toolshed install: Non-existent wheel file

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-15.2-arm64-arm-64bit
ChimeraX Version: 1.9rc202411130312 (2024-11-13 03:12:11 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9rc202411130312 (2024-11-13)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 4x6u format mmcif fromDatabase pdb

4x6u title:  
Crystal Structure of lipase from Geobacillus stearothermophilus T6 [more
info...]  
  
Chain information for 4x6u #1  
---  
Chain | Description | UniProt  
A | Lipase | Q93A71_GEOSE 4-389  
  
Non-standard residues in 4x6u #1  
---  
CA — calcium ion  
ZN — zinc ion  
  

> select ~sel & ##selected

Nothing selected  

> select sidechain

1931 atoms, 1612 bonds, 392 residues, 1 model selected  

> cliper

Unknown command: cliper  

> ui tool show Updates

> toolshed show

> open
> /Users/nitsanyehishalom/Downloads/ChimeraX_Clipper-0.24.0-cp311-cp311-macosx_10_13_universal2.whl

Unrecognized file suffix '.whl'  

> select clear

[Repeated 1 time(s)]

> select /A:287

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select add /A:358

12 atoms, 10 bonds, 2 residues, 1 model selected  

> select add /A:361

21 atoms, 18 bonds, 3 residues, 1 model selected  

> select clear

> select add /A:358

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

> select add /A:287

12 atoms, 10 bonds, 2 residues, 1 model selected  

> select add /A:368

20 atoms, 17 bonds, 3 residues, 1 model selected  

> select up

118 atoms, 119 bonds, 15 residues, 1 model selected  

> select down

20 atoms, 17 bonds, 3 residues, 1 model selected  

> select up

118 atoms, 119 bonds, 15 residues, 1 model selected  

> show sel

> select clear

> select /A:288@SD

1 atom, 1 residue, 1 model selected  

> select up

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

> show sel surfaces

> hide sel surfaces

> Hbond sel

Unknown command: Hbond sel  

> H-bond sel

Unknown command: H-bond sel  

> ui tool show H-Bonds

> hbonds sel color #61f6ef dashes 6 saltOnly true select true reveal true
> retainCurrent true

0 hydrogen bonds found  

> select /A:288

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

> swapaa sel ASP

Using Dunbrack library  
/A MET 288: phi -55.8, psi 141.0 trans  
Applying ASP rotamer (chi angles: -173.1 84.4) to /A ASP 288  

> ui tool show Rotamers

Populating font family aliases took 148 ms. Replace uses of missing font
family "Times" with one that exists to avoid this cost.  

> swapaa interactive sel ASP rotLib Dunbrack

/A ASP 288: phi -55.8, psi 141.0 trans  
Changed 90 bond radii  

> hbonds #!1 & ~#!1/A:288 & ~solvent saltOnly true reveal true restrict #1.4 &
> ~@c,ca,n

0 hydrogen bonds found  

> hbonds #!1 & ~#!1/A:288 & ~solvent reveal true restrict #1.4 & ~@c,ca,n

0 hydrogen bonds found  

> clashes #!1 & ~#!1/A:288 & ~solvent radius 0.075 reveal true restrict #1.4 &
> ~@c,ca,n

30 clashes  

> hbonds #!1 & ~#!1/A:288 & ~solvent reveal true restrict #1.4 & ~@c,ca,n

0 hydrogen bonds found  

> coulombic sel

The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics:  
4x6u #!1/A HIS 395 OXT  

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for 4x6u_A SES surface #1.2: minimum, -21.20, mean -1.42,
maximum 8.67  
To also show corresponding color key, enter the above coulombic command and
add key true  

> hide surfaces

> swapaa sel SER

Using Dunbrack library  
/A ASP 288: phi -55.8, psi 141.0 trans  
Applying SER rotamer (chi angles: -63.9) to /A SER 288  

> ui tool show Rotamers

> swapaa interactive sel SER rotLib Dunbrack

/A SER 288: phi -55.8, psi 141.0 trans  
Changed 9 bond radii  

> clashes #!1 & ~#!1/A:288 & ~solvent radius 0.075 reveal true restrict #1.3 &
> ~@c,ca,n

No clashes  

> hbonds #!1 & ~#!1/A:288 & ~solvent reveal true restrict #1.3 & ~@c,ca,n

4 hydrogen bonds found  

> ui tool show Rotamers

> swapaa sel LYS

Using Dunbrack library  
4x6u #!1/A SER 288: phi -55.8, psi 141.0 trans  
Applying LYS rotamer (chi angles: -178.2 179.3 -70.6 77.4) to 4x6u #!1/A LYS
288  

> ui tool show Rotamers

> swapaa interactive sel LYS rotLib Dunbrack

/A LYS 288: phi -55.8, psi 141.0 trans  
Changed 438 bond radii  

> clashes #!1 & ~#!1/A:288 & ~solvent radius 0.075 reveal true restrict #1.3 &
> ~@c,ca,n

701 clashes  

> hbonds #!1 & ~#!1/A:288 & ~solvent reveal true restrict #1.3 & ~@c,ca,n

44 hydrogen bonds found  

> ui tool show "Volume Viewer"

> toolshed show

Downloading bundle
ChimeraX_Clipper-0.24.0-cp311-cp311-macosx_10_13_universal2.whl  

> help help:user

> toolshed show

[Repeated 1 time(s)]

> toolshed install Cliper

Cliper does not match any bundles  

> toolshed install
> ChimeraX_Clipper-0.24.0-cp311-cp311-macosx_10_13_universal2.whl

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.9-rc2024.11.13.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX-1.9-rc2024.11.13.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9-rc2024.11.13.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/toolshed.py", line 305, in toolshed_install  
ts.install_bundle(bundles, logger, **kw)  
File
"/Applications/ChimeraX-1.9-rc2024.11.13.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1028, in install_bundle  
_install_bundle(  
File
"/Applications/ChimeraX-1.9-rc2024.11.13.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/toolshed_utils/__init__.py", line 216, in _install_bundle  
raise ValueError("Non-existent wheel file")  
ValueError: Non-existent wheel file  
  
ValueError: Non-existent wheel file  
  
File
"/Applications/ChimeraX-1.9-rc2024.11.13.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/toolshed_utils/__init__.py", line 216, in _install_bundle  
raise ValueError("Non-existent wheel file")  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 89.3
OpenGL renderer: Apple M2 Pro
OpenGL vendor: Apple

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: Mac14,9
      Model Number: MPHE3HB/A
      Chip: Apple M2 Pro
      Total Number of Cores: 10 (6 performance and 4 efficiency)
      Memory: 16 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: 1 day, 3 hours, 36 minutes

Graphics/Displays:

    Apple M2 Pro:

      Chipset Model: Apple M2 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 16
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        DELL P2419H:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3024 x 1964 Retina
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 2.4.1
    auditwheel: 6.1.0
    babel: 2.16.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.7.1
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    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: 2.16.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58.7
    ChimeraX-AtomicLibrary: 14.1.11
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.7
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    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: 2.3
    ChimeraX-clix: 0.1.9
    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: 1.9rc202411130312
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.5
    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: 1.4.1
    ChimeraX-Hbonds: 2.5
    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: 1.2.1
    ChimeraX-Label: 1.1.11
    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: 2.1.6
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    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-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
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.6
    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: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.1
    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: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.3.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.14
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    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: 1.18.1
    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
    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: 1.41
    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: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.8
    decorator: 5.1.1
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.54.1
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.12.1
    html2text: 2024.2.26
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jedi: 0.19.1
    Jinja2: 3.1.4
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.7
    line_profiler: 4.1.3
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    MolecularDynamicsViewer: 1.6
    msgpack: 1.0.8
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.1
    numpy: 2.1.3
    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: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    plotly: 5.24.1
    prompt_toolkit: 3.0.48
    psutil: 6.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.31
    Pygments: 2.18.0
    pyKVFinder: 0.7.1
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.0
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.7.1
    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.3
    PyQt6-WebEngineSubwheel-Qt6: 6.7.3
    PyQt6_sip: 13.8.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.2
    qtshim: 1.0
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    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: 0.6.3
    tables: 3.10.1
    tcia_utils: 1.5.1
    tenacity: 9.0.0
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    toml: 0.10.2
    tornado: 6.4.1
    traitlets: 5.14.3
    typing_extensions: 4.12.2
    tzdata: 2024.2
    urllib3: 2.2.3
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13

[Eric Pettersen]

Maybe you should raise UserError instead of ValueError?