Opened 9 months ago

Closed 9 months ago

#16635 closed defect (can't reproduce)

Crash in chem_group

Reported by: chimerax-bug-report@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Structure Analysis Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description (last modified by Eric Pettersen) 

The following bug report has been submitted:
Platform:        Windows-10-10.0.22631
ChimeraX Version: 1.10.dev202501142332 (2025-01-14 23:32:44 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Windows fatal exception: access violation

Thread 0x000046e0 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202501142332\bin\Lib\threading.py", line 324 in wait
  File "C:\Program Files\ChimeraX 1.10.dev202501142332\bin\Lib\threading.py", line 622 in wait
  File "C:\Program Files\ChimeraX 1.10.dev202501142332\bin\Lib\threading.py", line 1392 in run
  File "C:\Program Files\ChimeraX 1.10.dev202501142332\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202501142332\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x000011c0 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202501142332\bin\Lib\site-packages\chimerax\chem_group\support.py", line 40 in call_c_plus_plus
  File "C:\Program Files\ChimeraX 1.10.dev202501142332\bin\Lib\site-packages\chimerax\chem_group\chem_group.py", line 233 in find_group
  File "C:\Program Files\ChimeraX 1.10.dev202501142332\bin\Lib\site-packages\chimerax\hbonds\hbond.py", line 770 in _find_acceptors
  File "C:\Program Files\ChimeraX 1.10.dev202501142332\bin\Lib\site-packages\chimerax\hbonds\hbond.py", line 498 in find_hbonds
  File "C:\Program Files\ChimeraX 1.10.dev202501142332\bin\Lib\site-packages\chimerax\addh\hbond.py", line 259 in add_hydrogens
  File "C:\Program Files\ChimeraX 1.10.dev202501142332\bin\Lib\site-packages\chimerax\addh\cmd.py", line 184 in hbond_add_hydrogens
  File "C:\Program Files\ChimeraX 1.10.dev202501142332\bin\Lib\site-packages\chimerax\addh\cmd.py", line 77 in cmd_addh
  File "C:\Program Files\ChimeraX 1.10.dev202501142332\bin\Lib\site-packages\chimerax\coulombic\coulombic.py", line 95 in assign_charges
  File "C:\Program Files\ChimeraX 1.10.dev202501142332\bin\Lib\site-packages\chimerax\coulombic\cmd.py", line 102 in cmd_coulombic
  File "C:\Program Files\ChimeraX 1.10.dev202501142332\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 3213 in run
  File "C:\Program Files\ChimeraX 1.10.dev202501142332\bin\Lib\site-packages\chimerax\core\commands\run.py", line 49 in run
  File "C:\Program Files\ChimeraX 1.10.dev202501142332\bin\Lib\site-packages\chimerax\shortcuts\shortcuts.py", line 536 in run
  File "C:\Program Files\ChimeraX 1.10.dev202501142332\bin\Lib\site-packages\chimerax\shortcuts\shortcuts.py", line 593 in run_expanded_command
  File "C:\Program Files\ChimeraX 1.10.dev202501142332\bin\Lib\site-packages\chimerax\shortcuts\shortcuts.py", line 72 in func_plus_tip
  File "C:\Program Files\ChimeraX 1.10.dev202501142332\bin\Lib\site-packages\chimerax\shortcuts\shortcuts.py", line 339 in run
  File "C:\Program Files\ChimeraX 1.10.dev202501142332\bin\Lib\site-packages\chimerax\shortcuts\shortcuts.py", line 420 in run_shortcut
  File "C:\Program Files\ChimeraX 1.10.dev202501142332\bin\Lib\site-packages\chimerax\shortcuts\shortcuts.py", line 402 in try_shortcut
  File "C:\Program Files\ChimeraX 1.10.dev202501142332\bin\Lib\site-packages\chimerax\shortcuts\shortcuts.py", line 1386 in run_provider
  File "C:\Program Files\ChimeraX 1.10.dev202501142332\bin\Lib\site-packages\chimerax\shortcuts\__init__.py", line 66 in run_provider
  File "C:\Program Files\ChimeraX 1.10.dev202501142332\bin\Lib\site-packages\chimerax\core\toolshed\__init__.py", line 1419 in run_provider
  File "C:\Program Files\ChimeraX 1.10.dev202501142332\bin\Lib\site-packages\chimerax\core\toolshed\info.py", line 397 in run_provider
  File "C:\Program Files\ChimeraX 1.10.dev202501142332\bin\Lib\site-packages\chimerax\toolbar\tool.py", line 215 in callback
  File "C:\Program Files\ChimeraX 1.10.dev202501142332\bin\Lib\site-packages\chimerax\ui\gui.py", line 339 in event_loop
  File "C:\Program Files\ChimeraX 1.10.dev202501142332\bin\Lib\site-packages\chimerax\core\__main__.py", line 1050 in init
  File "C:\Program Files\ChimeraX 1.10.dev202501142332\bin\Lib\site-packages\chimerax\core\__main__.py", line 1213 in 
  File "", line 88 in _run_code
  File "", line 198 in _run_module_as_main
===== Log before crash start =====
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.10.dev202501142332 (2025-01-14)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 9bw1

9bw1 title:  
TnsABCD-DNA transpososome [more info...]  
  
Chain information for 9bw1 #1  
---  
Chain | Description | UniProt  
2 | LE_polyA |   
4 | RE_target |   
5 | RE_polyA |   
6 | Target_downstream |   
H | Target_val |   
I | tRNA_LE_LUEGO |   
J | TnsD | A0A235IGG7_9NOSO 1-462  
M N O P a b c d | Integrase | A0A235IFR8_9NOSO 1-898  
Q R S T U V W x y | TnsC | A0A235IFM2_9NOSO 1-383  
  
Non-standard residues in 9bw1 #1  
---  
ATP — adenosine-5'-triphosphate  
MG — magnesium ion  
ZN — zinc ion  
  

> preset cartoons/nucleotides ribbons/slabs

Using preset: Cartoons/Nucleotides / Ribbons/Slabs  
Changed 47046 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    ~worm
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    nucleotides tube/slab shape box

  

> open C:/Users/olawu/Downloads/emd_44944.mrc

Opened emd_44944.mrc as #2, grid size 480,480,480, pixel 0.822, shown at level
0.00442, step 2, values float32  

> volume #2 level -0.002399

> volume #2 level 0.01643

> close #2

> open C:/Users/olawu/Downloads/emd_44944.mrc

Opened emd_44944.mrc as #2, grid size 480,480,480, pixel 0.822, shown at level
0.00442, step 2, values float32  

> color bfactor

Collection has bfactors  
47283 atoms, 5431 residues, atom bfactor range 2.36 to 276  

> volume #2 style image region 0,0,238,479,479,238 step 1 showOutlineBox true

> style ball

Changed 47283 atom styles  

> style ball

Changed 47283 atom styles  

> style sphere

Changed 47283 atom styles  

> style ball

Changed 47283 atom styles  

> volume #2 region 0,0,0,479,479,479 step 2

> volume #2 style surface region 0,0,0,479,479,479 step 2

> volume #2 color #0055ff

> volume #2 color white

> ui tool show "Side View"

> coulombic

The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:  
/4 DA -30  
/6 DG 6  
/I DC -15  
/J LEU 462  
/a PHE 898  
/b PHE 898  
/c PHE 898  
/d PHE 898  


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

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.10.dev202501142332 (2025-01-14)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 - Build 31.0.101.5333
OpenGL renderer: Intel(R) Iris(R) Xe Graphics
OpenGL vendor: Intel

Python: 3.11.4
Locale: en_US.cp1252
Qt version: PyQt6 6.8.0, Qt 6.8.1
Qt runtime version: 6.8.1
Qt platform: windows

Manufacturer: Dell Inc.
Model: Inspiron 15 3511
OS: Microsoft Windows 11 Home (Build 22631)
Memory: 8,311,836,672
MaxProcessMemory: 137,438,953,344
CPU: 8 11th Gen Intel(R) Core(TM) i5-1135G7 @ 2.40GHz
OSLanguage: en-US

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.dev202501142332
    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: 1.43
    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-commercial: 6.8.0
    PyQt6-Qt6: 6.8.1
    PyQt6-WebEngine-commercial: 6.8.0
    PyQt6-WebEngine-Qt6: 6.8.1
    PyQt6_sip: 13.9.1
    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

Change History (3)

comment:1 by Eric Pettersen, 9 months ago

Component: Unassigned → Structure Analysis
Description: modified (diff)
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Crash in chem_group

comment:2 by Eric Pettersen, 9 months ago

Works on the Windows 10 box here (vive)

comment:3 by Eric Pettersen, 9 months ago

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