id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
14499	Crash opening PDB file	chimerax-bug-report@…	Eric Pettersen	"{{{
The following bug report has been submitted:
Platform:        macOS-14.2.1-arm64-arm-64bit
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: Segmentation fault

Current thread 0x00000001e3e1d000 (most recent call first):
 File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/pdb/pdb.py"", line 78 in open_pdb
 File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/pdb/__init__.py"", line 34 in open
 File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/open_command/cmd.py"", line 435 in remember_data_format
 File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/open_command/cmd.py"", line 464 in collated_open
 File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/open_command/cmd.py"", line 194 in provider_open
 File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/commands/cli.py"", line 2897 in run
 File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/open_command/cmd.py"", line 119 in cmd_open
 File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/commands/cli.py"", line 2897 in run
 File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/commands/run.py"", line 38 in run
 File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py"", line 1918 in _open_dropped_file
 File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py"", line 240 in event
 File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py"", line 275 in event_loop
 File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py"", line 892 in init
 File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py"", line 1043 in 
 File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py"", line 87 in _run_code
 File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py"", line 197 in _run_module_as_main


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Log:
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  




OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M2
OpenGL vendor: Apple

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:

   Hardware Overview:

     Model Name: MacBook Air
     Model Identifier: Mac14,2
     Model Number: Z15S001DBCH/A
     Chip: Apple M2
     Total Number of Cores: 8 (4 performance and 4 efficiency)
     Memory: 16 GB
     System Firmware Version: 10151.61.4
     OS Loader Version: 10151.61.4

Software:

   System Software Overview:

     System Version: macOS 14.2.1 (23C71)
     Kernel Version: Darwin 23.2.0
     Time since boot: 9\u592921\u5c0f\u65f618\u5206\u949f

Graphics/Displays:

   Apple M2:

     Chipset Model: Apple M2
     Type: GPU
     Bus: Built-In
     Total Number of Cores: 8
     Vendor: Apple (0x106b)
     Metal Support: Metal 3
     Displays:
       Color LCD:
         Display Type: Built-in Liquid Retina Display
         Resolution: 2560 x 1664 Retina
         Main Display: Yes
         Mirror: Off
         Online: Yes
         Automatically Adjust Brightness: Yes
         Connection Type: Internal


Installed Packages:
   alabaster: 0.7.13
   appdirs: 1.4.4
   appnope: 0.1.3
   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: 2021.10.8
   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-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-ItemsInspection: 1.0.1
   ChimeraX-Label: 1.1.7
   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
   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: 2022.2.22
   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: 21.3
   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
   setuptools-scm: 7.0.5
   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


}}}
"	defect	closed	normal		Input/Output		can't reproduce						all	ChimeraX