Unknown problem

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.22621
ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
UCSF ChimeraX version: 1.10.1 (2025-07-24)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open
> E:\xwechat_files\wxid_a4mi7llka1ea12_6660\msg\file\2025-10\1F7A-substrate-
> analysis.cxs format session

Log from Mon Oct 16 22:16:33 2023UCSF ChimeraX version: 1.5.dev202208240008
(2022-08-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> open /Users/xiangyuliu/Documents/Teaching/2023/2023-teaching-
> preparation/第四课/structures/1F7A-substrate-analysis.cxs

Log from Fri Oct 13 16:59:05 2023UCSF ChimeraX version: 1.5.dev202208240008
(2022-08-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/xiangyuliu/Documents/Projects/Xiuqing-FP-
> receptor/manuscript/structure-models/FP_miniGqiN-coot-9.pdb

Chain information for FP_miniGqiN-coot-9.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
G | No description available  
N | No description available  
R | No description available  
  

> open /Users/xiangyuliu/Documents/Teaching/2023/2023-teaching-
> preparation/第四课/structures/1f7a-2000-substrate.pdb

1f7a-2000-substrate.pdb title:  
How does A symmetric dimer recognize an asymmetric substrate? A substrate
complex of hiv-1 protease. [more info...]  
  
Chain information for 1f7a-2000-substrate.pdb #2  
---  
Chain | Description | UniProt  
A B | pol polyprotein | POL_HV1A2  
P | Ca-P2 substrate |   
  
Non-standard residues in 1f7a-2000-substrate.pdb #2  
---  
ACT — acetate ion  
  

> hide #!1 models

> open /Users/xiangyuliu/Documents/Teaching/2023/2023-teaching-
> preparation/第四课/structures/1f7a-2000-substrate.pdb

1f7a-2000-substrate.pdb title:  
How does A symmetric dimer recognize an asymmetric substrate? A substrate
complex of hiv-1 protease. [more info...]  
  
Chain information for 1f7a-2000-substrate.pdb #3  
---  
Chain | Description | UniProt  
A B | pol polyprotein | POL_HV1A2  
P | Ca-P2 substrate |   
  
Non-standard residues in 1f7a-2000-substrate.pdb #3  
---  
ACT — acetate ion  
  

> close #3

> view #2

> color #2 & C bychain

> select #2/P

68 atoms, 62 bonds, 14 residues, 1 model selected  

> select add sel :<4

285 atoms, 260 bonds, 50 residues, 1 model selected  

> show sel

> select off

Expected an objects specifier or a keyword  

> select clear

> select #2/P

68 atoms, 62 bonds, 14 residues, 1 model selected  

> select add sel :<4

285 atoms, 260 bonds, 50 residues, 1 model selected  

> hide sel cartoons

> set bgColor white

> select off

Expected an objects specifier or a keyword  

> select clear

> select #2/P

68 atoms, 62 bonds, 14 residues, 1 model selected  

> select add sel :<4

285 atoms, 260 bonds, 50 residues, 1 model selected  

> show sel cartoons

> style sel stick

Changed 285 atom styles  

> style sel ball

Changed 285 atom styles  

> hide sel cartoons

> select clear

> save /Users/xiangyuliu/Documents/Teaching/2023/2023-teaching-
> preparation/第四课/structures/1F7A-substrate-analysis.cxs

> select #2/P:5

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

> select #2/P:5-10

35 atoms, 34 bonds, 5 residues, 1 model selected  

> select #2/P:1-5

36 atoms, 35 bonds, 5 residues, 1 model selected  

> color sel & C orange

> select clear

> select #2/B:25

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

> color sel & C forestgreen

> save /Users/xiangyuliu/Documents/Teaching/2023/2023-teaching-
> preparation/第四课/structures/1F7A-substrate-analysis.cxs

> ui tool show "Side View"

> lighting soft

> view name view1

> save /Users/xiangyuliu/Documents/Teaching/2023/2023-teaching-
> preparation/第四课/structures/1F7A-substrate-analysis.cxs

——— End of log from Fri Oct 13 16:59:05 2023 ———

opened ChimeraX session  

> select #2/A:25

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

> color sel & C forestgreen

> select #2/A,B:26

14 atoms, 12 bonds, 2 residues, 1 model selected  

> hide sel cartoons

> show sel

> style sel ball

Changed 14 atom styles  

> select clear

> view list

Named views: view1  

> view view1

> ui tool show "Side View"

> view name view2

> view list

Named views: view1, view2  

> view view2

> save /Users/xiangyuliu/Documents/Teaching/2023/2023-teaching-
> preparation/第四课/structures/1F7A-substrate-analysis.cxs

> open /Users/xiangyuliu/Documents/Teaching/2023/2023-teaching-
> preparation/第四课/structures/1f7a-2000-substrate.pdb

1f7a-2000-substrate.pdb title:  
How does A symmetric dimer recognize an asymmetric substrate? A substrate
complex of hiv-1 protease. [more info...]  
  
Chain information for 1f7a-2000-substrate.pdb #3  
---  
Chain | Description | UniProt  
A B | pol polyprotein | POL_HV1A2  
P | Ca-P2 substrate |   
  
Non-standard residues in 1f7a-2000-substrate.pdb #3  
---  
ACT — acetate ion  
  

> hide #2 models

> color #3 & C bychain

> hide #3/A,B

> select #3/A,B:25

16 atoms, 14 bonds, 2 residues, 1 model selected  

> show sel

> style sel ball

Changed 16 atom styles  

> save /Users/xiangyuliu/Documents/Teaching/2023/2023-teaching-
> preparation/第四课/structures/1F7A-substrate-analysis.cxs

> select off

Expected an objects specifier or a keyword  

> select clear

> cd /Users/xiangyuliu/Documents/Teaching/2023/2023-teaching-
> preparation/第四课/Figures

Current working directory is:
/Users/xiangyuliu/Documents/Teaching/2023/2023-teaching-
preparation/第四课/Figures  

> save 2.png width 1200 transparentBackground true

> save /Users/xiangyuliu/Documents/Teaching/2023/2023-teaching-
> preparation/第四课/structures/1F7A-substrate-analysis.cxs

——— End of log from Mon Oct 16 22:16:33 2023 ———

> view name session-start

opened ChimeraX session  

> select add #3

1663 atoms, 1588 bonds, 309 residues, 1 model selected  

> select add #2

3326 atoms, 3176 bonds, 618 residues, 2 models selected  

> select add #1

10666 atoms, 10665 bonds, 4 pseudobonds, 1603 residues, 4 models selected  

> close #1

> close

> set bgColor black

> open "E:/Desktop/str 10.27/1atp-Mn-ATP.pdb"

1atp-Mn-ATP.pdb title:  
2.2 angstrom refined crystal structure of the catalytic subunit of camp-
dependent protein kinase complexed with mnatp and A peptide inhibitor [more
info...]  
  
Chain information for 1atp-Mn-ATP.pdb #1  
---  
Chain | Description | UniProt  
E | camp-dependent protein kinase | KAPCA_MOUSE 1-350  
I | peptide inhibitor pki(5-24) | IPKA_MOUSE 5-24  
  
Non-standard residues in 1atp-Mn-ATP.pdb #1  
---  
ATP — adenosine-5&#x27;-triphosphate  
MN — manganese (II) ion  
  

> set bgColor black

> hide #!1 models

> show #!1 models

> select add #1

3070 atoms, 3040 bonds, 11 pseudobonds, 462 residues, 2 models selected  

> show sel atoms

> show sel cartoons

> show sel surfaces




OpenGL version: 3.3.0 NVIDIA 581.29
OpenGL renderer: NVIDIA GeForce RTX 4070 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: zh_CN.cp936
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: windows

Manufacturer: ASUS
Model: System Product Name
OS: Microsoft Windows 11 专业版 (Build 22621)
Memory: 34,164,097,024
MaxProcessMemory: 137,438,953,344
CPU: 20 13th Gen Intel(R) Core(TM) i5-13600KF
OSLanguage: zh-CN

Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    asttokens: 3.0.0
    babel: 2.17.0
    beautifulsoup4: 4.13.3
    blockdiag: 3.0.0
    blosc2: 3.6.1
    build: 1.2.2.post1
    certifi: 2025.7.14
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.2
    ChimeraX-AddCharge: 1.5.19
    ChimeraX-AddH: 2.2.7
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.20.2
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Aniso: 1.1.4
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60.7
    ChimeraX-AtomicLibrary: 14.1.19
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.3
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-Boltz: 1.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.5.1
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.10.1
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.5
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.4
    ChimeraX-Dicom: 1.2.7
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.4
    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: 1.4.1
    ChimeraX-Hbonds: 2.5.1
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.6.2
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    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: 2.2.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.10.1
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.19
    ChimeraX-ModelPanel: 1.5.1
    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-MutationScores: 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: 1.14.1
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.10
    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: 1.1.3
    ChimeraX-ProfileGrids: 1.1.3
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.3
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    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: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.7
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17.1
    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.19.1
    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: 2.5.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.45.2
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    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: 1.1.5
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    comtypes: 1.4.10
    contourpy: 1.3.2
    coverage: 7.10.0
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.12
    debugpy: 1.8.15
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.0
    filelock: 3.18.0
    fonttools: 4.59.0
    funcparserlib: 2.0.0a0
    glfw: 2.9.0
    grako: 3.16.5
    h5py: 3.14.0
    html2text: 2024.2.26
    idna: 3.10
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.1.0
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.7
    jedi: 0.19.1
    Jinja2: 3.1.6
    jupyter_client: 8.6.3
    jupyter_core: 5.8.1
    jupyterlab_widgets: 3.0.15
    kiwisolver: 1.4.8
    line_profiler: 4.2.0
    lxml: 5.3.1
    lz4: 4.3.2
    MarkupSafe: 3.0.2
    matplotlib: 3.10.1
    matplotlib-inline: 0.1.7
    msgpack: 1.1.0
    ndindex: 1.10.0
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.11.0
    numpy: 1.26.4
    nvidia-nvjitlink-cu12: 12.9.86
    OpenMM: 8.2.0
    OpenMM-CUDA-12: 8.2.0
    openvr: 1.26.701
    packaging: 24.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pickleshare: 0.7.5
    pillow: 10.4.0
    pip: 25.0.1
    pkginfo: 1.11.1
    platformdirs: 4.3.8
    pluggy: 1.6.0
    prompt_toolkit: 3.0.51
    psutil: 7.0.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    Pygments: 2.18.0
    pynmrstar: 3.3.5
    pynrrd: 1.0.0
    PyOpenGL: 3.1.9
    PyOpenGL-accelerate: 3.1.9
    pyopenxr: 1.1.4501
    pyparsing: 3.2.3
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.8.1
    PyQt6-Qt6: 6.8.2
    PyQt6-WebEngine-commercial: 6.8.0
    PyQt6-WebEngine-Qt6: 6.8.2
    PyQt6_sip: 13.10.0
    pytest: 8.4.1
    pytest-cov: 6.2.1
    python-dateutil: 2.9.0.post0
    pytz: 2025.2
    pywin32: 310
    pyzmq: 27.0.0
    qtconsole: 5.5.2
    QtPy: 2.4.3
    qtshim: 1.1
    RandomWords: 0.4.0
    requests: 2.32.3
    roman-numerals-py: 3.1.0
    scipy: 1.14.0
    setuptools: 78.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 3.0.1
    sortedcontainers: 2.4.0
    soupsieve: 2.7
    Sphinx: 8.2.3
    sphinx-autodoc-typehints: 3.1.0
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.7.1
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.4
    tornado: 6.5.1
    traitlets: 5.14.3
    typing_extensions: 4.14.1
    tzdata: 2025.2
    urllib3: 2.5.0
    wcwidth: 0.2.13
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.14
    WMI: 1.5.1