id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
16900	Crash getting secondary structure ID	chimerax-bug-report@…	Eric Pettersen	"{{{
The following bug report has been submitted:
Platform:        macOS-15.2-arm64-arm-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
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}
===== Log before crash start =====
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/geqijun/Documents/Projects/model_building/Foldseek/P14_J90_006/P14—J90—coot-0.pdb

Chain information for P14—J90—coot-0.pdb #1  
---  
Chain | Description  
0 | No description available  
1 | No description available  
2 e | No description available  
3 | No description available  
4 | No description available  
5 9 c o q w | No description available  
6 | No description available  
7 | No description available  
8 X Y z | No description available  
A | No description available  
B F x | No description available  
C | No description available  
D | No description available  
E V y | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L Q | No description available  
M | No description available  
N | No description available  
O | No description available  
P | No description available  
R | No description available  
S n | No description available  
T | No description available  
U | No description available  
W s | No description available  
Z | No description available  
a | No description available  
b | No description available  
d | No description available  
f | No description available  
g | No description available  
h | No description available  
i | No description available  
j v | No description available  
k | No description available  
l | No description available  
m | No description available  
p | No description available  
r | No description available  
t | No description available  
u | No description available  
  

> select clear

Drag select of 732 atoms, 2 pseudobonds, 333 bonds  

> delete sel

Drag select of 2295 atoms, 10 pseudobonds, 1364 bonds  

> delete sel

Drag select of 1228 atoms, 9 pseudobonds, 722 bonds  

> delete sel

Drag select of 322 atoms, 4 pseudobonds, 127 bonds  

> delete sel

Drag select of 2 atoms, 1 bonds  

> delete sel

Drag select of 1291 atoms, 13 pseudobonds, 520 bonds  

> delete sel

Drag select of 1924 atoms, 15 pseudobonds, 1218 bonds  

> delete sel

Drag select of 125 atoms, 2 pseudobonds, 62 bonds  

> delete sel

Drag select of 656 atoms, 16 pseudobonds, 429 bonds  

> delete sel

Drag select of 610 atoms, 7 pseudobonds, 383 bonds  

> delete sel

Drag select of 406 atoms, 3 pseudobonds, 280 bonds  

> delete sel

Drag select of 18 atoms, 9 bonds  

> delete sel

Drag select of 55 atoms, 1 pseudobonds, 27 bonds  

> delete sel

Drag select of 10 atoms, 5 bonds  

> delete sel

Drag select of 11 atoms, 5 bonds  

> delete sel

Drag select of 7 atoms  

> delete sel

Drag select of 4 atoms, 1 pseudobonds  

> delete sel

Drag select of 34 atoms, 19 bonds  

> delete sel

Drag select of 3 atoms  

> delete sel

Drag select of 2 atoms  

> delete sel

Drag select of 1 atoms  

> delete sel

Drag select of 1 atoms  

> delete sel

> select /A:3@ND2

1 atom, 1 residue, 1 model selected  

> delete sel

> select /A:3@CA

1 atom, 1 residue, 1 model selected  

> delete sel

> select /A:3@CG

1 atom, 1 residue, 1 model selected  

> delete sel

> select /A:3@CB

1 atom, 1 residue, 1 model selected  

> delete sel

> select /A:3@OD1

1 atom, 1 residue, 1 model selected  

> delete sel

> select /A:3@C

1 atom, 1 residue, 1 model selected  

> delete sel

> select /A:3@O

1 atom, 1 residue, 1 model selected  

> delete sel

Drag select of 4 atoms, 3 bonds  

> delete sel

Drag select of 4 atoms, 3 bonds  

> delete sel

Drag select of 1 atoms  

> delete sel

Drag select of 1 atoms  

> delete sel

Drag select of 3 atoms, 2 bonds  

> delete sel

Drag select of 2 atoms  

> delete sel

Drag select of 1 atoms  

> delete sel

Drag select of 1 atoms  

> delete sel

Drag select of 3 atoms  

> delete sel

Drag select of 2 atoms  

> delete sel

Drag select of 11 atoms, 9 bonds  

> delete sel

Drag select of 5 atoms, 4 bonds  

> delete sel

Drag select of 2 atoms, 1 bonds  

> delete sel

> select clear

Drag select of 17 atoms, 14 bonds  

> delete sel

Drag select of 5 atoms, 4 bonds  

> delete sel

Drag select of 17 atoms, 10 bonds  

> delete sel

Drag select of 19 atoms, 11 bonds  

> delete sel

Drag select of 1 atoms  

> delete sel

Drag select of 14 atoms, 14 bonds  

> delete sel

Drag select of 5 atoms, 5 bonds  

> delete sel

> select @@serial_number=9574

1 atom, 1 residue, 1 model selected  

> delete sel

Drag select of 13 atoms, 10 bonds  

> delete sel

Drag select of 2 atoms  

> delete sel

Drag select of 1 atoms  

> delete sel

Drag select of 4 atoms, 2 bonds  

> delete sel

Drag select of 5 atoms, 3 bonds  

> delete sel

Drag select of 5 atoms, 5 bonds  

> delete sel

Drag select of 5 atoms, 5 bonds  

> delete sel

Drag select of 8 atoms, 4 bonds  

> delete sel

Drag select of 3 atoms, 2 bonds  

> delete sel

Drag select of 5 atoms, 4 bonds  

> delete sel

Drag select of 2 atoms, 1 bonds  

> delete sel

Drag select of 1 atoms, 2 bonds  

> delete sel

Drag select of 4 atoms, 2 bonds  

> delete sel

Drag select of 5 atoms, 3 bonds  

> delete sel

Drag select of 5 atoms, 3 bonds  

> delete sel

> select /V:1@CA

1 atom, 1 residue, 1 model selected  

> delete sel

Drag select of 3 atoms, 1 bonds  

> delete sel

Drag select of 1 atoms  

> delete sel

Drag select of 2 atoms  

> delete sel

Drag select of 2 atoms, 1 bonds  

> delete sel

Drag select of 1 atoms  

> delete sel

Drag select of 2 atoms, 1 bonds  

> delete sel

> select /g:1@O3'

1 atom, 1 residue, 1 model selected  

> delete sel

Drag select of 20 atoms, 18 bonds  

> delete sel

Drag select of 23 atoms, 23 bonds  

> delete sel

Drag select of 3 atoms, 1 bonds  

> delete sel

Drag select of 4 atoms, 5 bonds  

> delete sel

Drag select of 1 atoms  

> delete sel

Drag select of 2 atoms  

> delete sel

Drag select of 1 atoms  

> delete sel

Drag select of 9 atoms, 8 bonds  

> delete sel

> save
> /Users/geqijun/Documents/Projects/model_building/Foldseek/P14_J90_006/P14_J90_1.pdb
> relModel #1


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

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/geqijun/Documents/Projects/model_building/Foldseek/P14_J90_006/P14_J90_1.pdb

Chain information for P14_J90_1.pdb #1  
---  
Chain | Description  
GG | No description available  
Ii | No description available  
  




OpenGL version: 4.1 Metal - 89.3
OpenGL renderer: Apple M3
OpenGL vendor: Apple

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: iMac
      Model Identifier: Mac15,5
      Model Number: Z19K0006YCH/A
      Chip: Apple M3
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 24 GB
      System Firmware Version: 11881.61.3
      OS Loader Version: 11881.61.3

Software:

    System Software Overview:

      System Version: macOS 15.2 (24C101)
      Kernel Version: Darwin 24.2.0
      Time since boot: 14天1小时21分钟

Graphics/Displays:

    Apple M3:

      Chipset Model: Apple M3
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 10
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        iMac:
          Display Type: Built-In Retina LCD
          Resolution: Retina 4.5K (4480 x 2520)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        Studio Display:
          Display Type: Retina LCD
          Resolution: 5120 x 2880 Retina
          Display Serial Number: GWPL2G1C92
          Display Firmware Version: Version 16.4 (Build 20E246)
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes


Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 2.4.1
    Babel: 2.15.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.7
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.57.1
    ChimeraX-AtomicLibrary: 14.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.6
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.7
    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: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.8
    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: 1.2.4
    ChimeraX-DiffPlot: 1.0
    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: 1.1.10
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.2
    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: 2.7.1
    ChimeraX-MedicalToolbar: 1.0.3
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.17
    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: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.5
    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: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.4.1
    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-Segmentations: 3.0.15
    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: 1.16.5
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    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: 1.39.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.3
    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: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.2.1
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.1
    decorator: 5.1.1
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.4
    fonttools: 4.53.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.11.0
    html2text: 2024.2.26
    idna: 3.7
    ihm: 1.0
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.3
    jedi: 0.19.1
    jinja2: 3.1.4
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.11
    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    lxml: 5.2.1
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.4
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.0
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.3.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.2
    prompt-toolkit: 3.0.47
    psutil: 5.9.8
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pygments: 2.17.2
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.1.2
    pyproject-hooks: 1.1.0
    PyQt6-commercial: 6.6.1
    PyQt6-Qt6: 6.6.3
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.3
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pyzmq: 26.0.3
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.13.0
    setuptools: 69.5.1
    setuptools-scm: 8.0.4
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 7.2.6
    sphinx-autodoc-typehints: 2.0.1
    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: 0.6.3
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    tornado: 6.4.1
    traitlets: 5.14.2
    typing-extensions: 4.12.2
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.11
}}}
"	defect	closed	normal		Core		can't reproduce						all	ChimeraX