id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
9480	Probable crash in garbage collection	chimerax-bug-report@…	Tom Goddard	"{{{
The following bug report has been submitted:
Platform:        Linux-5.15.0-76-generic-x86_64-with-glibc2.31
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 0x00007f2d9295c740 (most recent call first):
  File ""/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/numpy/core/_internal.py"", line 283 in data_as
  File ""/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/atomic/molc.py"", line 322 in pointer
  File ""/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/atomic/molc.py"", line 197 in get_prop
  File ""/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/atomic/structure.py"", line 1805 in _update_graphics_if_needed
  File ""/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/triggerset.py"", line 138 in invoke
  File ""/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/triggerset.py"", line 237 in _activate
  File ""/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/triggerset.py"", line 206 in activate
  File ""/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/triggerset.py"", line 382 in activate_trigger
  File ""/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/graphics/view.py"", line 283 in check_for_drawing_change
  File ""/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/updateloop.py"", line 65 in draw_new_frame
  File ""/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/updateloop.py"", line 139 in _redraw_timer_callback
  File ""/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/open_command/dialog.py"", line 135 in show_open_file_dialog
  File ""/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/open_command/dialog.py"", line 107 in 
  File ""/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py"", line 275 in event_loop
  File ""/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/__main__.py"", line 892 in init
  File ""/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/__main__.py"", line 1043 in 
  File ""/usr/lib/ucsf-chimerax/lib/python3.9/runpy.py"", line 87 in _run_code
  File ""/usr/lib/ucsf-chimerax/lib/python3.9/runpy.py"", line 197 in _run_module_as_main
===== Log before crash start =====
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 /home/cclab04/Downloads/5a43.pdb format pdb

5a43.pdb title:  
Crystal structure of A dual topology fluoride ion channel. [more info...]  
  
Chain information for 5a43.pdb #1  
---  
Chain | Description | UniProt  
A B | fluoride channel | B7LI20_ECO45 1-126  
C D | monobodies |  
  
Non-standard residues in 5a43.pdb #1  
---  
DMU — decyl-β-D-maltopyranoside (decylmaltoside)  
F — fluoride ion  
NA — sodium ion  
  

> ui tool show ""Show Sequence Viewer""

> sequence chain /A /B

Alignment identifier is 1  

> select /A-B:2-30,34-58,62-70,72-78,80-93,95-125

1770 atoms, 1804 bonds, 230 residues, 1 model selected  

> ui tool show ""Modeller Comparative""

> select /A/B

1983 atoms, 2028 bonds, 4 pseudobonds, 259 residues, 2 models selected  

> save /home/cclab04/research/myresearch/PDB/channel_00.pdb relModel #1

> close

> open /home/cclab04/research/myresearch/PDB/channel_00.pdb

channel_00.pdb title:  
Crystal structure of A dual topology fluoride ion channel. [more info...]  
  
Chain information for channel_00.pdb #1  
---  
Chain | Description | UniProt  
A B | fluoride channel | B7LI20_ECO45 1-126  
C D | monobodies |  
  
Non-standard residues in channel_00.pdb #1  
---  
DMU — decyl-β-D-maltopyranoside (decylmaltoside)  
F — fluoride ion  
NA — sodium ion  
  

> close

> open /home/cclab04/Downloads/5a43.pdb format pdb

5a43.pdb title:  
Crystal structure of A dual topology fluoride ion channel. [more info...]  
  
Chain information for 5a43.pdb #1  
---  
Chain | Description | UniProt  
A B | fluoride channel | B7LI20_ECO45 1-126  
C D | monobodies |  
  
Non-standard residues in 5a43.pdb #1  
---  
DMU — decyl-β-D-maltopyranoside (decylmaltoside)  
F — fluoride ion  
NA — sodium ion  
  

> select /A/B

1983 atoms, 2028 bonds, 4 pseudobonds, 259 residues, 2 models selected  

> save /home/cclab04/research/myresearch/PDB/channel_00.pdb selectedOnly true
> relModel #1

> open /home/cclab04/research/myresearch/PDB/channel_00.pdb

Summary of feedback from opening
/home/cclab04/research/myresearch/PDB/channel_00.pdb  
---  
warnings | Start residue of secondary structure not found: SHEET 1 1 1 THR C 7
THR C 15 0  
Start residue of secondary structure not found: SHEET 2 2 1 SER C 18 ASP C 24
0  
Start residue of secondary structure not found: SHEET 3 3 1 THR C 29 GLU C 39
0  
Start residue of secondary structure not found: SHEET 4 4 1 GLN C 47 PRO C 52
0  
Start residue of secondary structure not found: SHEET 5 5 1 THR C 57 SER C 61
0  
11 messages similar to the above omitted  
  
channel_00.pdb title:  
Crystal structure of A dual topology fluoride ion channel. [more info...]  
  
Chain information for channel_00.pdb #2  
---  
Chain | Description | UniProt  
A B | fluoride channel | B7LI20_ECO45 1-126  
  
Non-standard residues in channel_00.pdb #2  
---  
DMU — decyl-β-D-maltopyranoside (decylmaltoside)  
F — fluoride ion  
NA — sodium ion  
  

> close


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

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: 4.6 (Core Profile) Mesa 22.2.0-devel (git-08da37035f)
OpenGL renderer: Mesa Intel(R) UHD Graphics 630 (CFL GT2)
OpenGL vendor: Intel

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=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:0
Manufacturer: HP
Model: HP ProDesk 600 G4 PCI MT IDS APJ
OS: Ubuntu 20.04 Focal Fossa
Architecture: 64bit ELF
Virtual Machine: none
CPU: 12 Intel(R) Core(TM) i7-8700 CPU @ 3.20GHz
Cache Size: 12288 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:          7.5Gi       3.4Gi       470Mi       564Mi       3.6Gi       3.3Gi
	Swap:           9Gi       316Mi       9.7Gi

Graphics:
	00:02.0 VGA compatible controller [0300]: Intel Corporation UHD Graphics 630 (Desktop) [8086:3e92]	
	DeviceName: Onboard IGD	
	Subsystem: Hewlett-Packard Company UHD Graphics 630 (Desktop) [103c:83ed]

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-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-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

}}}
"	defect	closed	normal		Graphics		can't reproduce		Eric Pettersen				all	ChimeraX