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#18847 closed defect (nonchimerax)

Crash during Boltz prediction

Reported by:	petr@…	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-10-10.0.22621
ChimeraX Version: 1.11.dev202509201954 (2025-09-20 19:54:21 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Aborted

Thread 0x000045a8 (most recent call first):
  File "C:\Program Files\ChimeraX 1.11.dev202509201954\bin\Lib\site-packages\chimerax\boltz\predict.py", line 1401 in _queue_output_in_thread
  File "C:\Program Files\ChimeraX 1.11.dev202509201954\bin\Lib\threading.py", line 982 in run
  File "C:\Program Files\ChimeraX 1.11.dev202509201954\bin\Lib\threading.py", line 1045 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.11.dev202509201954\bin\Lib\threading.py", line 1002 in _bootstrap

Thread 0x00004324 (most recent call first):
  File "C:\Program Files\ChimeraX 1.11.dev202509201954\bin\Lib\site-packages\chimerax\boltz\predict.py", line 1401 in _queue_output_in_thread
  File "C:\Program Files\ChimeraX 1.11.dev202509201954\bin\Lib\threading.py", line 982 in run
  File "C:\Program Files\ChimeraX 1.11.dev202509201954\bin\Lib\threading.py", line 1045 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.11.dev202509201954\bin\Lib\threading.py", line 1002 in _bootstrap

Current thread 0x00005cfc (most recent call first):
  File "C:\Program Files\ChimeraX 1.11.dev202509201954\bin\Lib\site-packages\chimerax\ui\gui.py", line 368 in event_loop
  File "C:\Program Files\ChimeraX 1.11.dev202509201954\bin\Lib\site-packages\chimerax\core\__main__.py", line 1064 in init
  File "C:\Program Files\ChimeraX 1.11.dev202509201954\bin\Lib\site-packages\chimerax\core\__main__.py", line 1229 in 
  File "", line 88 in _run_code
  File "", line 198 in _run_module_as_main

Extension modules: _win32sysloader, win32api, win32com.shell.shell, chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.surface._surface, chimerax.pdb_lib._load_libs, lxml._elementpath, lxml.etree, chimerax.map._map, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, PIL._imaging, PIL._imagingmath, psutil._psutil_windows, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, win32event (total: 47)
===== Log before crash start =====
UCSF ChimeraX version: 1.11.dev202509201954 (2025-09-20)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> ui tool show Boltz

> boltz predict protein
> MEGSGGGAGERAPLLGARRAAAAAAAAGAFAGRRAACGAVLLTELLERAAFYGITSNLVLFLNGAPFCWEGAQASEALLLFMGLTYLGSPFGGWLADARLGRARAILLSLALYLLGMLAFPLLAAPATRAALCGSARLLNCTAPGPDAAARCCSPATFAGLVLVGLGVATVKANITPFGADQVKDRGPEATRRFFNWFYWSINLGAILSLGGIAYIQQNVSFVTGYAIPTVCVGLAFVVFLCGQSVFITKPPDGSAFTDMFKILTYSCCSQKRSGERQSNGEGIGVFQQSSKQSLFDSCKMSHGGPFTEEKVEDVKALVKIVPVFLALIPYWTVYFQMQTTYVLQSLHLRIPEISNITTTPHTLPAAWLTMFDAVLILLLIPLKDKLVDPILRRHGLLPSSLKRIAVGMFFVMCSAFAAGILESKRLNLVKEKTINQTIGNVVYHAADLSLWWQVPQYLLIGISEIFASIAGLEFAYSAAPKSMQSAIMGLFFFFSGVGSFVGSGLLALVSIKAIGWMSSHTDFGNINGCYLNYYFFLLAAIQGATLLLFLIISVKYDHHRDHQRSRANGVPTSRRA
> forEachSmilesLigand
> 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=O)N1C2CCC1CN(C(=O)C1=C3C(=CC=C1)C1=C(CCCC1)N3)C2,BGI-0029972,CCOC1=CC=C(C2=NC3=CC=CC=C3C(S(=O)(=O)NCCCN3CCN(CC4=CC=CC=C4)CC3C)=C2)C=C1,BGI-0029971,CCOC1=CC=C(C2=NC3=CC=CC=C3C(S(=O)(=O)NCCCN3[C@H](C)CCC[C@H]3C)=C2)C=C1,BGI-0029969,CCOC1=CC=C(C2=NC3=CC=CC=C3C(S(=O)(=O)NCCCN3CCN(C)CC3C)=C2)C=C1,BGI-0029968,CCOC1=CC=C(C2=NC3=CC=CC=C3C(S(=O)(=O)NCCCN3CCN(C4=CC=CC=C4)CC3C)=C2)C=C1,BGI-0029967,CCOC1=CC=C(C2=NC3=CC=CC=C3C(S(=O)(=O)NCCCN3CCCCC3C(C)C)=C2)C=C1,BGI-0029966,CCOC1=CC=C(C2=NC3=C(OC(F)(F)F)C=CC=C3C(S(=O)(=O)NCCCN3CCCCC3C)=C2)C=C1,BGI-0029743,CCOC1=CC=C(C2=NC3=CC=CC=C3C(S(=O)(=O)NCCCN3CC4CC(C4)C3)=C2)C=C1,BGI-0029742,CCOC1=CC=C(C2=NC3=CC=CC=C3C(S(=O)(=O)NCCCN3CC4CCC(C4)C3)=C2)C=C1,BGI-0029740,CCOC1=CC=C(C2=NC3=CC=CC=C3C(S(=O)(=O)NCCCN3CCCC(C4=CC=CC=C4)C3)=C2)C=C1,BGI-0029738,CCOC1=CC=C(C2=NC3=CC=CC=C3C(S(=O)(=O)NCCCN3CCCC(N(C)C)C3)=C2)C=C1,BGI-0028911,CCOC1=CC=C(C2=NC3=C(C(S(=O)(NCCCN4CCCCC4C)=O)=C2)C=CC=C3)C=C1,BGI-0028909,CC1CCCCN1CCC1=CN(C)C(=O)C(C2=CC(C3=CC=C(OCC)C=C3)=NC3=CC=CC=C23)=N1,BGI-0028908,CC1CCCCN1CCC1=CN=C(C2=CC(C3=CC=C(OCC)C=C3)=NC3=CC=CC=C23)N1,BGI-0028907,CC1CCCCN1CCC1=NN=C(C2=CC(C3=CC=C(OCC)C=C3)=NC3=CC=CC=C23)N1,BGI-0023870,COC1=C(C(=O)N2CCC(N3CCN(C(=O)C=C)CC3)C2)C=C(C#C)C=C1,BGI-0020671,C#CCNC1CCCC2=NC(C3=CC=C(NC(=O)C=C)C=C3)=CC=C12,BGI-0020577,C#CC1=NC2=C(S1)C(N1CC(CNC(C=C)=O)C1)CCC2,BGI-0019272,C#CC1=CC=C2C(=C1)C(CN1CCC(NC(C=C)=O)CC1)=CS2,BGI-0019193,CC1=CC2=C(NC3=C2CCCC3N2CC(CNC(C=C)=O)C2)C=C1,BGI-0019192,C#CC1=CC2=C(NC3=C2CCCC3N2CC(CNC(C=C)=O)C2)C=C1,BGI-0018508,FC1=CC=CC(C#C)=C1OC1CC2(C1)CC(NC(C=C)=O)C2,BGI-0018360,C#CCOC1=C(C(N2CC(NC(C=C)=O)C2)C)C=CC2=C1CCC2,BGI-0018338,O=C(C=C)N[C@H]1CC[C@H](CN(C)C2C3=C(C=CC=C3)C3=C2C(C#C)=CC=C3)CC1,BGI-0018337,CC1=CC2=C(NC3=C2CCCC3N2CC(NC(C=C)=O)C2)C=C1,BGI-0017728,O=C(C=C)NC1CN(C2CCCC3=C2NC2=C(CC)C=CC=C32)CCC1,BGI-0017727,C#CC1=C2NC3=C(CCCC3N3CCCC(NC(C=C)=O)C3)C2=CC=C1,BGI-0017423,C#CCN1CCC2=CC=CC(C3=CC=CC=C3NC(C=C)=O)=C2C1,BGI-0017309,C#CC1=CC2=C(N=CC=C2OC2CC3(C2)CC(NC(C=C)=O)C3)C=C1,BGI-0017233,C#CC1=C(C2=NC(N3CC(NC(C=C)=O)CCC3)=CC=C2)C=CC=C1,BGI-0017229,C#CC1=C(C2=NC(N3CC(CNC(C=C)=O)CCC3)=CC=C2)C=CC=C1"
> affinity each steering true

Running Boltz prediction of 367 ligands on gpu  
Using cached multiple sequence alignment  

Invalid texture upload for 0x20e583226f0 layer=0 mip=0  

QDxgiVSyncService not destroyed in time  

QThreadStorage: entry 3 destroyed before end of thread 0x20e7ec46ca0  

QThreadStorage: entry 2 destroyed before end of thread 0x20e7ec46ca0  

QThreadStorage: entry 1 destroyed before end of thread 0x20e7ec46ca0  


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

Log:
UCSF ChimeraX version: 1.11.dev202509201954 (2025-09-20)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 NVIDIA 560.94
OpenGL renderer: NVIDIA GeForce RTX 4090/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.9
Locale: en_US.cp1252
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: windows

Manufacturer: Giga Computing
Model: MZ73-LM0-000
OS: Microsoft Windows 11 Pro for Workstations (Build 22621)
Memory: 549,502,214,144
MaxProcessMemory: 137,438,953,344
CPU: 192 AMD EPYC 9654 96-Core Processor                
OSLanguage: en-US

Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    asttokens: 3.0.0
    babel: 2.17.0
    beautifulsoup4: 4.13.5
    blockdiag: 3.0.0
    blosc2: 3.8.0
    build: 1.3.0
    certifi: 2025.8.3
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.3
    ChimeraX-AddCharge: 1.5.20
    ChimeraX-AddH: 2.2.7
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 3.0.2
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Aniso: 1.3.2
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60.17
    ChimeraX-AtomicLibrary: 14.2
    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: 1.1
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.6.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    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: 1.3.0
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.11.dev202509201954
    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: 2.5.3
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.4
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.7.1
    ChimeraX-Label: 1.2
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2.1
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.2
    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: 2.2.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.17.1
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-Minimize: 1.2
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.22
    ChimeraX-ModelPanel: 1.6
    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: 1.0.1
    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: 1.15.1
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.11
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.5
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.3
    ChimeraX-ProfileGrids: 1.4
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.5
    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: 1.5.2
    ChimeraX-Scenes: 0.2.2
    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: 2.17.2
    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.1
    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: 1.48.2
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDock: 1.4.1
    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: 0.2.3
    comtypes: 1.4.11
    contourpy: 1.3.3
    coverage: 7.10.7
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.1.3
    debugpy: 1.8.17
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.1
    filelock: 3.19.1
    fonttools: 4.60.0
    funcparserlib: 2.0.0a0
    glfw: 2.10.0
    grako: 3.16.5
    h5py: 3.14.0
    html2text: 2025.4.15
    idna: 3.10
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.1.0
    ipykernel: 6.30.1
    ipython: 9.5.0
    ipython_pygments_lexers: 1.1.1
    ipywidgets: 8.1.7
    jedi: 0.19.2
    Jinja2: 3.1.6
    jupyter_client: 8.6.3
    jupyter_core: 5.8.1
    jupyterlab_widgets: 3.0.15
    kiwisolver: 1.4.9
    line_profiler: 5.0.0
    lxml: 6.0.1
    lz4: 4.3.2
    Markdown: 3.8.2
    MarkupSafe: 3.0.2
    matplotlib: 3.10.5
    matplotlib-inline: 0.1.7
    msgpack: 1.1.1
    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: 2.12.1
    numpy: 1.26.4
    nvidia-nvjitlink-cu12: 12.9.86
    OpenMM: 8.2.0
    OpenMM-CUDA-12: 8.2.0
    openvr: 1.26.701
    packaging: 25.0
    ParmEd: 4.2.2
    parso: 0.8.5
    pep517: 0.13.1
    pickleshare: 0.7.5
    pillow: 11.3.0
    pip: 25.2
    pkginfo: 1.12.1.2
    platformdirs: 4.4.0
    pluggy: 1.6.0
    prompt_toolkit: 3.0.52
    psutil: 7.0.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pybind11: 3.0.1
    pycollada: 0.8
    pydicom: 2.4.4
    Pygments: 2.18.0
    pynmrstar: 3.3.6
    pynrrd: 1.0.0
    PyOpenGL: 3.1.10
    PyOpenGL-accelerate: 3.1.10
    pyopenxr: 1.1.4501
    pyparsing: 3.2.5
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.9.1
    PyQt6-Qt6: 6.9.2
    PyQt6-WebEngine-commercial: 6.9.0
    PyQt6-WebEngine-Qt6: 6.9.2
    PyQt6_sip: 13.10.2
    pytest: 8.4.2
    pytest-cov: 7.0.0
    python-dateutil: 2.9.0.post0
    pytz: 2025.2
    pywin32: 311
    pyzmq: 27.1.0
    qtconsole: 5.7.0
    QtPy: 2.4.3
    qtshim: 1.2
    RandomWords: 0.4.0
    requests: 2.32.4
    roman-numerals-py: 3.1.0
    scipy: 1.14.0
    setuptools: 80.9.0
    sfftk-rw: 0.8.1
    six: 1.17.0
    snowballstemmer: 3.0.1
    sortedcontainers: 2.4.0
    soupsieve: 2.8
    Sphinx: 8.2.3
    sphinx-autodoc-typehints: 3.2.0
    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: 0.7.6
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.5
    tornado: 6.5.2
    traitlets: 5.14.3
    typing_extensions: 4.15.0
    tzdata: 2025.2
    urllib3: 2.5.0
    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 (4)

comment:1 by Eric Pettersen, 7 weeks ago

Component:	Unassigned → Structure Prediction
Owner:	set to Tom Goddard
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → Crash during Boltz prediction

Reported by Petr Jansa

comment:2 by Tom Goddard, 7 weeks ago

Resolution:	→ nonchimerax
Status:	assigned → closed

The Log shows the following error before ChimeraX crashed

Invalid texture upload for 0x20e583226f0 layer=0 mip=0

which is an OpenGL graphics error that came from the Qt window toolkit. Possibly the boltz structure prediction was hogging all the GPU memory and caused ChimeraX Qt graphical user interface to crash. I have been using an Nvidia RTX 4090 with Boltz and ChimeraX for about a year now on Linux and never seen ChimeraX crash, so possibly it is something about the Nvidia driver on Windows. I suspect this won't be reproducible, I think you are not too likely to see this crash again if you try running the prediction.

If you would prefer to run your boltz prediction outside ChimeraX so a ChimeraX crash won't stop the prediction you can go to a command prompt on Windows, go to the directory where ChimeraX setup the boltz run (e.g. ~/Desktop/boltz_abc). In that directory will be the input files for the boltz prediction (for predicting multiple ligands there will be one per ligand), and there will be a file named "command" that contains the command ChimeraX ran to start the Boltz predictions. The results will later appear in the subdirectory boltz_results_boltz_abc.

comment:3 by petr@…, 7 weeks ago

Dear all,

Thank you very much for a quick response. Yes, this happened when a batch of 350 ligands was submitted (run with 50 was executed with no issues). Testing it also on a computer with Nvidia RTX 4090 (24 BG) on Windows.

Do you have any recommendation how to run couple of thousands ligands using Boltz in ChimeraX? With our set up it takes ~1min for each ligand for this particular protein we are testing it on and we are OK to let the computer to work on it for couple of days. Is there a way to automate and run it in chunks of the batch? Do you plan any KNIME nodes for Boltz ChimeraX?

Best regards

Petr

BTW: So far very happy licensing ChimeraX and excited to try other functionalities.

---- On Tue, 23 Sep 2025 10:34:51 -0700 ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> wrote ---

#18847: Crash during Boltz prediction
-------------------------------------------+-------------------------
Reporter: petr@… | Owner: Tom Goddard
Type: defect | Status: closed
Priority: normal | Milestone:
Component: Structure Prediction | Version:
Resolution: nonchimerax | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
-------------------------------------------+-------------------------
Changes (by Tom Goddard):

* resolution: => nonchimerax
* status: assigned => closed

Comment:

The Log shows the following error before ChimeraX crashed

Invalid texture upload for 0x20e583226f0 layer=0 mip=0

which is an OpenGL graphics error that came from the Qt window toolkit.
Possibly the boltz structure prediction was hogging all the GPU memory and
caused ChimeraX Qt graphical user interface to crash. I have been using
an Nvidia RTX 4090 with Boltz and ChimeraX for about a year now on Linux
and never seen ChimeraX crash, so possibly it is something about the
Nvidia driver on Windows. I suspect this won't be reproducible, I think
you are not too likely to see this crash again if you try running the
prediction.

If you would prefer to run your boltz prediction outside ChimeraX so a
ChimeraX crash won't stop the prediction you can go to a command prompt on
Windows, go to the directory where ChimeraX setup the boltz run (e.g.
~/Desktop/boltz_abc). In that directory will be the input files for the
boltz prediction (for predicting multiple ligands there will be one per
ligand), and there will be a file named "command" that contains the
command ChimeraX ran to start the Boltz predictions. The results will
later appear in the subdirectory boltz_results_boltz_abc.

comment:4 by Tom Goddard, 7 weeks ago

I replied directly to Petr.

Petr, the ChimeraX bug reports are public, so don't send confidential info to the bug report email address.

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