Windows 10 Pro (Build 19045)
Memory: 16,891,580,416
MaxProcessMemory: 137,438,953,344
CPU: 16 11th Gen Intel(R) Core(TM) i7-11700 @ 2.50GHz
OSLanguage: zh-CN

Installed Packages:
    alabaster: 1.0.0
    anyio: 4.8.0
    appdirs: 1.4.4
    asttokens: 3.0.0
    auditwheel: 6.2.0
    babel: 2.17.0
    beautifulsoup4: 4.13.3
    blockdiag: 3.0.0
    blosc2: 3.1.0
    build: 1.2.1
    certifi: 2025.1.31
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.1
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.19.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Aniso: 1.0.1
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60.5
    ChimeraX-AtomicLibrary: 14.1.13
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.3
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.10.dev202502131920
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.7
    ChimeraX-DistMonitor: 1.4.2
    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: 1.4.1
    ChimeraX-Hbonds: 2.5
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.5.1
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    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: 2.1.7
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.18
    ChimeraX-ModelPanel: 1.5
    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-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14.1
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.7
    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: 1.1.2
    ChimeraX-ProfileGrids: 1.0.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.3
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    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: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.7
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17
    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.19.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.43
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    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: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    comtypes: 1.4.5
    contourpy: 1.3.1
    coverage: 7.6.12
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.12
    debugpy: 1.8.12
    decorator: 5.1.1
    docutils: 0.21.2
    executing: 2.2.0
    filelock: 3.17.0
    fonttools: 4.56.0
    funcparserlib: 2.0.0a0
    glfw: 2.8.0
    grako: 3.16.5
    h11: 0.14.0
    h5py: 3.12.1
    html2text: 2024.2.26
    httpcore: 1.0.7
    httpx: 0.28.1
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.0.0
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jedi: 0.19.1
    Jinja2: 3.1.5
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.8
    line_profiler: 4.2.0
    lxml: 5.2.2
    lz4: 4.4.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    msgpack: 1.1.0
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    numpy: 1.26.4
    OpenMM: 8.2.0
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pickleshare: 0.7.5
    pillow: 10.4.0
    pip: 25.0.1
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    pluggy: 1.5.0
    prompt_toolkit: 3.0.50
    psutil: 6.0.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.31
    Pygments: 2.18.0
    pynmrstar: 3.3.5
    pynrrd: 1.0.0
    PyOpenGL: 3.1.9
    PyOpenGL-accelerate: 3.1.9
    pyopenxr: 1.0.3401
    pyparsing: 3.2.1
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.8.1
    PyQt6-Qt6: 6.8.2
    PyQt6-WebEngine-commercial: 6.8.0
    PyQt6-WebEngine-Qt6: 6.8.2
    PyQt6_sip: 13.10.0
    pytest: 8.3.4
    pytest-cov: 6.0.0
    python-dateutil: 2.9.0.post0
    pytz: 2025.1
    pywin32: 306
    pyzmq: 26.2.1
    qtconsole: 5.5.2
    QtPy: 2.4.3
    qtshim: 1.1
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    sniffio: 1.3.1
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.1.3
    sphinx-autodoc-typehints: 3.0.1
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.7.1
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    tornado: 6.4.2
    traitlets: 5.14.3
    typing_extensions: 4.12.2
    tzdata: 2025.1
    urllib3: 2.3.0
    wcwidth: 0.2.13
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.13
    WMI: 1.5.1

Change History (4)

comment:1 by pett, 8 months ago

Component: Unassigned → Structure Prediction
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Crash showing tool resulting from "alphafold predict"

comment:2 by Tom Goddard, 8 months ago

Resolution: → can't reproduce
Status: assigned → closed
Summary: Crash showing tool resulting from "alphafold predict" → Crash after "alphafold predict"

On Windows the Python faulthandler output is confusing often showing many fatal errors that apparently aren't really fatal errors. In this ticket the fault handler output shows two "current thread" tracebacks. One is showing some tool, no indication what tool, and the other is in the Qt event loop. The tool being shown is almost surely not the AlphaFold tool since the log shows the AlphaFold prediction command that was already run by the AlphaFold tool. When the prediction completes, not tool is shown, it just loads the structure. So there is no indication of what the tool was being shown in the faulthandler output where it says "access violation".

We recently reenabled faulthandler on Windows to see if it gave any useful info about Windows crashes. It hasn't seemed too useful so far.

comment:3 by pett, 8 months ago

Both "current threads" have the same thread number, despite different stacks.

Couldn't the window being shown be the "Alphafold Run" window that comes up when you start a prediction?

comment:4 by Tom Goddard, 8 months ago

Yes, the AlphaFold Run window is a new tool and you are right that probably is the tool that causes the crash. That is also not surprising as that is a Qt html widget and running fancy Google Colab UI javascript and probably crashed due to QWebEngine issues.

Also maybe you are right that the two current threads really are the same active thread with the one ending in the Qt event loop which then is in Qt C++ code, and the other is the C++ code calling back into Python (processing an event, e.g. pressing the "Predict" button on the AlphaFold tool).

That could all make sense. Still useless with just a suggestion of a QWebEngineView crashing.

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