Crash using open/save dialog

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Linux-5.14.0-284.30.1.el9_2.x86_64-x86_64-with-glibc2.34
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Bus error

Current thread 0x00007fc8807d9f00 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/open_command/dialog.py", line 135 in show_open_file_dialog
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/toolbar/providers.py", line 17 in _file_open
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/toolbar/providers.py", line 45 in run_provider
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/toolbar/__init__.py", line 37 in run_provider
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/core/toolshed/__init__.py", line 1289 in run_provider
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/core/toolshed/info.py", line 386 in run_provider
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/toolbar/tool.py", line 165 in callback
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/ui/gui.py", line 275 in event_loop
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/core/__main__.py", line 892 in init
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1043 in 
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/runpy.py", line 87 in _run_code
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/runpy.py", line 197 in _run_module_as_main
===== Log before crash start =====
Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open J141_focusedFII_sharpen_centered.mrc

Opened J141_focusedFII_sharpen_centered.mrc as #1, grid size 256,256,256,
pixel 1.1, shown at level 0.189, step 1, values float32  

> surface dust #1 size 11

> volume #1 level 0.07401

> volume #1 level 0.2149

> volume #1 level 0.1679

> open /panfs/home/vsreddy/ma000657/modeling/Ad5-FII/hx2_FII_Ad5_FII.pdb

Chain information for hx2_FII_Ad5_FII.pdb #2  
---  
Chain | Description  
D | No description available  
E | No description available  
F | No description available  
X | No description available  
  

> select add #2

26494 atoms, 27189 bonds, 12 pseudobonds, 3310 residues, 2 models selected  

> ui mousemode right "translate selected models"

> view matrix models #2,1,0,0,-145.71,0,1,0,-135.76,0,0,1,-155.81

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.96399,-0.25867,-0.061775,-95.462,0.23655,0.94014,-0.2453,-111.96,0.12153,0.22186,0.96748,-194.4

> view matrix models
> #2,0.93961,-0.3155,0.13262,-122.67,0.31589,0.94861,0.018649,-175,-0.13168,0.02437,0.99099,-139.59

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.93961,-0.3155,0.13262,-116.02,0.31589,0.94861,0.018649,-167.87,-0.13168,0.02437,0.99099,-134.6

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.92208,-0.33937,0.18601,-120.98,0.32581,0.94012,0.10014,-183.94,-0.20886,-0.031737,0.97743,-114.4

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.92208,-0.33937,0.18601,-111.98,0.32581,0.94012,0.10014,-188.41,-0.20886,-0.031737,0.97743,-114.92

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.93891,-0.33346,0.085161,-95.379,0.3169,0.93417,0.16403,-198.87,-0.13425,-0.12703,0.98277,-113.63

> view matrix models
> #2,0.96458,-0.24351,0.10144,-113.6,0.22575,0.96093,0.16014,-189.38,-0.13647,-0.13157,0.98187,-112.57

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.96458,-0.24351,0.10144,-113.85,0.22575,0.96093,0.16014,-188.9,-0.13647,-0.13157,0.98187,-112.55

> ui tool show "Fit in Map"

> fitmap #2 inMap #1

Fit molecule hx2_FII_Ad5_FII.pdb (#2) to map
J141_focusedFII_sharpen_centered.mrc (#1) using 26494 atoms  
average map value = 0.2649, steps = 88  
shifted from previous position = 4.32  
rotated from previous position = 9.24 degrees  
atoms outside contour = 12582, contour level = 0.16794  
  
Position of hx2_FII_Ad5_FII.pdb (#2) relative to
J141_focusedFII_sharpen_centered.mrc (#1) coordinates:  
Matrix rotation and translation  
0.98636295 -0.08916068 0.13834202 -147.71105610  
0.07200294 0.98961277 0.12442725 -166.12141544  
-0.14799905 -0.11276940 0.98253720 -112.21785208  
Axis -0.58531013 0.70657968 0.39768984  
Axis point -710.65770587 0.00000000 1317.31087853  
Rotation angle (degrees) 11.69048998  
Shift along axis -75.54913971  
  

> select subtract #2

Nothing selected  

> select add #1

2 models selected  

> transparency sel 50

> select subtract #1

Nothing selected  

> volume #1 level 0.4492

> volume #1 level 0.4075

> volume #1 level 0.1315

> volume #1 level 0.1992


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

Log:
Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open J141_focusedFII_sharpen_centered.mrc

Opened J141_focusedFII_sharpen_centered.mrc as #1, grid size 256,256,256,
pixel 1.1, shown at level 0.189, step 1, values float32  




OpenGL version: 3.3.0 NVIDIA 535.104.05
OpenGL renderer: Quadro RTX 6000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: en_US.UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=gnome
XDG_SESSION_DESKTOP=gnome
XDG_CURRENT_DESKTOP=GNOME
DISPLAY=:1
Manufacturer: Dell Inc.
Model: Precision 5820 Tower
OS: Rocky Linux 9.2 Blue Onyx
Architecture: 64bit ELF
Virtual Machine: none
CPU: 8 Intel(R) Xeon(R) W-2123 CPU @ 3.60GHz
Cache Size: 8448 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:           124Gi       6.4Gi        27Gi       117Mi        91Gi       118Gi
	Swap:          4.0Gi       3.2Gi       783Mi

Graphics:
	65:00.0 VGA compatible controller [0300]: NVIDIA Corporation TU102GL [Quadro RTX 6000/8000] [10de:1e30] (rev a1)	
	Subsystem: NVIDIA Corporation Quadro RTX 6000 [10de:12ba]	
	Kernel driver in use: nvidia

Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2023.5.7
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9.1
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.10
    ChimeraX-AtomicLibrary: 10.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.8
    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: 1.3.2
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.21.0
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6.1
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    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
    ChimeraX-DockPrep: 1.1.1
    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: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.6.0
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-LinuxSupport: 1.0.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    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: 2.0.12
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.3.7
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.1
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.28.4
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    distro: 1.7.0
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.39.3
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.9.26
    imagesize: 1.4.1
    importlib-metadata: 6.6.0
    ipykernel: 6.21.1
    ipython: 8.10.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.6
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.0.2
    jupyter-core: 5.3.0
    jupyterlab-widgets: 3.0.7
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.2
    matplotlib: 3.6.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 2.8.8
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 23.1
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.5.0
    prompt-toolkit: 3.0.38
    psutil: 5.9.4
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.4.2
    PyQt6-Qt6: 6.4.3
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pyzmq: 25.0.2
    qtconsole: 5.4.0
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.28.2
    scipy: 1.9.3
    setuptools: 67.4.0
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4.1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.1
    traitlets: 5.9.0
    typing-extensions: 4.5.0
    tzdata: 2023.3
    urllib3: 1.26.15
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7
    zipp: 3.15.0