KVFinder on old MacOS

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-14.3.1-arm64-arm-64bit
ChimeraX Version: 1.11.1 (2026-01-23 05:51:34 UTC)
Description
Replace this text with list of actions that caused this problem to occur

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

> open /Users/xiongwenling/Downloads/tspan4.cxs format session

Log from Thu Mar 19 18:35:17 2026UCSF ChimeraX version: 1.11.1 (2026-01-23)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/xiongwenling/Downloads/fold_tspan4-2 2/tspan4 .cif"

Chain information for tspan4 .cif #1  
---  
Chain | Description  
A | .  
  
Computing secondary structure  

> open /Users/xiongwenling/Downloads/5TCX.cif

5TCX.cif title:  
Crystal structure of human tetraspanin CD81 [more info...]  
  
Chain information for 5TCX.cif #2  
---  
Chain | Description | UniProt  
A | CD81 antigen | CD81_HUMAN 2-236  
  
Non-standard residues in 5TCX.cif #2  
---  
CLR — cholesterol  
  

> color #1 lightblue

> color #2 salmon

> cartoon #1,2

> hide #1,2 atoms

> show #1,2 cartoons

> select #1:12-34,54-76,83-105,202-224

690 atoms, 702 bonds, 92 residues, 1 model selected  

> select #2:13-35,62-84,91-113,204-226

701 atoms, 716 bonds, 92 residues, 1 model selected  

> select #1:12-34,54-76,83-105,202-224

690 atoms, 702 bonds, 92 residues, 1 model selected  

> select #2:13-35,62-84,91-113,204-226

701 atoms, 716 bonds, 92 residues, 1 model selected  

> select #1:12-34,54-76,83-105,202-224

690 atoms, 702 bonds, 92 residues, 1 model selected  

> select #1:12-34,54-76,83-105,202-224

690 atoms, 702 bonds, 92 residues, 1 model selected  

> select #2:13-35,62-84,91-113,204-226

701 atoms, 716 bonds, 92 residues, 1 model selected  

> select #1:12-34,54-76,83-105,202-224

690 atoms, 702 bonds, 92 residues, 1 model selected  

> select #2:13-35,62-84,91-113,204-226

701 atoms, 716 bonds, 92 residues, 1 model selected  

> matchmaker #1 to #2 pairing ss #1:12-34,54-76,83-105,202-224
> #2:13-35,62-84,91-113,204-226

Expected a keyword  

> select #1:12-34,54-76,83-105,202-224

690 atoms, 702 bonds, 92 residues, 1 model selected  

> select #1:12-34,54-76,83-105,202-224

690 atoms, 702 bonds, 92 residues, 1 model selected  

> select #1:12-34,54-76,83-105,202-224 select #2:13-35,62-84,91-113,204-226

Expected a keyword  

> select #1:12-34,54-76,83-105,202-224

690 atoms, 702 bonds, 92 residues, 1 model selected  

> select #2:13-35,62-84,91-113,204-226

701 atoms, 716 bonds, 92 residues, 1 model selected  

> select /#1:12-34,54-76,83-105,202-224/#2:13-35,62-84,91-113,204-226

Expected an objects specifier or a keyword  

> sel#1:12-34,54-76,83-105,202-224/#2:13-35,62-84,91-113,204-226

Unknown command:
sel#1:12-34,54-76,83-105,202-224/#2:13-35,62-84,91-113,204-226  

> selext #1:12-34,54-76,83-105,202-224,#2:13-35,62-84,91-113,204-226

Unknown command: selext
#1:12-34,54-76,83-105,202-224,#2:13-35,62-84,91-113,204-226  

> selext #1:12-34,54-76,83-105,202-224 and #2:13-35,62-84,91-113,204-226

Unknown command: selext #1:12-34,54-76,83-105,202-224 and
#2:13-35,62-84,91-113,204-226  

> select #1:12-34,54-76,83-105,202-224 and #2:13-35,62-84,91-113,204-226

Expected a keyword  

> select #1:12-34,54-76,83-105,202-224, #2:13-35,62-84,91-113,204-226

Expected an objects specifier or a keyword  

> select #1:12-34,54-76,83-105,202-224/ #2:13-35,62-84,91-113,204-226

Expected an objects specifier or a keyword  

> select #1:12-34,54-76,83-105,202-224 add #2:13-35,62-84,91-113,204-226

Expected a keyword  

> select #1/A

1835 atoms, 1880 bonds, 238 residues, 1 model selected  

> select #2/A

1628 atoms, 1660 bonds, 2 pseudobonds, 212 residues, 2 models selected  

> ui tool show Matchmaker

> matchmaker #!2 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker tspan4 .cif, chain A (#1) with 5TCX.cif, chain A (#2), sequence
alignment score = 429.9  
RMSD between 80 pruned atom pairs is 1.008 angstroms; (across all 202 pairs:
9.992)  
  

> ui tool show Matchmaker

> matchmaker #1:12-34,54-76,83-105,202-224 to #2:13-35,62-84,91-113,204-226

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 5TCX.cif, chain A (#2) with tspan4 .cif, chain A (#1), sequence
alignment score = 279.9  
RMSD between 83 pruned atom pairs is 1.015 angstroms; (across all 90 pairs:
1.216)  
  

> show #2:CLR

> surface #1

> surface #2

> select #2:18,219

17 atoms, 15 bonds, 2 residues, 1 model selected  

> color sel yellow

> sequence chain #1

Alignment identifier is 1/A  

> sequence chain #2

Alignment identifier is 2/A  

> show #2:CLR

[Repeated 1 time(s)]

> surface #1,2

> transparency 50 surfaces

> save /Users/xiongwenling/Desktop/image1.png supersample 3

> save /Users/xiongwenling/Desktop/image2.png supersample 3

> save /Users/xiongwenling/Downloads/tspan4.cxs

——— End of log from Thu Mar 19 18:35:17 2026 ———

> view name session-start

opened ChimeraX session  

> ui tool show "File History"

> select add #1

1852 atoms, 1895 bonds, 240 residues, 2 models selected  

> select subtract #1

17 atoms, 15 bonds, 2 residues, 2 models selected  

> open /Users/xiongwenling/Downloads/5TCX.cif format mmcif

5TCX.cif title:  
Crystal structure of human tetraspanin CD81 [more info...]  
  
Chain information for 5TCX.cif #3  
---  
Chain | Description | UniProt  
A | CD81 antigen | CD81_HUMAN 2-236  
  
Non-standard residues in 5TCX.cif #3  
---  
CLR — cholesterol  
  

> undo

> redo

> undo

[Repeated 1 time(s)]

> select add #2

1628 atoms, 1660 bonds, 2 pseudobonds, 212 residues, 3 models selected  

> hide #!3 models

> select subtract #2

1 model selected  

> select add #2

1628 atoms, 1660 bonds, 2 pseudobonds, 212 residues, 3 models selected  

> select subtract #2

1 model selected  

> matchmaker #1:12-34,54-76,83-105,202-224 to #2:13-35,62-84,91-113,204-226

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 5TCX.cif, chain A (#2) with tspan4 .cif, chain A (#1), sequence
alignment score = 279.9  
RMSD between 83 pruned atom pairs is 1.015 angstroms; (across all 90 pairs:
1.216)  
  

> sequence chain #1

Alignment identifier is 1/A  

> sequence chain #2

Destroying pre-existing alignment with identifier 2/A  
Alignment identifier is 2/A  

> select #2:18,219

17 atoms, 15 bonds, 2 residues, 1 model selected  

> ~select

Nothing selected  

> color sel yellow

[Repeated 1 time(s)]

> select #2:18,21,64,68,71,72,75,94,98,101,212,216,219

107 atoms, 97 bonds, 13 residues, 1 model selected  

> namesel cd81_pocket

Unknown command: namesel cd81_pocket  

> color sel red

>

Unknown command: sequence #1  

>

Unknown command: sequence #2  

>

Unknown command: sequence #1  

>

Unknown command: sequence #2  

> open aligned_tspan4.pdb

No such file/path: aligned_tspan4.pdb  

> open "/Users/xiongwenling/Downloads/fold_tspan4-2 2/tspan4 .cif"

Chain information for tspan4 .cif #4  
---  
Chain | Description  
A | .  
  
Computing secondary structure  

> addh hbond true pH 7.4

Expected a keyword  

> addh hbond true pH 7.4

Expected a keyword  

> ui tool show "File History"

> undo

[Repeated 2 time(s)]

> hide #4 models

> select #2:18,21,64,68,71,72,75,94,98,101,212,216,219

107 atoms, 97 bonds, 13 residues, 1 model selected  

> namesel cd81_pocket

Unknown command: namesel cd81_pocket  

> color sel red

> select #2:18,21,64,68,71,72,75,94,98,101,212,216,219

107 atoms, 97 bonds, 13 residues, 1 model selected  

> namesel cd81_pocket

Unknown command: namesel cd81_pocket  

> color sel red

> select add #1

1942 atoms, 1977 bonds, 251 residues, 3 models selected  

> select subtract #1

107 atoms, 97 bonds, 13 residues, 3 models selected  

> select add #2

1628 atoms, 1660 bonds, 2 pseudobonds, 212 residues, 4 models selected  

> select subtract #2

1 model selected  

> select add #2

1628 atoms, 1660 bonds, 2 pseudobonds, 212 residues, 3 models selected  

> select subtract #2

1 model selected  

> select add #1

1835 atoms, 1880 bonds, 238 residues, 1 model selected  

> select subtract #1

1 model selected  

> select #2:18,21,64,68,71,72,75,94,98,101,212,216,219

107 atoms, 97 bonds, 13 residues, 1 model selected  

> namesel cd81_pocket

Unknown command: namesel cd81_pocket  

> color sel red

> select #2:18,21,64,68,71,72,75,94,98,101,212,216,219

107 atoms, 97 bonds, 13 residues, 1 model selected  

> named cd81_pocket

Unknown command: named cd81_pocket  

> color sel red

> select #2:18,64,68,71,72,75,94,98,101,212,216,219

96 atoms, 86 bonds, 12 residues, 1 model selected  

> namesel cd81_pocket

Unknown command: namesel cd81_pocket  

> color sel red

> 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  
╰─> [60 lines of output]  
running bdist_wheel  
running build  
running build_py  
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder  
copying pyKVFinder/__init__.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder  
copying pyKVFinder/utils.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder  
copying pyKVFinder/main.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder  
copying pyKVFinder/argparser.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder  
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/hydropathy.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/__init__.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/export.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/spatial.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/depth.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/constitutional.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/geometry.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/cavity.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/openings.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/detect.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
running egg_info  
writing pyKVFinder.egg-info/PKG-INFO  
writing dependency_links to pyKVFinder.egg-info/dependency_links.txt  
writing entry points to pyKVFinder.egg-info/entry_points.txt  
writing requirements to pyKVFinder.egg-info/requires.txt  
writing top-level names to pyKVFinder.egg-info/top_level.txt  
reading manifest file 'pyKVFinder.egg-info/SOURCES.txt'  
reading manifest template 'MANIFEST.in'  
warning: no files found matching 'requirements.txt'  
adding license file 'LICENSE'  
writing manifest file 'pyKVFinder.egg-info/SOURCES.txt'  
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data  
copying pyKVFinder/data/WimleyWhite.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data  
copying pyKVFinder/data/EisenbergWeiss.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data  
copying pyKVFinder/data/ZhaoLondon.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data  
copying pyKVFinder/data/RadzickaWolfenden.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data  
copying pyKVFinder/data/MoonFleming.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data  
copying pyKVFinder/data/KyteDoolittle.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data  
copying pyKVFinder/data/HessaHeijne.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data  
copying pyKVFinder/data/vdw.dat ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data  
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests  
copying pyKVFinder/data/tests/ADN.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests  
copying pyKVFinder/data/tests/C1.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests  
copying pyKVFinder/data/tests/PKI.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests  
copying pyKVFinder/data/tests/1FMO.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests  
copying pyKVFinder/data/tests/1FMO.KVFinder.output.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests  
copying pyKVFinder/data/tests/ClO4.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests  
copying pyKVFinder/data/tests/1FMO.xyz ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests  
copying pyKVFinder/data/tests/custom-box.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests  
copying pyKVFinder/data/tests/ADN.xyz ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests  
copying pyKVFinder/data/tests/residues-box.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests  
running build_ext  
building 'pyKVFinder._pyKVFinder' extension  
swigging C/pyKVFinder.i to C/pyKVFinder_wrap.c  
swig -python -o C/pyKVFinder_wrap.c C/pyKVFinder.i  
creating build/temp.macosx-10.9-universal2-cpython-311/C  
clang -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g
-fwrapv -O3 -Wall -arch arm64 -arch x86_64 -g
-I/private/var/folders/v0/f2w4v_zj5sq88xplfv5k35640000gn/T/pip-build-env-
ckw0i262/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/Applications/ChimeraX-1.11.1.app/Contents/include/python3.11 -c
C/pyKVFinder.c -o build/temp.macosx-10.9-universal2-cpython-311/C/pyKVFinder.o
-Xpreprocessor -fopenmp=libomp -O3 -ffast-math  
xcode-select: note: No developer tools were found, requesting install.  
If developer tools are located at a non-default location on disk, use `sudo
xcode-select --switch path/to/Xcode.app` to specify the Xcode that you wish to
use for command line developer tools, and cancel the installation dialog.  
See `man xcode-select` for more details.  
error: command '/usr/bin/clang' failed with exit code 1  
[end of output]  
  
note: This error originates from a subprocess, and is likely not a problem
with pip.  
ERROR: Failed building wheel for pyKVFinder  
error: failed-wheel-build-for-install  
  
× Failed to build installable wheels for some pyproject.toml based projects  
╰─> pyKVFinder  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/kvfinder/__init__.py", line 48, in check_pyKVFinder  
import pyKVFinder  
ModuleNotFoundError: No module named 'pyKVFinder'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 571, in start_tool  
ti = api._api_caller.start_tool(api, session, self, tool_info)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1400, in start_tool  
return cls._get_func(api, "start_tool")(session, ti.name)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/kvfinder/__init__.py", line 42, in start_tool  
check_pyKVFinder(session.logger)  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/kvfinder/__init__.py", line 54, in check_pyKVFinder  
run(logger.session, pip_cmd, log=False)  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/pip.py", line 84, in pip  
run_logged_pip(pip_cmd, session.logger)  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/python_utils.py", line 148, in run_logged_pip  
raise RuntimeError(s)  
RuntimeError: error: subprocess-exited-with-error  
  
× Building wheel for pyKVFinder (pyproject.toml) did not run successfully.  
│ exit code: 1  
╰─> [60 lines of output]  
running bdist_wheel  
running build  
running build_py  
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder  
copying pyKVFinder/__init__.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder  
copying pyKVFinder/utils.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder  
copying pyKVFinder/main.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder  
copying pyKVFinder/argparser.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder  
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/hydropathy.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/__init__.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/export.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/spatial.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/depth.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/constitutional.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/geometry.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/cavity.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/openings.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/detect.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
running egg_info  
writing pyKVFinder.egg-info/PKG-INFO  
writing dependency_links to pyKVFinder.egg-info/dependency_links.txt  
writing entry points to pyKVFinder.egg-info/entry_points.txt  
writing requirements to pyKVFinder.egg-info/requires.txt  
writing top-level names to pyKVFinder.egg-info/top_level.txt  
reading manifest file 'pyKVFinder.egg-info/SOURCES.txt'  
reading manifest template 'MANIFEST.in'  
warning: no files found matching 'requirements.txt'  
adding license file 'LICENSE'  
writing manifest file 'pyKVFinder.egg-info/SOURCES.txt'  
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data  
copying pyKVFinder/data/WimleyWhite.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data  
copying pyKVFinder/data/EisenbergWeiss.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data  
copying pyKVFinder/data/ZhaoLondon.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data  
copying pyKVFinder/data/RadzickaWolfenden.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data  
copying pyKVFinder/data/MoonFleming.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data  
copying pyKVFinder/data/KyteDoolittle.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data  
copying pyKVFinder/data/HessaHeijne.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data  
copying pyKVFinder/data/vdw.dat ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data  
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests  
copying pyKVFinder/data/tests/ADN.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests  
copying pyKVFinder/data/tests/C1.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests  
copying pyKVFinder/data/tests/PKI.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests  
copying pyKVFinder/data/tests/1FMO.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests  
copying pyKVFinder/data/tests/1FMO.KVFinder.output.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests  
copying pyKVFinder/data/tests/ClO4.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests  
copying pyKVFinder/data/tests/1FMO.xyz ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests  
copying pyKVFinder/data/tests/custom-box.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests  
copying pyKVFinder/data/tests/ADN.xyz ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests  
copying pyKVFinder/data/tests/residues-box.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests  
running build_ext  
building 'pyKVFinder._pyKVFinder' extension  
swigging C/pyKVFinder.i to C/pyKVFinder_wrap.c  
swig -python -o C/pyKVFinder_wrap.c C/pyKVFinder.i  
creating build/temp.macosx-10.9-universal2-cpython-311/C  
clang -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g
-fwrapv -O3 -Wall -arch arm64 -arch x86_64 -g
-I/private/var/folders/v0/f2w4v_zj5sq88xplfv5k35640000gn/T/pip-build-env-
ckw0i262/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/Applications/ChimeraX-1.11.1.app/Contents/include/python3.11 -c
C/pyKVFinder.c -o build/temp.macosx-10.9-universal2-cpython-311/C/pyKVFinder.o
-Xpreprocessor -fopenmp=libomp -O3 -ffast-math  
xcode-select: note: No developer tools were found, requesting install.  
If developer tools are located at a non-default location on disk, use `sudo
xcode-select --switch path/to/Xcode.app` to specify the Xcode that you wish to
use for command line developer tools, and cancel the installation dialog.  
See `man xcode-select` for more details.  
error: command '/usr/bin/clang' failed with exit code 1  
[end of output]  
  
note: This error originates from a subprocess, and is likely not a problem
with pip.  
ERROR: Failed building wheel for pyKVFinder  
error: failed-wheel-build-for-install  
  
× Failed to build installable wheels for some pyproject.toml based projects  
╰─> pyKVFinder  
  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1939, in <lambda>  
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/cmd.py", line 219, in ui_tool_show  
return bi.start_tool(session, name)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 578, in start_tool  
raise ToolshedError(  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Find
Cavities in bundle ChimeraX-KVFinder:  
error: subprocess-exited-with-error  
  
× Building wheel for pyKVFinder (pyproject.toml) did not run successfully.  
│ exit code: 1  
╰─> [60 lines of output]  
running bdist_wheel  
running build  
running build_py  
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder  
copying pyKVFinder/__init__.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder  
copying pyKVFinder/utils.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder  
copying pyKVFinder/main.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder  
copying pyKVFinder/argparser.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder  
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/hydropathy.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/__init__.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/export.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/spatial.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/depth.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/constitutional.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/geometry.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/cavity.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/openings.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/detect.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
running egg_info  
writing pyKVFinder.egg-info/PKG-INFO  
writing dependency_links to pyKVFinder.egg-info/dependency_links.txt  
writing entry points to pyKVFinder.egg-info/entry_points.txt  
writing requirements to pyKVFinder.egg-info/requires.txt  
writing top-level names to pyKVFinder.egg-info/top_level.txt  
reading manifest file 'pyKVFinder.egg-info/SOURCES.txt'  
reading manifest template 'MANIFEST.in'  
warning: no files found matching 'requirements.txt'  
adding license file 'LICENSE'  
writing manifest file 'pyKVFinder.egg-info/SOURCES.txt'  
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data  
copying pyKVFinder/data/WimleyWhite.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data  
copying pyKVFinder/data/EisenbergWeiss.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data  
copying pyKVFinder/data/ZhaoLondon.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data  
copying pyKVFinder/data/RadzickaWolfenden.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data  
copying pyKVFinder/data/MoonFleming.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data  
copying pyKVFinder/data/KyteDoolittle.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data  
copying pyKVFinder/data/HessaHeijne.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data  
copying pyKVFinder/data/vdw.dat ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data  
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests  
copying pyKVFinder/data/tests/ADN.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests  
copying pyKVFinder/data/tests/C1.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests  
copying pyKVFinder/data/tests/PKI.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests  
copying pyKVFinder/data/tests/1FMO.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests  
copying pyKVFinder/data/tests/1FMO.KVFinder.output.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests  
copying pyKVFinder/data/tests/ClO4.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests  
copying pyKVFinder/data/tests/1FMO.xyz ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests  
copying pyKVFinder/data/tests/custom-box.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests  
copying pyKVFinder/data/tests/ADN.xyz ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests  
copying pyKVFinder/data/tests/residues-box.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests  
running build_ext  
building 'pyKVFinder._pyKVFinder' extension  
swigging C/pyKVFinder.i to C/pyKVFinder_wrap.c  
swig -python -o C/pyKVFinder_wrap.c C/pyKVFinder.i  
creating build/temp.macosx-10.9-universal2-cpython-311/C  
clang -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g
-fwrapv -O3 -Wall -arch arm64 -arch x86_64 -g
-I/private/var/folders/v0/f2w4v_zj5sq88xplfv5k35640000gn/T/pip-build-env-
ckw0i262/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/Applications/ChimeraX-1.11.1.app/Contents/include/python3.11 -c
C/pyKVFinder.c -o build/temp.macosx-10.9-universal2-cpython-311/C/pyKVFinder.o
-Xpreprocessor -fopenmp=libomp -O3 -ffast-math  
xcode-select: note: No developer tools were found, requesting install.  
If developer tools are located at a non-default location on disk, use `sudo
xcode-select --switch path/to/Xcode.app` to specify the Xcode that you wish to
use for command line developer tools, and cancel the installation dialog.  
See `man xcode-select` for more details.  
error: command '/usr/bin/clang' failed with exit code 1  
[end of output]  
  
note: This error originates from a subprocess, and is likely not a problem
with pip.  
ERROR: Failed building wheel for pyKVFinder  
error: failed-wheel-build-for-install  
  
× Failed to build installable wheels for some pyproject.toml based projects  
╰─> pyKVFinder  
  
  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Find
Cavities in bundle ChimeraX-KVFinder:  
error: subprocess-exited-with-error  
  
× Building wheel for pyKVFinder (pyproject.toml) did not run successfully.  
│ exit code: 1  
╰─> [60 lines of output]  
running bdist_wheel  
running build  
running build_py  
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder  
copying pyKVFinder/__init__.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder  
copying pyKVFinder/utils.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder  
copying pyKVFinder/main.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder  
copying pyKVFinder/argparser.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder  
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/hydropathy.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/__init__.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/export.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/spatial.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/depth.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/constitutional.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/geometry.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/cavity.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/openings.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/detect.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
running egg_info  
writing pyKVFinder.egg-info/PKG-INFO  
writing dependency_links to pyKVFinder.egg-info/dependency_links.txt  
writing entry points to pyKVFinder.egg-info/entry_points.txt  
writing requirements to pyKVFinder.egg-info/requires.txt  
writing top-level names to pyKVFinder.egg-info/top_level.txt  
reading manifest file 'pyKVFinder.egg-info/SOURCES.txt'  
reading manifest template 'MANIFEST.in'  
warning: no files found matching 'requirements.txt'  
adding license file 'LICENSE'  
writing manifest file 'pyKVFinder.egg-info/SOURCES.txt'  
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data  
copying pyKVFinder/data/WimleyWhite.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data  
copying pyKVFinder/data/EisenbergWeiss.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data  
copying pyKVFinder/data/ZhaoLondon.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data  
copying pyKVFinder/data/RadzickaWolfenden.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data  
copying pyKVFinder/data/MoonFleming.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data  
copying pyKVFinder/data/KyteDoolittle.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data  
copying pyKVFinder/data/HessaHeijne.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data  
copying pyKVFinder/data/vdw.dat ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data  
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests  
copying pyKVFinder/data/tests/ADN.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests  
copying pyKVFinder/data/tests/C1.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests  
copying pyKVFinder/data/tests/PKI.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests  
copying pyKVFinder/data/tests/1FMO.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests  
copying pyKVFinder/data/tests/1FMO.KVFinder.output.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests  
copying pyKVFinder/data/tests/ClO4.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests  
copying pyKVFinder/data/tests/1FMO.xyz ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests  
copying pyKVFinder/data/tests/custom-box.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests  
copying pyKVFinder/data/tests/ADN.xyz ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests  
copying pyKVFinder/data/tests/residues-box.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests  
running build_ext  
building 'pyKVFinder._pyKVFinder' extension  
swigging C/pyKVFinder.i to C/pyKVFinder_wrap.c  
swig -python -o C/pyKVFinder_wrap.c C/pyKVFinder.i  
creating build/temp.macosx-10.9-universal2-cpython-311/C  
clang -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g
-fwrapv -O3 -Wall -arch arm64 -arch x86_64 -g
-I/private/var/folders/v0/f2w4v_zj5sq88xplfv5k35640000gn/T/pip-build-env-
ckw0i262/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/Applications/ChimeraX-1.11.1.app/Contents/include/python3.11 -c
C/pyKVFinder.c -o build/temp.macosx-10.9-universal2-cpython-311/C/pyKVFinder.o
-Xpreprocessor -fopenmp=libomp -O3 -ffast-math  
xcode-select: note: No developer tools were found, requesting install.  
If developer tools are located at a non-default location on disk, use `sudo
xcode-select --switch path/to/Xcode.app` to specify the Xcode that you wish to
use for command line developer tools, and cancel the installation dialog.  
See `man xcode-select` for more details.  
error: command '/usr/bin/clang' failed with exit code 1  
[end of output]  
  
note: This error originates from a subprocess, and is likely not a problem
with pip.  
ERROR: Failed building wheel for pyKVFinder  
error: failed-wheel-build-for-install  
  
× Failed to build installable wheels for some pyproject.toml based projects  
╰─> pyKVFinder  
  
  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 578, in start_tool  
raise ToolshedError(  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M2
OpenGL vendor: Apple

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

    Hardware Overview:

      Model Name: MacBook Air
      Model Identifier: Mac14,2
      Model Number: Z1600072UCH/A
      Chip: Apple M2
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 8 GB
      System Firmware Version: 10151.81.1
      OS Loader Version: 10151.81.1

Software:

    System Software Overview:

      System Version: macOS 14.3.1 (23D60)
      Kernel Version: Darwin 23.3.0
      Time since boot: 2天12小时55分钟

Graphics/Displays:

    Apple M2:

      Chipset Model: Apple M2
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 8
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina Display
          Resolution: 2560 x 1664 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    aiohappyeyeballs: 2.6.1
    aiohttp: 3.13.1
    aiosignal: 1.4.0
    alabaster: 1.0.0
    annotated-types: 0.7.0
    anyio: 4.12.1
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.1
    attrs: 25.4.0
    babel: 2.17.0
    beautifulsoup4: 4.13.5
    blockdiag: 3.0.0
    blosc2: 3.12.2
    build: 1.3.0
    certifi: 2025.7.14
    cftime: 1.6.5
    charset-normalizer: 3.4.4
    ChimeraX-AddCharge: 1.5.20
    ChimeraX-AddH: 2.2.8
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 3.1.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Animations: 1.0
    ChimeraX-Aniso: 1.3.2
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.61.4
    ChimeraX-AtomicLibrary: 14.2.1
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.3
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-Boltz: 1.1
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.6.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3.0
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.11.1
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.5
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.4
    ChimeraX-Dicom: 1.2.7
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.4
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.4.1
    ChimeraX-Hbonds: 2.5.3
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.4
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.7.3
    ChimeraX-Label: 1.2
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.2
    ChimeraX-Map: 1.3
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.2.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MCPServer: 0.1.0
    ChimeraX-MDcrds: 2.17.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-Minimize: 1.3.2
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.22
    ChimeraX-ModelPanel: 1.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0.1
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.15.2
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.12
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.5
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.4
    ChimeraX-ProfileGrids: 1.4.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.5
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.3
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.2
    ChimeraX-Scenes: 0.3.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.10
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17.3
    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.19.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.49.1
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDock: 1.5.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.5
    ChimeraX-Zone: 1.0.1
    click: 8.3.1
    colorama: 0.4.6
    comm: 0.2.3
    contourpy: 1.3.3
    coverage: 7.13.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.1.4
    debugpy: 1.8.19
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.1
    filelock: 3.19.1
    fonttools: 4.61.1
    frozenlist: 1.8.0
    funcparserlib: 2.0.0a0
    glfw: 2.10.0
    grako: 3.16.5
    h11: 0.16.0
    h5py: 3.15.1
    html2text: 2025.4.15
    httpcore: 1.0.9
    httpx: 0.28.1
    httpx-sse: 0.4.3
    idna: 3.11
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.3.0
    ipykernel: 6.30.1
    ipython: 9.5.0
    ipython_pygments_lexers: 1.1.1
    ipywidgets: 8.1.8
    jedi: 0.19.2
    Jinja2: 3.1.6
    jsonschema: 4.26.0
    jsonschema-specifications: 2025.9.1
    jupyter_client: 8.6.3
    jupyter_core: 5.9.1
    jupyterlab_widgets: 3.0.16
    kiwisolver: 1.4.9
    line_profiler: 5.0.0
    lxml: 6.0.2
    lz4: 4.3.2
    Markdown: 3.8.2
    MarkupSafe: 3.0.3
    matplotlib: 3.10.7
    matplotlib-inline: 0.2.1
    mcp: 1.18.0
    msgpack: 1.1.1
    multidict: 6.7.0
    ndindex: 1.10.1
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.14.1
    numpy: 1.26.4
    OpenMM: 8.2.0
    openvr: 1.26.701
    packaging: 25.0
    ParmEd: 4.2.2
    parso: 0.8.5
    pep517: 0.13.1
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 11.3.0
    pip: 25.2
    pkginfo: 1.12.1.2
    platformdirs: 4.5.1
    pluggy: 1.6.0
    prompt_toolkit: 3.0.52
    propcache: 0.4.1
    psutil: 7.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pybind11: 3.0.1
    pycollada: 0.8
    pydantic: 2.12.5
    pydantic-settings: 2.12.0
    pydantic_core: 2.41.5
    pydicom: 2.4.4
    Pygments: 2.18.0
    pynmrstar: 3.3.6
    pynrrd: 1.0.0
    PyOpenGL: 3.1.10
    PyOpenGL-accelerate: 3.1.10
    pyopenxr: 1.1.4501
    pyparsing: 3.3.2
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.9.1
    PyQt6-Qt6: 6.9.2
    PyQt6-WebEngine-commercial: 6.9.0
    PyQt6-WebEngine-Qt6: 6.9.2
    PyQt6_sip: 13.10.2
    pytest: 9.0.2
    pytest-cov: 7.0.0
    python-dateutil: 2.9.0.post0
    python-dotenv: 1.2.1
    python-multipart: 0.0.21
    pyzmq: 27.1.0
    qtconsole: 5.7.0
    QtPy: 2.4.3
    qtshim: 1.2
    RandomWords: 0.4.0
    referencing: 0.37.0
    requests: 2.32.5
    roman-numerals: 4.1.0
    roman-numerals-py: 4.1.0
    rpds-py: 0.30.0
    scipy: 1.14.0
    setuptools: 80.9.0
    sfftk-rw: 0.8.1
    six: 1.17.0
    snowballstemmer: 3.0.1
    sortedcontainers: 2.4.0
    soupsieve: 2.8.3
    Sphinx: 8.2.3
    sphinx-autodoc-typehints: 3.2.0
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    sse-starlette: 3.2.0
    stack-data: 0.6.3
    starlette: 0.52.1
    superqt: 0.7.6
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.5
    tornado: 6.5.4
    traitlets: 5.14.3
    typing-inspection: 0.4.2
    typing_extensions: 4.15.0
    urllib3: 2.6.3
    uvicorn: 0.40.0
    wcwidth: 0.3.2
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.15
    yarl: 1.22.0