'ChimeraX-ISOLDE' custom initialization failed: Clipper distribution not found

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19044
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Errors  
---  
error | Bundle 'ChimeraX-ISOLDE' custom initialization failed  
warning | Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 490, in get_module  
m = importlib.import_module(self.package_name)  
File "C:\Program Files\ChimeraX\bin\lib\importlib\\__init__.py", line 127, in
import_module  
return _bootstrap._gcd_import(name[level:], package, level)  
File "<frozen importlib._bootstrap>", line 1030, in _gcd_import  
File "<frozen importlib._bootstrap>", line 1007, in _find_and_load  
File "<frozen importlib._bootstrap>", line 986, in _find_and_load_unlocked  
File "<frozen importlib._bootstrap>", line 680, in _load_unlocked  
File "<frozen importlib._bootstrap_external>", line 850, in exec_module  
File "<frozen importlib._bootstrap>", line 228, in _call_with_frames_removed  
File "C:\Users\edgar.llontop\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\\__init__.py", line 51, in <module>  
__version__ = _version()  
File "C:\Users\edgar.llontop\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\\__init__.py", line 49, in _version  
return pkg_resources.require('ChimeraX-ISOLDE')[0].version  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\pkg_resources\\__init__.py", line 956, in require  
needed = self.resolve(parse_requirements(requirements))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\pkg_resources\\__init__.py", line 815, in resolve  
dist = self._resolve_dist(  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\pkg_resources\\__init__.py", line 856, in _resolve_dist  
raise DistributionNotFound(req, requirers)  
pkg_resources.DistributionNotFound: The 'ChimeraX-Clipper~=0.21.0'
distribution was not found and is required by ChimeraX-ISOLDE  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 364, in initialize  
api = self._get_api(session.logger)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 509, in _get_api  
m = self.get_module()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 492, in get_module  
raise ToolshedError("Error importing bundle %s's module: %s" % (self.name,
str(e)))  
chimerax.core.toolshed.ToolshedError: Error importing bundle ChimeraX-ISOLDE's
module: The 'ChimeraX-Clipper~=0.21.0' distribution was not found and is
required by ChimeraX-ISOLDE  
  
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  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 490, in get_module  
m = importlib.import_module(self.package_name)  
File "C:\Program Files\ChimeraX\bin\lib\importlib\\__init__.py", line 127, in
import_module  
return _bootstrap._gcd_import(name[level:], package, level)  
File "<frozen importlib._bootstrap>", line 1030, in _gcd_import  
File "<frozen importlib._bootstrap>", line 1007, in _find_and_load  
File "<frozen importlib._bootstrap>", line 986, in _find_and_load_unlocked  
File "<frozen importlib._bootstrap>", line 680, in _load_unlocked  
File "<frozen importlib._bootstrap_external>", line 850, in exec_module  
File "<frozen importlib._bootstrap>", line 228, in _call_with_frames_removed  
File "C:\Users\edgar.llontop\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\\__init__.py", line 51, in <module>  
__version__ = _version()  
File "C:\Users\edgar.llontop\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\\__init__.py", line 49, in _version  
return pkg_resources.require('ChimeraX-ISOLDE')[0].version  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\pkg_resources\\__init__.py", line 956, in require  
needed = self.resolve(parse_requirements(requirements))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\pkg_resources\\__init__.py", line 815, in resolve  
dist = self._resolve_dist(  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\pkg_resources\\__init__.py", line 856, in _resolve_dist  
raise DistributionNotFound(req, requirers)  
pkg_resources.DistributionNotFound: The 'ChimeraX-Clipper~=0.21.0'
distribution was not found and is required by ChimeraX-ISOLDE  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\toolbar\tool.py", line 205, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 385, in run_provider  
api = self._get_api(session.logger)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 509, in _get_api  
m = self.get_module()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 492, in get_module  
raise ToolshedError("Error importing bundle %s's module: %s" % (self.name,
str(e)))  
chimerax.core.toolshed.ToolshedError: Error importing bundle ChimeraX-ISOLDE's
module: The 'ChimeraX-Clipper~=0.21.0' distribution was not found and is
required by ChimeraX-ISOLDE  
  
chimerax.core.toolshed.ToolshedError: Error importing bundle ChimeraX-ISOLDE's
module: The 'ChimeraX-Clipper~=0.21.0' distribution was not found and is
required by ChimeraX-ISOLDE  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 492, in get_module  
raise ToolshedError("Error importing bundle %s's module: %s" % (self.name,
str(e)))  
  
See log for complete Python traceback.  
  

> toolshed show

Downloading bundle ChimeraX_ISOLDE-1.6.0-cp39-cp39-win_amd64.whl  

> open Y:\People\micael.cunha\CRYO-EM\TRPML_139bound.pdb format pdb

Chain information for TRPML_139bound.pdb #1  
---  
Chain | Description  
A B C D | No description available  
  

> open Y:\People\micael.cunha\CRYO-EM\TRPML_139bound.pdb format pdb

Chain information for TRPML_139bound.pdb #2  
---  
Chain | Description  
A B C D | No description available  
  

> open Y:\People\micael.cunha\CRYO-EM\TRPML_139bound.mrc format mrc

Opened TRPML_139bound.mrc as #3, grid size 288,288,288, pixel 0.83, shown at
level 0.0107, step 2, values float32  

> transparency 60

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 490, in get_module  
m = importlib.import_module(self.package_name)  
File "C:\Program Files\ChimeraX\bin\lib\importlib\\__init__.py", line 127, in
import_module  
return _bootstrap._gcd_import(name[level:], package, level)  
File "<frozen importlib._bootstrap>", line 1030, in _gcd_import  
File "<frozen importlib._bootstrap>", line 1007, in _find_and_load  
File "<frozen importlib._bootstrap>", line 986, in _find_and_load_unlocked  
File "<frozen importlib._bootstrap>", line 680, in _load_unlocked  
File "<frozen importlib._bootstrap_external>", line 850, in exec_module  
File "<frozen importlib._bootstrap>", line 228, in _call_with_frames_removed  
File "C:\Users\edgar.llontop\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\\__init__.py", line 51, in <module>  
__version__ = _version()  
File "C:\Users\edgar.llontop\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\\__init__.py", line 49, in _version  
return pkg_resources.require('ChimeraX-ISOLDE')[0].version  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\pkg_resources\\__init__.py", line 956, in require  
needed = self.resolve(parse_requirements(requirements))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\pkg_resources\\__init__.py", line 815, in resolve  
dist = self._resolve_dist(  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\pkg_resources\\__init__.py", line 856, in _resolve_dist  
raise DistributionNotFound(req, requirers)  
pkg_resources.DistributionNotFound: The 'ChimeraX-Clipper~=0.21.0'
distribution was not found and is required by ChimeraX-ISOLDE  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\toolbar\tool.py", line 205, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 385, in run_provider  
api = self._get_api(session.logger)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 509, in _get_api  
m = self.get_module()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 492, in get_module  
raise ToolshedError("Error importing bundle %s's module: %s" % (self.name,
str(e)))  
chimerax.core.toolshed.ToolshedError: Error importing bundle ChimeraX-ISOLDE's
module: The 'ChimeraX-Clipper~=0.21.0' distribution was not found and is
required by ChimeraX-ISOLDE  
  
chimerax.core.toolshed.ToolshedError: Error importing bundle ChimeraX-ISOLDE's
module: The 'ChimeraX-Clipper~=0.21.0' distribution was not found and is
required by ChimeraX-ISOLDE  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 492, in get_module  
raise ToolshedError("Error importing bundle %s's module: %s" % (self.name,
str(e)))  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 369.39
OpenGL renderer: Quadro K620/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: pt_BR.cp1252
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: windows

Manufacturer: Dell Inc.
Model: Precision Tower 5810
OS: Microsoft Windows 10 Pro (Build 19044)
Memory: 34,277,900,288
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Xeon(R) CPU E5-1620 v3 @ 3.50GHz
OSLanguage: pt-BR

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-ISOLDE: 1.6.0
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    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-PhenixUI: 1.1.13
    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
    comtypes: 1.1.14
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    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
    MolecularDynamicsViewer: 1.4
    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
    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
    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
    pywin32: 305
    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
    WMI: 1.5.1
    zipp: 3.15.0

[Tristan Croll]

I'm confused. Clipper 0.21.0 is there on the Toolshed, for all three operating systems. ​https://cxtoolshed.rbvi.ucsf.edu/apps/chimeraxclipper:

Version 0.21.0
Released 11 May 2023
Works with ChimeraX (<1.7,>=1.6.dev202303162359)

[pett]

Greg's on vacation until next week, so you may not get any feedback until then.