Opened 4 years ago

Closed 4 years ago

Last modified 4 years ago

#5714 closed defect (can't reproduce)

Crash showing AlphaFold model

Reported by: swayam.singh@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Graphics Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.19042
ChimeraX Version: 1.3rc202112010754 (2021-12-01 07:54:47 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Aborted

Thread 0x0000394c (most recent call first):
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\multiprocessing\pool.py", line 576 in _handle_results
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00005354 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\multiprocessing\pool.py", line 528 in _handle_tasks
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00005a68 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\multiprocessing\connection.py", line 816 in _exhaustive_wait
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\multiprocessing\connection.py", line 884 in wait
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\multiprocessing\pool.py", line 499 in _wait_for_updates
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\multiprocessing\pool.py", line 519 in _handle_workers
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x000038ec (most recent call first):
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x000050a8 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00005754 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x0000152c (most recent call first):
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00003c80 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00005f68 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00003b10 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00005254 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00003c5c (most recent call first):
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00003204 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x000056c0 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x0000510c (most recent call first):
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\threading.py", line 930 in _bootstrap

Current thread 0x00003b84 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\runpy.py", line 197 in _run_module_as_main
===== Log before crash start =====
UCSF ChimeraX version: 1.3rc202112010754 (2021-12-01)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "D:\Patha\SEM 5\BI3134 BIO INFORMATICS\MODELLING
> ASSIGNMENT\Q05FL0.fasta" format fasta

Summary of feedback from opening D:\Patha\SEM 5\BI3134 BIO
INFORMATICS\MODELLING ASSIGNMENT\Q05FL0.fasta  
---  
note | Alignment identifier is Q05FL0.fasta  
  
Opened 1 sequences from Q05FL0.fasta  

> ui tool show AlphaFold

Fetching Q05FL0 UniProt info from https://www.uniprot.org/uniprot/Q05FL0.xml  

> alphafold search Q05FL0

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

> alphafold match Q05FL0

1 UniProt id does not have an AlphaFold database model: Q05FL0 (UniProt
Q05FL0)  

No AlphaFold model with similar sequence for UniProt Q05FL0  

Opened 0 AlphaFold model  

> alphafold predict Q05FL0

Running AlphaFold prediction  
Chain information for best_model.pdb #2  
---  
Chain | Description  
A | No description available  
  
Associated best_model.pdb chain A to tr|Q05FJ4|Q05FJ4_CARRP Ribosomal protein
L5 OS=Carsonella ruddii (strain PV) OX=387662 GN=CRP_146 PE=3 SV=1 with 0
mismatches  
AlphaFold prediction finished  
Results in C:\Users\Swayam Prakash
Singh/Downloads\ChimeraX\AlphaFold\prediction_1  

> hide #1 models

> show #1 models

> hide #1 models

> show #1 models


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

Log:
UCSF ChimeraX version: 1.3rc202112010754 (2021-12-01)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 NVIDIA 471.96
OpenGL renderer: NVIDIA GeForce RTX 2060/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: LENOVO
Model: 81SX
OS: Microsoft Windows 10 Home Single Language (Build 19042)
Memory: 17,095,184,384
MaxProcessMemory: 137,438,953,344
CPU: 12 Intel(R) Core(TM) i7-9750H CPU @ 2.60GHz
OSLanguage: en-US
Locale: ('en_IN', 'cp1252')
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: 2021.10.8
    cftime: 1.5.1.1
    charset-normalizer: 2.0.8
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.31
    ChimeraX-AtomicLibrary: 4.2
    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: 2.6.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.2
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3rc202112010754
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    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: 2.1.2
    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: 2.0.4
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    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: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    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: 2.4.6
    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: 1.6.1
    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: 1.13.7
    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: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.7.3
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.3
    ParmEd: 3.2.0
    parso: 0.8.3
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.23
    psutil: 5.8.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.6
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pywin32: 228
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.2
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    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: 5.1.1
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0
    WMI: 1.5.1

Change History (5)

comment:1 by pett, 4 years ago

Component: Unassigned → Graphics
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Crash showing AlphaFold model

comment:2 by Tom Goddard, 4 years ago

Crashed after opening a fasta sequence, using alphafold search to do a blast search, using alphafold match to find a uniprot entry (none found), using alphafold predict that returned a structure, hiding and showing the PDB file computed by alphafold. When the alphafold model was opened it got automatically associated with a sequence that was previously opened from a fasta file.

None of this suggests a cause for the crash.

comment:3 by Tom Goddard, 4 years ago

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

I tried exactly the same steps on the same uniprot sequence using the same Dec 1, 2021 release candidate and on Windows. It worked correctly without crashes. Possibly the crash was from the graphics driver. I wonder if the reporter hid and showed the model twice (probably using model panel) because the graphics did not draw it -- that also would suggest a graphics driver problem. Another possibility is that some Qt bug caused the crash, for instance, dragging and dropping a panel or closing a panel.

in reply to:  4 ; comment:4 by swayam.singh@…, 4 years ago 

I think it was caused due to an auto update of my graphics driver happening
in the middle of a run.

On Thu, 2 Dec 2021, 02:16 ChimeraX, <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

in reply to:  5 ; comment:5 by goddard@…, 4 years ago 

That might cause a crash.
Note: See TracTickets for help on using tickets.