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Opened 5 weeks ago
Closed 5 weeks ago
#19043 closed defect (can't reproduce)
'pip install pyKVFinder' fails with empty error message
| Reported by: | Owned by: | Greg Couch | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | Eric Pettersen | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.26100
ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 UTC)
Description
It doesnt have the Find cavities plugin.
Log:
You can double click a model's Name or ID in the model panel to edit those
fields
UCSF ChimeraX version: 1.10.1 (2025-07-24)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "C:/Users/juligonz/OneDrive - University of Texas Medical Branch/Marino
> Lab/Juliana/Experiments/Alphafold/Reelin-
> WT_ROBO1/fold_reelin_wt_robo1_model_0.cif"
Chain information for fold_reelin_wt_robo1_model_0.cif #1
---
Chain | Description
A | .
B | .
> open "C:/Users/juligonz/OneDrive - University of Texas Medical Branch/Marino
> Lab/Juliana/Experiments/Alphafold/Reelin-
> WT_ROBO1/fold_reelin_wt_robo1_model_1.cif"
Chain information for fold_reelin_wt_robo1_model_1.cif #2
---
Chain | Description
A | .
B | .
> open "C:/Users/juligonz/OneDrive - University of Texas Medical Branch/Marino
> Lab/Juliana/Experiments/Alphafold/Reelin-
> WT_ROBO1/fold_reelin_wt_robo1_model_2.cif"
Chain information for fold_reelin_wt_robo1_model_2.cif #3
---
Chain | Description
A | .
B | .
> open "C:/Users/juligonz/OneDrive - University of Texas Medical Branch/Marino
> Lab/Juliana/Experiments/Alphafold/Reelin-
> WT_ROBO1/fold_reelin_wt_robo1_model_3.cif"
Chain information for fold_reelin_wt_robo1_model_3.cif #4
---
Chain | Description
A | .
B | .
> open "C:/Users/juligonz/OneDrive - University of Texas Medical Branch/Marino
> Lab/Juliana/Experiments/Alphafold/Reelin-
> WT_ROBO1/fold_reelin_wt_robo1_model_4.cif"
Chain information for fold_reelin_wt_robo1_model_4.cif #5
---
Chain | Description
A | .
B | .
> hide #2 models
> hide #3 models
> hide #4 models
> hide #5 models
> select add #1
40054 atoms, 41120 bonds, 5111 residues, 1 model selected
> select subtract #1
Nothing selected
> hide #1 models
> select add #1
40054 atoms, 41120 bonds, 5111 residues, 1 model selected
> select subtract #1
Nothing selected
> show #1 models
> hide #1 models
> show #2 models
> show #1 models
> hide #2 models
> show #1 cartoons
Computing secondary structure
> show #1 atoms
> hide #1 atoms
> hide #1 cartoons
> show #1 cartoons
> show #2 models
> hide #1 models
> show #2 cartoons
Computing secondary structure
> hide #2 atoms
> show #1 models
> hide #2 models
> show #2 models
> hide #1 models
> show #3 models
> hide #2 models
> hide #3 atoms
> show #3 cartoons
Computing secondary structure
> show #4 models
> hide #3 models
> hide #4 atoms
> show #4 cartoons
Computing secondary structure
> show #5 models
> hide #4 models
> show #5 cartoons
Computing secondary structure
> hide #5 atoms
> show #4 models
> show #3 models
> show #2 models
> show #1 models
> hide #5 models
> hide #4 models
> hide #2 models
> hide #3 models
> ui tool show Matchmaker
> matchmaker #3-5 to #1
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 fold_reelin_wt_robo1_model_0.cif, chain A (#1) with
fold_reelin_wt_robo1_model_2.cif, chain A (#3), sequence alignment score =
17945.5
RMSD between 313 pruned atom pairs is 1.403 angstroms; (across all 3460 pairs:
17.039)
Matchmaker fold_reelin_wt_robo1_model_0.cif, chain A (#1) with
fold_reelin_wt_robo1_model_3.cif, chain A (#4), sequence alignment score =
17974.9
RMSD between 1442 pruned atom pairs is 1.282 angstroms; (across all 3460
pairs: 5.731)
Matchmaker fold_reelin_wt_robo1_model_0.cif, chain A (#1) with
fold_reelin_wt_robo1_model_4.cif, chain A (#5), sequence alignment score =
18041.5
RMSD between 1065 pruned atom pairs is 0.923 angstroms; (across all 3460
pairs: 10.653)
> show #2 models
> show #3 models
> show #4 models
> hide #4 models
> hide #3 models
> hide #2 models
> show #2 models
> show #3 models
> show #5 models
> show #4 models
> hide #4 models
> show #4 models
> ui tool show Matchmaker
> matchmaker #2-5 to #1
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 fold_reelin_wt_robo1_model_0.cif, chain A (#1) with
fold_reelin_wt_robo1_model_1.cif, chain A (#2), sequence alignment score =
18018.7
RMSD between 1300 pruned atom pairs is 0.860 angstroms; (across all 3460
pairs: 10.126)
Matchmaker fold_reelin_wt_robo1_model_0.cif, chain A (#1) with
fold_reelin_wt_robo1_model_2.cif, chain A (#3), sequence alignment score =
17945.5
RMSD between 313 pruned atom pairs is 1.403 angstroms; (across all 3460 pairs:
17.039)
Matchmaker fold_reelin_wt_robo1_model_0.cif, chain A (#1) with
fold_reelin_wt_robo1_model_3.cif, chain A (#4), sequence alignment score =
17974.9
RMSD between 1442 pruned atom pairs is 1.282 angstroms; (across all 3460
pairs: 5.731)
Matchmaker fold_reelin_wt_robo1_model_0.cif, chain A (#1) with
fold_reelin_wt_robo1_model_4.cif, chain A (#5), sequence alignment score =
18041.5
RMSD between 1065 pruned atom pairs is 0.923 angstroms; (across all 3460
pairs: 10.653)
> ui tool show "Find Cavities"
pyKVFinder module not installed; fetching from PyPi repository...
'pip install pyKVFinder' failed. Error from pip:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\kvfinder\\__init__.py", line 48, in check_pyKVFinder
import pyKVFinder
ModuleNotFoundError: No module named 'pyKVFinder'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 571, in start_tool
ti = api._api_caller.start_tool(api, session, self, tool_info)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1399, in start_tool
return cls._get_func(api, "start_tool")(session, ti.name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\kvfinder\\__init__.py", line 42, in start_tool
check_pyKVFinder(session.logger)
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\kvfinder\\__init__.py", line 54, in check_pyKVFinder
run(logger.session, pip_cmd, log=False)
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3221, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\commands\pip.py", line 88, in pip
run_logged_pip(pip_cmd, session.logger)
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\python_utils.py", line 143, in run_logged_pip
raise RuntimeError(s)
RuntimeError
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\gui.py", line 1891, in <lambda>
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3221, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\cmd.py", line 219, in ui_tool_show
return bi.start_tool(session, name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 578, in start_tool
raise ToolshedError(
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Find
Cavities in bundle ChimeraX-KVFinder:
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Find
Cavities in bundle ChimeraX-KVFinder:
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 578, in start_tool
raise ToolshedError(
See log for complete Python traceback.
> ui tool show "Find Cavities"
pyKVFinder module not installed; fetching from PyPi repository...
'pip install pyKVFinder' failed. Error from pip:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\kvfinder\\__init__.py", line 48, in check_pyKVFinder
import pyKVFinder
ModuleNotFoundError: No module named 'pyKVFinder'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 571, in start_tool
ti = api._api_caller.start_tool(api, session, self, tool_info)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1399, in start_tool
return cls._get_func(api, "start_tool")(session, ti.name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\kvfinder\\__init__.py", line 42, in start_tool
check_pyKVFinder(session.logger)
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\kvfinder\\__init__.py", line 54, in check_pyKVFinder
run(logger.session, pip_cmd, log=False)
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3221, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\commands\pip.py", line 88, in pip
run_logged_pip(pip_cmd, session.logger)
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\python_utils.py", line 143, in run_logged_pip
raise RuntimeError(s)
RuntimeError
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\gui.py", line 1891, in <lambda>
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3221, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\cmd.py", line 219, in ui_tool_show
return bi.start_tool(session, name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 578, in start_tool
raise ToolshedError(
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Find
Cavities in bundle ChimeraX-KVFinder:
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Find
Cavities in bundle ChimeraX-KVFinder:
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 578, in start_tool
raise ToolshedError(
See log for complete Python traceback.
> lighting simple
[Repeated 1 time(s)]
> undo
> show #4 models
> lighting soft
> lighting simple
[Repeated 1 time(s)]
> lighting soft
> ui tool show "Find Cavities"
pyKVFinder module not installed; fetching from PyPi repository...
'pip install pyKVFinder' failed. Error from pip:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\kvfinder\\__init__.py", line 48, in check_pyKVFinder
import pyKVFinder
ModuleNotFoundError: No module named 'pyKVFinder'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 571, in start_tool
ti = api._api_caller.start_tool(api, session, self, tool_info)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1399, in start_tool
return cls._get_func(api, "start_tool")(session, ti.name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\kvfinder\\__init__.py", line 42, in start_tool
check_pyKVFinder(session.logger)
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\kvfinder\\__init__.py", line 54, in check_pyKVFinder
run(logger.session, pip_cmd, log=False)
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3221, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\commands\pip.py", line 88, in pip
run_logged_pip(pip_cmd, session.logger)
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\python_utils.py", line 143, in run_logged_pip
raise RuntimeError(s)
RuntimeError
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\gui.py", line 1891, in <lambda>
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3221, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\ui\cmd.py", line 219, in ui_tool_show
return bi.start_tool(session, name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 578, in start_tool
raise ToolshedError(
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Find
Cavities in bundle ChimeraX-KVFinder:
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Find
Cavities in bundle ChimeraX-KVFinder:
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 578, in start_tool
raise ToolshedError(
See log for complete Python traceback.
OpenGL version: 3.3.0 - Build 32.0.101.6647
OpenGL renderer: Intel(R) Graphics
OpenGL vendor: Intel
Python: 3.11.4
Locale: en_US.cp1252
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: windows
Manufacturer: Dell Inc.
Model: Dell Pro Slim Plus QBS1250
OS: Microsoft Windows 11 Enterprise (Build 26100)
Memory: 16,595,546,112
MaxProcessMemory: 137,438,953,344
CPU: 14 Intel(R) Core(TM) Ultra 5 235
OSLanguage: en-US
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
narwhals: 2.7.0
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: 2.3.3
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
plotly: 6.3.1
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
tomlkit: 0.13.3
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
Change History (2)
comment:1 by , 5 weeks ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Core |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → 'pip install pyKVFinder' fails with empty error message |
comment:2 by , 5 weeks ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | assigned → closed |
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Hi Juliana,
--Eric