Opened 2 days ago

Closed 3 hours ago

#20779 closed defect (limitation)

KVFinder on old MacOS

Reported by: stuti_sharma@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Surface/Binding Analysis Version:
Keywords: Cc: Zach Pearson
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-12.7.6-arm64-arm-64bit
ChimeraX Version: 1.11.1 (2026-01-23 05:51:34 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
UCSF ChimeraX version: 1.11.1 (2026-01-23)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/stutisharma2/Documents/Manuscript_a2-isoform/Figures/a2Vo_real_space_refined_010-R543A_D768S_kvfinder.pdb
> format pdb

Chain information for a2Vo_real_space_refined_010-R543A_D768S_kvfinder.pdb #1  
---  
Chain | Description  
0 | No description available  
1 2 9 | No description available  
C | No description available  
F | No description available  
S | No description available  
  

> set bgColor white

> hide atoms

> show cartoons

> graphics silhouettes true

> lighting soft

> open
> /Users/stutisharma/Downloads/KVFinder_structures_9925176794514289572/cavity_9925176794514289572.pdb

Summary of feedback from opening
/Users/stutisharma/Downloads/KVFinder_structures_9925176794514289572/cavity_9925176794514289572.pdb  
---  
warning | Ignored bad PDB record found on line 25065  
  

> open
> /Users/stutisharma/Downloads/KVFinder_structures_9925176794514289572/input_9925176794514289572.pdb

Summary of feedback from opening
/Users/stutisharma/Downloads/KVFinder_structures_9925176794514289572/input_9925176794514289572.pdb  
---  
warning | Ignored bad PDB record found on line 12108  
  
Chain information for input_9925176794514289572.pdb #3  
---  
Chain | Description  
0 | No description available  
1 2 9 | No description available  
C | No description available  
F | No description available  
S | No description available  
  

> hide #!1 models

> hide #2 models

> hide #!3 atoms

> show #!3 cartoons

Computing secondary structure  

> show #2 models

> select #2@@serial_number=18518

1 atom, 1 residue, 1 model selected  

> ui tool show "Find Cavities"

pyKVFinder module not installed; fetching from PyPi repository...  
'pip install pyKVFinder' failed. Error from pip: error: subprocess-exited-
with-error  
  
× Building wheel for pyKVFinder (pyproject.toml) did not run successfully.  
│ exit code: 1  
╰─> [58 lines of output]  
running bdist_wheel  
running build  
running build_py  
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder  
copying pyKVFinder/__init__.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder  
copying pyKVFinder/utils.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder  
copying pyKVFinder/main.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder  
copying pyKVFinder/argparser.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder  
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/hydropathy.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/__init__.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/export.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/spatial.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/depth.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/constitutional.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/geometry.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/cavity.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/openings.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/detect.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
running egg_info  
writing pyKVFinder.egg-info/PKG-INFO  
writing dependency_links to pyKVFinder.egg-info/dependency_links.txt  
writing entry points to pyKVFinder.egg-info/entry_points.txt  
writing requirements to pyKVFinder.egg-info/requires.txt  
writing top-level names to pyKVFinder.egg-info/top_level.txt  
reading manifest file 'pyKVFinder.egg-info/SOURCES.txt'  
reading manifest template 'MANIFEST.in'  
warning: no files found matching 'requirements.txt'  
adding license file 'LICENSE'  
writing manifest file 'pyKVFinder.egg-info/SOURCES.txt'  
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data  
copying pyKVFinder/data/WimleyWhite.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data  
copying pyKVFinder/data/EisenbergWeiss.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data  
copying pyKVFinder/data/ZhaoLondon.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data  
copying pyKVFinder/data/RadzickaWolfenden.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data  
copying pyKVFinder/data/MoonFleming.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data  
copying pyKVFinder/data/KyteDoolittle.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data  
copying pyKVFinder/data/HessaHeijne.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data  
copying pyKVFinder/data/vdw.dat ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data  
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests  
copying pyKVFinder/data/tests/ADN.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests  
copying pyKVFinder/data/tests/C1.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests  
copying pyKVFinder/data/tests/PKI.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests  
copying pyKVFinder/data/tests/1FMO.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests  
copying pyKVFinder/data/tests/1FMO.KVFinder.output.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests  
copying pyKVFinder/data/tests/ClO4.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests  
copying pyKVFinder/data/tests/1FMO.xyz ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests  
copying pyKVFinder/data/tests/custom-box.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests  
copying pyKVFinder/data/tests/ADN.xyz ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests  
copying pyKVFinder/data/tests/residues-box.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests  
running build_ext  
building 'pyKVFinder._pyKVFinder' extension  
swigging C/pyKVFinder.i to C/pyKVFinder_wrap.c  
swig -python -o C/pyKVFinder_wrap.c C/pyKVFinder.i  
creating build/temp.macosx-10.9-universal2-cpython-311/C  
clang -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g
-fwrapv -O3 -Wall -arch arm64 -arch x86_64 -g
-I/private/var/folders/gc/1prrbz4d08d0s08m3kl9ksg00000gn/T/pip-build-
env-n4xk8o3s/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/Applications/ChimeraX-1.11.1.app/Contents/include/python3.11 -c
C/pyKVFinder.c -o build/temp.macosx-10.9-universal2-cpython-311/C/pyKVFinder.o
-Xpreprocessor -fopenmp=libomp -O3 -ffast-math  
error: unknown argument: '-fopenmp=libomp'  
error: command '/usr/bin/clang' failed with exit code 1  
[end of output]  
  
note: This error originates from a subprocess, and is likely not a problem
with pip.  
ERROR: Failed building wheel for pyKVFinder  
error: failed-wheel-build-for-install  
  
× Failed to build installable wheels for some pyproject.toml based projects  
╰─> pyKVFinder  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/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
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 571, in start_tool  
ti = api._api_caller.start_tool(api, session, self, tool_info)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1400, in start_tool  
return cls._get_func(api, "start_tool")(session, ti.name)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/kvfinder/__init__.py", line 42, in start_tool  
check_pyKVFinder(session.logger)  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/kvfinder/__init__.py", line 54, in check_pyKVFinder  
run(logger.session, pip_cmd, log=False)  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/pip.py", line 84, in pip  
run_logged_pip(pip_cmd, session.logger)  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/python_utils.py", line 148, in run_logged_pip  
raise RuntimeError(s)  
RuntimeError: error: subprocess-exited-with-error  
  
× Building wheel for pyKVFinder (pyproject.toml) did not run successfully.  
│ exit code: 1  
╰─> [58 lines of output]  
running bdist_wheel  
running build  
running build_py  
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder  
copying pyKVFinder/__init__.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder  
copying pyKVFinder/utils.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder  
copying pyKVFinder/main.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder  
copying pyKVFinder/argparser.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder  
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/hydropathy.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/__init__.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/export.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/spatial.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/depth.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/constitutional.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/geometry.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/cavity.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/openings.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/detect.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
running egg_info  
writing pyKVFinder.egg-info/PKG-INFO  
writing dependency_links to pyKVFinder.egg-info/dependency_links.txt  
writing entry points to pyKVFinder.egg-info/entry_points.txt  
writing requirements to pyKVFinder.egg-info/requires.txt  
writing top-level names to pyKVFinder.egg-info/top_level.txt  
reading manifest file 'pyKVFinder.egg-info/SOURCES.txt'  
reading manifest template 'MANIFEST.in'  
warning: no files found matching 'requirements.txt'  
adding license file 'LICENSE'  
writing manifest file 'pyKVFinder.egg-info/SOURCES.txt'  
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data  
copying pyKVFinder/data/WimleyWhite.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data  
copying pyKVFinder/data/EisenbergWeiss.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data  
copying pyKVFinder/data/ZhaoLondon.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data  
copying pyKVFinder/data/RadzickaWolfenden.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data  
copying pyKVFinder/data/MoonFleming.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data  
copying pyKVFinder/data/KyteDoolittle.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data  
copying pyKVFinder/data/HessaHeijne.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data  
copying pyKVFinder/data/vdw.dat ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data  
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests  
copying pyKVFinder/data/tests/ADN.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests  
copying pyKVFinder/data/tests/C1.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests  
copying pyKVFinder/data/tests/PKI.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests  
copying pyKVFinder/data/tests/1FMO.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests  
copying pyKVFinder/data/tests/1FMO.KVFinder.output.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests  
copying pyKVFinder/data/tests/ClO4.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests  
copying pyKVFinder/data/tests/1FMO.xyz ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests  
copying pyKVFinder/data/tests/custom-box.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests  
copying pyKVFinder/data/tests/ADN.xyz ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests  
copying pyKVFinder/data/tests/residues-box.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests  
running build_ext  
building 'pyKVFinder._pyKVFinder' extension  
swigging C/pyKVFinder.i to C/pyKVFinder_wrap.c  
swig -python -o C/pyKVFinder_wrap.c C/pyKVFinder.i  
creating build/temp.macosx-10.9-universal2-cpython-311/C  
clang -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g
-fwrapv -O3 -Wall -arch arm64 -arch x86_64 -g
-I/private/var/folders/gc/1prrbz4d08d0s08m3kl9ksg00000gn/T/pip-build-
env-n4xk8o3s/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/Applications/ChimeraX-1.11.1.app/Contents/include/python3.11 -c
C/pyKVFinder.c -o build/temp.macosx-10.9-universal2-cpython-311/C/pyKVFinder.o
-Xpreprocessor -fopenmp=libomp -O3 -ffast-math  
error: unknown argument: '-fopenmp=libomp'  
error: command '/usr/bin/clang' failed with exit code 1  
[end of output]  
  
note: This error originates from a subprocess, and is likely not a problem
with pip.  
ERROR: Failed building wheel for pyKVFinder  
error: failed-wheel-build-for-install  
  
× Failed to build installable wheels for some pyproject.toml based projects  
╰─> pyKVFinder  
  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1939, in <lambda>  
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/cmd.py", line 219, in ui_tool_show  
return bi.start_tool(session, name)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/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:  
error: subprocess-exited-with-error  
  
× Building wheel for pyKVFinder (pyproject.toml) did not run successfully.  
│ exit code: 1  
╰─> [58 lines of output]  
running bdist_wheel  
running build  
running build_py  
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder  
copying pyKVFinder/__init__.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder  
copying pyKVFinder/utils.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder  
copying pyKVFinder/main.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder  
copying pyKVFinder/argparser.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder  
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/hydropathy.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/__init__.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/export.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/spatial.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/depth.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/constitutional.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/geometry.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/cavity.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/openings.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/detect.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
running egg_info  
writing pyKVFinder.egg-info/PKG-INFO  
writing dependency_links to pyKVFinder.egg-info/dependency_links.txt  
writing entry points to pyKVFinder.egg-info/entry_points.txt  
writing requirements to pyKVFinder.egg-info/requires.txt  
writing top-level names to pyKVFinder.egg-info/top_level.txt  
reading manifest file 'pyKVFinder.egg-info/SOURCES.txt'  
reading manifest template 'MANIFEST.in'  
warning: no files found matching 'requirements.txt'  
adding license file 'LICENSE'  
writing manifest file 'pyKVFinder.egg-info/SOURCES.txt'  
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data  
copying pyKVFinder/data/WimleyWhite.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data  
copying pyKVFinder/data/EisenbergWeiss.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data  
copying pyKVFinder/data/ZhaoLondon.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data  
copying pyKVFinder/data/RadzickaWolfenden.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data  
copying pyKVFinder/data/MoonFleming.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data  
copying pyKVFinder/data/KyteDoolittle.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data  
copying pyKVFinder/data/HessaHeijne.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data  
copying pyKVFinder/data/vdw.dat ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data  
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests  
copying pyKVFinder/data/tests/ADN.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests  
copying pyKVFinder/data/tests/C1.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests  
copying pyKVFinder/data/tests/PKI.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests  
copying pyKVFinder/data/tests/1FMO.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests  
copying pyKVFinder/data/tests/1FMO.KVFinder.output.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests  
copying pyKVFinder/data/tests/ClO4.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests  
copying pyKVFinder/data/tests/1FMO.xyz ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests  
copying pyKVFinder/data/tests/custom-box.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests  
copying pyKVFinder/data/tests/ADN.xyz ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests  
copying pyKVFinder/data/tests/residues-box.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests  
running build_ext  
building 'pyKVFinder._pyKVFinder' extension  
swigging C/pyKVFinder.i to C/pyKVFinder_wrap.c  
swig -python -o C/pyKVFinder_wrap.c C/pyKVFinder.i  
creating build/temp.macosx-10.9-universal2-cpython-311/C  
clang -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g
-fwrapv -O3 -Wall -arch arm64 -arch x86_64 -g
-I/private/var/folders/gc/1prrbz4d08d0s08m3kl9ksg00000gn/T/pip-build-
env-n4xk8o3s/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/Applications/ChimeraX-1.11.1.app/Contents/include/python3.11 -c
C/pyKVFinder.c -o build/temp.macosx-10.9-universal2-cpython-311/C/pyKVFinder.o
-Xpreprocessor -fopenmp=libomp -O3 -ffast-math  
error: unknown argument: '-fopenmp=libomp'  
error: command '/usr/bin/clang' failed with exit code 1  
[end of output]  
  
note: This error originates from a subprocess, and is likely not a problem
with pip.  
ERROR: Failed building wheel for pyKVFinder  
error: failed-wheel-build-for-install  
  
× Failed to build installable wheels for some pyproject.toml based projects  
╰─> pyKVFinder  
  
  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Find
Cavities in bundle ChimeraX-KVFinder:  
error: subprocess-exited-with-error  
  
× Building wheel for pyKVFinder (pyproject.toml) did not run successfully.  
│ exit code: 1  
╰─> [58 lines of output]  
running bdist_wheel  
running build  
running build_py  
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder  
copying pyKVFinder/__init__.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder  
copying pyKVFinder/utils.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder  
copying pyKVFinder/main.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder  
copying pyKVFinder/argparser.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder  
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/hydropathy.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/__init__.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/export.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/spatial.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/depth.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/constitutional.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/geometry.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/cavity.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/openings.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/detect.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
running egg_info  
writing pyKVFinder.egg-info/PKG-INFO  
writing dependency_links to pyKVFinder.egg-info/dependency_links.txt  
writing entry points to pyKVFinder.egg-info/entry_points.txt  
writing requirements to pyKVFinder.egg-info/requires.txt  
writing top-level names to pyKVFinder.egg-info/top_level.txt  
reading manifest file 'pyKVFinder.egg-info/SOURCES.txt'  
reading manifest template 'MANIFEST.in'  
warning: no files found matching 'requirements.txt'  
adding license file 'LICENSE'  
writing manifest file 'pyKVFinder.egg-info/SOURCES.txt'  
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data  
copying pyKVFinder/data/WimleyWhite.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data  
copying pyKVFinder/data/EisenbergWeiss.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data  
copying pyKVFinder/data/ZhaoLondon.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data  
copying pyKVFinder/data/RadzickaWolfenden.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data  
copying pyKVFinder/data/MoonFleming.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data  
copying pyKVFinder/data/KyteDoolittle.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data  
copying pyKVFinder/data/HessaHeijne.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data  
copying pyKVFinder/data/vdw.dat ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data  
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests  
copying pyKVFinder/data/tests/ADN.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests  
copying pyKVFinder/data/tests/C1.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests  
copying pyKVFinder/data/tests/PKI.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests  
copying pyKVFinder/data/tests/1FMO.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests  
copying pyKVFinder/data/tests/1FMO.KVFinder.output.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests  
copying pyKVFinder/data/tests/ClO4.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests  
copying pyKVFinder/data/tests/1FMO.xyz ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests  
copying pyKVFinder/data/tests/custom-box.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests  
copying pyKVFinder/data/tests/ADN.xyz ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests  
copying pyKVFinder/data/tests/residues-box.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests  
running build_ext  
building 'pyKVFinder._pyKVFinder' extension  
swigging C/pyKVFinder.i to C/pyKVFinder_wrap.c  
swig -python -o C/pyKVFinder_wrap.c C/pyKVFinder.i  
creating build/temp.macosx-10.9-universal2-cpython-311/C  
clang -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g
-fwrapv -O3 -Wall -arch arm64 -arch x86_64 -g
-I/private/var/folders/gc/1prrbz4d08d0s08m3kl9ksg00000gn/T/pip-build-
env-n4xk8o3s/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/Applications/ChimeraX-1.11.1.app/Contents/include/python3.11 -c
C/pyKVFinder.c -o build/temp.macosx-10.9-universal2-cpython-311/C/pyKVFinder.o
-Xpreprocessor -fopenmp=libomp -O3 -ffast-math  
error: unknown argument: '-fopenmp=libomp'  
error: command '/usr/bin/clang' failed with exit code 1  
[end of output]  
  
note: This error originates from a subprocess, and is likely not a problem
with pip.  
ERROR: Failed building wheel for pyKVFinder  
error: failed-wheel-build-for-install  
  
× Failed to build installable wheels for some pyproject.toml based projects  
╰─> pyKVFinder  
  
  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 578, in start_tool  
raise ToolshedError(  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M1
OpenGL vendor: Apple

Python: 3.11.9
Locale: UTF-8
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: iMac
      Model Identifier: iMac21,1
      Chip: Apple M1
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 16 GB
      System Firmware Version: 10151.140.19
      OS Loader Version: 7459.141.1.701.1

Software:

    System Software Overview:

      System Version: macOS 12.7.6 (21H1320)
      Kernel Version: Darwin 21.6.0
      Time since boot: 2 days 3:07

Graphics/Displays:

    Apple M1:

      Chipset Model: Apple M1
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 8
      Vendor: Apple (0x106b)
      Metal Family: Supported, Metal GPUFamily Apple 7
      Displays:
        iMac:
          Display Type: Built-In Retina LCD
          Resolution: Retina 4.5K (4480 x 2520)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        PHL 288E2:
          Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus)
          UI Looks like: 2560 x 1440 @ 30.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported


Installed Packages:
    aiohappyeyeballs: 2.6.1
    aiohttp: 3.13.1
    aiosignal: 1.4.0
    alabaster: 1.0.0
    annotated-types: 0.7.0
    anyio: 4.12.1
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.1
    attrs: 25.4.0
    babel: 2.17.0
    beautifulsoup4: 4.13.5
    blockdiag: 3.0.0
    blosc2: 3.12.2
    build: 1.3.0
    certifi: 2025.7.14
    cftime: 1.6.5
    charset-normalizer: 3.4.4
    ChimeraX-AddCharge: 1.5.20
    ChimeraX-AddH: 2.2.8
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 3.1.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Animations: 1.0
    ChimeraX-Aniso: 1.3.2
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.61.4
    ChimeraX-AtomicLibrary: 14.2.1
    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: 1.1
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.6.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.3
    ChimeraX-Clipper: 0.26.1
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3.0
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.11.1
    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: 2.5.3
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.4
    ChimeraX-ISOLDE: 1.11.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.7.3
    ChimeraX-Label: 1.2
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.2
    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-MCPServer: 0.1.0
    ChimeraX-MDcrds: 2.17.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-Minimize: 1.3.2
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.22
    ChimeraX-ModelPanel: 1.6
    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: 1.0.1
    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: 1.15.2
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.12
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.5
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.4
    ChimeraX-ProfileGrids: 1.4.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.5
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.3
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.2
    ChimeraX-Scenes: 0.3.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.10
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17.3
    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: 1.49.1
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDock: 1.5.2
    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
    click: 8.3.1
    colorama: 0.4.6
    comm: 0.2.3
    contourpy: 1.3.3
    coverage: 7.13.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.1.4
    debugpy: 1.8.19
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.1
    filelock: 3.19.1
    fonttools: 4.61.1
    frozenlist: 1.8.0
    funcparserlib: 2.0.0a0
    glfw: 2.10.0
    grako: 3.16.5
    h11: 0.16.0
    h5py: 3.15.1
    html2text: 2025.4.15
    httpcore: 1.0.9
    httpx: 0.28.1
    httpx-sse: 0.4.3
    idna: 3.11
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.3.0
    ipykernel: 6.30.1
    ipython: 9.5.0
    ipython_pygments_lexers: 1.1.1
    ipywidgets: 8.1.8
    jedi: 0.19.2
    Jinja2: 3.1.6
    jsonschema: 4.26.0
    jsonschema-specifications: 2025.9.1
    jupyter_client: 8.6.3
    jupyter_core: 5.9.1
    jupyterlab_widgets: 3.0.16
    kiwisolver: 1.4.9
    line_profiler: 5.0.0
    lxml: 6.0.2
    lz4: 4.3.2
    Markdown: 3.8.2
    MarkupSafe: 3.0.3
    matplotlib: 3.10.7
    matplotlib-inline: 0.2.1
    mcp: 1.18.0
    msgpack: 1.1.1
    multidict: 6.7.0
    ndindex: 1.10.1
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.14.1
    numpy: 1.26.4
    OpenMM: 8.2.0
    openvr: 1.26.701
    packaging: 25.0
    ParmEd: 4.2.2
    parso: 0.8.5
    pep517: 0.13.1
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 11.3.0
    pip: 26.1.2
    pkginfo: 1.12.1.2
    platformdirs: 4.5.1
    pluggy: 1.6.0
    prompt_toolkit: 3.0.52
    propcache: 0.4.1
    psutil: 7.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pybind11: 3.0.1
    pycollada: 0.8
    pydantic: 2.12.5
    pydantic-settings: 2.12.0
    pydantic_core: 2.41.5
    pydicom: 2.4.4
    Pygments: 2.18.0
    pynmrstar: 3.3.6
    pynrrd: 1.0.0
    PyOpenGL: 3.1.10
    PyOpenGL-accelerate: 3.1.10
    pyopenxr: 1.1.4501
    pyparsing: 3.3.2
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.9.1
    PyQt6-Qt6: 6.9.2
    PyQt6-WebEngine-commercial: 6.9.0
    PyQt6-WebEngine-Qt6: 6.9.2
    PyQt6_sip: 13.10.2
    pytest: 9.0.2
    pytest-cov: 7.0.0
    python-dateutil: 2.9.0.post0
    python-dotenv: 1.2.1
    python-multipart: 0.0.21
    pyzmq: 27.1.0
    qtconsole: 5.7.0
    QtPy: 2.4.3
    qtshim: 1.2
    RandomWords: 0.4.0
    referencing: 0.37.0
    requests: 2.32.5
    roman-numerals: 4.1.0
    roman-numerals-py: 4.1.0
    rpds-py: 0.30.0
    scipy: 1.14.0
    setuptools: 80.9.0
    sfftk-rw: 0.8.1
    six: 1.17.0
    snowballstemmer: 3.0.1
    sortedcontainers: 2.4.0
    soupsieve: 2.8.3
    Sphinx: 8.2.3
    sphinx-autodoc-typehints: 3.2.0
    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
    sse-starlette: 3.2.0
    stack-data: 0.6.3
    starlette: 0.52.1
    superqt: 0.7.6
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.5
    tornado: 6.5.4
    traitlets: 5.14.3
    typing-inspection: 0.4.2
    typing_extensions: 4.15.0
    urllib3: 2.6.3
    uvicorn: 0.40.0
    wcwidth: 0.3.2
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.15
    yarl: 1.22.0

Change History (4)

comment:1 by Tom Goddard, 28 hours ago

Component: Unassigned → Structure Analysis
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → pyKVFinder on Mac: '/usr/bin/clang' failed with exit code 1

comment:2 by Zach Pearson, 26 hours ago

Cc: Eric Pettersen added
Owner: changed from Eric Pettersen to Zach Pearson

It looks like a build operation is failing on -fopenmp=libomp; that's my bug.

comment:3 by Zach Pearson, 26 hours ago

Cc: Zach Pearson added; Eric Pettersen removed
Owner: changed from Zach Pearson to Eric Pettersen

pyKVfinder's build process requires OpenMP to be installed via homebrew for local builds. macOS 12.7 is too old to use the binary version of 0.8.x or 0.9.x; the most recent version that would work is 0.7.2.

You should update your macOS version if possible.

Reassigning to Eric

comment:4 by Eric Pettersen, 3 hours ago

Component: Structure Analysis → Surface/Binding Analysis
Resolution: → limitation
Status: assigned → closed
Summary: pyKVFinder on Mac: '/usr/bin/clang' failed with exit code 1 → KVFinder on old MacOS

Hi Stuti,

Unfortunately, the underlying pyKVFinder program that ChimeraX uses to find the pockets only runs on MacOS 15 and newer, so other than upgrading your OS or getting a newer Mac, there isn't really any solution for the problem you're having.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

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