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#5182 closed defect (can't reproduce)

Crash handling AlphaFold results

Reported by:	gmszhuf@…	Owned by:	Tom Goddard
Priority:	normal	Milestone:
Component:	Sequence	Version:
Keywords:		Cc:	Zach Pearson
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        Windows-10-10.0.22000
ChimeraX Version: 1.3.dev202109070604 (2021-09-07 06:04:33 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Windows fatal exception: access violation

Thread 0x0000ba50 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3.dev202109070604\bin\lib\multiprocessing\pool.py", line 576 in _handle_results
  File "C:\Program Files\ChimeraX 1.3.dev202109070604\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3.dev202109070604\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3.dev202109070604\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x0000a4a4 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3.dev202109070604\bin\lib\multiprocessing\pool.py", line 528 in _handle_tasks
  File "C:\Program Files\ChimeraX 1.3.dev202109070604\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3.dev202109070604\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3.dev202109070604\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00009f94 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3.dev202109070604\bin\lib\multiprocessing\connection.py", line 816 in _exhaustive_wait
  File "C:\Program Files\ChimeraX 1.3.dev202109070604\bin\lib\multiprocessing\connection.py", line 884 in wait
  File "C:\Program Files\ChimeraX 1.3.dev202109070604\bin\lib\multiprocessing\pool.py", line 499 in _wait_for_updates
  File "C:\Program Files\ChimeraX 1.3.dev202109070604\bin\lib\multiprocessing\pool.py", line 519 in _handle_workers
  File "C:\Program Files\ChimeraX 1.3.dev202109070604\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3.dev202109070604\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3.dev202109070604\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x000047e0 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3.dev202109070604\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.3.dev202109070604\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3.dev202109070604\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3.dev202109070604\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x0000b1bc (most recent call first):
  File "C:\Program Files\ChimeraX 1.3.dev202109070604\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.3.dev202109070604\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3.dev202109070604\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3.dev202109070604\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00009c04 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3.dev202109070604\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.3.dev202109070604\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3.dev202109070604\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3.dev202109070604\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x0000ba60 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3.dev202109070604\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.3.dev202109070604\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3.dev202109070604\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3.dev202109070604\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x0000b4a0 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3.dev202109070604\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.3.dev202109070604\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3.dev202109070604\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3.dev202109070604\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x0000c77c (most recent call first):
  File "C:\Program Files\ChimeraX 1.3.dev202109070604\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.3.dev202109070604\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3.dev202109070604\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3.dev202109070604\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x0000b9e4 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3.dev202109070604\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.3.dev202109070604\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3.dev202109070604\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3.dev202109070604\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x0000b634 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3.dev202109070604\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.3.dev202109070604\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3.dev202109070604\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3.dev202109070604\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x0000ae24 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3.dev202109070604\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.3.dev202109070604\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3.dev202109070604\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3.dev202109070604\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00003e40 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3.dev202109070604\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.3.dev202109070604\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3.dev202109070604\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3.dev202109070604\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x0000c754 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3.dev202109070604\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.3.dev202109070604\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3.dev202109070604\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3.dev202109070604\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x0000d530 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3.dev202109070604\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.3.dev202109070604\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3.dev202109070604\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3.dev202109070604\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x0000bf00 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3.dev202109070604\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.3.dev202109070604\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3.dev202109070604\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3.dev202109070604\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x000035c4 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3.dev202109070604\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.3.dev202109070604\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3.dev202109070604\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3.dev202109070604\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x0000c92c (most recent call first):
  File "C:\Program Files\ChimeraX 1.3.dev202109070604\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.3.dev202109070604\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3.dev202109070604\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3.dev202109070604\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00000900 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3.dev202109070604\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.3.dev202109070604\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3.dev202109070604\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3.dev202109070604\bin\lib\threading.py", line 930 in _bootstrap

Current thread 0x0000ce48 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3.dev202109070604\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files\ChimeraX 1.3.dev202109070604\bin\lib\site-packages\ChimeraX_main.py", line 880 in init
  File "C:\Program Files\ChimeraX 1.3.dev202109070604\bin\lib\site-packages\ChimeraX_main.py", line 1029 in 
  File "C:\Program Files\ChimeraX 1.3.dev202109070604\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.3.dev202109070604\bin\lib\runpy.py", line 197 in _run_module_as_main
===== Log before crash start =====
> open
> C:\Users\fengz\OneDrive\Documents\GitHub\panSARS\docking\docking\S309_docking\S309_RBD_docking.pdb
> format pdb

Summary of feedback from opening
C:\Users\fengz\OneDrive\Documents\GitHub\panSARS\docking\docking\S309_docking\S309_RBD_docking.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 PHE A 29
SER A 31 1 3  
Start residue of secondary structure not found: HELIX 2 2 GLN A 62 PHE A 64 1
3  
Start residue of secondary structure not found: HELIX 3 3 SER A 88 ASP A 90 1
3  
Start residue of secondary structure not found: HELIX 4 4 SER B 31 SER B 33 1
3  
Start residue of secondary structure not found: HELIX 5 5 PRO B 81 ASP B 83 1
3  
19 messages similar to the above omitted  
  
Chain information for S309_RBD_docking.pdb  
---  
Chain | Description  
1.1/A 1.2/A 1.3/A 1.4/A 1.5/A 1.6/A 1.7/A 1.8/A 1.9/A 1.10/A | No description
available  
1.1/B 1.2/B 1.3/B 1.4/B 1.5/B 1.6/B 1.7/B 1.8/B 1.9/B 1.10/B | No description
available  
1.11/E | No description available  
  

> ui tool show AlphaFold

> alphafold match #1.1

Fetching compressed AlphaFold A0A0C4DH31 from
https://alphafold.ebi.ac.uk/files/AF-A0A0C4DH31-F1-model_v1.cif  
Fetching compressed AlphaFold P01619 from
https://alphafold.ebi.ac.uk/files/AF-P01619-F1-model_v1.cif  
2 AlphaFold models found using sequence similarity searches: A0A0C4DH31 (chain
A), P01619 (chain B)  
AlphaFold chains matching S309_RBD_docking.pdb  
---  
Chain| UniProt Name| UniProt Id| RMSD| Length| Seen| % Id  
A | HV118_HUMAN | A0A0C4DH31 | 0.25 | 98 | 127 | 94  
B | KV320_HUMAN | P01619 | 1.39 | 96 | 107 | 93  
  
Opened 2 AlphaFold models  

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #1.2 models

> hide #1.3 models

> hide #1.4 models

> hide #1.5 models

> hide #1.7 models

> hide #1.6 models

> hide #1.8 models

> hide #1.9 models

> hide #1.10 models

> hide #!1.11 models

> show #!1.11 models

> color #2::c_alpha_distance>=3.0 red

> show #2::c_alpha_distance>=3.0 atoms,ribbons

> show #2.1::c_alpha_distance>=3.0 atoms,ribbons

> select #2.1::c_alpha_distance>=3.0

Nothing selected  

> color #2.2::c_alpha_distance>=3.0 red

> show #2.2::c_alpha_distance>=3.0 atoms,ribbons

> color #2.2::missing_structure=true lime

> show #2.2::missing_structure=true atoms,ribbons

> color #2.1::missing_structure=true lime

> show #2.1::missing_structure=true atoms,ribbons

> select #2.1::missing_structure=true

Nothing selected  

> color #2.1::missing_structure=true red

> color #2.1::missing_structure=true lime

> alphafold match #1.11

No AlphaFold model with similar sequence for chain E  

Opened 0 AlphaFold model  

> alphafold search #1.11

ChimeraX REST job id: job_zywlpwvc  
BlastProtein finished.  
Parsing BLAST results.  

> alphafold predict #1.11

Running AlphaFold prediction  


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

Log:
UCSF ChimeraX version: 1.3.dev202109070604 (2021-09-07)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 NVIDIA 471.35
OpenGL renderer: NVIDIA GeForce RTX 2080 Super/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Alienware
Model: Alienware m17 R3
OS: Microsoft Windows 11 Pro (Build 22000)
Memory: 34,075,373,568
MaxProcessMemory: 137,438,953,344
CPU: 16 Intel(R) Core(TM) i9-10980HK CPU @ 2.40GHz
OSLanguage: en-US
Locale: ('en_US', 'cp936')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.5.30
    cftime: 1.5.0
    chardet: 4.0.0
    ChimeraX-AddCharge: 1.1.4
    ChimeraX-AddH: 2.1.10
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.2
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.29.1
    ChimeraX-AtomicLibrary: 4.1.4
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.3
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.4.1
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3.dev202109070604
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.4
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.1
    ChimeraX-Help: 1.2
    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
    ChimeraX-Label: 1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.1
    ChimeraX-MDcrds: 2.5
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.1
    ChimeraX-ModelPanel: 1.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.1
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.12
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    comtypes: 1.1.10
    cxservices: 1.1
    cycler: 0.10.0
    Cython: 0.29.23
    decorator: 5.0.9
    distlib: 0.3.1
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.4.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.20
    imagecodecs: 2021.4.28
    imagesize: 1.2.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 2.11.3
    jupyter-client: 6.1.12
    jupyter-core: 4.7.1
    kiwisolver: 1.3.2
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 1.1.1
    matplotlib: 3.4.2
    matplotlib-inline: 0.1.2
    msgpack: 1.0.2
    netCDF4: 1.5.6
    networkx: 2.6.2
    numexpr: 2.7.3
    numpy: 1.21.0
    openvr: 1.16.801
    packaging: 21.0
    ParmEd: 3.2.0
    parso: 0.8.2
    pickleshare: 0.7.5
    Pillow: 8.2.0
    pip: 21.1.1
    pkginfo: 1.7.0
    prompt-toolkit: 3.0.20
    psutil: 5.8.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.9.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.1
    pytz: 2021.1
    pywin32: 228
    pyzmq: 22.2.1
    qtconsole: 5.1.0
    QtPy: 1.11.0
    RandomWords: 0.3.0
    requests: 2.25.1
    scipy: 1.6.3
    setuptools: 57.0.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.4.0
    Sphinx: 4.0.1
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.0
    urllib3: 1.26.6
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.2
    wheel-filename: 1.3.0
    WMI: 1.5.1

Change History (4)

comment:1 by Eric Pettersen, 4 years ago

Cc:	Zach Pearson added
Component:	Unassigned → Sequence
Owner:	set to Tom Goddard
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → Crash handling AlphaFold results

comment:2 by Eric Pettersen, 4 years ago

Reported by Zhu Feng

comment:3 by Tom Goddard, 4 years ago

I don't see any clues about why ChimeraX crashed. It seems the last operations was command "alphafold predict #1.11". The Qt window toolkit was in the event loop so it does not look like any ChimeraX code was running in the main thread. There are 19 other Python running threads -- I do not know what created those. Maybe the Qt window toolkit crashed somehow associated with the AlphaFold predict Google Colab browser window.

comment:4 by Tom Goddard, 4 years ago

Resolution:	→ can't reproduce
Status:	assigned → closed

I tried running AlphaFold prediction on Windows in ChimeraX Sep 8, 2021 build and it worked without errors or crashes.

If you see this crash running AlphaFold please report again. My suspicion is the crash is unrelated to AlphaFold and is instead some bug in the Qt window toolkit.

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