Opened 2 months ago

Closed 2 months ago

#18494 closed defect (can't reproduce)

Crash in Qt event loop after alphafold prediction

Reported by: akshitavinod00@… 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-10-10.0.26100
ChimeraX Version: 1.10rc202505210000 (2025-05-21 00:00:04 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Windows fatal exception: code 0x8001010d

Thread 0x00006358 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10rc202505210000\bin\Lib\multiprocessing\pool.py", line 579 in _handle_results
  File "C:\Program Files\ChimeraX 1.10rc202505210000\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10rc202505210000\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10rc202505210000\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00003aa8 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10rc202505210000\bin\Lib\multiprocessing\pool.py", line 531 in _handle_tasks
  File "C:\Program Files\ChimeraX 1.10rc202505210000\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10rc202505210000\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10rc202505210000\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00004ebc (most recent call first):
  File "C:\Program Files\ChimeraX 1.10rc202505210000\bin\Lib\multiprocessing\connection.py", line 810 in _exhaustive_wait
  File "C:\Program Files\ChimeraX 1.10rc202505210000\bin\Lib\multiprocessing\connection.py", line 878 in wait
  File "C:\Program Files\ChimeraX 1.10rc202505210000\bin\Lib\multiprocessing\pool.py", line 502 in _wait_for_updates
  File "C:\Program Files\ChimeraX 1.10rc202505210000\bin\Lib\multiprocessing\pool.py", line 522 in _handle_workers
  File "C:\Program Files\ChimeraX 1.10rc202505210000\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10rc202505210000\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10rc202505210000\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x000076f8 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10rc202505210000\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10rc202505210000\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10rc202505210000\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10rc202505210000\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00004da4 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10rc202505210000\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10rc202505210000\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10rc202505210000\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10rc202505210000\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x000014f8 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10rc202505210000\bin\Lib\ssl.py", line 1134 in read
  File "C:\Program Files\ChimeraX 1.10rc202505210000\bin\Lib\ssl.py", line 1278 in recv_into
  File "C:\Program Files\ChimeraX 1.10rc202505210000\bin\Lib\socket.py", line 706 in readinto
  File "C:\Program Files\ChimeraX 1.10rc202505210000\bin\Lib\http\client.py", line 279 in _read_status
  File "C:\Program Files\ChimeraX 1.10rc202505210000\bin\Lib\http\client.py", line 318 in begin
  File "C:\Program Files\ChimeraX 1.10rc202505210000\bin\Lib\http\client.py", line 1378 in getresponse
  File "C:\Program Files\ChimeraX 1.10rc202505210000\bin\Lib\urllib\request.py", line 1352 in do_open
  File "C:\Program Files\ChimeraX 1.10rc202505210000\bin\Lib\urllib\request.py", line 1391 in https_open
  File "C:\Program Files\ChimeraX 1.10rc202505210000\bin\Lib\urllib\request.py", line 496 in _call_chain
  File "C:\Program Files\ChimeraX 1.10rc202505210000\bin\Lib\urllib\request.py", line 536 in _open
  File "C:\Program Files\ChimeraX 1.10rc202505210000\bin\Lib\urllib\request.py", line 519 in open
  File "C:\Program Files\ChimeraX 1.10rc202505210000\bin\Lib\urllib\request.py", line 216 in urlopen
  File "C:\Program Files\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\chimerax\core\toolshed\available.py", line 62 in load
  File "C:\Program Files\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\chimerax\core\toolshed\__init__.py", line 516 in reload_available
  File "C:\Program Files\ChimeraX 1.10rc202505210000\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10rc202505210000\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10rc202505210000\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x000018bc (most recent call first):
  File "C:\Program Files\ChimeraX 1.10rc202505210000\bin\Lib\threading.py", line 324 in wait
  File "C:\Program Files\ChimeraX 1.10rc202505210000\bin\Lib\threading.py", line 622 in wait
  File "C:\Program Files\ChimeraX 1.10rc202505210000\bin\Lib\threading.py", line 1392 in run
  File "C:\Program Files\ChimeraX 1.10rc202505210000\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10rc202505210000\bin\Lib\threading.py", line 995 in _bootstrap

Current thread 0x000048d8 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\chimerax\ui\gui.py", line 368 in event_loop
  File "C:\Program Files\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\chimerax\core\__main__.py", line 1057 in init
  File "C:\Program Files\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\chimerax\core\__main__.py", line 1220 in 
  File "", line 88 in _run_code
  File "", line 198 in _run_module_as_main
===== Log before crash start =====
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.10rc202505210000 (2025-05-21)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> ui tool show AlphaFold

> alphafold search
> >MPHRSRGSSRWRFSSRTAARLLVTFYAGLALATASRSSYHNQFPIIPPQIPQEEEGPSRGNGQHEFTLRHIHLRGTHQDPDLHLKLDVTPETRLVTIAEDTGLPEPAETSHLEALSIKSDSIYIQRLADRRPSVIESHLEYARSSGAATVLSDDAWVMDEVDGPDVTSKDTILTLAKMTANDYIEEPGTGDWNIISGRFNWSTNFGWQGDSLRGHIYADATNSTVVISLKGTSPALFDGAETTTNDKVNDNLYFGCCCGQGNSYLSRQACDCSTSVYTANLTCIVEAMRDRNRYYQAAIDLYTNVTALYPQANVWLTGHSLGGAMSGLLGLTFGLPTVTFEAIPDALPAARLGLPTPPGYDPLLPQLRKNTGIFHVGHTADPIYTGTCNGVGATCTWWGYSLESACHAGSMCVYDTVEDKGWRVGIGTHRIKSVIKDVLKAYDEVPPCVPEVECYDCQLWKYFKSNGSEITTTTTTTSTSTSTSITRTSTCQTPGWWGCLDKTTSTSMPITTTEDITTTATTSTSTSTCQTPGWFGCLDKTTSIVSTTAEITTTTAISTPTSTSTCETPGWFGCYDKTTSTGESTTITPEVTATSISDKGKR

Missing or invalid "sequence" argument: Sequences argument
">MPHRSRGSSRWRFSSRTAARLLVTFYAGLALATASRSSYHNQFPIIPPQIPQEEEGPSRGNGQHEFTLRHIHLRGTHQDPDLHLKLDVTPETRLVTIAEDTGLPEPAETSHLEALSIKSDSIYIQRLADRRPSVIESHLEYARSSGAATVLSDDAWVMDEVDGPDVTSKDTILTLAKMTANDYIEEPGTGDWNIISGRFNWSTNFGWQGDSLRGHIYADATNSTVVISLKGTSPALFDGAETTTNDKVNDNLYFGCCCGQGNSYLSRQACDCSTSVYTANLTCIVEAMRDRNRYYQAAIDLYTNVTALYPQANVWLTGHSLGGAMSGLLGLTFGLPTVTFEAIPDALPAARLGLPTPPGYDPLLPQLRKNTGIFHVGHTADPIYTGTCNGVGATCTWWGYSLESACHAGSMCVYDTVEDKGWRVGIGTHRIKSVIKDVLKAYDEVPPCVPEVECYDCQLWKYFKSNGSEITTTTTTTSTSTSTSITRTSTCQTPGWWGCLDKTTSTSMPITTTEDITTTATTSTSTSTCQTPGWFGCLDKTTSIVSTTAEITTTTAISTPTSTSTCETPGWFGCYDKTTSTGESTTITPEVTATSISDKGKR"
is not a chain specifier, alignment id, UniProt id, or sequence characters  

> alphafold predict
> >MSHEGLKIGVLLTDPVQLLDLAPIDLFNMATPEYLEIWKKASASSLKNENAVQEVTATSGVRLTHTTADEEVSPGNLDLLFLPGPDPNSEPDDEVKEFLRAHNKHKTTFLVICTAAFVAGYSGIYDSKHVTGPRFLIPNLRKLFPKTEWDESVRWKQDGHIWTAGGITNGNDLVAAYIRATYPSSVAETVCTMAEVGDRPMKFDIGLKRNDTIFPELQRAALLSSAAYSGCIGSAFDINITKQIRDIVTDTQGYIGYSEEKKRIAVVMRGSTAPMDLFNDLDTVLVTPKLSGVDFPPDAMIMSGINIPWSAVHDEVIMEVKRLVTKYPDYTLESTGHSLGGALTYLSYVSLCQNFPDKAVTSNALAAFPIGNQAFADFGSSQHGTLNRGNNALDGVPNIYVTPFNFAHYGTEFYSDGSASNTLKCINERDMDCSAGNGMYGITPQHVFSFGVLEMGAGCGSSL

Missing or invalid "sequences" argument: Sequences argument
">MSHEGLKIGVLLTDPVQLLDLAPIDLFNMATPEYLEIWKKASASSLKNENAVQEVTATSGVRLTHTTADEEVSPGNLDLLFLPGPDPNSEPDDEVKEFLRAHNKHKTTFLVICTAAFVAGYSGIYDSKHVTGPRFLIPNLRKLFPKTEWDESVRWKQDGHIWTAGGITNGNDLVAAYIRATYPSSVAETVCTMAEVGDRPMKFDIGLKRNDTIFPELQRAALLSSAAYSGCIGSAFDINITKQIRDIVTDTQGYIGYSEEKKRIAVVMRGSTAPMDLFNDLDTVLVTPKLSGVDFPPDAMIMSGINIPWSAVHDEVIMEVKRLVTKYPDYTLESTGHSLGGALTYLSYVSLCQNFPDKAVTSNALAAFPIGNQAFADFGSSQHGTLNRGNNALDGVPNIYVTPFNFAHYGTEFYSDGSASNTLKCINERDMDCSAGNGMYGITPQHVFSFGVLEMGAGCGSSL"
is not a chain specifier, alignment id, UniProt id, or sequence characters  

> alphafold predict
> MSHEGLKIGVLLTDPVQLLDLAPIDLFNMATPEYLEIWKKASASSLKNENAVQEVTATSGVRLTHTTADEEVSPGNLDLLFLPGPDPNSEPDDEVKEFLRAHNKHKTTFLVICTAAFVAGYSGIYDSKHVTGPRFLIPNLRKLFPKTEWDESVRWKQDGHIWTAGGITNGNDLVAAYIRATYPSSVAETVCTMAEVGDRPMKFDIGLKRNDTIFPELQRAALLSSAAYSGCIGSAFDINITKQIRDIVTDTQGYIGYSEEKKRIAVVMRGSTAPMDLFNDLDTVLVTPKLSGVDFPPDAMIMSGINIPWSAVHDEVIMEVKRLVTKYPDYTLESTGHSLGGALTYLSYVSLCQNFPDKAVTSNALAAFPIGNQAFADFGSSQHGTLNRGNNALDGVPNIYVTPFNFAHYGTEFYSDGSASNTLKCINERDMDCSAGNGMYGITPQHVFSFGVLEMGAGCGSSL


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

Log:
UCSF ChimeraX version: 1.10rc202505210000 (2025-05-21)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 - Build 30.0.100.9864
OpenGL renderer: Intel(R) UHD Graphics 600
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: ASUSTeK COMPUTER INC.
Model: VivoBook_ASUSLaptop X515MA_X515MA
OS: Microsoft Windows 11 Home Single Language (Build 26100)
Memory: 4,109,103,104
MaxProcessMemory: 137,438,953,344
CPU: 2 Intel(R) Celeron(R) N4020 CPU @ 1.10GHz
OSLanguage: en-US

Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    asttokens: 3.0.0
    auditwheel: 6.3.0
    babel: 2.17.0
    beautifulsoup4: 4.13.3
    blockdiag: 3.0.0
    blosc2: 3.3.3
    build: 1.2.2.post1
    certifi: 2025.4.26
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.2
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.7
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.20.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Aniso: 1.1.3
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60.6
    ChimeraX-AtomicLibrary: 14.1.18
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.3
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-Boltz: 1.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.5.1
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.10rc202505210000
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.5
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.4
    ChimeraX-Dicom: 1.2.7
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.4
    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: 2.5.1
    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: 1.6.2
    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: 2.2.1
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.10.1
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.19
    ChimeraX-ModelPanel: 1.5.1
    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: 2.7.10
    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: 1.1.3
    ChimeraX-ProfileGrids: 1.1.2
    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: 2.17.1
    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: 1.45.1
    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: 1.1.5
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    comtypes: 1.4.10
    contourpy: 1.3.2
    coverage: 7.8.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.12
    debugpy: 1.8.14
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.0
    filelock: 3.18.0
    fonttools: 4.58.0
    funcparserlib: 2.0.0a0
    glfw: 2.9.0
    grako: 3.16.5
    h5py: 3.13.0
    html2text: 2024.2.26
    idna: 3.10
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.1.0
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.7
    jedi: 0.19.1
    Jinja2: 3.1.6
    jupyter_client: 8.6.3
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.15
    kiwisolver: 1.4.8
    line_profiler: 4.2.0
    lxml: 5.3.1
    lz4: 4.4.4
    MarkupSafe: 3.0.2
    matplotlib: 3.10.1
    matplotlib-inline: 0.1.7
    msgpack: 1.1.0
    ndindex: 1.10.0
    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: 24.2
    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: 4.3.8
    pluggy: 1.6.0
    prompt_toolkit: 3.0.51
    psutil: 7.0.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.32
    Pygments: 2.18.0
    pynmrstar: 3.3.5
    pynrrd: 1.0.0
    PyOpenGL: 3.1.9
    PyOpenGL-accelerate: 3.1.9
    pyopenxr: 1.1.4501
    pyparsing: 3.2.3
    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: 8.3.5
    pytest-cov: 6.1.1
    python-dateutil: 2.9.0.post0
    pytz: 2025.2
    pywin32: 310
    pyzmq: 26.4.0
    qtconsole: 5.5.2
    QtPy: 2.4.3
    qtshim: 1.1
    RandomWords: 0.4.0
    requests: 2.32.3
    roman-numerals-py: 3.1.0
    scipy: 1.14.0
    setuptools: 78.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 3.0.1
    sortedcontainers: 2.4.0
    soupsieve: 2.7
    Sphinx: 8.2.3
    sphinx-autodoc-typehints: 3.1.0
    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: 2025.3.13
    tinyarray: 1.2.4
    tornado: 6.5
    traitlets: 5.14.3
    typing_extensions: 4.13.2
    tzdata: 2025.2
    urllib3: 2.4.0
    wcwidth: 0.2.13
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.14
    WMI: 1.5.1

Change History (2)

comment:1 by pett, 2 months ago

Component: UnassignedStructure Prediction
Owner: set to Tom Goddard
Platform: all
Project: ChimeraX
Status: newassigned
Summary: ChimeraX bug report submissionCrash in alphafold predict

Reported by Akshita Rajbhar

comment:2 by Tom Goddard, 2 months ago

Resolution: can't reproduce
Status: assignedclosed
Summary: Crash in alphafold predictCrash in Qt event loop after alphafold prediction

The crash report only says that it crashed in the Qt event loop. Possibly this was caused by some mouse interaction with the AlphaFold Run window since the log shows some alphafold prediction was started. The AlphaFold Run window is a Qt html window and I suspect that this has some bugs that can lead to crashes. But I have no reproducible case and the bug would be in the Qt project not in ChimeraX.

If the crash happened when you were using the mouse in the AlphaFold Run window or when doing some other mouse interaction with ChimeraX I would like to know what mouse action caused the crash.

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