Opened 4 weeks ago

Closed 4 weeks ago

#19281 closed defect (can't reproduce)

Crash during Boltz output

Reported by: jszot@… 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-10-10.0.26200
ChimeraX Version: 1.11.dev202509291912 (2025-09-29 19:12:18 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Aborted

Thread 0x00004a2c (most recent call first):
  File "C:\Program Files\ChimeraX 1.11.dev202509291912\bin\Lib\site-packages\chimerax\boltz\predict.py", line 1401 in _queue_output_in_thread
  File "C:\Program Files\ChimeraX 1.11.dev202509291912\bin\Lib\threading.py", line 982 in run
  File "C:\Program Files\ChimeraX 1.11.dev202509291912\bin\Lib\threading.py", line 1045 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.11.dev202509291912\bin\Lib\threading.py", line 1002 in _bootstrap

Thread 0x00005af8 (most recent call first):
  File "C:\Program Files\ChimeraX 1.11.dev202509291912\bin\Lib\site-packages\chimerax\boltz\predict.py", line 1401 in _queue_output_in_thread
  File "C:\Program Files\ChimeraX 1.11.dev202509291912\bin\Lib\threading.py", line 982 in run
  File "C:\Program Files\ChimeraX 1.11.dev202509291912\bin\Lib\threading.py", line 1045 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.11.dev202509291912\bin\Lib\threading.py", line 1002 in _bootstrap

Thread 0x000012f0 (most recent call first):
  File "C:\Program Files\ChimeraX 1.11.dev202509291912\bin\Lib\multiprocessing\pool.py", line 579 in _handle_results
  File "C:\Program Files\ChimeraX 1.11.dev202509291912\bin\Lib\threading.py", line 982 in run
  File "C:\Program Files\ChimeraX 1.11.dev202509291912\bin\Lib\threading.py", line 1045 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.11.dev202509291912\bin\Lib\threading.py", line 1002 in _bootstrap

Thread 0x00005c20 (most recent call first):
  File "C:\Program Files\ChimeraX 1.11.dev202509291912\bin\Lib\multiprocessing\pool.py", line 531 in _handle_tasks
  File "C:\Program Files\ChimeraX 1.11.dev202509291912\bin\Lib\threading.py", line 982 in run
  File "C:\Program Files\ChimeraX 1.11.dev202509291912\bin\Lib\threading.py", line 1045 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.11.dev202509291912\bin\Lib\threading.py", line 1002 in _bootstrap

Thread 0x00006918 (most recent call first):
  File "C:\Program Files\ChimeraX 1.11.dev202509291912\bin\Lib\multiprocessing\connection.py", line 828 in _exhaustive_wait
  File "C:\Program Files\ChimeraX 1.11.dev202509291912\bin\Lib\multiprocessing\connection.py", line 896 in wait
  File "C:\Program Files\ChimeraX 1.11.dev202509291912\bin\Lib\multiprocessing\pool.py", line 502 in _wait_for_updates
  File "C:\Program Files\ChimeraX 1.11.dev202509291912\bin\Lib\multiprocessing\pool.py", line 522 in _handle_workers
  File "C:\Program Files\ChimeraX 1.11.dev202509291912\bin\Lib\threading.py", line 982 in run
  File "C:\Program Files\ChimeraX 1.11.dev202509291912\bin\Lib\threading.py", line 1045 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.11.dev202509291912\bin\Lib\threading.py", line 1002 in _bootstrap

Thread 0x00009a8c (most recent call first):
  File "C:\Program Files\ChimeraX 1.11.dev202509291912\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.11.dev202509291912\bin\Lib\threading.py", line 982 in run
  File "C:\Program Files\ChimeraX 1.11.dev202509291912\bin\Lib\threading.py", line 1045 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.11.dev202509291912\bin\Lib\threading.py", line 1002 in _bootstrap

Thread 0x000009c0 (most recent call first):
  File "C:\Program Files\ChimeraX 1.11.dev202509291912\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.11.dev202509291912\bin\Lib\threading.py", line 982 in run
  File "C:\Program Files\ChimeraX 1.11.dev202509291912\bin\Lib\threading.py", line 1045 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.11.dev202509291912\bin\Lib\threading.py", line 1002 in _bootstrap

Thread 0x0000a97c (most recent call first):
  File "C:\Program Files\ChimeraX 1.11.dev202509291912\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.11.dev202509291912\bin\Lib\threading.py", line 982 in run
  File "C:\Program Files\ChimeraX 1.11.dev202509291912\bin\Lib\threading.py", line 1045 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.11.dev202509291912\bin\Lib\threading.py", line 1002 in _bootstrap

Thread 0x0000847c (most recent call first):
  File "C:\Program Files\ChimeraX 1.11.dev202509291912\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.11.dev202509291912\bin\Lib\threading.py", line 982 in run
  File "C:\Program Files\ChimeraX 1.11.dev202509291912\bin\Lib\threading.py", line 1045 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.11.dev202509291912\bin\Lib\threading.py", line 1002 in _bootstrap

Thread 0x00008ee0 (most recent call first):
  File "C:\Program Files\ChimeraX 1.11.dev202509291912\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.11.dev202509291912\bin\Lib\threading.py", line 982 in run
  File "C:\Program Files\ChimeraX 1.11.dev202509291912\bin\Lib\threading.py", line 1045 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.11.dev202509291912\bin\Lib\threading.py", line 1002 in _bootstrap

Thread 0x000035f4 (most recent call first):
  File "C:\Program Files\ChimeraX 1.11.dev202509291912\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.11.dev202509291912\bin\Lib\threading.py", line 982 in run
  File "C:\Program Files\ChimeraX 1.11.dev202509291912\bin\Lib\threading.py", line 1045 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.11.dev202509291912\bin\Lib\threading.py", line 1002 in _bootstrap

Thread 0x00007c70 (most recent call first):
  File "C:\Program Files\ChimeraX 1.11.dev202509291912\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.11.dev202509291912\bin\Lib\threading.py", line 982 in run
  File "C:\Program Files\ChimeraX 1.11.dev202509291912\bin\Lib\threading.py", line 1045 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.11.dev202509291912\bin\Lib\threading.py", line 1002 in _bootstrap

Thread 0x00008904 (most recent call first):
  File "C:\Program Files\ChimeraX 1.11.dev202509291912\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.11.dev202509291912\bin\Lib\threading.py", line 982 in run
  File "C:\Program Files\ChimeraX 1.11.dev202509291912\bin\Lib\threading.py", line 1045 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.11.dev202509291912\bin\Lib\threading.py", line 1002 in _bootstrap

Thread 0x00000f84 (most recent call first):
  File "C:\Program Files\ChimeraX 1.11.dev202509291912\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.11.dev202509291912\bin\Lib\threading.py", line 982 in run
  File "C:\Program Files\ChimeraX 1.11.dev202509291912\bin\Lib\threading.py", line 1045 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.11.dev202509291912\bin\Lib\threading.py", line 1002 in _bootstrap

Thread 0x00005be8 (most recent call first):
  File "C:\Program Files\ChimeraX 1.11.dev202509291912\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.11.dev202509291912\bin\Lib\threading.py", line 982 in run
  File "C:\Program Files\ChimeraX 1.11.dev202509291912\bin\Lib\threading.py", line 1045 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.11.dev202509291912\bin\Lib\threading.py", line 1002 in _bootstrap

Thread 0x00001bfc (most recent call first):
  File "C:\Program Files\ChimeraX 1.11.dev202509291912\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.11.dev202509291912\bin\Lib\threading.py", line 982 in run
  File "C:\Program Files\ChimeraX 1.11.dev202509291912\bin\Lib\threading.py", line 1045 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.11.dev202509291912\bin\Lib\threading.py", line 1002 in _bootstrap

Thread 0x00006824 (most recent call first):
  File "C:\Program Files\ChimeraX 1.11.dev202509291912\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.11.dev202509291912\bin\Lib\threading.py", line 982 in run
  File "C:\Program Files\ChimeraX 1.11.dev202509291912\bin\Lib\threading.py", line 1045 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.11.dev202509291912\bin\Lib\threading.py", line 1002 in _bootstrap

Thread 0x00005314 (most recent call first):
  File "C:\Program Files\ChimeraX 1.11.dev202509291912\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.11.dev202509291912\bin\Lib\threading.py", line 982 in run
  File "C:\Program Files\ChimeraX 1.11.dev202509291912\bin\Lib\threading.py", line 1045 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.11.dev202509291912\bin\Lib\threading.py", line 1002 in _bootstrap

Thread 0x00003364 (most recent call first):
  File "C:\Program Files\ChimeraX 1.11.dev202509291912\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.11.dev202509291912\bin\Lib\threading.py", line 982 in run
  File "C:\Program Files\ChimeraX 1.11.dev202509291912\bin\Lib\threading.py", line 1045 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.11.dev202509291912\bin\Lib\threading.py", line 1002 in _bootstrap

Thread 0x0000750c (most recent call first):
  File "C:\Program Files\ChimeraX 1.11.dev202509291912\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.11.dev202509291912\bin\Lib\threading.py", line 982 in run
  File "C:\Program Files\ChimeraX 1.11.dev202509291912\bin\Lib\threading.py", line 1045 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.11.dev202509291912\bin\Lib\threading.py", line 1002 in _bootstrap

Thread 0x00007890 (most recent call first):
  File "C:\Program Files\ChimeraX 1.11.dev202509291912\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.11.dev202509291912\bin\Lib\threading.py", line 982 in run
  File "C:\Program Files\ChimeraX 1.11.dev202509291912\bin\Lib\threading.py", line 1045 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.11.dev202509291912\bin\Lib\threading.py", line 1002 in _bootstrap

Thread 0x00008540 (most recent call first):
  File "C:\Program Files\ChimeraX 1.11.dev202509291912\bin\Lib\site-packages\chimerax\ui\gui.py", line 368 in event_loop
  File "C:\Program Files\ChimeraX 1.11.dev202509291912\bin\Lib\site-packages\chimerax\core\__main__.py", line 1064 in init
  File "C:\Program Files\ChimeraX 1.11.dev202509291912\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, psutil._psutil_windows, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, chimerax.surface._surface, chimerax.pdb_lib._load_libs, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio (total: 47)
===== 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: 1.11.dev202509291912 (2025-09-29)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 7EVZ format mmcif fromDatabase pdb

7evz title:  
Cryo-EM structure of cenerimod -bound Sphingosine-1-phosphate receptor 1 in
complex with Gi protein [more info...]  
  
Chain information for 7evz #1  
---  
Chain | Description | UniProt  
A | Guanine nucleotide-binding protein G(i) subunit alpha-1 | GNAI1_HUMAN 1-354  
B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | GBB1_HUMAN 2-340  
C | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | GBG2_HUMAN 1-71  
D | Sphingosine 1-phosphate receptor 1 |   
E | scFv16 |   
  
Non-standard residues in 7evz #1  
---  
JER — (2~{S})-3-[4-[5-(2-cyclopentyl-6-methoxy-
pyridin-4-yl)-1,2,4-oxadiazol-3-yl]-2-ethyl-6-methyl-phenoxy]propane-1,2-diol  
PLM — palmitic acid  
  
1983 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.  

> ui tool show Boltz

> boltz predict protein /D ligandCcd S1P name test1103_7evz device gpu
> affinity S1P

Running Boltz prediction of protein with 531 residues, 1 ligands S1P on gpu  
Using cached multiple sequence alignment
C:\Users\Votab/Downloads/ChimeraX/BoltzMSA\7evz_D_test1  

Invalid texture upload for 0x205ef9d4bf0 layer=0 mip=0  

QDxgiVSyncService not destroyed in time  


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

Log:
UCSF ChimeraX version: 1.11.dev202509291912 (2025-09-29)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 NVIDIA 581.57
OpenGL renderer: NVIDIA GeForce RTX 3060 Ti/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: Dell Inc.
Model: XPS 8940
OS: Microsoft Windows 11 Home (Build 26200)
Memory: 33,941,618,688
MaxProcessMemory: 137,438,953,344
CPU: 16 11th Gen Intel(R) Core(TM) i7-11700 @ 2.50GHz
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: 3.9.0
    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.dev202509291912
    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: 1.2.2
    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: 3.5.9
    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: 1.48.3
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDock: 1.5
    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: 3.1.4
    debugpy: 1.8.17
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.1
    filelock: 3.19.1
    fonttools: 4.60.1
    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: 6.0.2
    lz4: 4.3.2
    Markdown: 3.8.2
    MarkupSafe: 3.0.3
    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: 2.13.0
    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: 2.32.5
    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: 0.2.14
    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 Eric Pettersen, 4 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 output

Reported by James Szot

comment:2 by Tom Goddard, 4 weeks ago

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

I suspect this crash was a graphics driver problem. The last messages logged to ChimeraX were about graphics and suggest that the Qt window toolkit crashed because of a graphics problem.

Invalid texture upload for 0x205ef9d4bf0 layer=0 mip=0

QDxgiVSyncService not destroyed in time

Boltz was using the GPU for computing a structure. You have a current graphics driver, so I don't have any suggestion about how you might avoid this crash.

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