id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
15065	Crash as menu teardown makes previous window key	chimerax-bug-report@…	Eric Pettersen	"{{{
The following bug report has been submitted:
Platform:        macOS-14.2.1-arm64-arm-64bit
ChimeraX Version: 1.7 (2023-12-19 08:36:03 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  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  
UCSF ChimeraX version: 1.7 (2023-12-19)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open ""/Users/mbell/Desktop/Papers/1. My Papers/2 Bell et al.,/Figures/Figure
> 1/FlaB_FliC_Monocolor.cxs"" format session

opened ChimeraX session  

> open ""/Users/mbell/Desktop/Projects/4. Full-length TLR5 &
> bound/AF_Models_TLR5/prediction_pSC254_FLhTLR5_bb20c/rank_1_model_5_ptm_seed_0_unrelaxed.pdb""

Chain information for rank_1_model_5_ptm_seed_0_unrelaxed.pdb #3  
---  
Chain | Description  
A | No description available  
  

> open 3v47 fromDatabase pdb format mmcif

3v47 title:  
Crystal structure of the N-terminal fragment of zebrafish TLR5 in complex with
Salmonella flagellin [more info...]  
  
Chain information for 3v47 #4  
---  
Chain | Description | UniProt  
A B | Toll-like receptor 5b and variable lymphocyte receptor B.61 chimeric
protein | B3DIN1_DANRE 22-390, Q4G1L2_EPTBU 391-465  
C D | Flagellin | FLIC_SALDU 47-465  
  
Non-standard residues in 3v47 #4  
---  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose  
  

> mmaker #2 to #4/C

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 3v47, chain C (#4) with FliCtest_d0959_unrelaxed_model_1.pdb, chain
A (#2), sequence alignment score = 756.2  
RMSD between 127 pruned atom pairs is 0.749 angstroms; (across all 258 pairs:
34.714)  
  

> mmaker #3 to #4/A

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 3v47, chain A (#4) with rank_1_model_5_ptm_seed_0_unrelaxed.pdb,
chain A (#3), sequence alignment score = 852  
RMSD between 351 pruned atom pairs is 0.948 angstroms; (across all 435 pairs:
5.992)  
  

> delete #4/B,D-Z

> select clear

> hide #!4 models

> select clear

> ui tool show ""Show Sequence Viewer""

> sequence chain #3/A

Alignment identifier is 3/A  

> select #3/A:1

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #3/A:1-18

146 atoms, 148 bonds, 18 residues, 1 model selected  

> select #3/A:1-18,31-34

171 atoms, 173 bonds, 22 residues, 1 model selected  

> select #3/A:1

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #3/A:1-40

302 atoms, 308 bonds, 40 residues, 1 model selected  

> select #3/A:1

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #3/A:1-42

314 atoms, 320 bonds, 42 residues, 1 model selected  

> hide sel atoms

> hide sel cartoons

Drag select of 5 residues  
Drag select of 78 residues  

> select clear

> combine #2,3 to #5 name FliC-Combined

Expected a keyword  

> combine #2,3 #5 name FliC-Combined

Remapping chain ID 'A' in rank_1_model_5_ptm_seed_0_unrelaxed.pdb #3 to 'B'  

> hide #5 models

> show #5 models

> select add #5

10746 atoms, 10940 bonds, 1380 residues, 1 model selected  

> ui mousemode right ""translate selected models""

> view matrix models
> #5,0.31386,0.94669,-0.072656,-82.655,-0.65458,0.16031,-0.7388,-55.545,-0.68776,0.27944,0.67,-58.696

> view matrix models
> #5,0.31386,0.94669,-0.072656,-121.59,-0.65458,0.16031,-0.7388,-101.42,-0.68776,0.27944,0.67,-138.84

> select clear

Drag select of 15 residues  
Drag select of 77 residues  

> ui mousemode right ""translate selected atoms""

> ui mousemode right pivot

> ui mousemode right ""translate selected atoms""

Drag select of 76 residues  
Drag select of 78 residues  
Drag select of 3 residues  

> undo

> mlp sel

Map values for surface ""FliC-Combined_A SES surface"": minimum -31.28, mean
-7.142, maximum 23.44  
To also show corresponding color key, enter the above mlp command and add key
true  

> hide sel surfaces

> select clear

Drag select of 44 residues  
Drag select of 128 residues  
Drag select of 147 residues  

> mlp sel

Map values for surface ""FliC-Combined_A SES surface"": minimum -34.34, mean
-7.203, maximum 21.47  
Map values for surface ""FliC-Combined_B SES surface"": minimum -29.93, mean
-3.844, maximum 25.63  
To also show corresponding color key, enter the above mlp command and add key
true  
Drag select of FliC-Combined_A SES surface, 22338 of 452520 triangles, FliC-
Combined_B SES surface, 26436 of 847080 triangles, 120 residues  

> mlp sel

Map values for surface ""FliC-Combined_A SES surface"": minimum -34.34, mean
-7.203, maximum 21.47  
Map values for surface ""FliC-Combined_B SES surface"": minimum -29.93, mean
-3.844, maximum 25.63  
To also show corresponding color key, enter the above mlp command and add key
true  

> hide sel surfaces

> select clear

Drag select of 80 residues  

> select #5/A:455

9 atoms, 8 bonds, 1 residue, 1 model selected  
Drag select of 80 residues  

> select subtract #5/B:622

589 atoms, 79 residues, 3 models selected  

> coulombic sel

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for FliC-Combined_A SES surface #5.1: minimum, -20.77, mean
-2.60, maximum 14.30  
To also show corresponding color key, enter the above coulombic command and
add key true  

> mlp sel

Map values for surface ""FliC-Combined_A SES surface"": minimum -33.32, mean
-7.217, maximum 21.68  
To also show corresponding color key, enter the above mlp command and add key
true  

> hide sel surfaces

> select clear

> undo

No undo action is available  

> select clear

> select #5/A:39

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select add #5/A:40

14 atoms, 12 bonds, 2 residues, 2 models selected  

> select add #5/A:38

22 atoms, 19 bonds, 3 residues, 2 models selected  

> select #5/A:40

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select #5/A:39

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #5/A:37

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select subtract #5/A:37

1 model selected  

> select #5/A:36

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #5/A:37

11 atoms, 10 bonds, 1 residue, 1 model selected  
Drag select of 145 residues  

> select clear

> select #2/A:495

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #2/A:459-495

279 atoms, 280 bonds, 37 residues, 1 model selected  

> select #2/A:461-462

16 atoms, 15 bonds, 2 residues, 1 model selected  

> select #2/A:461-468

62 atoms, 61 bonds, 8 residues, 1 model selected  

> select
> #2/A:9-34,45-100,106-129,200-206,260-262,290-298,383-386,408-455,459-494

1571 atoms, 1568 bonds, 213 residues, 1 model selected  


===== 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: 1.7 (2023-12-19)  
© 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 M3 Max
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 Pro
      Model Identifier: Mac15,11
      Model Number: Z1AH000BGD/A
      Chip: Apple M3 Max
      Total Number of Cores: 14 (10 performance and 4 efficiency)
      Memory: 36 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: 67 days, 21 hours, 9 minutes

Graphics/Displays:

    Apple M3 Max:

      Chipset Model: Apple M3 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 30
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3456 x 2234 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        DELL U2415:
          Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array)
          UI Looks like: 1920 x 1200 @ 60.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported


Installed Packages:
    alabaster: 0.7.13
    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: 2.12.1
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1.3
    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-Clipper: 0.22.4
    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
    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-ISOLDE: 1.7.1
    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
    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: 1.5.13
    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-PDBImages: 1.2
    ChimeraX-PDBLibrary: 1.0.3
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-QScore: 1.1
    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: 1.12.3
    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: 2.2.2
    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: 1.33.2
    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: 0.2.0
    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: 4.47.0
    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: 5.5.1
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.3
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    MolecularDynamicsViewer: 1.4
    msgpack: 1.0.4
    nest-asyncio: 1.5.8
    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: 10.0.1
    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: 1.0.7
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.5
    sphinxcontrib-htmlhelp: 2.0.4
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.6
    sphinxcontrib-serializinghtml: 1.1.9
    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: 2023.3
    urllib3: 2.1.0
    wcwidth: 0.2.12
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9

}}}
"	defect	closed	normal		Platform		can't reproduce		Tom Goddard				all	ChimeraX