Crash in event loop

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19045
ChimeraX Version: 1.11.dev202509030023 (2025-09-03 00:23:25 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Windows fatal exception: access violation

Thread 0x00002190 (most recent call first):
  File "C:\Program Files\ChimeraX 1.11.dev202509030023\bin\Lib\threading.py", line 331 in wait
  File "C:\Program Files\ChimeraX 1.11.dev202509030023\bin\Lib\threading.py", line 629 in wait
  File "C:\Program Files\ChimeraX 1.11.dev202509030023\bin\Lib\threading.py", line 1399 in run
  File "C:\Program Files\ChimeraX 1.11.dev202509030023\bin\Lib\threading.py", line 1045 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.11.dev202509030023\bin\Lib\threading.py", line 1002 in _bootstrap

Current thread 0x000022d4 (most recent call first):
  File "C:\Program Files\ChimeraX 1.11.dev202509030023\bin\Lib\site-packages\chimerax\ui\gui.py", line 368 in event_loop
  File "C:\Program Files\ChimeraX 1.11.dev202509030023\bin\Lib\site-packages\chimerax\core\__main__.py", line 1064 in init
  File "C:\Program Files\ChimeraX 1.11.dev202509030023\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.dev202509030023 (2025-09-03)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "C:\Users\Emiliana Pia Imbrice\Downloads\2MMN.cif" format mmcif

2MMN.cif title:  
Solution Structure of the Reduced Thioredoxin from Plasmodium falciparum [more
info...]  
  
Chain information for 2MMN.cif  
---  
Chain | Description | UniProt  
1.1/A 1.2/A 1.3/A 1.4/A 1.5/A 1.6/A 1.7/A 1.8/A 1.9/A 1.10/A | Thioredoxin | THIO_PLAF7 2-104  
  

> open "C:\Users\Emiliana Pia Imbrice\Downloads\2MMN.cif" format mmcif

2MMN.cif title:  
Solution Structure of the Reduced Thioredoxin from Plasmodium falciparum [more
info...]  
  
Chain information for 2MMN.cif  
---  
Chain | Description | UniProt  
2.1/A 2.2/A 2.3/A 2.4/A 2.5/A 2.6/A 2.7/A 2.8/A 2.9/A 2.10/A | Thioredoxin | THIO_PLAF7 2-104  
  

> set bgColor white

> select
> #1.1/A#1.2/A#1.3/A#1.4/A#1.5/A#1.6/A#1.7/A#1.8/A#1.9/A#1.10/A#2.1/A#2.2/A#2.3/A#2.4/A#2.5/A#2.6/A#2.7/A#2.8/A#2.9/A#2.10/A

32620 atoms, 32900 bonds, 2080 residues, 20 models selected  

> hide sel atoms

> hide sel cartoons

> select #1.1/A

1631 atoms, 1645 bonds, 104 residues, 1 model selected  

> hide sel cartoons

> show sel cartoons

> show sel atoms

> hide sel atoms

> color sel cornflower blue

> graphics silhouettes true

> select clear

> ui tool show "Show Sequence Viewer"

> sequence chain #1.1/A #1.2/A #1.3/A #1.4/A #1.5/A #1.6/A #1.7/A #1.8/A
> #1.9/A #1.10/A #2.1/A #2.2/A #2.3/A #2.4/A #2.5/A #2.6/A #2.7/A #2.8/A
> #2.9/A #2.10/A

Alignment identifier is 1  

> select #1.1/A:7-17,31-47,60-67,91-103 #1.2/A:7-17,31-47,60-67,91-103
> #1.3/A:7-17,31-47,60-67,91-103 #1.4/A:7-17,31-47,60-67,91-103
> #1.5/A:7-17,31-47,60-67,91-103 #1.6/A:7-17,31-47,60-67,91-103
> #1.7/A:7-17,31-47,60-67,91-103 #1.8/A:7-17,31-47,60-67,91-103
> #1.9/A:7-17,31-47,60-67,91-103 #1.10/A:7-17,31-47,60-67,91-103
> #2.1/A:7-17,31-47,60-67,91-103 #2.2/A:7-17,31-47,60-67,91-103
> #2.3/A:7-17,31-47,60-67,91-103 #2.4/A:7-17,31-47,60-67,91-103
> #2.5/A:7-17,31-47,60-67,91-103 #2.6/A:7-17,31-47,60-67,91-103
> #2.7/A:7-17,31-47,60-67,91-103 #2.8/A:7-17,31-47,60-67,91-103
> #2.9/A:7-17,31-47,60-67,91-103 #2.10/A:7-17,31-47,60-67,91-103

15380 atoms, 15440 bonds, 980 residues, 20 models selected  

> select #1.1/A:33 #1.2/A:33 #1.3/A:33 #1.4/A:33 #1.5/A:33 #1.6/A:33 #1.7/A:33
> #1.8/A:33 #1.9/A:33 #1.10/A:33 #2.1/A:33 #2.2/A:33 #2.3/A:33 #2.4/A:33
> #2.5/A:33 #2.6/A:33 #2.7/A:33 #2.8/A:33 #2.9/A:33 #2.10/A:33

220 atoms, 200 bonds, 20 residues, 20 models selected  

> select #1.1/A:33 #1.2/A:33 #1.3/A:33 #1.4/A:33 #1.5/A:33 #1.6/A:33 #1.7/A:33
> #1.8/A:33 #1.9/A:33 #1.10/A:33 #2.1/A:33 #2.2/A:33 #2.3/A:33 #2.4/A:33
> #2.5/A:33 #2.6/A:33 #2.7/A:33 #2.8/A:33 #2.9/A:33 #2.10/A:33

220 atoms, 200 bonds, 20 residues, 20 models selected  
Thioredoxin [ID: 1] region 20 chains [33] RMSD: 0.598  
  

> show sel atoms

> hide sel atoms

> show sel cartoons

> hide sel cartoons

> color sel lime

> show sel atoms

> select #1.1/A:30 #1.2/A:30 #1.3/A:30 #1.4/A:30 #1.5/A:30 #1.6/A:30 #1.7/A:30
> #1.8/A:30 #1.9/A:30 #1.10/A:30 #2.1/A:30 #2.2/A:30 #2.3/A:30 #2.4/A:30
> #2.5/A:30 #2.6/A:30 #2.7/A:30 #2.8/A:30 #2.9/A:30 #2.10/A:30

220 atoms, 200 bonds, 20 residues, 20 models selected  

> select #1.1/A:30 #1.2/A:30 #1.3/A:30 #1.4/A:30 #1.5/A:30 #1.6/A:30 #1.7/A:30
> #1.8/A:30 #1.9/A:30 #1.10/A:30 #2.1/A:30 #2.2/A:30 #2.3/A:30 #2.4/A:30
> #2.5/A:30 #2.6/A:30 #2.7/A:30 #2.8/A:30 #2.9/A:30 #2.10/A:30

220 atoms, 200 bonds, 20 residues, 20 models selected  
Thioredoxin [ID: 1] region 20 chains [30] RMSD: 0.587  
  

> color sel lime

> select #1.1/A:7-17,31-47,60-67,91-103 #1.2/A:7-17,31-47,60-67,91-103
> #1.3/A:7-17,31-47,60-67,91-103 #1.4/A:7-17,31-47,60-67,91-103
> #1.5/A:7-17,31-47,60-67,91-103 #1.6/A:7-17,31-47,60-67,91-103
> #1.7/A:7-17,31-47,60-67,91-103 #1.8/A:7-17,31-47,60-67,91-103
> #1.9/A:7-17,31-47,60-67,91-103 #1.10/A:7-17,31-47,60-67,91-103
> #2.1/A:7-17,31-47,60-67,91-103 #2.2/A:7-17,31-47,60-67,91-103
> #2.3/A:7-17,31-47,60-67,91-103 #2.4/A:7-17,31-47,60-67,91-103
> #2.5/A:7-17,31-47,60-67,91-103 #2.6/A:7-17,31-47,60-67,91-103
> #2.7/A:7-17,31-47,60-67,91-103 #2.8/A:7-17,31-47,60-67,91-103
> #2.9/A:7-17,31-47,60-67,91-103 #2.10/A:7-17,31-47,60-67,91-103

15380 atoms, 15440 bonds, 980 residues, 20 models selected  

> select #1.1/A:33 #1.2/A:33 #1.3/A:33 #1.4/A:33 #1.5/A:33 #1.6/A:33 #1.7/A:33
> #1.8/A:33 #1.9/A:33 #1.10/A:33 #2.1/A:33 #2.2/A:33 #2.3/A:33 #2.4/A:33
> #2.5/A:33 #2.6/A:33 #2.7/A:33 #2.8/A:33 #2.9/A:33 #2.10/A:33

220 atoms, 200 bonds, 20 residues, 20 models selected  

> select #1.1/A:33 #1.2/A:33 #1.3/A:33 #1.4/A:33 #1.5/A:33 #1.6/A:33 #1.7/A:33
> #1.8/A:33 #1.9/A:33 #1.10/A:33 #2.1/A:33 #2.2/A:33 #2.3/A:33 #2.4/A:33
> #2.5/A:33 #2.6/A:33 #2.7/A:33 #2.8/A:33 #2.9/A:33 #2.10/A:33

220 atoms, 200 bonds, 20 residues, 20 models selected  
Thioredoxin [ID: 1] region 20 chains [33] RMSD: 0.598  
  

> hide sel atoms

> hide sel cartoons

> show sel cartoons


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

Log:
UCSF ChimeraX version: 1.11.dev202509030023 (2025-09-03)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 NVIDIA 516.40
OpenGL renderer: NVIDIA GeForce MX230/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

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

Manufacturer: Acer
Model: Aspire A315-55G
OS: Microsoft Windows 10 Home (Build 19045)
Memory: 8,403,275,776
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i5-10210U CPU @ 1.60GHz
OSLanguage: it-IT

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.dev202509030023
    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: 8.4.1
    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
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