Opened 12 months ago

Last modified 10 months ago

#16158 assigned defect

ISOLDE: Clipper distribution was not found

Reported by: chimerax-bug-report@… Owned by: Greg Couch
Priority: normal Milestone: 1.10
Component: Tool Shed Version:
Keywords: Cc: Tristan Croll, chimerax-programmers, olibclarke@…
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.22631
ChimeraX Version: 1.6rc202303280104 (2023-03-28 01:04:53 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
warnings | QWindowsWindow::setDarkBorderToWindow: Unable to set dark window
border.  
QWindowsWindow::setDarkBorderToWindow: Unable to set dark window border.  
  
UCSF ChimeraX version: 1.6rc202303280104 (2023-03-28)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> ui tool show Updates

Errors may have occurred when running pip:  

pip standard error:  
\---  
  
[notice] A new release of pip is available: 23.0 -> 24.2  
[notice] To update, run: C:\Program Files\ChimeraX\bin\ChimeraX.exe -m pip
install --upgrade pip  
\---  

pip standard output:  
\---  
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/  
Collecting ChimeraX-ISOLDE==1.6.dev1  
Downloading
https://cxtoolshed.rbvi.ucsf.edu/media/chimeraxisolde/releases/1.6.dev1/ChimeraX_ISOLDE-1.6.dev1-cp39-cp39-win_amd64.whl
(87.4 MB)  
\--------------------------------------- 87.4/87.4 MB 12.8 MB/s eta 0:00:00  
Installing collected packages: ChimeraX-ISOLDE  
Successfully installed ChimeraX-ISOLDE-1.6.dev1  
\---  

Successfully installed ChimeraX-ISOLDE-1.6.dev1  
Installed ChimeraX-ISOLDE (1.6.dev1)  

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\andre\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\\__init__.py", line 51, in <module>  
__version__ = _version()  
File "C:\Users\andre\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~=0.20.0'
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~=0.20.0' distribution was not found and is
required by ChimeraX-ISOLDE  
  

ChimeraX-ISOLDE (installed) [version: 1.6.dev1] [api package: chimerax.isolde]
[category: General] [tool: ISOLDE [categories: General] [synopsis: Interactive
Molecular Dynamics Flexible Fitting (iMDFF)]] [tool: Ramachandran Plot
[categories: Validation] [synopsis: Interactive Ramachandran plot]] [command:
isolde [categories: General] [synopsis: Command-line control of ISOLDE
simulations]] [command: rama [categories: General] [synopsis: Live
Ramachandran validation of models]] [command: rota [categories: General]
[synopsis: Live rotamer validation of models]] [command: ~rama [categories:
General] [synopsis: Turn off live Ramachandran validation of models]]
[command: ~rota [categories: General] [synopsis: Turn off live rotamer
validation of models]]: custom initialization failed  

> open
> C:\Users\andre\Downloads\cryosparc_P46_J209_006_volume_map_sym_sharp.mrc\cryosparc_P46_J209_006_volume_map_sym_sharp.mrc
> format mrc

Opened cryosparc_P46_J209_006_volume_map_sym_sharp.mrc as #1, grid size
448,448,448, pixel 0.844, shown at level 0.206, step 2, values float32  

> open
> C:/Users/andre/Downloads/fold_2024_10_21_14_07/fold_2024_10_21_14_07_model_0.cif

Chain information for fold_2024_10_21_14_07_model_0.cif #2  
---  
Chain | Description  
A | .  
  

> set bgColor white

> ui tool show ISOLDE

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\andre\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\\__init__.py", line 51, in <module>  
__version__ = _version()  
File "C:\Users\andre\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~=0.20.0'
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 559, in start_tool  
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~=0.20.0' 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\ui\gui.py",
line 1665, in <lambda>  
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\cmd.py",
line 219, in ui_tool_show  
bi.start_tool(session, name)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 567, in start_tool  
raise ToolshedError(  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in
bundle ChimeraX-ISOLDE:  
Error importing bundle ChimeraX-ISOLDE's module: The 'ChimeraX-
Clipper~=0.20.0' distribution was not found and is required by ChimeraX-ISOLDE  
  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in
bundle ChimeraX-ISOLDE:  
Error importing bundle ChimeraX-ISOLDE's module: The 'ChimeraX-
Clipper~=0.20.0' 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 567, in start_tool  
raise ToolshedError(  
  
See log for complete Python traceback.  
  

> ui tool show ISOLDE

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\andre\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\\__init__.py", line 51, in <module>  
__version__ = _version()  
File "C:\Users\andre\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~=0.20.0'
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 559, in start_tool  
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~=0.20.0' 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\ui\gui.py",
line 1665, in <lambda>  
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\cmd.py",
line 219, in ui_tool_show  
bi.start_tool(session, name)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 567, in start_tool  
raise ToolshedError(  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in
bundle ChimeraX-ISOLDE:  
Error importing bundle ChimeraX-ISOLDE's module: The 'ChimeraX-
Clipper~=0.20.0' distribution was not found and is required by ChimeraX-ISOLDE  
  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in
bundle ChimeraX-ISOLDE:  
Error importing bundle ChimeraX-ISOLDE's module: The 'ChimeraX-
Clipper~=0.20.0' 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 567, in start_tool  
raise ToolshedError(  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 556.13
OpenGL renderer: NVIDIA GeForce GTX 1660 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

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

Manufacturer: HP
Model: OMEN Laptop 15-en0xxx
OS: Microsoft Windows 11 Home (Build 22631)
Memory: 16,495,435,776
MaxProcessMemory: 137,438,953,344
CPU: 16 AMD Ryzen 7 4800H with Radeon Graphics         
OSLanguage: en-US

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: 2022.12.7
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9
    ChimeraX-AddH: 2.2.3
    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: 1.6rc202303280104
    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.dev1
    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
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    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: 1.10.2
    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: 1.6.6
    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: 6.1.0
    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
    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: 23.0
    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: 3.2.0
    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: 2023.2
    pywin32: 305
    pyzmq: 25.0.2
    qtconsole: 5.4.0
    QtPy: 2.3.0
    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
    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: 6.2
    traitlets: 5.9.0
    typing-extensions: 4.5.0
    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

Change History (6)

comment:1 by Eric Pettersen, 12 months ago

Component: Unassigned → Third Party
Owner: set to Tristan Croll
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → ISOLDE: Clipper distribution was not found

comment:2 by Tristan Croll, 12 months ago

Component: Third Party → Tool Shed
Owner: changed from Tristan Croll to Eric Pettersen

Looks like something is (or a *couple* of things are) broken in the ToolShed... reassigning to Eric to decide who to pass it to:

I just uninstalled ISOLDE and Clipper from ChimeraX 1.8 on my Linux machine, and restarted ChimeraX. First thing I noticed in the log on startup:

isolde shorthand
isolde is provided by the uninstalled bundle ISOLDE versions 1.7rc1 – 1.7.1
UCSF ChimeraX version: 1.8 (2024-06-10)

The latest version of ISOLDE on the ToolShed is 1.8 - this is also the only version _actually_ compatible with ChimeraX 1.8 (I accidentally specified "ChimeraX~=1.7" instead of "ChimeraX ~=1.7.0" for that release; ISOLDE 1.8 specifies "ChimeraX~=1.8.0" and ISOLDE 1.8.dev0 specifies "ChimeraX~=1.8.dev202403220040").

If I do "ui tool show Updates" as this user did, and choose to show "All Available" then ISOLDE 1.7.1 is the latest available in the list.

If I go ahead and choose to install 1.7.1, then I get essentially the same traceback as the user (see below). Upshot (I think) is that installing a new package from the Updates UI is failing to install necessary dependencies.

Installed ChimeraX-ISOLDE (1.7.1)
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/toolshed/info.py", line 501, in get_module
m = importlib.import_module(self.package_name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/importlib/__init__.py", line 126, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "<frozen importlib._bootstrap>", line 1204, in _gcd_import
File "<frozen importlib._bootstrap>", line 1176, in _find_and_load
File "<frozen importlib._bootstrap>", line 1147, in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 690, in _load_unlocked
File "<frozen importlib._bootstrap_external>", line 940, in exec_module
File "<frozen importlib._bootstrap>", line 241, in _call_with_frames_removed
File "/home/tcroll/.local/share/ChimeraX/1.8/lib/python3.11/site-packages/chimerax/isolde/__init__.py", line 51, in <module>
__version__ = _version()
^^^^^^^^^^
File "/home/tcroll/.local/share/ChimeraX/1.8/lib/python3.11/site-packages/chimerax/isolde/__init__.py", line 49, in _version
return pkg_resources.require('ChimeraX-ISOLDE')[0].version
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/pkg_resources/__init__.py", line 937, in require
needed = self.resolve(parse_requirements(requirements))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/pkg_resources/__init__.py", line 798, in resolve
dist = self._resolve_dist(
^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/pkg_resources/__init__.py", line 839, in _resolve_dist
raise DistributionNotFound(req, requirers)
pkg_resources.DistributionNotFound: The 'ChimeraX-Clipper~=0.22.0' 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 "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/toolshed/info.py", line 375, in initialize
api = self._get_api(session.logger)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/toolshed/info.py", line 520, in _get_api
m = self.get_module()
^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/toolshed/info.py", line 503, 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~=0.22.0' distribution was not found and is required by ChimeraX-ISOLDE

ChimeraX-ISOLDE (installed) [version: 1.7.1] [api package: chimerax.isolde] [category: General] [tool: ISOLDE [categories: General] [synopsis: Interactive Molecular Dynamics Flexible Fitting (iMDFF)]] [tool: Ramachandran Plot [categories: Validation] [synopsis: Interactive Ramachandran plot]] [command: isolde [categories: General] [synopsis: Command-line control of ISOLDE simulations]] [command: rama [categories: General] [synopsis: Live Ramachandran validation of models]] [command: rota [categories: General] [synopsis: Live rotamer validation of models]] [command: ~rama [categories: General] [synopsis: Turn off live Ramachandran validation of models]] [command: ~rota [categories: General] [synopsis: Turn off live rotamer validation of models]]: custom initialization failed

comment:3 by Tristan Croll, 12 months ago

Cc: Tristan Croll added

(forgot to add myself to the CC)

comment:4 by Eric Pettersen, 12 months ago

Cc: chimerax-programmers added
Milestone: → 1.9
Owner: changed from Eric Pettersen to Greg Couch

comment:5 by Eric Pettersen, 12 months ago

Cc: olibclarke@… added

comment:6 by Greg Couch, 10 months ago

Milestone: 1.9 → 1.10

Ticket retargeted after milestone closed

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