The following bug report has been submitted:
Platform: Windows-10-10.0.26100
ChimeraX Version: 1.10.dev202501081858 (2025-01-08 18:58:24 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Windows fatal exception: code 0x8001010d
Thread 0x00008f04 (most recent call first):
File "C:\Program Files\ChimeraX 1.10.dev202501081858\bin\Lib\socket.py", line 836 in create_connection
File "C:\Program Files\ChimeraX 1.10.dev202501081858\bin\Lib\http\client.py", line 945 in connect
File "C:\Program Files\ChimeraX 1.10.dev202501081858\bin\Lib\http\client.py", line 1451 in connect
File "C:\Program Files\ChimeraX 1.10.dev202501081858\bin\Lib\http\client.py", line 979 in send
File "C:\Program Files\ChimeraX 1.10.dev202501081858\bin\Lib\http\client.py", line 1041 in _send_output
File "C:\Program Files\ChimeraX 1.10.dev202501081858\bin\Lib\http\client.py", line 1281 in endheaders
File "C:\Program Files\ChimeraX 1.10.dev202501081858\bin\Lib\http\client.py", line 1332 in _send_request
File "C:\Program Files\ChimeraX 1.10.dev202501081858\bin\Lib\http\client.py", line 1286 in request
File "C:\Program Files\ChimeraX 1.10.dev202501081858\bin\Lib\urllib\request.py", line 1348 in do_open
File "C:\Program Files\ChimeraX 1.10.dev202501081858\bin\Lib\urllib\request.py", line 1391 in https_open
File "C:\Program Files\ChimeraX 1.10.dev202501081858\bin\Lib\urllib\request.py", line 496 in _call_chain
File "C:\Program Files\ChimeraX 1.10.dev202501081858\bin\Lib\urllib\request.py", line 536 in _open
File "C:\Program Files\ChimeraX 1.10.dev202501081858\bin\Lib\urllib\request.py", line 519 in open
File "C:\Program Files\ChimeraX 1.10.dev202501081858\bin\Lib\urllib\request.py", line 216 in urlopen
File "C:\Program Files\ChimeraX 1.10.dev202501081858\bin\Lib\site-packages\chimerax\core\toolshed\available.py", line 62 in load
File "C:\Program Files\ChimeraX 1.10.dev202501081858\bin\Lib\site-packages\chimerax\core\toolshed\__init__.py", line 516 in reload_available
File "C:\Program Files\ChimeraX 1.10.dev202501081858\bin\Lib\threading.py", line 975 in run
File "C:\Program Files\ChimeraX 1.10.dev202501081858\bin\Lib\threading.py", line 1038 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.10.dev202501081858\bin\Lib\threading.py", line 995 in _bootstrap
Current thread 0x00004318 (most recent call first):
File "C:\Program Files\ChimeraX 1.10.dev202501081858\bin\Lib\site-packages\chimerax\ui\gui.py", line 339 in event_loop
File "C:\Program Files\ChimeraX 1.10.dev202501081858\bin\Lib\site-packages\chimerax\core\__main__.py", line 1054 in init
File "C:\Program Files\ChimeraX 1.10.dev202501081858\bin\Lib\site-packages\chimerax\core\__main__.py", line 1217 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
===== Log before crash start =====
> open 2hyy
2hyy title:
Human Abl kinase domain in complex with imatinib (STI571, Glivec) [more
info...]
Chain information for 2hyy #1
---
Chain | Description | UniProt
A B C D | Proto-oncogene tyrosine-protein kinase ABL1 | ABL1_HUMAN 228-500
Non-standard residues in 2hyy #1
---
STI — 4-(4-methyl-piperazin-1-ylmethyl)-N-[4-methyl-3-(4-pyridin-3-yl-
pyrimidin-2-ylamino)-phenyl]-benzamide (sti-571; imatinib)
2hyy mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
3| author_defined_assembly
4| author_defined_assembly
> sym #1 assembly 1 copies true
Made 1 copies for 2hyy assembly 1
> select #2.1/A:259
4 atoms, 3 bonds, 1 residue, 1 model selected
> mousemode
left: rotate
control left: select
middle: translate
right: translate
wheel: zoom
pause: identify object
Available modes: select, select add, select subtract, select toggle, rotate,
rotate and select, rotate selected models, rotate z selected models, rotate
selected atoms, rotate independent, translate, translate selected models,
translate xy selected models, move picked models, translate selected atoms,
zoom, clip, clip rotate, identify object, pivot, center, center or translate,
swipe as scroll, none, next docked, pick blobs, hide blobs, create
segmentations, erase segmentations, move segmentation cursor, resize
segmentation cursor, toggle segmentation visibility, swapaa, mark maximum,
mark plane, mark surface, mark center, mark point, link markers, move markers,
resize markers, delete markers, zone, bond rotation, map eraser, distance,
play coordinates, orthopick, play map series, tape measure, tug, minimize,
label, move label, contour level, move planes, crop volume, windowing, rotate
slab
> select clear
> select #2.1/A:267
7 atoms, 6 bonds, 1 residue, 1 model selected
> select clear
> preset "initial styles" sticks
Using preset: Initial Styles / Sticks
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset sticks
Using preset: Initial Styles / Sticks
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset original
Using preset: Initial Styles / Original Look
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset sticks
Using preset: Initial Styles / Sticks
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> style ball
Changed 10863 atom styles
> style ball
Changed 10863 atom styles
> preset stivkes
No preset name matches 'stivkes'
> preset sticks
Using preset: Initial Styles / Sticks
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> style :STT sphere
Changed 0 atom styles
> style ball
Changed 10863 atom styles
> style :STI sphere
Changed 185 atom styles
> style :STI sphere
Changed 185 atom styles
> style stick
Changed 10863 atom styles
> color :sti & C salmon
Drag select of 405 atoms, 407 bonds
> select clear
> preset original
Using preset: Initial Styles / Original Look
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> select clear
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.10.dev202501081858 (2025-01-08)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 3.3.0 - Build 32.0.101.5768
OpenGL renderer: Intel(R) Arc(TM) Graphics
OpenGL vendor: Intel
Python: 3.11.4
Locale: zh_CN.cp936
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: windows
Manufacturer: LENOVO
Model: 83D2
OS: Microsoft Windows 11 家庭中文版 (Build 26100)
Memory: 33,945,935,872
MaxProcessMemory: 137,438,953,344
CPU: 18 Intel(R) Core(TM) Ultra 5 125H
OSLanguage: zh-CN
Installed Packages:
alabaster: 1.0.0
anyio: 4.8.0
appdirs: 1.4.4
asttokens: 3.0.0
auditwheel: 6.2.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2024.12.14
cftime: 1.6.4.post1
charset-normalizer: 3.4.1
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.10.dev202501081858
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
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
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: 1.5.1
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: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
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
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.7
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: 1.1.2
ChimeraX-ProfileGrids: 1.0.1
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: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.15
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: 2.5.1
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: 1.42.2
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: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
comtypes: 1.4.5
contourpy: 1.3.1
coverage: 7.6.10
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.11
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.0.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.5
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.8
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
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: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pickleshare: 0.7.5
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
pluggy: 1.5.0
prompt_toolkit: 3.0.48
psutil: 6.0.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.1
pyproject_hooks: 1.2.0
PyQt6: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
pytest: 8.3.4
pytest-cov: 6.0.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pywin32: 306
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.1
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
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: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.3.0
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
WMI: 1.5.1
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Could be the toolshed update does some Qt call in the wrong thread. The command log doesn't suggest anything the user ran would cause a problem and after many commands the toolshed is finally checking for an update and Qt mysteriously crashes. I think Greg should check that absolutely no Qt is used in the async thread that is doing the Toolshed update, including logging messages.