Crash in python_instances_of_class

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.22631
ChimeraX Version: 1.8.dev202403200605 (2024-03-20 06:05:36 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.8.dev202403200605 (2024-03-20)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "C:/Users/hanbi/Box/Bing, Randall, and
> Anne/AF2models_2.2/A0A267DS21/A0A267DS21_11mer_AF2.2_new/best_model.pdb"

Chain information for best_model.pdb #1  
---  
Chain | Description  
A B C D E F G H I J K | No description available  
  

> show surfaces

> coulombic

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for best_model.pdb_A SES surface #1.1: minimum, -23.57, mean
-0.44, maximum 14.26  
Coulombic values for best_model.pdb_B SES surface #1.2: minimum, -19.60, mean
-0.42, maximum 13.88  
Coulombic values for best_model.pdb_C SES surface #1.3: minimum, -17.49, mean
-0.44, maximum 14.46  
Coulombic values for best_model.pdb_D SES surface #1.4: minimum, -18.79, mean
-0.45, maximum 14.01  
Coulombic values for best_model.pdb_E SES surface #1.5: minimum, -19.55, mean
-0.44, maximum 14.12  
Coulombic values for best_model.pdb_F SES surface #1.6: minimum, -15.99, mean
-0.44, maximum 14.10  
Coulombic values for best_model.pdb_G SES surface #1.7: minimum, -18.70, mean
-0.44, maximum 14.50  
Coulombic values for best_model.pdb_H SES surface #1.8: minimum, -14.14, mean
-0.44, maximum 14.26  
Coulombic values for best_model.pdb_I SES surface #1.9: minimum, -17.57, mean
-0.43, maximum 14.23  
Coulombic values for best_model.pdb_J SES surface #1.10: minimum, -22.66, mean
-0.43, maximum 14.32  
Coulombic values for best_model.pdb_K SES surface #1.11: minimum, -19.41, mean
-0.42, maximum 14.22  
To also show corresponding color key, enter the above coulombic command and
add key true  

> close

> open "C:/Users/hanbi/Box/Bing, Randall, and
> Anne/AF2models_2.2/A0A1I8J849/A0A1I8J849_11mer_AF2.2/best_model.pdb"

Chain information for best_model.pdb #1  
---  
Chain | Description  
A B C D E F G H I J K | No description available  
  

> show surfaces

> coulombic

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for best_model.pdb_A SES surface #1.1: minimum, -13.96, mean
0.07, maximum 14.65  
Coulombic values for best_model.pdb_B SES surface #1.2: minimum, -14.51, mean
0.04, maximum 14.12  
Coulombic values for best_model.pdb_C SES surface #1.3: minimum, -13.81, mean
0.06, maximum 14.71  
Coulombic values for best_model.pdb_D SES surface #1.4: minimum, -14.56, mean
0.08, maximum 14.93  
Coulombic values for best_model.pdb_E SES surface #1.5: minimum, -14.09, mean
0.04, maximum 14.00  
Coulombic values for best_model.pdb_F SES surface #1.6: minimum, -18.98, mean
0.09, maximum 14.26  
Coulombic values for best_model.pdb_G SES surface #1.7: minimum, -14.22, mean
0.09, maximum 14.52  
Coulombic values for best_model.pdb_H SES surface #1.8: minimum, -13.87, mean
0.11, maximum 22.75  
Coulombic values for best_model.pdb_I SES surface #1.9: minimum, -13.95, mean
0.10, maximum 14.21  
Coulombic values for best_model.pdb_J SES surface #1.10: minimum, -13.98, mean
0.08, maximum 14.11  
Coulombic values for best_model.pdb_K SES surface #1.11: minimum, -14.54, mean
0.06, maximum 14.88  
To also show corresponding color key, enter the above coulombic command and
add key true  

> close

> open "C:/Users/hanbi/Box/Bing, Randall, and
> Anne/AF2models_2.2/A0A267FNG7/A0A267FNG7_11mer_AF2.2_new/best_model.pdb"

Chain information for best_model.pdb #1  
---  
Chain | Description  
A B C D E F G H I J K | No description available  
  

> show surfaces

> coulombic

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX_daily_032024\bin\Lib\site-
packages\chimerax\toolbar\tool.py", line 205, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File "C:\Program Files\ChimeraX_daily_032024\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 397, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX_daily_032024\bin\Lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1302, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX_daily_032024\bin\Lib\site-
packages\chimerax\shortcuts\\__init__.py", line 66, in run_provider  
shortcuts.run_provider(session, name)  
File "C:\Program Files\ChimeraX_daily_032024\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 1387, in run_provider  
keyboard_shortcuts(session).try_shortcut(name)  
File "C:\Program Files\ChimeraX_daily_032024\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 402, in try_shortcut  
self.run_shortcut(keys)  
File "C:\Program Files\ChimeraX_daily_032024\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 420, in run_shortcut  
sc.run(self.session, status = self._enabled)  
File "C:\Program Files\ChimeraX_daily_032024\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 339, in run  
f(s)  
File "C:\Program Files\ChimeraX_daily_032024\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 72, in func_plus_tip  
func(cmd + " %s")(session)  
File "C:\Program Files\ChimeraX_daily_032024\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 593, in run_expanded_command  
run(session, cmd)  
File "C:\Program Files\ChimeraX_daily_032024\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 536, in run  
run_command(session, command, **kw)  
File "C:\Program Files\ChimeraX_daily_032024\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX_daily_032024\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2904, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX_daily_032024\bin\Lib\site-
packages\chimerax\coulombic\cmd.py", line 102, in cmd_coulombic  
assign_charges(session, needs_assignment, his_scheme, charge_method,  
File "C:\Program Files\ChimeraX_daily_032024\bin\Lib\site-
packages\chimerax\coulombic\coulombic.py", line 73, in assign_charges  
charged_struct = struct.copy(name="copy of " + struct.name)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX_daily_032024\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 162, in copy  
m._copy_custom_attrs(self)  
File "C:\Program Files\ChimeraX_daily_032024\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 176, in _copy_custom_attrs  
py_objs = [py_obj for py_obj in python_instances_of_class(class_obj)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX_daily_032024\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 61, in python_instances_of_class  
return [x for x in instances if filt(x)]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX_daily_032024\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 61, in <listcomp>  
return [x for x in instances if filt(x)]  
^^^^^^^  
File "C:\Program Files\ChimeraX_daily_032024\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 52, in <lambda>  
filt = lambda x: open_structure(x.structure)  
^^^^^^^^^^^  
File "atomic_cpp\\\cymol.pyx", line 536, in
chimerax.atomic.cymol.CyAtom.structure.__get__  
RuntimeError: Atom already deleted  
  
RuntimeError: Atom already deleted  
  
File "atomic_cpp\\\cymol.pyx", line 536, in
chimerax.atomic.cymol.CyAtom.structure.__get__  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 528.92
OpenGL renderer: NVIDIA GeForce RTX 3060 Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: en_US.cp1252
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.2
Qt platform: windows

Manufacturer: Micro-Star International Co., Ltd.
Model: Raider GE76 12UE
OS: Microsoft Windows 11 Home (Build 22631)
Memory: 16,866,566,144
MaxProcessMemory: 137,438,953,344
CPU: 20 12th Gen Intel(R) Core(TM) i9-12900H
OSLanguage: en-US

Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    asttokens: 2.4.1
    Babel: 2.14.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.5.1
    build: 1.1.1
    certifi: 2024.2.2
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.16
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.3
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.5
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.56
    ChimeraX-AtomicLibrary: 14.0.2
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    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: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.8.dev202403200605
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    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: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.9
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.1.4
    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: 2.1.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.13
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.15
    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-Neuron: 1.0
    ChimeraX-Nifti: 1.1
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.3
    ChimeraX-PDB: 2.7.5
    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: 1.1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.3
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    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: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.16.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.37.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 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: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    comtypes: 1.3.1
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.9
    debugpy: 1.8.1
    decorator: 5.1.1
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.1
    fonttools: 4.50.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2024.2.26
    idna: 3.6
    ihm: 0.43
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.2
    jedi: 0.19.1
    Jinja2: 3.1.3
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.10
    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    lxml: 5.1.0
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.8
    ndindex: 1.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.2.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.9.0
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 24.0
    ParmEd: 4.2.2
    parso: 0.8.3
    pep517: 0.13.1
    pillow: 10.2.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.0
    prompt-toolkit: 3.0.43
    psutil: 5.9.8
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.3.0
    pygments: 2.17.2
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3302
    pyparsing: 3.1.2
    pyproject-hooks: 1.0.0
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    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.2
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pywin32: 306
    pyzmq: 25.1.2
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.12.0
    Send2Trash: 1.8.3
    SEQCROW: 1.8.8
    setuptools: 69.2.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
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    sphinx-autodoc-typehints: 2.0.0
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.6.1
    tables: 3.9.2
    tcia-utils: 1.5.1
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    tornado: 6.4
    traitlets: 5.14.1
    typing-extensions: 4.10.0
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.10
    WMI: 1.5.1