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Opened 30 hours ago
Last modified 7 hours ago
#19863 feedback defect
Crash in event loop
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.22631
ChimeraX Version: 1.11.dev202509050043 (2025-09-05 00:43:43 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Windows fatal exception: access violation
Current thread 0x00005128 (most recent call first):
File "C:\Users\cheinen\AppData\Local\Programs\ChimeraX 1.11.dev202509050043\bin\Lib\site-packages\chimerax\ui\gui.py", line 368 in event_loop
File "C:\Users\cheinen\AppData\Local\Programs\ChimeraX 1.11.dev202509050043\bin\Lib\site-packages\chimerax\core\__main__.py", line 1064 in init
File "C:\Users\cheinen\AppData\Local\Programs\ChimeraX 1.11.dev202509050043\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
===== Log before crash start =====
UCSF ChimeraX version: 1.11.dev202509050043 (2025-09-05)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open C:/Users/cheinen/Desktop/murineMutations_interfaceStructure.pdb
Summary of feedback from opening
C:/Users/cheinen/Desktop/murineMutations_interfaceStructure.pdb
---
warnings | Ignored bad PDB record found on line 62
HELIX 1 1 GLU L 86 VAL L 88 5 Generated by MOE 3
Ignored bad PDB record found on line 63
HELIX 2 2 SER H 88 ASP H 90 5 Generated by MOE 3
Ignored bad PDB record found on line 64
HELIX 3 3 ALA A 283 ALA A 301 1 Generated by MOE 19
Ignored bad PDB record found on line 65
HELIX 4 4 ARG A 328 ASN A 331 1 Generated by MOE 4
Ignored bad PDB record found on line 66
HELIX 5 5 VAL A 335 GLN A 341 1 Generated by MOE 7
56 messages similar to the above omitted
Chain information for murineMutations_interfaceStructure.pdb #1
---
Chain | Description
A | No description available
H | No description available
L | No description available
Computing secondary structure
> select /L:1-112
1704 atoms, 1724 bonds, 112 residues, 1 model selected
> sequence chain #1/L
Alignment identifier is 1/L
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.11.dev202509050043 (2025-09-05)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 3.3.0 - Build 30.0.101.1692
OpenGL renderer: Intel(R) UHD Graphics 630
OpenGL vendor: Intel
Python: 3.11.9
Locale: en_US.cp1252
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.1
Qt platform: windows
Manufacturer: Dell Inc.
Model: OptiPlex 7070
OS: Microsoft Windows 11 Enterprise (Build 22631)
Memory: 16,951,218,176
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-9700 CPU @ 3.00GHz
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: 3.7.2
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: 1.60.16
ChimeraX-AtomicLibrary: 14.1.23
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.dev202509050043
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
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: 1.5.1
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: 1.0.1
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: 2.7.10
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: 1.3.1
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: 0.2.1
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: 2.17.2
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: 1.3.2
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: 7.10.6
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.1.3
debugpy: 1.8.16
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.1
filelock: 3.19.1
fonttools: 4.59.2
funcparserlib: 2.0.0a0
glfw: 2.9.0
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: 2.11.0
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: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.10
PyOpenGL-accelerate: 3.1.10
pyopenxr: 1.1.4501
pyparsing: 3.2.3
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.9.1
PyQt6-Qt6: 6.9.1
PyQt6-WebEngine-commercial: 6.9.0
PyQt6-WebEngine-Qt6: 6.9.1
PyQt6_sip: 13.10.2
pytest: 8.4.2
pytest-cov: 6.2.1
python-dateutil: 2.9.0.post0
pytz: 2025.2
pywin32: 311
pyzmq: 27.0.2
qtconsole: 5.6.1
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
Attachments (1)
Change History (5)
comment:1 by , 8 hours ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Core |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in event loop |
comment:2 by , 8 hours ago
| Status: | accepted → feedback |
|---|
comment:3 by , 7 hours ago
Hello,
It crashes each time I exit out of the sequence viewer tab.
Thanks,
Cobey Donelson
Molecular Physiology and Biophysics PhD Student, Molecular Otolaryngology and Renal Research Laboratories
University of Iowa Health Care
285 Newton Rd, 5256 CBRB, Iowa City, Iowa 52242
https://morl.lab.uiowa.edu<https://morl.lab.uiowa.edu/>
[cid:67aaf869-9659-412b-a26e-035dddcac58f]
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Thursday, February 19, 2026 12:26 PM
To: Donelson, Cobey J H <cobey-heinen@uiowa.edu>; pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>
Cc: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>
Subject: [External] Re: [ChimeraX] #19863: Crash in event loop
[You don't often get email from chimerax-bugs-admin@cgl.ucsf.edu. Learn why this is important at https://aka.ms/LearnAboutSenderIdentification ]
#19863: Crash in event loop
-------------------------------------+----------------------------
Reporter: cobey-heinen@… | Owner: Eric Pettersen
Type: defect | Status: feedback
Priority: normal | Milestone:
Component: Core | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
-------------------------------------+----------------------------
Changes (by Eric Pettersen):
* status: accepted => feedback
Comment:
Hi Cobey,
Thanks for reporting this problem. Do you remember what you were
doing when this crash occurred?
--Eric
Eric Pettersen
UCSF Computer Graphics Lab
--
Ticket URL: <https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Ftrac%2FChimeraX%2Fticket%2F19863%23comment%3A2&data=05%7C02%7Ccobey-heinen%40uiowa.edu%7C3ec46b7ca1624a489e2408de6fe47266%7C1bc445959aba4fc3b8ec7b94a5586fdc%7C1%7C0%7C639071224182025747%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=2xp9m2eWvREUaz7kA7dnPSXTXHwJbRGozsuuGF%2B%2FBfY%3D&reserved=0<https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/19863#comment:2>>
ChimeraX <https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimerax%2F&data=05%7C02%7Ccobey-heinen%40uiowa.edu%7C3ec46b7ca1624a489e2408de6fe47266%7C1bc445959aba4fc3b8ec7b94a5586fdc%7C1%7C0%7C639071224182063533%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=QVwPa3Y%2FRLY9oFaXvWidUIGT1jYDIwlI%2BI6eTvjg7jo%3D&reserved=0<https://www.rbvi.ucsf.edu/chimerax/>>
ChimeraX Issue Tracker
comment:4 by , 7 hours ago
This suggests to me a problem with the Qt windowing toolkit that ChimeraX uses. Can you try upgrading to the ChimeraX 1.11.1 production release which includes a later version of the Qt toolkit, and let me know if the behavior persists?
Note:
See TracTickets
for help on using tickets.
Hi Cobey,
--Eric