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Opened 4 hours ago
#19399 new defect
ChimeraX bug report submission
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Unassigned | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | ||
| Project: |
Description
The following bug report has been submitted:
Platform: macOS-13.7.6-x86_64-i386-64bit
ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 UTC)
Description
Unable to run find cavities tool
Log:
UCSF ChimeraX version: 1.10.1 (2025-07-24)
© 2016-2025 Regents of the University of California. All rights reserved.
> open
> /Users/cjh30/Documents/Crystallography/Bd0967/Images_chimera/Bd0967_surface_coloured.cxs
> format session
Log from Tue Nov 18 13:53:38 2025 Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.7rc202311070653 (2023-11-07)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/cjh30/Library/CloudStorage/GoogleDrive-
> chrisharding1234@gmail.com/My
> Drive/Lecturer/Project_work/2023_work_onwards/Bd0967/AlphaFold_predictions/0967_0606/fold_0967_0606_model_0.cif"
Chain information for fold_0967_0606_model_0.cif #1
---
Chain | Description
A | .
B | .
> ui tool show "Color Actions"
> color bychain
> close session
> open
> /Users/cjh30/Documents/Crystallography/Bd0967/WT/Deposition/Bd0967_WT.pdb
Summary of feedback from opening
/Users/cjh30/Documents/Crystallography/Bd0967/WT/Deposition/Bd0967_WT.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK Date 2025-07-02 Time 13:43:33 BST +0100 (1751460213.73 s)
Ignored bad PDB record found on line 2
REMARK PHENIX refinement
Ignored bad PDB record found on line 4
REMARK ****************** INPUT FILES AND LABELS
******************************
Ignored bad PDB record found on line 5
REMARK Reflections:
Ignored bad PDB record found on line 6
REMARK file name : /Users/cjh30/Documents/Crystallography/Bd0967/Older_da
31 messages similar to the above omitted
Chain information for Bd0967_WT.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E F G H I | No description available
J K | No description available
> show cartoons
> select
21757 atoms, 20206 bonds, 7 pseudobonds, 4381 residues, 2 models selected
> hide sel surfaces
[Repeated 1 time(s)]
> hide sel atoms
> ui tool show "Color Actions"
> set bgColor white
> hide sel cartoons
> select /A
4934 atoms, 5007 bonds, 2 pseudobonds, 628 residues, 2 models selected
> show sel cartoons
> cartoon style (#!1 & sel) modeHelix tube sides 20
> select /A :233-332
729 atoms, 731 bonds, 1 pseudobond, 96 residues, 2 models selected
> ui tool show "Color Actions"
> color sel khaki
> color sel pale goldenrod
> color sel beige
> color sel wheat
> color sel khaki
> select /A :24-220
1569 atoms, 1599 bonds, 191 residues, 1 model selected
> ui tool show "Color Actions"
> color sel powder blue
> ui tool show "Color Actions"
> color sel light coral
> ui tool show "Color Actions"
> color sel medium purple
> color sel light coral
> select /A :333-566
1719 atoms, 1750 bonds, 1 pseudobond, 229 residues, 2 models selected
> ui tool show "Color Actions"
> color sel medium purple
> select /A :567-666
815 atoms, 821 bonds, 100 residues, 1 model selected
> ui tool show "Color Actions"
> color sel dark sea green
> select /A :221-233
113 atoms, 113 bonds, 13 residues, 1 model selected
> color sel light gray
> hide #1.1 models
> graphics silhouettes true
> lighting flat
> lighting shadows true intensity 0.5
> lighting simple
> lighting full
> lighting soft
> lighting full
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting flat
[Repeated 1 time(s)]
> lighting simple
> graphics silhouettes false
> graphics silhouettes true
> select clear
> save
> /Users/cjh30/Documents/Crystallography/Bd0967/Images_chimera/Bd0967_overall.cxs
> select /A :567-666
815 atoms, 821 bonds, 100 residues, 1 model selected
> ui tool show "Color Actions"
> color sel plum
> color sel thistle
> color sel dark orchid
> color sel dark magenta
> color sel purple
> color sel medium purple
> color sel violet
> color sel plum
> color sel light cyan
> color sel lavender
> color sel #a566ffff
> color sel #b197c3ff
> color sel #dc4ba4ff
> color sel #b197c3ff
> color sel #af3790ff
> color sel #f396bdff
> color sel #b197c3ff
> select /A :333-566
1719 atoms, 1750 bonds, 1 pseudobond, 229 residues, 2 models selected
> color (#!1 & sel) #00ab7dff
> color (#!1 & sel) #00af7dff
> color (#!1 & sel) #008c7dff
> color (#!1 & sel) #00697dff
> color (#!1 & sel) #008c7dff
> color sel light blue
> color sel cadet blue
> ui tool show "Color Actions"
> color sel olive
> undo
> select /A :234-332
718 atoms, 720 bonds, 1 pseudobond, 95 residues, 2 models selected
> ui tool show "Color Actions"
> color sel dark khaki
> color sel olive
> color sel dark khaki
> select clear
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> save
> /Users/cjh30/Documents/Crystallography/Bd0967/Images_chimera/Bd0967_overall.cxs
> save
> /Users/cjh30/Documents/Crystallography/Bd0967/Images_chimera/Bd0967_overall_view1.cxs
> turn x90
Expected an axis vector or a keyword
> turn x 90
[Repeated 7 time(s)]
> turn y 90
[Repeated 2 time(s)]
> turn x 90
> turn y 90
[Repeated 7 time(s)]
> turn x 90
[Repeated 3 time(s)]
> turn z 90
[Repeated 20 time(s)]
> turn x 90
[Repeated 7 time(s)]
> turn x 30
[Repeated 10 time(s)]
> turn x 10
[Repeated 37 time(s)]
> turn x -10
> turn z -10
[Repeated 1 time(s)]
> turn z 10
[Repeated 4 time(s)]
> turn z -10
[Repeated 1 time(s)]
> save /Users/cjh30/Desktop/image1.png supersample 3
> turn z -10
> turn z 10
[Repeated 1 time(s)]
> turn x 10
[Repeated 31 time(s)]
> turn x -10
[Repeated 3 time(s)]
> turn x 10
[Repeated 1 time(s)]
> turn z 10
[Repeated 1 time(s)]
> turn z -10
[Repeated 2 time(s)]
> turn y -10
> turn y 10
> turn z 10
> turn z -10
[Repeated 1 time(s)]
> turn z 10
[Repeated 1 time(s)]
> turn z -10
> turn x -10
[Repeated 1 time(s)]
> turn x 10
> save /Users/cjh30/Desktop/image2.png supersample 3
> turn y 10
> turn y -10
[Repeated 2 time(s)]
> turn y 10
> save /Users/cjh30/Desktop/image3.png supersample 3
> turn x 10
[Repeated 7 time(s)]
> turn x -10
> turn x -70
> turn x 70
> save /Users/cjh30/Desktop/image4.png supersample 3
> turn x -70
> save
> /Users/cjh30/Documents/Crystallography/Bd0967/Images_chimera/Bd0967_overall_view1.cxs
> select /E
21 atoms, 20 bonds, 4 residues, 1 model selected
> show sel atoms
> style sel sphere
Changed 21 atom styles
> select /I
21 atoms, 20 bonds, 4 residues, 1 model selected
> show sel atoms
> style sel sphere
Changed 21 atom styles
> turn z 10
> turn z -10
> turn y -10
> turn y 10
[Repeated 1 time(s)]
> turn y -10
> turn y 5
> turn x 70
> select /A :457, 483, 487
24 atoms, 21 bonds, 3 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 24 atom styles
> style sel stick
Changed 24 atom styles
> style sel stick
Changed 24 atom styles
> show sel atoms
> ui tool show "Color Actions"
> color sel byhetero
> color sel orange
> color sel byhetero
> undo
[Repeated 1 time(s)]
> ui tool show "Color Actions"
> color sel orange target a
> color sel byhetero target a
> select ::name="MG"
4 atoms, 4 residues, 1 model selected
> show sel atoms
> select /mg mg 2
Expected a keyword
> select /mg 2
Expected a keyword
> select /Mg
4 atoms, 4 residues, 1 model selected
> select /Mg 2
Expected a keyword
> select /Mg Mg 2
Expected a keyword
> select /Mg:2@MG
1 atom, 1 residue, 1 model selected
> select /Mg:5@MG
1 atom, 1 residue, 1 model selected
> select /Mg :2
1 atom, 1 residue, 1 model selected
> select /Mg
4 atoms, 4 residues, 1 model selected
> hide sel atoms
> select /Mg :2
1 atom, 1 residue, 1 model selected
> show sel atoms
> color sel cyan
> style sel sphere
Changed 1 atom style
> select /A :33, 100
12 atoms, 10 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 12 atom styles
> color sel byhetero
> select /A:100@SG
1 atom, 1 residue, 1 model selected
> select add /A:96
10 atoms, 8 bonds, 2 residues, 1 model selected
> select add /A:33@SG
11 atoms, 8 bonds, 3 residues, 1 model selected
> select subtract /A:96
2 atoms, 2 residues, 1 model selected
> select subtract /A:33
1 atom, 1 residue, 1 model selected
> select add /A:33@SG
2 atoms, 2 residues, 1 model selected
> bond sel
Created 1 bond
> select clear
> select /E
21 atoms, 20 bonds, 4 residues, 1 model selected
> color sel hot pink
> color sel byhetero
> select /I
21 atoms, 20 bonds, 4 residues, 1 model selected
> color sel hot pink
> color sel byhetero
> select clear
> select /I
21 atoms, 20 bonds, 4 residues, 1 model selected
> hide sel atoms
> show sel atoms
> style sel stick
Changed 21 atom styles
> style sel sphere
Changed 21 atom styles
> select clear
> save
> /Users/cjh30/Documents/Crystallography/Bd0967/Images_chimera/Bd0967_overall_view1_extras.cxs
> save /Users/cjh30/Desktop/image5.png supersample 3
> turn y 70
> turn y -70
> save /Users/cjh30/Desktop/image6.png supersample 3
> turn x 70
> turn x 5
[Repeated 3 time(s)]
> show #1.1 models
> hide #1.1 models
> show #1.1 models
> hide #1.1 models
> show #1.1 models
> save /Users/cjh30/Desktop/image7.png supersample 3
> turn x -80
> turn x -5
[Repeated 1 time(s)]
> save /Users/cjh30/Desktop/image8.png supersample 3
> turn x 90
> select /A
4934 atoms, 5008 bonds, 2 pseudobonds, 628 residues, 2 models selected
> hide sel atoms
> hide sel cartoons
> show sel surfaces
> select /I
21 atoms, 20 bonds, 4 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> select /E
21 atoms, 20 bonds, 4 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> select /A :24-220
1569 atoms, 1600 bonds, 191 residues, 1 model selected
> ui tool show "Color Actions"
> color sel light coral target s
> ui tool show "Color Actions"
> color sel dark khaki target s
> color sel light coral target s
> select /A :234-332
718 atoms, 720 bonds, 1 pseudobond, 95 residues, 2 models selected
> ui tool show "Color Actions"
> color sel dark khaki target s
> select /A :333-566
1719 atoms, 1750 bonds, 1 pseudobond, 229 residues, 2 models selected
> ui tool show "Color Actions"
> color sel cadet blue target s
[Repeated 1 time(s)]
> select /A :567-666
815 atoms, 821 bonds, 100 residues, 1 model selected
> ui tool show "Color Actions"
> color (#!1 & sel) #bb9bc3ff target s
> select /A :221-233
113 atoms, 113 bonds, 13 residues, 1 model selected
> ui tool show "Color Actions"
> color sel light gray target s
> select clear
> save
> /Users/cjh30/Documents/Crystallography/Bd0967/Images_chimera/Bd0967_surface_coloured.cxs
——— End of log from Tue Nov 18 13:53:38 2025 ———
> view name session-start
opened ChimeraX session
> 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/xx/gkd4k61s4yg7sg5twfyh99xr0000gq/T/pip-build-
env-2blq5tgy/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/Applications/ChimeraX-1.10.1.app/Contents/include/python3.11 -c
C/pyKVFinder.c -o build/temp.macosx-10.9-universal2-cpython-311/C/pyKVFinder.o
-Xpreprocessor -fopenmp=libomp -O3 -ffast-math
error: unknown argument: '-fopenmp=libomp'
error: command '/usr/bin/clang' failed with exit code 1
[end of output]
note: This error originates from a subprocess, and is likely not a problem
with pip.
ERROR: Failed building wheel for pyKVFinder
ERROR: Failed to build installable wheels for some pyproject.toml based
projects (pyKVFinder)
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10.1.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-1.10.1.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-1.10.1.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-1.10.1.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-1.10.1.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-1.10.1.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-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3221, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.1.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-1.10.1.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/xx/gkd4k61s4yg7sg5twfyh99xr0000gq/T/pip-build-
env-2blq5tgy/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/Applications/ChimeraX-1.10.1.app/Contents/include/python3.11 -c
C/pyKVFinder.c -o build/temp.macosx-10.9-universal2-cpython-311/C/pyKVFinder.o
-Xpreprocessor -fopenmp=libomp -O3 -ffast-math
error: unknown argument: '-fopenmp=libomp'
error: command '/usr/bin/clang' failed with exit code 1
[end of output]
note: This error originates from a subprocess, and is likely not a problem
with pip.
ERROR: Failed building wheel for pyKVFinder
ERROR: Failed 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-1.10.1.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-1.10.1.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-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3221, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.1.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-1.10.1.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
╰─> [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/xx/gkd4k61s4yg7sg5twfyh99xr0000gq/T/pip-build-
env-2blq5tgy/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/Applications/ChimeraX-1.10.1.app/Contents/include/python3.11 -c
C/pyKVFinder.c -o build/temp.macosx-10.9-universal2-cpython-311/C/pyKVFinder.o
-Xpreprocessor -fopenmp=libomp -O3 -ffast-math
error: unknown argument: '-fopenmp=libomp'
error: command '/usr/bin/clang' failed with exit code 1
[end of output]
note: This error originates from a subprocess, and is likely not a problem
with pip.
ERROR: Failed building wheel for pyKVFinder
ERROR: Failed 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/xx/gkd4k61s4yg7sg5twfyh99xr0000gq/T/pip-build-
env-2blq5tgy/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/Applications/ChimeraX-1.10.1.app/Contents/include/python3.11 -c
C/pyKVFinder.c -o build/temp.macosx-10.9-universal2-cpython-311/C/pyKVFinder.o
-Xpreprocessor -fopenmp=libomp -O3 -ffast-math
error: unknown argument: '-fopenmp=libomp'
error: command '/usr/bin/clang' failed with exit code 1
[end of output]
note: This error originates from a subprocess, and is likely not a problem
with pip.
ERROR: Failed building wheel for pyKVFinder
ERROR: Failed to build installable wheels for some pyproject.toml based
projects (pyKVFinder)
File
"/Applications/ChimeraX-1.10.1.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 INTEL-20.7.3
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 640
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: MacBookPro14,1
Processor Name: Dual-Core Intel Core i5
Processor Speed: 2.3 GHz
Number of Processors: 1
Total Number of Cores: 2
L2 Cache (per Core): 256 KB
L3 Cache: 4 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 529.140.2.0.0
OS Loader Version: 577.140.2~30
SMC Version (system): 2.43f11
Software:
System Software Overview:
System Version: macOS 13.7.6 (22H625)
Kernel Version: Darwin 22.6.0
Time since boot: 3 days, 38 minutes
Graphics/Displays:
Intel Iris Plus Graphics 640:
Chipset Model: Intel Iris Plus Graphics 640
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x5926
Revision ID: 0x0006
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
HP P24h G5:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: 3CM3421QC5
Mirror: Off
Online: Yes
Rotation: Supported
Connection Type: DVI or HDMI
Adapter Firmware Version: 5.06
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
babel: 2.17.0
beautifulsoup4: 4.13.3
blockdiag: 3.0.0
blosc2: 3.6.1
build: 1.2.2.post1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.2
ChimeraX-AddCharge: 1.5.19
ChimeraX-AddH: 2.2.7
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.20.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.1.4
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.7
ChimeraX-AtomicLibrary: 14.1.19
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.5.1
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.10.1
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5.1
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.6.2
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.10.1
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.19
ChimeraX-ModelPanel: 1.5.1
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14.1
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.10
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.3
ChimeraX-ProfileGrids: 1.1.3
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.3
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.1
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.45.2
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.5
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.2
coverage: 7.10.0
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.12
debugpy: 1.8.15
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.0
filelock: 3.18.0
fonttools: 4.59.0
funcparserlib: 2.0.0a0
glfw: 2.9.0
grako: 3.16.5
h5py: 3.14.0
html2text: 2024.2.26
idna: 3.10
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.1.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.7
jedi: 0.19.1
Jinja2: 3.1.6
jupyter_client: 8.6.3
jupyter_core: 5.8.1
jupyterlab_widgets: 3.0.15
kiwisolver: 1.4.8
line_profiler: 4.2.0
lxml: 5.3.1
lz4: 4.3.2
MarkupSafe: 3.0.2
matplotlib: 3.10.1
matplotlib-inline: 0.1.7
msgpack: 1.1.0
ndindex: 1.10.0
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.11.0
numpy: 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: 1.6.0
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
Pygments: 2.18.0
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.9
PyOpenGL-accelerate: 3.1.9
pyopenxr: 1.1.4501
pyparsing: 3.2.3
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.8.1
PyQt6-Qt6: 6.8.2
PyQt6-WebEngine-commercial: 6.8.0
PyQt6-WebEngine-Qt6: 6.8.2
PyQt6_sip: 13.10.0
pytest: 8.4.1
pytest-cov: 6.2.1
python-dateutil: 2.9.0.post0
pytz: 2025.2
pyzmq: 27.0.0
qtconsole: 5.5.2
QtPy: 2.4.3
qtshim: 1.1
RandomWords: 0.4.0
requests: 2.32.3
roman-numerals-py: 3.1.0
scipy: 1.14.0
setuptools: 78.1.0
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.7
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.1.0
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.7.1
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.4
tornado: 6.5.1
traitlets: 5.14.3
typing_extensions: 4.14.1
tzdata: 2025.2
urllib3: 2.5.0
wcwidth: 0.2.13
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.14
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