Opened 6 months ago

Closed 6 months ago

#17775 closed defect (duplicate)

No compiled Mac Intel version of pyKVFinder

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

Description 

The following bug report has been submitted:
Platform:        macOS-14.7.3-x86_64-i386-64bit
ChimeraX Version: 1.10rc202505150242 (2025-05-15 02:42:12 UTC)
Description
Just installed ChimeraX. Cannot use 'Find Cavities'. I receive the following error - pyKVFinder not installed. Please advise.  Many thanks, Rachel

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.10rc202505150242 (2025-05-15)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> ui tool show "Dock Prep"

> 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  
╰─> [51 lines of output]  
running bdist_wheel  
running build  
running build_py  
file _pyKVFinder.py (for module _pyKVFinder) not found  
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder  
copying pyKVFinder/grid.py ->
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  
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  
file _pyKVFinder.py (for module _pyKVFinder) not found  
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/EisenbergWeiss.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/KyteDoolittle.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/RadzickaWolfenden.toml ->
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/ZhaoLondon.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/1FMO.KVFinder.output.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.xyz ->
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/ADN.xyz ->
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/ClO4.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/custom-box.toml ->
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  
file _pyKVFinder.py (for module _pyKVFinder) not found  
running build_ext  
building '_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/l0/r98wv9m51rb1yc_v93sr4byw0000gn/T/pip-build-env-
r_6pjv50/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/Applications/ChimeraX-1.10-rc2025.05.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/Applications/ChimeraX-1.10-rc2025.05.21.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 to build installable wheels for some pyproject.toml based
projects (pyKVFinder)  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.10-rc2025.05.21.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-1.10-rc2025.05.21.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-1.10-rc2025.05.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1399, in start_tool  
return cls._get_func(api, "start_tool")(session, ti.name)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10-rc2025.05.21.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-1.10-rc2025.05.21.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-1.10-rc2025.05.21.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-1.10-rc2025.05.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3219, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10-rc2025.05.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/pip.py", line 88, in pip  
run_logged_pip(pip_cmd, session.logger)  
File
"/Applications/ChimeraX-1.10-rc2025.05.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/python_utils.py", line 143, 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  
╰─> [51 lines of output]  
running bdist_wheel  
running build  
running build_py  
file _pyKVFinder.py (for module _pyKVFinder) not found  
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder  
copying pyKVFinder/grid.py ->
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  
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  
file _pyKVFinder.py (for module _pyKVFinder) not found  
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/EisenbergWeiss.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/KyteDoolittle.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/RadzickaWolfenden.toml ->
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/ZhaoLondon.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/1FMO.KVFinder.output.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.xyz ->
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/ADN.xyz ->
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/ClO4.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/custom-box.toml ->
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  
file _pyKVFinder.py (for module _pyKVFinder) not found  
running build_ext  
building '_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/l0/r98wv9m51rb1yc_v93sr4byw0000gn/T/pip-build-env-
r_6pjv50/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/Applications/ChimeraX-1.10-rc2025.05.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/Applications/ChimeraX-1.10-rc2025.05.21.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 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-1.10-rc2025.05.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1891, in <lambda>  
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10-rc2025.05.21.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-1.10-rc2025.05.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3219, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10-rc2025.05.21.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-1.10-rc2025.05.21.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  
╰─> [51 lines of output]  
running bdist_wheel  
running build  
running build_py  
file _pyKVFinder.py (for module _pyKVFinder) not found  
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder  
copying pyKVFinder/grid.py ->
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  
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  
file _pyKVFinder.py (for module _pyKVFinder) not found  
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/EisenbergWeiss.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/KyteDoolittle.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/RadzickaWolfenden.toml ->
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/ZhaoLondon.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/1FMO.KVFinder.output.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.xyz ->
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/ADN.xyz ->
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/ClO4.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/custom-box.toml ->
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  
file _pyKVFinder.py (for module _pyKVFinder) not found  
running build_ext  
building '_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/l0/r98wv9m51rb1yc_v93sr4byw0000gn/T/pip-build-env-
r_6pjv50/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/Applications/ChimeraX-1.10-rc2025.05.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/Applications/ChimeraX-1.10-rc2025.05.21.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 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  
╰─> [51 lines of output]  
running bdist_wheel  
running build  
running build_py  
file _pyKVFinder.py (for module _pyKVFinder) not found  
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder  
copying pyKVFinder/grid.py ->
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  
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  
file _pyKVFinder.py (for module _pyKVFinder) not found  
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/EisenbergWeiss.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/KyteDoolittle.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/RadzickaWolfenden.toml ->
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/ZhaoLondon.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/1FMO.KVFinder.output.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.xyz ->
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/ADN.xyz ->
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/ClO4.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/custom-box.toml ->
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  
file _pyKVFinder.py (for module _pyKVFinder) not found  
running build_ext  
building '_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/l0/r98wv9m51rb1yc_v93sr4byw0000gn/T/pip-build-env-
r_6pjv50/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/Applications/ChimeraX-1.10-rc2025.05.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/Applications/ChimeraX-1.10-rc2025.05.21.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 to build installable wheels for some pyproject.toml based
projects (pyKVFinder)  
  
  
File
"/Applications/ChimeraX-1.10-rc2025.05.21.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.  
  

> open /Users/rachel/Downloads/result.dock4 format swissdock

> viewdockx #1.1-133

> close session

> open /Users/rachel/Downloads/3CLproandhydroxychloroquine/files/receptor.pdb
> format pdb

Summary of feedback from opening
/Users/rachel/Downloads/3CLproandhydroxychloroquine/files/receptor.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK NONE *  
  
Ignored bad PDB record found on line 2  
REMARK DATE: 1/29/25 13:36:42 CREATED BY USER: root  
  
Chain information for receptor.pdb #1  
---  
Chain | Description  
? | No description available  
  
Computing secondary structure  

> 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  
╰─> [51 lines of output]  
running bdist_wheel  
running build  
running build_py  
file _pyKVFinder.py (for module _pyKVFinder) not found  
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder  
copying pyKVFinder/grid.py ->
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  
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  
file _pyKVFinder.py (for module _pyKVFinder) not found  
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/EisenbergWeiss.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/KyteDoolittle.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/RadzickaWolfenden.toml ->
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/ZhaoLondon.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/1FMO.KVFinder.output.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.xyz ->
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/ADN.xyz ->
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/ClO4.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/custom-box.toml ->
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  
file _pyKVFinder.py (for module _pyKVFinder) not found  
running build_ext  
building '_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/l0/r98wv9m51rb1yc_v93sr4byw0000gn/T/pip-build-
env-3e_na_iu/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/Applications/ChimeraX-1.10-rc2025.05.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/Applications/ChimeraX-1.10-rc2025.05.21.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 to build installable wheels for some pyproject.toml based
projects (pyKVFinder)  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.10-rc2025.05.21.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-1.10-rc2025.05.21.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-1.10-rc2025.05.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1399, in start_tool  
return cls._get_func(api, "start_tool")(session, ti.name)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10-rc2025.05.21.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-1.10-rc2025.05.21.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-1.10-rc2025.05.21.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-1.10-rc2025.05.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3219, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10-rc2025.05.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/pip.py", line 88, in pip  
run_logged_pip(pip_cmd, session.logger)  
File
"/Applications/ChimeraX-1.10-rc2025.05.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/python_utils.py", line 143, 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  
╰─> [51 lines of output]  
running bdist_wheel  
running build  
running build_py  
file _pyKVFinder.py (for module _pyKVFinder) not found  
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder  
copying pyKVFinder/grid.py ->
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  
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  
file _pyKVFinder.py (for module _pyKVFinder) not found  
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/EisenbergWeiss.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/KyteDoolittle.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/RadzickaWolfenden.toml ->
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/ZhaoLondon.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/1FMO.KVFinder.output.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.xyz ->
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/ADN.xyz ->
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/ClO4.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/custom-box.toml ->
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  
file _pyKVFinder.py (for module _pyKVFinder) not found  
running build_ext  
building '_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/l0/r98wv9m51rb1yc_v93sr4byw0000gn/T/pip-build-
env-3e_na_iu/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/Applications/ChimeraX-1.10-rc2025.05.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/Applications/ChimeraX-1.10-rc2025.05.21.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 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-1.10-rc2025.05.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1891, in <lambda>  
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10-rc2025.05.21.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-1.10-rc2025.05.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3219, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10-rc2025.05.21.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-1.10-rc2025.05.21.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  
╰─> [51 lines of output]  
running bdist_wheel  
running build  
running build_py  
file _pyKVFinder.py (for module _pyKVFinder) not found  
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder  
copying pyKVFinder/grid.py ->
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  
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  
file _pyKVFinder.py (for module _pyKVFinder) not found  
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/EisenbergWeiss.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/KyteDoolittle.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/RadzickaWolfenden.toml ->
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/ZhaoLondon.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/1FMO.KVFinder.output.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.xyz ->
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/ADN.xyz ->
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/ClO4.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/custom-box.toml ->
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  
file _pyKVFinder.py (for module _pyKVFinder) not found  
running build_ext  
building '_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/l0/r98wv9m51rb1yc_v93sr4byw0000gn/T/pip-build-
env-3e_na_iu/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/Applications/ChimeraX-1.10-rc2025.05.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/Applications/ChimeraX-1.10-rc2025.05.21.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 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  
╰─> [51 lines of output]  
running bdist_wheel  
running build  
running build_py  
file _pyKVFinder.py (for module _pyKVFinder) not found  
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder  
copying pyKVFinder/grid.py ->
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  
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  
file _pyKVFinder.py (for module _pyKVFinder) not found  
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/EisenbergWeiss.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/KyteDoolittle.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/RadzickaWolfenden.toml ->
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/ZhaoLondon.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/1FMO.KVFinder.output.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.xyz ->
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/ADN.xyz ->
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/ClO4.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/custom-box.toml ->
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  
file _pyKVFinder.py (for module _pyKVFinder) not found  
running build_ext  
building '_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/l0/r98wv9m51rb1yc_v93sr4byw0000gn/T/pip-build-
env-3e_na_iu/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/Applications/ChimeraX-1.10-rc2025.05.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/Applications/ChimeraX-1.10-rc2025.05.21.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 to build installable wheels for some pyproject.toml based
projects (pyKVFinder)  
  
  
File
"/Applications/ChimeraX-1.10-rc2025.05.21.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.  
  

> 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  
╰─> [51 lines of output]  
running bdist_wheel  
running build  
running build_py  
file _pyKVFinder.py (for module _pyKVFinder) not found  
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder  
copying pyKVFinder/grid.py ->
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  
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  
file _pyKVFinder.py (for module _pyKVFinder) not found  
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/EisenbergWeiss.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/KyteDoolittle.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/RadzickaWolfenden.toml ->
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/ZhaoLondon.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/1FMO.KVFinder.output.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.xyz ->
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/ADN.xyz ->
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/ClO4.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/custom-box.toml ->
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  
file _pyKVFinder.py (for module _pyKVFinder) not found  
running build_ext  
building '_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/l0/r98wv9m51rb1yc_v93sr4byw0000gn/T/pip-build-
env-j2miyg3i/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/Applications/ChimeraX-1.10-rc2025.05.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/Applications/ChimeraX-1.10-rc2025.05.21.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 to build installable wheels for some pyproject.toml based
projects (pyKVFinder)  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.10-rc2025.05.21.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-1.10-rc2025.05.21.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-1.10-rc2025.05.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1399, in start_tool  
return cls._get_func(api, "start_tool")(session, ti.name)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10-rc2025.05.21.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-1.10-rc2025.05.21.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-1.10-rc2025.05.21.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-1.10-rc2025.05.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3219, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10-rc2025.05.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/pip.py", line 88, in pip  
run_logged_pip(pip_cmd, session.logger)  
File
"/Applications/ChimeraX-1.10-rc2025.05.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/python_utils.py", line 143, 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  
╰─> [51 lines of output]  
running bdist_wheel  
running build  
running build_py  
file _pyKVFinder.py (for module _pyKVFinder) not found  
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder  
copying pyKVFinder/grid.py ->
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  
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  
file _pyKVFinder.py (for module _pyKVFinder) not found  
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/EisenbergWeiss.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/KyteDoolittle.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/RadzickaWolfenden.toml ->
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/ZhaoLondon.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/1FMO.KVFinder.output.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.xyz ->
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/ADN.xyz ->
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/ClO4.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/custom-box.toml ->
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  
file _pyKVFinder.py (for module _pyKVFinder) not found  
running build_ext  
building '_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/l0/r98wv9m51rb1yc_v93sr4byw0000gn/T/pip-build-
env-j2miyg3i/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/Applications/ChimeraX-1.10-rc2025.05.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/Applications/ChimeraX-1.10-rc2025.05.21.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 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-1.10-rc2025.05.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1891, in <lambda>  
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10-rc2025.05.21.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-1.10-rc2025.05.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3219, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10-rc2025.05.21.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-1.10-rc2025.05.21.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  
╰─> [51 lines of output]  
running bdist_wheel  
running build  
running build_py  
file _pyKVFinder.py (for module _pyKVFinder) not found  
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder  
copying pyKVFinder/grid.py ->
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  
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  
file _pyKVFinder.py (for module _pyKVFinder) not found  
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/EisenbergWeiss.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/KyteDoolittle.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/RadzickaWolfenden.toml ->
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/ZhaoLondon.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/1FMO.KVFinder.output.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.xyz ->
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/ADN.xyz ->
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/ClO4.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/custom-box.toml ->
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  
file _pyKVFinder.py (for module _pyKVFinder) not found  
running build_ext  
building '_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/l0/r98wv9m51rb1yc_v93sr4byw0000gn/T/pip-build-
env-j2miyg3i/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/Applications/ChimeraX-1.10-rc2025.05.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/Applications/ChimeraX-1.10-rc2025.05.21.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 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  
╰─> [51 lines of output]  
running bdist_wheel  
running build  
running build_py  
file _pyKVFinder.py (for module _pyKVFinder) not found  
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder  
copying pyKVFinder/grid.py ->
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  
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  
file _pyKVFinder.py (for module _pyKVFinder) not found  
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/EisenbergWeiss.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/KyteDoolittle.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/RadzickaWolfenden.toml ->
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/ZhaoLondon.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/1FMO.KVFinder.output.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.xyz ->
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/ADN.xyz ->
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/ClO4.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/custom-box.toml ->
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  
file _pyKVFinder.py (for module _pyKVFinder) not found  
running build_ext  
building '_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/l0/r98wv9m51rb1yc_v93sr4byw0000gn/T/pip-build-
env-j2miyg3i/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/Applications/ChimeraX-1.10-rc2025.05.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/Applications/ChimeraX-1.10-rc2025.05.21.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 to build installable wheels for some pyproject.toml based
projects (pyKVFinder)  
  
  
File
"/Applications/ChimeraX-1.10-rc2025.05.21.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.  
  

> select add #1

4682 atoms, 4735 bonds, 306 residues, 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  
╰─> [51 lines of output]  
running bdist_wheel  
running build  
running build_py  
file _pyKVFinder.py (for module _pyKVFinder) not found  
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder  
copying pyKVFinder/grid.py ->
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  
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  
file _pyKVFinder.py (for module _pyKVFinder) not found  
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/EisenbergWeiss.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/KyteDoolittle.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/RadzickaWolfenden.toml ->
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/ZhaoLondon.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/1FMO.KVFinder.output.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.xyz ->
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/ADN.xyz ->
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/ClO4.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/custom-box.toml ->
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  
file _pyKVFinder.py (for module _pyKVFinder) not found  
running build_ext  
building '_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/l0/r98wv9m51rb1yc_v93sr4byw0000gn/T/pip-build-env-
upu0dx_0/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/Applications/ChimeraX-1.10-rc2025.05.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/Applications/ChimeraX-1.10-rc2025.05.21.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 to build installable wheels for some pyproject.toml based
projects (pyKVFinder)  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.10-rc2025.05.21.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-1.10-rc2025.05.21.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-1.10-rc2025.05.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1399, in start_tool  
return cls._get_func(api, "start_tool")(session, ti.name)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10-rc2025.05.21.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-1.10-rc2025.05.21.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-1.10-rc2025.05.21.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-1.10-rc2025.05.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3219, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10-rc2025.05.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/pip.py", line 88, in pip  
run_logged_pip(pip_cmd, session.logger)  
File
"/Applications/ChimeraX-1.10-rc2025.05.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/python_utils.py", line 143, 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  
╰─> [51 lines of output]  
running bdist_wheel  
running build  
running build_py  
file _pyKVFinder.py (for module _pyKVFinder) not found  
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder  
copying pyKVFinder/grid.py ->
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  
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  
file _pyKVFinder.py (for module _pyKVFinder) not found  
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/EisenbergWeiss.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/KyteDoolittle.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/RadzickaWolfenden.toml ->
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/ZhaoLondon.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/1FMO.KVFinder.output.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.xyz ->
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/ADN.xyz ->
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/ClO4.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/custom-box.toml ->
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  
file _pyKVFinder.py (for module _pyKVFinder) not found  
running build_ext  
building '_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/l0/r98wv9m51rb1yc_v93sr4byw0000gn/T/pip-build-env-
upu0dx_0/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/Applications/ChimeraX-1.10-rc2025.05.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/Applications/ChimeraX-1.10-rc2025.05.21.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 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-1.10-rc2025.05.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1891, in <lambda>  
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10-rc2025.05.21.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-1.10-rc2025.05.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3219, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10-rc2025.05.21.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-1.10-rc2025.05.21.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  
╰─> [51 lines of output]  
running bdist_wheel  
running build  
running build_py  
file _pyKVFinder.py (for module _pyKVFinder) not found  
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder  
copying pyKVFinder/grid.py ->
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  
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  
file _pyKVFinder.py (for module _pyKVFinder) not found  
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/EisenbergWeiss.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/KyteDoolittle.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/RadzickaWolfenden.toml ->
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/ZhaoLondon.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/1FMO.KVFinder.output.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.xyz ->
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/ADN.xyz ->
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/ClO4.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/custom-box.toml ->
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  
file _pyKVFinder.py (for module _pyKVFinder) not found  
running build_ext  
building '_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/l0/r98wv9m51rb1yc_v93sr4byw0000gn/T/pip-build-env-
upu0dx_0/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/Applications/ChimeraX-1.10-rc2025.05.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/Applications/ChimeraX-1.10-rc2025.05.21.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 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  
╰─> [51 lines of output]  
running bdist_wheel  
running build  
running build_py  
file _pyKVFinder.py (for module _pyKVFinder) not found  
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder  
copying pyKVFinder/grid.py ->
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  
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  
file _pyKVFinder.py (for module _pyKVFinder) not found  
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/EisenbergWeiss.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/KyteDoolittle.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/RadzickaWolfenden.toml ->
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/ZhaoLondon.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/1FMO.KVFinder.output.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.xyz ->
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/ADN.xyz ->
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/ClO4.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/custom-box.toml ->
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  
file _pyKVFinder.py (for module _pyKVFinder) not found  
running build_ext  
building '_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/l0/r98wv9m51rb1yc_v93sr4byw0000gn/T/pip-build-env-
upu0dx_0/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/Applications/ChimeraX-1.10-rc2025.05.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/Applications/ChimeraX-1.10-rc2025.05.21.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 to build installable wheels for some pyproject.toml based
projects (pyKVFinder)  
  
  
File
"/Applications/ChimeraX-1.10-rc2025.05.21.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.  
  

> ui tool show ViewDockX

No suitable models found for ViewDockX  

> color sel orange

> preset "initial styles" cartoon

Using preset: Initial Styles / Cartoon  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> help help:user

> help help:quickstart

Select a database from the database table  

> toolshed show

> open 1ewl fromDatabase pdb format mmcif

Summary of feedback from opening 1ewl fetched from pdb  
---  
notes | Fetching compressed mmCIF 1ewl from http://files.rcsb.org/download/1ewl.cif  
Fetching CCD R99 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/9/R99/R99.cif  
  
1ewl title:  
Crystal structure of cruzain bound to WRR-99 [more info...]  
  
Chain information for 1ewl #2  
---  
Chain | Description | UniProt  
A | CRUZAIN | CYSP_TRYCR 1-212  
  
Non-standard residues in 1ewl #2  
---  
R99 — N-[3-carboxy-2-hydroxy-propionyl]-D-homophenylalanyl-
amino-2-methylbutane (WRR-99)  
  

> hide #1 models

> select subtract #1

Nothing selected  

> ui tool show "Dock Prep"

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Summary of feedback from adding hydrogens to 1ewl #2  
---  
notes | Termini for 1ewl (#2) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini: 1ewl #2/A ALA 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: 1ewl #2/A GLY 212  
Chain-final residues that are not actual C termini:  
205 hydrogen bonds  
1518 hydrogens added  
  
Closest equivalent command: addcharge #2 standardizeResidues none  
Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue R99+CYS (net charge -1) with gasteiger
method  
Running ANTECHAMBER command:
/Applications/ChimeraX-1.10-rc2025.05.21.app/Contents/bin/amber20/bin/antechamber
-i /var/folders/l0/r98wv9m51rb1yc_v93sr4byw0000gn/T/tmpfksn6dhl/ante.in.mol2
-fi mol2 -o
/var/folders/l0/r98wv9m51rb1yc_v93sr4byw0000gn/T/tmpfksn6dhl/ante.out.mol2 -fo
mol2 -c gas -nc -1 -j 5 -s 2 -dr n  
(R99+CYS) ``  
(R99+CYS) `Welcome to antechamber 20.0: molecular input file processor.`  
(R99+CYS) ``  
(R99+CYS) `Info: Finished reading file
(/var/folders/l0/r98wv9m51rb1yc_v93sr4byw0000gn/T/tmpfksn6dhl/ante.in.mol2);
atoms read (74), bonds read (74).`  
(R99+CYS) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(R99+CYS) `Running:
/Applications/ChimeraX-1.10-rc2025.05.21.app/Contents/bin/amber20/bin/bondtype
-j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(R99+CYS) ``  
(R99+CYS) ``  
(R99+CYS) `Running:
/Applications/ChimeraX-1.10-rc2025.05.21.app/Contents/bin/amber20/bin/atomtype
-i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(R99+CYS) `Running:
/Applications/ChimeraX-1.10-rc2025.05.21.app/Contents/bin/amber20/bin/atomtype
-i ANTECHAMBER_GAS.AC -o ANTECHAMBER_GAS_AT.AC -d
/Applications/ChimeraX-1.10-rc2025.05.21.app/Contents/bin/amber20/dat/antechamber/ATOMTYPE_GAS.DEF`  
(R99+CYS) ``  
Charges for residue R99+CYS determined  
Dock prep finished  

> save "/Users/rachel/Desktop/1ewl chimerax.mol2"

> 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  
╰─> [51 lines of output]  
running bdist_wheel  
running build  
running build_py  
file _pyKVFinder.py (for module _pyKVFinder) not found  
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder  
copying pyKVFinder/grid.py ->
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  
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  
file _pyKVFinder.py (for module _pyKVFinder) not found  
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/EisenbergWeiss.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/KyteDoolittle.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/RadzickaWolfenden.toml ->
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/ZhaoLondon.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/1FMO.KVFinder.output.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.xyz ->
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/ADN.xyz ->
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/ClO4.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/custom-box.toml ->
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  
file _pyKVFinder.py (for module _pyKVFinder) not found  
running build_ext  
building '_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/l0/r98wv9m51rb1yc_v93sr4byw0000gn/T/pip-build-env-
mvsko130/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/Applications/ChimeraX-1.10-rc2025.05.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/Applications/ChimeraX-1.10-rc2025.05.21.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 to build installable wheels for some pyproject.toml based
projects (pyKVFinder)  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.10-rc2025.05.21.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-1.10-rc2025.05.21.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-1.10-rc2025.05.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1399, in start_tool  
return cls._get_func(api, "start_tool")(session, ti.name)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10-rc2025.05.21.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-1.10-rc2025.05.21.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-1.10-rc2025.05.21.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-1.10-rc2025.05.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3219, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10-rc2025.05.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/pip.py", line 88, in pip  
run_logged_pip(pip_cmd, session.logger)  
File
"/Applications/ChimeraX-1.10-rc2025.05.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/python_utils.py", line 143, 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  
╰─> [51 lines of output]  
running bdist_wheel  
running build  
running build_py  
file _pyKVFinder.py (for module _pyKVFinder) not found  
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder  
copying pyKVFinder/grid.py ->
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  
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  
file _pyKVFinder.py (for module _pyKVFinder) not found  
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/EisenbergWeiss.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/KyteDoolittle.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/RadzickaWolfenden.toml ->
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/ZhaoLondon.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/1FMO.KVFinder.output.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.xyz ->
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/ADN.xyz ->
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/ClO4.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/custom-box.toml ->
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  
file _pyKVFinder.py (for module _pyKVFinder) not found  
running build_ext  
building '_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/l0/r98wv9m51rb1yc_v93sr4byw0000gn/T/pip-build-env-
mvsko130/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/Applications/ChimeraX-1.10-rc2025.05.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/Applications/ChimeraX-1.10-rc2025.05.21.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 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-1.10-rc2025.05.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1891, in <lambda>  
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10-rc2025.05.21.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-1.10-rc2025.05.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3219, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10-rc2025.05.21.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-1.10-rc2025.05.21.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  
╰─> [51 lines of output]  
running bdist_wheel  
running build  
running build_py  
file _pyKVFinder.py (for module _pyKVFinder) not found  
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder  
copying pyKVFinder/grid.py ->
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  
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  
file _pyKVFinder.py (for module _pyKVFinder) not found  
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/EisenbergWeiss.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/KyteDoolittle.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/RadzickaWolfenden.toml ->
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/ZhaoLondon.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/1FMO.KVFinder.output.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.xyz ->
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/ADN.xyz ->
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/ClO4.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/custom-box.toml ->
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  
file _pyKVFinder.py (for module _pyKVFinder) not found  
running build_ext  
building '_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/l0/r98wv9m51rb1yc_v93sr4byw0000gn/T/pip-build-env-
mvsko130/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/Applications/ChimeraX-1.10-rc2025.05.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/Applications/ChimeraX-1.10-rc2025.05.21.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 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  
╰─> [51 lines of output]  
running bdist_wheel  
running build  
running build_py  
file _pyKVFinder.py (for module _pyKVFinder) not found  
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder  
copying pyKVFinder/grid.py ->
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  
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  
file _pyKVFinder.py (for module _pyKVFinder) not found  
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/EisenbergWeiss.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/KyteDoolittle.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/RadzickaWolfenden.toml ->
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/ZhaoLondon.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/1FMO.KVFinder.output.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.xyz ->
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/ADN.xyz ->
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/ClO4.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/custom-box.toml ->
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  
file _pyKVFinder.py (for module _pyKVFinder) not found  
running build_ext  
building '_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/l0/r98wv9m51rb1yc_v93sr4byw0000gn/T/pip-build-env-
mvsko130/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/Applications/ChimeraX-1.10-rc2025.05.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/Applications/ChimeraX-1.10-rc2025.05.21.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 to build installable wheels for some pyproject.toml based
projects (pyKVFinder)  
  
  
File
"/Applications/ChimeraX-1.10-rc2025.05.21.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.  
  

> select #2/A

3137 atoms, 3180 bonds, 216 residues, 1 model selected  

> select solvent

Nothing selected  

> ui tool show "Dock Prep"

> 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  
╰─> [51 lines of output]  
running bdist_wheel  
running build  
running build_py  
file _pyKVFinder.py (for module _pyKVFinder) not found  
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder  
copying pyKVFinder/grid.py ->
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  
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  
file _pyKVFinder.py (for module _pyKVFinder) not found  
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/EisenbergWeiss.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/KyteDoolittle.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/RadzickaWolfenden.toml ->
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/ZhaoLondon.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/1FMO.KVFinder.output.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.xyz ->
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/ADN.xyz ->
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/ClO4.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/custom-box.toml ->
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  
file _pyKVFinder.py (for module _pyKVFinder) not found  
running build_ext  
building '_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/l0/r98wv9m51rb1yc_v93sr4byw0000gn/T/pip-build-env-
bqxet7h3/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/Applications/ChimeraX-1.10-rc2025.05.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/Applications/ChimeraX-1.10-rc2025.05.21.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 to build installable wheels for some pyproject.toml based
projects (pyKVFinder)  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.10-rc2025.05.21.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-1.10-rc2025.05.21.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-1.10-rc2025.05.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1399, in start_tool  
return cls._get_func(api, "start_tool")(session, ti.name)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10-rc2025.05.21.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-1.10-rc2025.05.21.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-1.10-rc2025.05.21.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-1.10-rc2025.05.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3219, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10-rc2025.05.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/pip.py", line 88, in pip  
run_logged_pip(pip_cmd, session.logger)  
File
"/Applications/ChimeraX-1.10-rc2025.05.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/python_utils.py", line 143, 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  
╰─> [51 lines of output]  
running bdist_wheel  
running build  
running build_py  
file _pyKVFinder.py (for module _pyKVFinder) not found  
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder  
copying pyKVFinder/grid.py ->
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  
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  
file _pyKVFinder.py (for module _pyKVFinder) not found  
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/EisenbergWeiss.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/KyteDoolittle.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/RadzickaWolfenden.toml ->
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/ZhaoLondon.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/1FMO.KVFinder.output.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.xyz ->
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/ADN.xyz ->
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/ClO4.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/custom-box.toml ->
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  
file _pyKVFinder.py (for module _pyKVFinder) not found  
running build_ext  
building '_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/l0/r98wv9m51rb1yc_v93sr4byw0000gn/T/pip-build-env-
bqxet7h3/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/Applications/ChimeraX-1.10-rc2025.05.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/Applications/ChimeraX-1.10-rc2025.05.21.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 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-1.10-rc2025.05.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1891, in <lambda>  
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10-rc2025.05.21.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-1.10-rc2025.05.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3219, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10-rc2025.05.21.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-1.10-rc2025.05.21.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  
╰─> [51 lines of output]  
running bdist_wheel  
running build  
running build_py  
file _pyKVFinder.py (for module _pyKVFinder) not found  
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder  
copying pyKVFinder/grid.py ->
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  
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  
file _pyKVFinder.py (for module _pyKVFinder) not found  
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/EisenbergWeiss.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/KyteDoolittle.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/RadzickaWolfenden.toml ->
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/ZhaoLondon.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/1FMO.KVFinder.output.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.xyz ->
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/ADN.xyz ->
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/ClO4.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/custom-box.toml ->
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  
file _pyKVFinder.py (for module _pyKVFinder) not found  
running build_ext  
building '_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/l0/r98wv9m51rb1yc_v93sr4byw0000gn/T/pip-build-env-
bqxet7h3/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/Applications/ChimeraX-1.10-rc2025.05.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/Applications/ChimeraX-1.10-rc2025.05.21.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 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  
╰─> [51 lines of output]  
running bdist_wheel  
running build  
running build_py  
file _pyKVFinder.py (for module _pyKVFinder) not found  
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder  
copying pyKVFinder/grid.py ->
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  
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  
file _pyKVFinder.py (for module _pyKVFinder) not found  
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/EisenbergWeiss.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/KyteDoolittle.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/RadzickaWolfenden.toml ->
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/ZhaoLondon.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/1FMO.KVFinder.output.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.xyz ->
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/ADN.xyz ->
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/ClO4.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/custom-box.toml ->
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  
file _pyKVFinder.py (for module _pyKVFinder) not found  
running build_ext  
building '_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/l0/r98wv9m51rb1yc_v93sr4byw0000gn/T/pip-build-env-
bqxet7h3/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/Applications/ChimeraX-1.10-rc2025.05.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/Applications/ChimeraX-1.10-rc2025.05.21.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 to build installable wheels for some pyproject.toml based
projects (pyKVFinder)  
  
  
File
"/Applications/ChimeraX-1.10-rc2025.05.21.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.  
  

> toolshed show

Downloading bundle ChimeraX_LigandRecognizer-0.2-py3-none-any.whl  
Bundle installation canceled  

> select ::name="HSD"::name="HSE"::name="R99"

171 atoms, 172 bonds, 8 residues, 2 models selected  

> log metadata #1

The model has no metadata

> log chains #1

Chain information for receptor.pdb #1  
---  
Chain | Description  
? | No description available  
  

> hide #1 target m

> ui tool show "Selection Inspector"

> remove

Unknown command: remove  

> remove r99

Unknown command: remove r99  

> select ::name="R99"

52 atoms, 52 bonds, 1 residue, 1 model selected  

> select ligand

52 atoms, 52 bonds, 1 residue, 1 model selected  

> remove ligand

Unknown command: remove ligand  

> ui mousemode right "map eraser"

[Repeated 4 time(s)]

> ui mousemode right "contour level"

> ui mousemode right "move planes"

> delete del

Missing or invalid "atoms" argument: invalid atoms specifier  

> select #2/A

3137 atoms, 3180 bonds, 216 residues, 1 model selected  

> select ligand

52 atoms, 52 bonds, 1 residue, 1 model selected  

> delete sel

> select ions

Nothing selected  

> select ::name="HSD"::name="HSE"

119 atoms, 120 bonds, 7 residues, 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  
╰─> [51 lines of output]  
running bdist_wheel  
running build  
running build_py  
file _pyKVFinder.py (for module _pyKVFinder) not found  
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder  
copying pyKVFinder/grid.py ->
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  
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  
file _pyKVFinder.py (for module _pyKVFinder) not found  
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/EisenbergWeiss.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/KyteDoolittle.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/RadzickaWolfenden.toml ->
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/ZhaoLondon.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/1FMO.KVFinder.output.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.xyz ->
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/ADN.xyz ->
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/ClO4.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/custom-box.toml ->
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  
file _pyKVFinder.py (for module _pyKVFinder) not found  
running build_ext  
building '_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/l0/r98wv9m51rb1yc_v93sr4byw0000gn/T/pip-build-
env-m9gvnf9q/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/Applications/ChimeraX-1.10-rc2025.05.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/Applications/ChimeraX-1.10-rc2025.05.21.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 to build installable wheels for some pyproject.toml based
projects (pyKVFinder)  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.10-rc2025.05.21.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-1.10-rc2025.05.21.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-1.10-rc2025.05.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1399, in start_tool  
return cls._get_func(api, "start_tool")(session, ti.name)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10-rc2025.05.21.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-1.10-rc2025.05.21.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-1.10-rc2025.05.21.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-1.10-rc2025.05.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3219, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10-rc2025.05.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/pip.py", line 88, in pip  
run_logged_pip(pip_cmd, session.logger)  
File
"/Applications/ChimeraX-1.10-rc2025.05.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/python_utils.py", line 143, 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  
╰─> [51 lines of output]  
running bdist_wheel  
running build  
running build_py  
file _pyKVFinder.py (for module _pyKVFinder) not found  
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder  
copying pyKVFinder/grid.py ->
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  
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  
file _pyKVFinder.py (for module _pyKVFinder) not found  
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/EisenbergWeiss.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/KyteDoolittle.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/RadzickaWolfenden.toml ->
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/ZhaoLondon.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/1FMO.KVFinder.output.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.xyz ->
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/ADN.xyz ->
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/ClO4.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/custom-box.toml ->
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  
file _pyKVFinder.py (for module _pyKVFinder) not found  
running build_ext  
building '_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/l0/r98wv9m51rb1yc_v93sr4byw0000gn/T/pip-build-
env-m9gvnf9q/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/Applications/ChimeraX-1.10-rc2025.05.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/Applications/ChimeraX-1.10-rc2025.05.21.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 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-1.10-rc2025.05.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1891, in <lambda>  
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10-rc2025.05.21.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-1.10-rc2025.05.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3219, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10-rc2025.05.21.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-1.10-rc2025.05.21.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  
╰─> [51 lines of output]  
running bdist_wheel  
running build  
running build_py  
file _pyKVFinder.py (for module _pyKVFinder) not found  
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder  
copying pyKVFinder/grid.py ->
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  
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  
file _pyKVFinder.py (for module _pyKVFinder) not found  
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/EisenbergWeiss.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/KyteDoolittle.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/RadzickaWolfenden.toml ->
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/ZhaoLondon.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/1FMO.KVFinder.output.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.xyz ->
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/ADN.xyz ->
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/ClO4.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/custom-box.toml ->
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  
file _pyKVFinder.py (for module _pyKVFinder) not found  
running build_ext  
building '_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/l0/r98wv9m51rb1yc_v93sr4byw0000gn/T/pip-build-
env-m9gvnf9q/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/Applications/ChimeraX-1.10-rc2025.05.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/Applications/ChimeraX-1.10-rc2025.05.21.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 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  
╰─> [51 lines of output]  
running bdist_wheel  
running build  
running build_py  
file _pyKVFinder.py (for module _pyKVFinder) not found  
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder  
copying pyKVFinder/grid.py ->
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  
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  
file _pyKVFinder.py (for module _pyKVFinder) not found  
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/EisenbergWeiss.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/KyteDoolittle.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/RadzickaWolfenden.toml ->
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/ZhaoLondon.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/1FMO.KVFinder.output.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.xyz ->
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/ADN.xyz ->
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/ClO4.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/custom-box.toml ->
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  
file _pyKVFinder.py (for module _pyKVFinder) not found  
running build_ext  
building '_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/l0/r98wv9m51rb1yc_v93sr4byw0000gn/T/pip-build-
env-m9gvnf9q/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/Applications/ChimeraX-1.10-rc2025.05.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/Applications/ChimeraX-1.10-rc2025.05.21.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 to build installable wheels for some pyproject.toml based
projects (pyKVFinder)  
  
  
File
"/Applications/ChimeraX-1.10-rc2025.05.21.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.  
  

> select #2/A

3085 atoms, 3127 bonds, 215 residues, 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  
╰─> [51 lines of output]  
running bdist_wheel  
running build  
running build_py  
file _pyKVFinder.py (for module _pyKVFinder) not found  
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder  
copying pyKVFinder/grid.py ->
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  
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  
file _pyKVFinder.py (for module _pyKVFinder) not found  
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/EisenbergWeiss.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/KyteDoolittle.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/RadzickaWolfenden.toml ->
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/ZhaoLondon.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/1FMO.KVFinder.output.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.xyz ->
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/ADN.xyz ->
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/ClO4.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/custom-box.toml ->
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  
file _pyKVFinder.py (for module _pyKVFinder) not found  
running build_ext  
building '_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/l0/r98wv9m51rb1yc_v93sr4byw0000gn/T/pip-build-
env-x55zd97o/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/Applications/ChimeraX-1.10-rc2025.05.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/Applications/ChimeraX-1.10-rc2025.05.21.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 to build installable wheels for some pyproject.toml based
projects (pyKVFinder)  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.10-rc2025.05.21.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-1.10-rc2025.05.21.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-1.10-rc2025.05.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1399, in start_tool  
return cls._get_func(api, "start_tool")(session, ti.name)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10-rc2025.05.21.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-1.10-rc2025.05.21.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-1.10-rc2025.05.21.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-1.10-rc2025.05.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3219, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10-rc2025.05.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/pip.py", line 88, in pip  
run_logged_pip(pip_cmd, session.logger)  
File
"/Applications/ChimeraX-1.10-rc2025.05.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/python_utils.py", line 143, 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  
╰─> [51 lines of output]  
running bdist_wheel  
running build  
running build_py  
file _pyKVFinder.py (for module _pyKVFinder) not found  
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder  
copying pyKVFinder/grid.py ->
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  
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  
file _pyKVFinder.py (for module _pyKVFinder) not found  
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/EisenbergWeiss.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/KyteDoolittle.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/RadzickaWolfenden.toml ->
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/ZhaoLondon.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/1FMO.KVFinder.output.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.xyz ->
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/ADN.xyz ->
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/ClO4.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/custom-box.toml ->
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  
file _pyKVFinder.py (for module _pyKVFinder) not found  
running build_ext  
building '_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/l0/r98wv9m51rb1yc_v93sr4byw0000gn/T/pip-build-
env-x55zd97o/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/Applications/ChimeraX-1.10-rc2025.05.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/Applications/ChimeraX-1.10-rc2025.05.21.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 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-1.10-rc2025.05.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1891, in <lambda>  
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10-rc2025.05.21.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-1.10-rc2025.05.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3219, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10-rc2025.05.21.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-1.10-rc2025.05.21.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  
╰─> [51 lines of output]  
running bdist_wheel  
running build  
running build_py  
file _pyKVFinder.py (for module _pyKVFinder) not found  
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder  
copying pyKVFinder/grid.py ->
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  
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  
file _pyKVFinder.py (for module _pyKVFinder) not found  
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/EisenbergWeiss.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/KyteDoolittle.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/RadzickaWolfenden.toml ->
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/ZhaoLondon.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/1FMO.KVFinder.output.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.xyz ->
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/ADN.xyz ->
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/ClO4.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/custom-box.toml ->
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  
file _pyKVFinder.py (for module _pyKVFinder) not found  
running build_ext  
building '_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/l0/r98wv9m51rb1yc_v93sr4byw0000gn/T/pip-build-
env-x55zd97o/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/Applications/ChimeraX-1.10-rc2025.05.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/Applications/ChimeraX-1.10-rc2025.05.21.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 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  
╰─> [51 lines of output]  
running bdist_wheel  
running build  
running build_py  
file _pyKVFinder.py (for module _pyKVFinder) not found  
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder  
copying pyKVFinder/grid.py ->
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  
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  
file _pyKVFinder.py (for module _pyKVFinder) not found  
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/EisenbergWeiss.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/KyteDoolittle.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/RadzickaWolfenden.toml ->
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/ZhaoLondon.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/1FMO.KVFinder.output.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.xyz ->
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/ADN.xyz ->
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/ClO4.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/custom-box.toml ->
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  
file _pyKVFinder.py (for module _pyKVFinder) not found  
running build_ext  
building '_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/l0/r98wv9m51rb1yc_v93sr4byw0000gn/T/pip-build-
env-x55zd97o/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/Applications/ChimeraX-1.10-rc2025.05.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/Applications/ChimeraX-1.10-rc2025.05.21.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 to build installable wheels for some pyproject.toml based
projects (pyKVFinder)  
  
  
File
"/Applications/ChimeraX-1.10-rc2025.05.21.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 INTEL-22.5.12
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine
OpenGL vendor: Intel Inc.

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro16,2
      Processor Name: Quad-Core Intel Core i5
      Processor Speed: 2 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 512 KB
      L3 Cache: 6 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      System Firmware Version: 2069.80.3.0.0 (iBridge: 22.16.13051.0.0,0)
      OS Loader Version: 580.140.1~51

Software:

    System Software Overview:

      System Version: macOS 14.7.3 (23H417)
      Kernel Version: Darwin 23.6.0
      Time since boot: 17 days, 1 hour, 32 minutes

Graphics/Displays:

    Intel Iris Plus Graphics:

      Chipset Model: Intel Iris Plus Graphics
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x8a53
      Revision ID: 0x0007
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    auditwheel: 6.3.0
    babel: 2.17.0
    beautifulsoup4: 4.13.3
    blockdiag: 3.0.0
    blosc2: 3.3.3
    build: 1.2.2.post1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.2
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.7
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.20.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Aniso: 1.1.3
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60.6
    ChimeraX-AtomicLibrary: 14.1.18
    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: 1.2.6
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.10rc202505150242
    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: 2.2.1
    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: 1.1.2
    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: 1.2.0
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.19.1
    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: 1.45.1
    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
    contourpy: 1.3.2
    coverage: 7.8.0
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.12
    debugpy: 1.8.14
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.0
    filelock: 3.18.0
    fonttools: 4.58.0
    funcparserlib: 2.0.0a0
    glfw: 2.9.0
    grako: 3.16.5
    h5py: 3.13.0
    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: 5.7.2
    jupyterlab_widgets: 3.0.15
    kiwisolver: 1.4.8
    line_profiler: 4.2.0
    lxml: 5.3.1
    lz4: 4.4.4
    MarkupSafe: 3.0.2
    matplotlib: 3.10.1
    matplotlib-inline: 0.1.7
    msgpack: 1.1.0
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    numpy: 1.26.4
    OpenMM: 8.2.0
    openvr: 1.26.701
    packaging: 24.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 10.4.0
    pip: 25.0.1
    pkginfo: 1.11.1
    platformdirs: 4.3.8
    pluggy: 1.5.0
    prompt_toolkit: 3.0.51
    psutil: 7.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.32
    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: 8.3.5
    pytest-cov: 6.1.1
    python-dateutil: 2.9.0.post0
    pytz: 2025.2
    pyzmq: 26.4.0
    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
    tornado: 6.4.2
    traitlets: 5.14.3
    typing_extensions: 4.13.2
    tzdata: 2025.2
    urllib3: 2.4.0
    wcwidth: 0.2.13
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.14

Change History (2)

comment:1 by Eric Pettersen, 6 months ago

Component: Unassigned → Surface/Binding Analysis
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → No compiled Mac Intel version of pyKVFinder

comment:2 by Eric Pettersen, 6 months ago

Resolution: → duplicate
Status: accepted → closed

Hi Rachel,

Thanks for reporting this problem. The issue is that part of the pyKVFinder Python module that Find Cavities uses is compiled, and there is no compiled version of the module available for Intel Mac computers. The maintainers of the pyKVFinder module are working on getting a compiled version for Intel Macs, but as I understand it they have a few other deadlines they have to meet this month, so it could be awhile.
In the interim, if you have access to any other type of machine than an Intel Mac, Find Cavities should work there. Also, I will add you to the main ticket we have open for this problem, so you will be notify as progress occurs.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

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