id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
16480	Crash in event loop	chimerax-bug-report@…	Eric Pettersen	"{{{
The following bug report has been submitted:
Platform:        macOS-14.4.1-arm64-arm-64bit
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Current thread 0x00000001ea38bac0 (most recent call first):
 File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 275 in event_loop
 File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 918 in init
 File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1069 in 
 File """", line 88 in _run_code
 File """", line 198 in _run_module_as_main

Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.pdb_lib._load_libs, chimerax.map._map, chimerax.surface._surface, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler (total: 47)


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===== Log before crash start =====
Startup Messages  
---  
warnings | Replacing fetcher for 'ngff' and format OME-Zarr from OME-Zarr
bundle with that from OME-Zarr bundle  
Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with
that from NMRSTAR bundle  

UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/anirudhmantri/Desktop/Relion/job074/run_class001_job074.mrc

Opened run_class001_job074.mrc as #1, grid size 324,324,324, pixel 1.72, shown
at level 0.00265, step 2, values float32  

> open /Users/anirudhmantri/Desktop/Relion/job076/run_class001_job076.mrc

Opened run_class001_job076.mrc as #2, grid size 324,324,324, pixel 1.72, shown
at level 0.00158, step 2, values float32  

> open /Users/anirudhmantri/Desktop/Relion/job078/run_it004_half1_class001.mrc

Opened run_it004_half1_class001.mrc as #3, grid size 324,324,324, pixel 1.72,
shown at level 0.00103, step 2, values float32  

> tile off

> shape cylinder center 125,125,108 radius 50 height 40 caps true


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

Log:
Startup Messages  
---  
warnings | Replacing fetcher for 'ngff' and format OME-Zarr from OME-Zarr
bundle with that from OME-Zarr bundle  
Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with
that from NMRSTAR bundle  

UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M1
OpenGL vendor: Apple

Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

   Hardware Overview:

     Model Name: MacBook Air
     Model Identifier: MacBookAir10,1
     Model Number: MGN93LL/A
     Chip: Apple M1
     Total Number of Cores: 8 (4 performance and 4 efficiency)
     Memory: 8 GB
     System Firmware Version: 10151.101.3
     OS Loader Version: 10151.101.3

Software:

   System Software Overview:

     System Version: macOS 14.4.1 (23E224)
     Kernel Version: Darwin 23.4.0
     Time since boot: 13 days, 2 hours, 6 minutes

Graphics/Displays:

   Apple M1:

     Chipset Model: Apple M1
     Type: GPU
     Bus: Built-In
     Total Number of Cores: 7
     Vendor: Apple (0x106b)
     Metal Support: Metal 3
     Displays:
       Color LCD:
         Display Type: Built-In Retina LCD
         Resolution: 2560 x 1600 Retina
         Main Display: Yes
         Mirror: Off
         Online: Yes
         Automatically Adjust Brightness: Yes
         Connection Type: Internal


Installed Packages:
   alabaster: 0.7.16
   appdirs: 1.4.4
   appnope: 0.1.3
   asttokens: 2.4.1
   Babel: 2.14.0
   backcall: 0.2.0
   beautifulsoup4: 4.11.2
   blockdiag: 3.0.0
   blosc2: 2.0.0
   build: 0.10.0
   certifi: 2022.12.7
   cftime: 1.6.3
   charset-normalizer: 3.3.2
   ChimeraX-AddCharge: 1.5.13
   ChimeraX-AddH: 2.2.5
   ChimeraX-AlignmentAlgorithms: 2.0.1
   ChimeraX-AlignmentHdrs: 3.4.1
   ChimeraX-AlignmentMatrices: 2.1
   ChimeraX-Alignments: 2.12.2
   ChimeraX-AlphaFold: 1.0
   ChimeraX-AltlocExplorer: 1.1.1
   ChimeraX-AmberInfo: 1.0
   ChimeraX-Arrays: 1.1
   ChimeraX-Atomic: 1.49.1
   ChimeraX-AtomicLibrary: 12.1.5
   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: 2.0.4
   ChimeraX-BugReporter: 1.0.1
   ChimeraX-BuildStructure: 2.10.5
   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: 1.1
   ChimeraX-CheckWaters: 1.3.2
   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: 1.7.1
   ChimeraX-CoreFormats: 1.2
   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: 1.1.3
   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: 1.1.8
   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: 2.1.2
   ChimeraX-MCopy: 1.0
   ChimeraX-MDcrds: 2.6.1
   ChimeraX-MedicalToolbar: 1.0.2
   ChimeraX-Meeting: 1.0.1
   ChimeraX-MLP: 1.1.1
   ChimeraX-mmCIF: 2.12.1
   ChimeraX-MMTF: 2.2
   ChimeraX-Modeller: 1.5.14
   ChimeraX-ModelPanel: 1.4
   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-NRRD: 1.1
   ChimeraX-Nucleotides: 2.0.3
   ChimeraX-OpenCommand: 1.13.1
   ChimeraX-PDB: 2.7.3
   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
   ChimeraX-PubChem: 2.1
   ChimeraX-ReadPbonds: 1.0.1
   ChimeraX-Registration: 1.1.2
   ChimeraX-RemoteControl: 1.0
   ChimeraX-RenderByAttr: 1.1
   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-SelInspector: 1.0
   ChimeraX-SeqView: 2.11
   ChimeraX-Shape: 1.0.1
   ChimeraX-Shell: 1.0.1
   ChimeraX-Shortcuts: 1.1.1
   ChimeraX-ShowSequences: 1.0.2
   ChimeraX-SideView: 1.0.1
   ChimeraX-Smiles: 2.1.2
   ChimeraX-SmoothLines: 1.0
   ChimeraX-SpaceNavigator: 1.0
   ChimeraX-StdCommands: 1.12.4
   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: 2.2.2
   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: 1.33.3
   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: 0.2.1
   contourpy: 1.2.0
   cxservices: 1.2.2
   cycler: 0.12.1
   Cython: 0.29.33
   debugpy: 1.8.0
   decorator: 5.1.1
   docutils: 0.19
   executing: 2.0.1
   filelock: 3.9.0
   fonttools: 4.47.2
   funcparserlib: 2.0.0a0
   glfw: 2.6.4
   grako: 3.16.5
   h5py: 3.10.0
   html2text: 2020.1.16
   idna: 3.6
   ihm: 0.38
   imagecodecs: 2023.9.18
   imagesize: 1.4.1
   ipykernel: 6.23.2
   ipython: 8.14.0
   ipython-genutils: 0.2.0
   ipywidgets: 8.1.1
   jedi: 0.18.2
   Jinja2: 3.1.2
   jupyter-client: 8.2.0
   jupyter-core: 5.7.1
   jupyterlab-widgets: 3.0.9
   kiwisolver: 1.4.5
   line-profiler: 4.0.2
   lxml: 4.9.2
   lz4: 4.3.2
   MarkupSafe: 2.1.4
   matplotlib: 3.7.2
   matplotlib-inline: 0.1.6
   msgpack: 1.0.4
   nest-asyncio: 1.6.0
   netCDF4: 1.6.2
   networkx: 3.1
   nibabel: 5.0.1
   nptyping: 2.5.0
   numexpr: 2.8.8
   numpy: 1.25.1
   openvr: 1.23.701
   packaging: 21.3
   ParmEd: 3.4.3
   parso: 0.8.3
   pep517: 0.13.0
   pexpect: 4.9.0
   pickleshare: 0.7.5
   pillow: 10.2.0
   pip: 23.0
   pkginfo: 1.9.6
   platformdirs: 4.1.0
   prompt-toolkit: 3.0.43
   psutil: 5.9.5
   ptyprocess: 0.7.0
   pure-eval: 0.2.2
   py-cpuinfo: 9.0.0
   pycollada: 0.7.2
   pydicom: 2.3.0
   Pygments: 2.16.1
   pynrrd: 1.0.0
   PyOpenGL: 3.1.7
   PyOpenGL-accelerate: 3.1.7
   pyopenxr: 1.0.2801
   pyparsing: 3.0.9
   pyproject-hooks: 1.0.0
   PyQt6-commercial: 6.3.1
   PyQt6-Qt6: 6.3.2
   PyQt6-sip: 13.4.0
   PyQt6-WebEngine-commercial: 6.3.1
   PyQt6-WebEngine-Qt6: 6.3.2
   python-dateutil: 2.8.2
   pytz: 2023.3.post1
   pyzmq: 25.1.2
   qtconsole: 5.4.3
   QtPy: 2.4.1
   RandomWords: 0.4.0
   requests: 2.31.0
   scipy: 1.11.1
   setuptools: 67.4.0
   setuptools-scm: 7.0.5
   sfftk-rw: 0.7.3
   six: 1.16.0
   snowballstemmer: 2.2.0
   sortedcontainers: 2.4.0
   soupsieve: 2.5
   sphinx: 6.1.3
   sphinx-autodoc-typehints: 1.22
   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: 0.5.0
   tables: 3.8.0
   tcia-utils: 1.5.1
   tifffile: 2023.7.18
   tinyarray: 1.2.4
   tomli: 2.0.1
   tornado: 6.4
   traitlets: 5.9.0
   typing-extensions: 4.9.0
   tzdata: 2023.4
   urllib3: 2.1.0
   wcwidth: 0.2.13
   webcolors: 1.12
   wheel: 0.38.4
   wheel-filename: 1.4.1
   widgetsnbextension: 4.0.9

}}}
"	defect	closed	normal		Window Toolkit		can't reproduce						all	ChimeraX