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Opened 12 hours ago
#20777 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-14.8.5-arm64-arm-64bit
ChimeraX Version: 1.12 (2026-06-12 03:42:34 UTC)
Description
Replace this text with list of actions that caused this problem to occur
Log:
UCSF ChimeraX version: 1.12 (2026-06-12)
© 2016-2026 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> close session
> open 4dpd
Summary of feedback from opening 4dpd fetched from pdb
---
notes | Fetching compressed mmCIF 4dpd from http://files.rcsb.org/download/4dpd.cif
Fetching CCD DHF from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/F/DHF/DHF.cif
Fetching CCD NAP from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/NAP/NAP.cif
Fetching CCD UMP from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/UMP/UMP.cif
4dpd title:
WILD TYPE PLASMODIUM FALCIPARUM DIHYDROFOLATE REDUCTASE-THYMIDYLATE SYNTHASE
(PfDHFR-TS), DHF COMPLEX, NADP+, dUMP [more info...]
Chain information for 4dpd #1
---
Chain | Description | UniProt
A B | Bifunctional dihydrofolate reductase-thymidylate synthase | A7UD81_PLAFA 1-608
Non-standard residues in 4dpd #1
---
DHF — dihydrofolic acid
NAP — nadp nicotinamide-adenine-dinucleotide phosphate
(2'-monophosphoadenosine 5'-diphosphoribose)
UMP — 2'-deoxyuridine 5'-monophosphate (DUMP)
> select /B
4719 atoms, 4640 bonds, 2 pseudobonds, 729 residues, 2 models selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> select /B:2-605
Nothing selected
> select ::name="DHF"
32 atoms, 34 bonds, 1 residue, 1 model selected
> style sel sphere
Changed 32 atom styles
> color sel purple
> open 4dpd
Summary of feedback from opening 4dpd fetched from pdb
---
warning | Cannot find consistent set of bond orders for ring system containing atom C12 in residue DHF /A:701
4dpd title:
WILD TYPE PLASMODIUM FALCIPARUM DIHYDROFOLATE REDUCTASE-THYMIDYLATE SYNTHASE
(PfDHFR-TS), DHF COMPLEX, NADP+, dUMP [more info...]
Chain information for 4dpd #2
---
Chain | Description | UniProt
A B | Bifunctional dihydrofolate reductase-thymidylate synthase | A7UD81_PLAFA 1-608
Non-standard residues in 4dpd #2
---
DHF — dihydrofolic acid
NAP — nadp nicotinamide-adenine-dinucleotide phosphate
(2'-monophosphoadenosine 5'-diphosphoribose)
UMP — 2'-deoxyuridine 5'-monophosphate (DUMP)
> select clear
> select #2/B
4719 atoms, 4640 bonds, 2 pseudobonds, 729 residues, 2 models selected
> delete atoms (#!2 & sel)
> delete bonds (#!2 & sel)
> select #1/A:288
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:287
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:288
8 atoms, 7 bonds, 1 residue, 1 model selected
> label sel text "/{0.chain_id} {0.name} {0.number}{0.insertion_code}"
> label height 2
> surface sel
> surface (#!1 & sel)
> surface style solid
> ui tool show "Color Actions"
> color sel dark blue
> select clear
> surface
> ui tool show "Color Actions"
> color blue violet
> select ::name="DHF"
64 atoms, 68 bonds, 2 residues, 2 models selected
> select ::name="DHF"
64 atoms, 68 bonds, 2 residues, 2 models selected
> select sel :< 5
472 atoms, 464 bonds, 48 residues, 2 models selected
> show (#!1-2 & sel) target ab
> color (#!1-2 & sel) red
> select ::name="DHF"
64 atoms, 68 bonds, 2 residues, 2 models selected
> ui tool show H-Bonds
> hbonds sel restrict cross reveal true
Cannot find consistent set of bond orders for ring system containing atom C12
in residue DHF /A:701
28 hydrogen bonds found
> ui tool show Contacts
> contacts sel restrict cross ignoreHiddenModels true
136 contacts
> transparency sel 90
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A #2/A
Alignment identifier is 1
> select
> #1/A:4-9,33-37,51-64,66-82,106-117,132-136,145-156,166-176,286-294,308-318,324-339,376-388,392-399,405-416,429-437,454-466,478-485,516-536,556-564,582-589
> #2/A:4-9,33-37,51-64,66-82,106-117,132-136,145-156,166-176,286-294,308-318,324-339,376-388,392-399,405-416,429-437,454-466,478-485,516-536,556-564,582-589
3702 atoms, 3750 bonds, 438 residues, 2 models selected
> select #1/A:299 #2/A:299
18 atoms, 16 bonds, 2 residues, 2 models selected
> select #1/A:299-306 #2/A:299-306
134 atoms, 132 bonds, 16 residues, 2 models selected
Bifunctional Dihydrofolate Reductase-Thymidylate Synthase [ID: 1] region 2
chains [299-306] RMSD: 0.000
> surface hidePatches (#!1-2 & sel)
> select clear
> transparency 70
> select #1/A:368-369 #2/A:368-369
32 atoms, 30 bonds, 4 residues, 2 models selected
> select #1/A:368-369 #2/A:368-369
32 atoms, 30 bonds, 4 residues, 2 models selected
Bifunctional Dihydrofolate Reductase-Thymidylate Synthase [ID: 1] region 2
chains [368-369] RMSD: 0.000
> open 1DHF
Summary of feedback from opening 1DHF fetched from pdb
---
notes | Fetching compressed mmCIF 1dhf from http://files.rcsb.org/download/1dhf.cif
Fetching CCD FOL from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/L/FOL/FOL.cif
1dhf title:
Crystal structures of recombinant human dihydrofolate reductase complexed with
folate and 5-deazofolate [more info...]
Chain information for 1dhf #5
---
Chain | Description | UniProt
A B | DIHYDROFOLATE REDUCTASE | DYR_HUMAN 1-186
Non-standard residues in 1dhf #5
---
FOL — folic acid
> select #5/B:4-185
1476 atoms, 1511 bonds, 182 residues, 1 model selected
> delete atoms sel
> delete bonds sel
Drag select of 4dpd_A SES surface, 53 of 481140 triangles, 4dpd_A SES surface,
53 of 481140 triangles, 36 atoms, 34 bonds
> delete atoms (#5 & sel)
> delete bonds (#5 & sel)
> surface hidePatches #1.3#2.2
> ui tool show Matchmaker
> matchmaker #5#!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 4dpd, chain A (#1) with 1dhf, chain A (#5), sequence alignment
score = 313.5
RMSD between 148 pruned atom pairs is 0.835 angstroms; (across all 171 pairs:
1.723)
Matchmaker 4dpd, chain A (#1) with 4dpd, chain A (#2), sequence alignment
score = 3111.2
RMSD between 530 pruned atom pairs is 0.000 angstroms; (across all 530 pairs:
0.000)
> save /Users/hkalin/Desktop/malaria.png width 930 height 675 supersample 3
> save /Users/hkalin/Desktop/4DPD_workshop_vr_HK.glb
> color modify #*lightness 40
Missing or invalid "adjuster" argument: Should be one of 'blackness', 'blue',
'contrast', 'green', 'hue', 'lightness', 'red', 'saturation', or 'whiteness'
> color modify #*lightness40
Missing or invalid "adjuster" argument: Should be one of 'blackness', 'blue',
'contrast', 'green', 'hue', 'lightness', 'red', 'saturation', or 'whiteness'
> colormodify #*lightness40
Unknown command: colormodify #*lightness40
> colormodify #*lightness 40
Unknown command: colormodify #*lightness 40
> colormodify #*lightness 40
Unknown command: colormodify #*lightness 40
> color modify #*lightness 40
Missing or invalid "adjuster" argument: Should be one of 'blackness', 'blue',
'contrast', 'green', 'hue', 'lightness', 'red', 'saturation', or 'whiteness'
> color modify #lightness 40
Missing or invalid "adjuster" argument: Should be one of 'blackness', 'blue',
'contrast', 'green', 'hue', 'lightness', 'red', 'saturation', or 'whiteness'
> color modify #lightness +40
Missing or invalid "adjuster" argument: Should be one of 'blackness', 'blue',
'contrast', 'green', 'hue', 'lightness', 'red', 'saturation', or 'whiteness'
> color modify #lightness -40
Missing or invalid "adjuster" argument: Should be one of 'blackness', 'blue',
'contrast', 'green', 'hue', 'lightness', 'red', 'saturation', or 'whiteness'
> color modify #1 lightness -40
> color modify #1 lightness +40
> color modify #1 lightness +70
> color modify # lightness +70
Missing or invalid "adjuster" argument: Should be one of 'blackness', 'blue',
'contrast', 'green', 'hue', 'lightness', 'red', 'saturation', or 'whiteness'
> color modify lightness +70
> color modify #2 lightness +70
> color modify #2 hue +70
> color modify #1 hue +70
> color modify lightness +70
> color modify lightness -70
> color modify lightness -10
> color modify lightness +50
> style ball
Changed 11090 atom styles
> style sphere
Changed 11090 atom styles
> style sphere
Changed 11090 atom styles
> style stick
Changed 11090 atom styles
> style sphere
Changed 11090 atom styles
> style sphere
Changed 11090 atom styles
> style ball
Changed 11090 atom styles
Drag select of 811 atoms, 1236 residues, 170 pseudobonds, 718 bonds
> style sel sphere
Changed 10509 atom styles
> style sel ball
Changed 10509 atom styles
> style sel sphere
Changed 10509 atom styles
> set bgColor white
> set bgColor black
> style sel ball
Changed 10509 atom styles
> lighting simple
> style sel sphere
Changed 10509 atom styles
> select #1/A#2/A
9470 atoms, 9248 bonds, 170 pseudobonds, 1510 residues, 6 models selected
> select #1/A
4735 atoms, 4624 bonds, 44 pseudobonds, 755 residues, 4 models selected
> select clear
> select #1/A
4735 atoms, 4624 bonds, 44 pseudobonds, 755 residues, 4 models selected
> select #5/A
1570 atoms, 1545 bonds, 245 residues, 1 model selected
> close session
> open 5WG8
Summary of feedback from opening 5WG8 fetched from pdb
---
notes | Fetching compressed mmCIF 5wg8 from http://files.rcsb.org/download/5wg8.cif
Fetching CCD LB1 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/1/LB1/LB1.cif
Fetching CCD MN from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/MN/MN.cif
Fetching CCD MPD from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/D/MPD/MPD.cif
Fetching CCD MRD from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/D/MRD/MRD.cif
5wg8 title:
Structure of PP5C with LB-100; 7-oxabicyclo[2.2.1]heptane-2,3-dicarbonyl
moiety modeled in the density [more info...]
Chain information for 5wg8 #1
---
Chain | Description | UniProt
A | Serine/threonine-protein phosphatase 5 | PPP5_HUMAN 169-499
Non-standard residues in 5wg8 #1
---
LB1 —
(1S,2R,3S,4R)-3-(4-methylpiperazine-1-carbonyl)-7-oxabicyclo[2.2.1]heptane-2-carboxylic
acid
MN — manganese (II) ion
MPD — (4S)-2-methyl-2,4-pentanediol
MRD — (4R)-2-methylpentane-2,4-diol
75 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
2553 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
Drag select of 118 atoms, 320 residues, 11 pseudobonds, 104 bonds
No Surface models open
> select clear
No Surface models open
[Repeated 1 time(s)]
> select :LB1
11 atoms, 12 bonds, 1 residue, 1 model selected
> select :MN
2 atoms, 2 residues, 1 model selected
> select :MPD
8 atoms, 7 bonds, 1 residue, 1 model selected
> select :MRD
8 atoms, 7 bonds, 1 residue, 1 model selected
Drag select of 1 atoms
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 5wg8_A SES surface #1.2: minimum, 0.00, mean 0.00,
maximum 0.00
To also show corresponding color key, enter the above coulombic command and
add key true
> coulombic sel
Coulombic values for 5wg8_A SES surface #1.2: minimum, 0.00, mean 0.00,
maximum 0.00
To also show corresponding color key, enter the above coulombic command and
add key true
> show sel surfaces
> open 5WG8 fromDatabase pdb format mmcif
5wg8 title:
Structure of PP5C with LB-100; 7-oxabicyclo[2.2.1]heptane-2,3-dicarbonyl
moiety modeled in the density [more info...]
Chain information for 5wg8 #2
---
Chain | Description | UniProt
A | Serine/threonine-protein phosphatase 5 | PPP5_HUMAN 169-499
Non-standard residues in 5wg8 #2
---
LB1 —
(1S,2R,3S,4R)-3-(4-methylpiperazine-1-carbonyl)-7-oxabicyclo[2.2.1]heptane-2-carboxylic
acid
MN — manganese (II) ion
MPD — (4S)-2-methyl-2,4-pentanediol
MRD — (4R)-2-methylpentane-2,4-diol
75 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
2553 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
> coulombic sel
Coulombic values for 5wg8_A SES surface #1.2: minimum, 0.00, mean 0.00,
maximum 0.00
To also show corresponding color key, enter the above coulombic command and
add key true
Drag select of 60 residues
Drag select of 26 residues
Drag select of 30 residues
Drag select of 64 residues
Drag select of 18 residues
> color modify #1 lightness 40
> color modify #* lightness 40
> color modify #1 lightness 40
> color modify #2 lightness 40
> color modify #2 lightness +40
> color modify #2 hue +40
> color modify #* hue +40
[Repeated 2 time(s)]
> color modify #* lightness +70
> select clear
[Repeated 1 time(s)]
> select #2/A
2815 atoms, 2613 bonds, 11 pseudobonds, 587 residues, 2 models selected
> delete atoms (#!2 & sel)
> delete bonds (#!2 & sel)
> graphics silhouettes true
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> lighting full
> lighting soft
> lighting simple
[Repeated 2 time(s)]
> lighting soft
> lighting simple
> ui tool show "Side View"
> view
[Repeated 1 time(s)]
> view orient
> lighting flat
> lighting simple
> lighting shadows true
> lighting shadows false
> graphics silhouettes false
Drag select of 106 atoms, 240 residues, 11 pseudobonds, 95 bonds
Drag select of 5wg8_A SES surface, 118 atoms, 320 residues, 11 pseudobonds,
104 bonds
> ui tool show "Find Cavities"
pyKVFinder module not installed; fetching from PyPi repository...
'pip install pyKVFinder' failed. Error from pip: error: subprocess-exited-
with-error
× Building wheel for pyKVFinder (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [58 lines of output]
running bdist_wheel
running build
running build_py
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder
copying pyKVFinder/__init__.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder
copying pyKVFinder/utils.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder
copying pyKVFinder/main.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder
copying pyKVFinder/argparser.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/hydropathy.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/__init__.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/export.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/spatial.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/depth.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/constitutional.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/geometry.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/cavity.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/openings.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/detect.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
running egg_info
writing pyKVFinder.egg-info/PKG-INFO
writing dependency_links to pyKVFinder.egg-info/dependency_links.txt
writing entry points to pyKVFinder.egg-info/entry_points.txt
writing requirements to pyKVFinder.egg-info/requires.txt
writing top-level names to pyKVFinder.egg-info/top_level.txt
reading manifest file 'pyKVFinder.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching 'requirements.txt'
adding license file 'LICENSE'
writing manifest file 'pyKVFinder.egg-info/SOURCES.txt'
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/WimleyWhite.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/EisenbergWeiss.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/ZhaoLondon.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/RadzickaWolfenden.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/MoonFleming.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/KyteDoolittle.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/HessaHeijne.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/vdw.dat ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/ADN.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/C1.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/PKI.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/1FMO.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/1FMO.KVFinder.output.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/ClO4.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/1FMO.xyz ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/custom-box.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/ADN.xyz ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/residues-box.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
running build_ext
building 'pyKVFinder._pyKVFinder' extension
swigging C/pyKVFinder.i to C/pyKVFinder_wrap.c
swig -python -o C/pyKVFinder_wrap.c C/pyKVFinder.i
creating build/temp.macosx-10.9-universal2-cpython-311/C
clang -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g
-fwrapv -O3 -Wall -arch arm64 -arch x86_64 -g
-I/private/var/folders/gd/ww67f0hx1mg613mfry6rddqsxqlhrx/T/pip-build-env-
jap6z4xt/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/Applications/ChimeraX-1.12.app/Contents/include/python3.11 -c
C/pyKVFinder.c -o build/temp.macosx-10.9-universal2-cpython-311/C/pyKVFinder.o
-Xpreprocessor -fopenmp=libomp -O3 -ffast-math
error: unknown argument: '-fopenmp=libomp'
error: command '/usr/bin/clang' failed with exit code 1
[end of output]
note: This error originates from a subprocess, and is likely not a problem
with pip.
ERROR: Failed building wheel for pyKVFinder
error: failed-wheel-build-for-install
× Failed to build installable wheels for some pyproject.toml based projects
╰─> pyKVFinder
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.12.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-1.12.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-1.12.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-1.12.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-1.12.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-1.12.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-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3245, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12.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-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/python_utils.py", line 148, in run_logged_pip
raise RuntimeError(s)
RuntimeError: error: subprocess-exited-with-error
× Building wheel for pyKVFinder (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [58 lines of output]
running bdist_wheel
running build
running build_py
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder
copying pyKVFinder/__init__.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder
copying pyKVFinder/utils.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder
copying pyKVFinder/main.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder
copying pyKVFinder/argparser.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/hydropathy.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/__init__.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/export.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/spatial.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/depth.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/constitutional.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/geometry.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/cavity.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/openings.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/detect.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
running egg_info
writing pyKVFinder.egg-info/PKG-INFO
writing dependency_links to pyKVFinder.egg-info/dependency_links.txt
writing entry points to pyKVFinder.egg-info/entry_points.txt
writing requirements to pyKVFinder.egg-info/requires.txt
writing top-level names to pyKVFinder.egg-info/top_level.txt
reading manifest file 'pyKVFinder.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching 'requirements.txt'
adding license file 'LICENSE'
writing manifest file 'pyKVFinder.egg-info/SOURCES.txt'
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/WimleyWhite.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/EisenbergWeiss.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/ZhaoLondon.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/RadzickaWolfenden.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/MoonFleming.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/KyteDoolittle.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/HessaHeijne.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/vdw.dat ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/ADN.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/C1.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/PKI.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/1FMO.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/1FMO.KVFinder.output.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/ClO4.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/1FMO.xyz ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/custom-box.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/ADN.xyz ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/residues-box.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
running build_ext
building 'pyKVFinder._pyKVFinder' extension
swigging C/pyKVFinder.i to C/pyKVFinder_wrap.c
swig -python -o C/pyKVFinder_wrap.c C/pyKVFinder.i
creating build/temp.macosx-10.9-universal2-cpython-311/C
clang -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g
-fwrapv -O3 -Wall -arch arm64 -arch x86_64 -g
-I/private/var/folders/gd/ww67f0hx1mg613mfry6rddqsxqlhrx/T/pip-build-env-
jap6z4xt/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/Applications/ChimeraX-1.12.app/Contents/include/python3.11 -c
C/pyKVFinder.c -o build/temp.macosx-10.9-universal2-cpython-311/C/pyKVFinder.o
-Xpreprocessor -fopenmp=libomp -O3 -ffast-math
error: unknown argument: '-fopenmp=libomp'
error: command '/usr/bin/clang' failed with exit code 1
[end of output]
note: This error originates from a subprocess, and is likely not a problem
with pip.
ERROR: Failed building wheel for pyKVFinder
error: failed-wheel-build-for-install
× Failed to build installable wheels for some pyproject.toml based projects
╰─> pyKVFinder
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1955, in <lambda>
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12.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-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3245, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12.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-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 578, in start_tool
raise ToolshedError(
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Find
Cavities in bundle ChimeraX-KVFinder:
error: subprocess-exited-with-error
× Building wheel for pyKVFinder (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [58 lines of output]
running bdist_wheel
running build
running build_py
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder
copying pyKVFinder/__init__.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder
copying pyKVFinder/utils.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder
copying pyKVFinder/main.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder
copying pyKVFinder/argparser.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/hydropathy.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/__init__.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/export.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/spatial.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/depth.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/constitutional.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/geometry.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/cavity.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/openings.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/detect.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
running egg_info
writing pyKVFinder.egg-info/PKG-INFO
writing dependency_links to pyKVFinder.egg-info/dependency_links.txt
writing entry points to pyKVFinder.egg-info/entry_points.txt
writing requirements to pyKVFinder.egg-info/requires.txt
writing top-level names to pyKVFinder.egg-info/top_level.txt
reading manifest file 'pyKVFinder.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching 'requirements.txt'
adding license file 'LICENSE'
writing manifest file 'pyKVFinder.egg-info/SOURCES.txt'
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/WimleyWhite.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/EisenbergWeiss.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/ZhaoLondon.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/RadzickaWolfenden.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/MoonFleming.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/KyteDoolittle.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/HessaHeijne.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/vdw.dat ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/ADN.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/C1.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/PKI.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/1FMO.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/1FMO.KVFinder.output.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/ClO4.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/1FMO.xyz ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/custom-box.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/ADN.xyz ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/residues-box.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
running build_ext
building 'pyKVFinder._pyKVFinder' extension
swigging C/pyKVFinder.i to C/pyKVFinder_wrap.c
swig -python -o C/pyKVFinder_wrap.c C/pyKVFinder.i
creating build/temp.macosx-10.9-universal2-cpython-311/C
clang -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g
-fwrapv -O3 -Wall -arch arm64 -arch x86_64 -g
-I/private/var/folders/gd/ww67f0hx1mg613mfry6rddqsxqlhrx/T/pip-build-env-
jap6z4xt/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/Applications/ChimeraX-1.12.app/Contents/include/python3.11 -c
C/pyKVFinder.c -o build/temp.macosx-10.9-universal2-cpython-311/C/pyKVFinder.o
-Xpreprocessor -fopenmp=libomp -O3 -ffast-math
error: unknown argument: '-fopenmp=libomp'
error: command '/usr/bin/clang' failed with exit code 1
[end of output]
note: This error originates from a subprocess, and is likely not a problem
with pip.
ERROR: Failed building wheel for pyKVFinder
error: failed-wheel-build-for-install
× Failed to build installable wheels for some pyproject.toml based projects
╰─> pyKVFinder
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Find
Cavities in bundle ChimeraX-KVFinder:
error: subprocess-exited-with-error
× Building wheel for pyKVFinder (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [58 lines of output]
running bdist_wheel
running build
running build_py
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder
copying pyKVFinder/__init__.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder
copying pyKVFinder/utils.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder
copying pyKVFinder/main.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder
copying pyKVFinder/argparser.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/hydropathy.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/__init__.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/export.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/spatial.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/depth.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/constitutional.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/geometry.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/cavity.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/openings.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/detect.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
running egg_info
writing pyKVFinder.egg-info/PKG-INFO
writing dependency_links to pyKVFinder.egg-info/dependency_links.txt
writing entry points to pyKVFinder.egg-info/entry_points.txt
writing requirements to pyKVFinder.egg-info/requires.txt
writing top-level names to pyKVFinder.egg-info/top_level.txt
reading manifest file 'pyKVFinder.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching 'requirements.txt'
adding license file 'LICENSE'
writing manifest file 'pyKVFinder.egg-info/SOURCES.txt'
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/WimleyWhite.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/EisenbergWeiss.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/ZhaoLondon.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/RadzickaWolfenden.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/MoonFleming.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/KyteDoolittle.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/HessaHeijne.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/vdw.dat ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/ADN.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/C1.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/PKI.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/1FMO.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/1FMO.KVFinder.output.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/ClO4.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/1FMO.xyz ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/custom-box.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/ADN.xyz ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/residues-box.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
running build_ext
building 'pyKVFinder._pyKVFinder' extension
swigging C/pyKVFinder.i to C/pyKVFinder_wrap.c
swig -python -o C/pyKVFinder_wrap.c C/pyKVFinder.i
creating build/temp.macosx-10.9-universal2-cpython-311/C
clang -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g
-fwrapv -O3 -Wall -arch arm64 -arch x86_64 -g
-I/private/var/folders/gd/ww67f0hx1mg613mfry6rddqsxqlhrx/T/pip-build-env-
jap6z4xt/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/Applications/ChimeraX-1.12.app/Contents/include/python3.11 -c
C/pyKVFinder.c -o build/temp.macosx-10.9-universal2-cpython-311/C/pyKVFinder.o
-Xpreprocessor -fopenmp=libomp -O3 -ffast-math
error: unknown argument: '-fopenmp=libomp'
error: command '/usr/bin/clang' failed with exit code 1
[end of output]
note: This error originates from a subprocess, and is likely not a problem
with pip.
ERROR: Failed building wheel for pyKVFinder
error: failed-wheel-build-for-install
× Failed to build installable wheels for some pyproject.toml based projects
╰─> pyKVFinder
File
"/Applications/ChimeraX-1.12.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.
> close session
> open /Users/hkalin/Downloads/AF-P53041-F1-model_v4.pdb format pdb
No such file/path: /Users/hkalin/Downloads/AF-P53041-F1-model_v4.pdb
> open 5WG8 format mmcif fromDatabase pdb
5wg8 title:
Structure of PP5C with LB-100; 7-oxabicyclo[2.2.1]heptane-2,3-dicarbonyl
moiety modeled in the density [more info...]
Chain information for 5wg8 #1
---
Chain | Description | UniProt
A | Serine/threonine-protein phosphatase 5 | PPP5_HUMAN 169-499
Non-standard residues in 5wg8 #1
---
LB1 —
(1S,2R,3S,4R)-3-(4-methylpiperazine-1-carbonyl)-7-oxabicyclo[2.2.1]heptane-2-carboxylic
acid
MN — manganese (II) ion
MPD — (4S)-2-methyl-2,4-pentanediol
MRD — (4R)-2-methylpentane-2,4-diol
75 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
2553 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
> close session
> open /Users/hkalin/Desktop/4DPD_workshop_vr_HK.glb format gltf
Opened glTF file containing 1 scenes, 29 nodes, 19 meshes
> select water
Expected an objects specifier or a keyword
> close session
> open
> /Users/hkalin/Desktop/fold_ppp5c_alphafold3/fold_ppp5c_alphafold3_full_data_0.json
Failed opening file
/Users/hkalin/Desktop/fold_ppp5c_alphafold3/fold_ppp5c_alphafold3_full_data_0.json:
Opening an AlphaFold PAE file requires first opening the predicted atomic
model. Did not find an open atomic model from the same directory. If the
atomic model is already open choose it using menu
Tools / Structure Prediction / AlphaFold Error Plot
or use the open command structure option, for example
open
/Users/hkalin/Desktop/fold_ppp5c_alphafold3/fold_ppp5c_alphafold3_full_data_0.json
structure #1
If you are trying to open a JSON file that is not AlphaFold PAE data then you
need to specify the specific JSON format such as
open mole_channels.json format mole
> open
> /Users/hkalin/Desktop/fold_ppp5c_alphafold3/fold_ppp5c_alphafold3_model_4.cif
> /Users/hkalin/Desktop/fold_ppp5c_alphafold3/fold_ppp5c_alphafold3_model_3.cif
> /Users/hkalin/Desktop/fold_ppp5c_alphafold3/fold_ppp5c_alphafold3_model_2.cif
> /Users/hkalin/Desktop/fold_ppp5c_alphafold3/fold_ppp5c_alphafold3_model_1.cif
> /Users/hkalin/Desktop/fold_ppp5c_alphafold3/fold_ppp5c_alphafold3_model_0.cif
Chain information for fold_ppp5c_alphafold3_model_4.cif #1
---
Chain | Description
A | .
Chain information for fold_ppp5c_alphafold3_model_3.cif #2
---
Chain | Description
A | .
Chain information for fold_ppp5c_alphafold3_model_2.cif #3
---
Chain | Description
A | .
Chain information for fold_ppp5c_alphafold3_model_1.cif #4
---
Chain | Description
A | .
Chain information for fold_ppp5c_alphafold3_model_0.cif #5
---
Chain | Description
A | .
Computing secondary structure
[Repeated 4 time(s)]
> select #1/A:1-499
3999 atoms, 4088 bonds, 499 residues, 1 model selected
> select #2/A:1-499
3999 atoms, 4088 bonds, 499 residues, 1 model selected
> select #3/A:1-499
3999 atoms, 4088 bonds, 499 residues, 1 model selected
> select #4/A:1-499
3999 atoms, 4088 bonds, 499 residues, 1 model selected
> select #5/A:1-499
3999 atoms, 4088 bonds, 499 residues, 1 model selected
> select #1/A:1-499
3999 atoms, 4088 bonds, 499 residues, 1 model selected
> select #5/A:1-499
3999 atoms, 4088 bonds, 499 residues, 1 model selected
> select clear
> select #2/A:1-499
3999 atoms, 4088 bonds, 499 residues, 1 model selected
> select #2/A:1-499
3999 atoms, 4088 bonds, 499 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #2/A:1-499
Nothing selected
> select #1/A:1-499
3999 atoms, 4088 bonds, 499 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #2/A:1-499
Nothing selected
> select #1/A:1-499
Nothing selected
> select #3/A:1-499
3999 atoms, 4088 bonds, 499 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #4/A:1-499
3999 atoms, 4088 bonds, 499 residues, 1 model selected
> select #5/A:1-499
3999 atoms, 4088 bonds, 499 residues, 1 model selected
> select #4/A:1-499
3999 atoms, 4088 bonds, 499 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select clear
[Repeated 1 time(s)]
> open 5WG8 fromDatabase pdb format mmcif
5wg8 title:
Structure of PP5C with LB-100; 7-oxabicyclo[2.2.1]heptane-2,3-dicarbonyl
moiety modeled in the density [more info...]
Chain information for 5wg8 #1
---
Chain | Description | UniProt
A | Serine/threonine-protein phosphatase 5 | PPP5_HUMAN 169-499
Non-standard residues in 5wg8 #1
---
LB1 —
(1S,2R,3S,4R)-3-(4-methylpiperazine-1-carbonyl)-7-oxabicyclo[2.2.1]heptane-2-carboxylic
acid
MN — manganese (II) ion
MPD — (4S)-2-methyl-2,4-pentanediol
MRD — (4R)-2-methylpentane-2,4-diol
75 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
2553 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
Drag select of 819 residues, 118 atoms, 11 pseudobonds, 104 bonds
> Matchmaker #2 to #1
Unknown command: Matchmaker #2 to #1
> select clear
> Matchmaker #2 to #1
Unknown command: Matchmaker #2 to #1
> Mmaker #2 to #1
Unknown command: Mmaker #2 to #1
> toolshed show
> ui tool show Match→Align
> msa3d #1/A#5/A
Match→Align cutoff: 5.0, in column if within cutoff of: any
48 residue pairs aligned
48 fully populated columns
Pairwise RMSDs across all fully populated columns
---
Model | 1 | 5
1 | 0.000 | 3.100
5 | 3.100 | 0.000
Overall RMSD: 3.100
Sequence lengths: 320 499
SDM (cutoff 5.0): 155.607
Q-score: 0.007
Alignment identifier is MA-1
Showing conservation header ("seq_conservation" residue attribute) for
alignment MA-1
Chains used in RMSD evaluation for alignment MA-1: 5wg8 #1/A,
fold_ppp5c_alphafold3_model_0.cif #5/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment MA-1
> select clear
Drag select of 819 residues, 118 atoms, 11 pseudobonds, 104 bonds
> Mmaker #2 to #1
Unknown command: Mmaker #2 to #1
> Mmaker #1 to #2
Unknown command: Mmaker #1 to #2
> select #5/A
3999 atoms, 4088 bonds, 499 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #5 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 5wg8, chain A (#1) with fold_ppp5c_alphafold3_model_0.cif, chain A
(#5), sequence alignment score = 1693.4
RMSD between 314 pruned atom pairs is 0.284 angstroms; (across all 320 pairs:
0.782)
> ui windowfill toggle
[Repeated 2 time(s)]
> ui mousemode right distance
[Repeated 1 time(s)]
> ui mousemode right "move label"
[Repeated 1 time(s)]Drag select of 10 residues
Drag select of 2 residues
> select clear
[Repeated 1 time(s)]
> select #5/A:80
12 atoms, 12 bonds, 1 residue, 1 model selected
> ui tool show "Find Cavities"
pyKVFinder module not installed; fetching from PyPi repository...
'pip install pyKVFinder' failed. Error from pip: error: subprocess-exited-
with-error
× Building wheel for pyKVFinder (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [58 lines of output]
running bdist_wheel
running build
running build_py
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder
copying pyKVFinder/__init__.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder
copying pyKVFinder/utils.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder
copying pyKVFinder/main.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder
copying pyKVFinder/argparser.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/hydropathy.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/__init__.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/export.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/spatial.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/depth.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/constitutional.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/geometry.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/cavity.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/openings.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/detect.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
running egg_info
writing pyKVFinder.egg-info/PKG-INFO
writing dependency_links to pyKVFinder.egg-info/dependency_links.txt
writing entry points to pyKVFinder.egg-info/entry_points.txt
writing requirements to pyKVFinder.egg-info/requires.txt
writing top-level names to pyKVFinder.egg-info/top_level.txt
reading manifest file 'pyKVFinder.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching 'requirements.txt'
adding license file 'LICENSE'
writing manifest file 'pyKVFinder.egg-info/SOURCES.txt'
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/WimleyWhite.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/EisenbergWeiss.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/ZhaoLondon.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/RadzickaWolfenden.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/MoonFleming.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/KyteDoolittle.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/HessaHeijne.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/vdw.dat ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/ADN.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/C1.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/PKI.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/1FMO.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/1FMO.KVFinder.output.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/ClO4.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/1FMO.xyz ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/custom-box.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/ADN.xyz ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/residues-box.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
running build_ext
building 'pyKVFinder._pyKVFinder' extension
swigging C/pyKVFinder.i to C/pyKVFinder_wrap.c
swig -python -o C/pyKVFinder_wrap.c C/pyKVFinder.i
creating build/temp.macosx-10.9-universal2-cpython-311/C
clang -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g
-fwrapv -O3 -Wall -arch arm64 -arch x86_64 -g
-I/private/var/folders/gd/ww67f0hx1mg613mfry6rddqsxqlhrx/T/pip-build-
env-n89hc9s1/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/Applications/ChimeraX-1.12.app/Contents/include/python3.11 -c
C/pyKVFinder.c -o build/temp.macosx-10.9-universal2-cpython-311/C/pyKVFinder.o
-Xpreprocessor -fopenmp=libomp -O3 -ffast-math
error: unknown argument: '-fopenmp=libomp'
error: command '/usr/bin/clang' failed with exit code 1
[end of output]
note: This error originates from a subprocess, and is likely not a problem
with pip.
ERROR: Failed building wheel for pyKVFinder
error: failed-wheel-build-for-install
× Failed to build installable wheels for some pyproject.toml based projects
╰─> pyKVFinder
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.12.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-1.12.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-1.12.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-1.12.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-1.12.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-1.12.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-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3245, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12.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-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/python_utils.py", line 148, in run_logged_pip
raise RuntimeError(s)
RuntimeError: error: subprocess-exited-with-error
× Building wheel for pyKVFinder (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [58 lines of output]
running bdist_wheel
running build
running build_py
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder
copying pyKVFinder/__init__.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder
copying pyKVFinder/utils.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder
copying pyKVFinder/main.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder
copying pyKVFinder/argparser.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/hydropathy.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/__init__.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/export.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/spatial.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/depth.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/constitutional.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/geometry.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/cavity.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/openings.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/detect.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
running egg_info
writing pyKVFinder.egg-info/PKG-INFO
writing dependency_links to pyKVFinder.egg-info/dependency_links.txt
writing entry points to pyKVFinder.egg-info/entry_points.txt
writing requirements to pyKVFinder.egg-info/requires.txt
writing top-level names to pyKVFinder.egg-info/top_level.txt
reading manifest file 'pyKVFinder.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching 'requirements.txt'
adding license file 'LICENSE'
writing manifest file 'pyKVFinder.egg-info/SOURCES.txt'
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/WimleyWhite.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/EisenbergWeiss.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/ZhaoLondon.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/RadzickaWolfenden.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/MoonFleming.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/KyteDoolittle.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/HessaHeijne.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/vdw.dat ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/ADN.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/C1.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/PKI.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/1FMO.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/1FMO.KVFinder.output.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/ClO4.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/1FMO.xyz ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/custom-box.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/ADN.xyz ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/residues-box.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
running build_ext
building 'pyKVFinder._pyKVFinder' extension
swigging C/pyKVFinder.i to C/pyKVFinder_wrap.c
swig -python -o C/pyKVFinder_wrap.c C/pyKVFinder.i
creating build/temp.macosx-10.9-universal2-cpython-311/C
clang -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g
-fwrapv -O3 -Wall -arch arm64 -arch x86_64 -g
-I/private/var/folders/gd/ww67f0hx1mg613mfry6rddqsxqlhrx/T/pip-build-
env-n89hc9s1/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/Applications/ChimeraX-1.12.app/Contents/include/python3.11 -c
C/pyKVFinder.c -o build/temp.macosx-10.9-universal2-cpython-311/C/pyKVFinder.o
-Xpreprocessor -fopenmp=libomp -O3 -ffast-math
error: unknown argument: '-fopenmp=libomp'
error: command '/usr/bin/clang' failed with exit code 1
[end of output]
note: This error originates from a subprocess, and is likely not a problem
with pip.
ERROR: Failed building wheel for pyKVFinder
error: failed-wheel-build-for-install
× Failed to build installable wheels for some pyproject.toml based projects
╰─> pyKVFinder
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1955, in <lambda>
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12.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-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3245, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12.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-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 578, in start_tool
raise ToolshedError(
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Find
Cavities in bundle ChimeraX-KVFinder:
error: subprocess-exited-with-error
× Building wheel for pyKVFinder (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [58 lines of output]
running bdist_wheel
running build
running build_py
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder
copying pyKVFinder/__init__.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder
copying pyKVFinder/utils.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder
copying pyKVFinder/main.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder
copying pyKVFinder/argparser.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/hydropathy.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/__init__.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/export.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/spatial.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/depth.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/constitutional.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/geometry.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/cavity.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/openings.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/detect.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
running egg_info
writing pyKVFinder.egg-info/PKG-INFO
writing dependency_links to pyKVFinder.egg-info/dependency_links.txt
writing entry points to pyKVFinder.egg-info/entry_points.txt
writing requirements to pyKVFinder.egg-info/requires.txt
writing top-level names to pyKVFinder.egg-info/top_level.txt
reading manifest file 'pyKVFinder.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching 'requirements.txt'
adding license file 'LICENSE'
writing manifest file 'pyKVFinder.egg-info/SOURCES.txt'
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/WimleyWhite.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/EisenbergWeiss.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/ZhaoLondon.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/RadzickaWolfenden.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/MoonFleming.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/KyteDoolittle.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/HessaHeijne.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/vdw.dat ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/ADN.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/C1.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/PKI.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/1FMO.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/1FMO.KVFinder.output.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/ClO4.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/1FMO.xyz ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/custom-box.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/ADN.xyz ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/residues-box.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
running build_ext
building 'pyKVFinder._pyKVFinder' extension
swigging C/pyKVFinder.i to C/pyKVFinder_wrap.c
swig -python -o C/pyKVFinder_wrap.c C/pyKVFinder.i
creating build/temp.macosx-10.9-universal2-cpython-311/C
clang -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g
-fwrapv -O3 -Wall -arch arm64 -arch x86_64 -g
-I/private/var/folders/gd/ww67f0hx1mg613mfry6rddqsxqlhrx/T/pip-build-
env-n89hc9s1/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/Applications/ChimeraX-1.12.app/Contents/include/python3.11 -c
C/pyKVFinder.c -o build/temp.macosx-10.9-universal2-cpython-311/C/pyKVFinder.o
-Xpreprocessor -fopenmp=libomp -O3 -ffast-math
error: unknown argument: '-fopenmp=libomp'
error: command '/usr/bin/clang' failed with exit code 1
[end of output]
note: This error originates from a subprocess, and is likely not a problem
with pip.
ERROR: Failed building wheel for pyKVFinder
error: failed-wheel-build-for-install
× Failed to build installable wheels for some pyproject.toml based projects
╰─> pyKVFinder
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Find
Cavities in bundle ChimeraX-KVFinder:
error: subprocess-exited-with-error
× Building wheel for pyKVFinder (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [58 lines of output]
running bdist_wheel
running build
running build_py
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder
copying pyKVFinder/__init__.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder
copying pyKVFinder/utils.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder
copying pyKVFinder/main.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder
copying pyKVFinder/argparser.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/hydropathy.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/__init__.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/export.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/spatial.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/depth.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/constitutional.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/geometry.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/cavity.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/openings.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
copying pyKVFinder/grid/detect.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid
running egg_info
writing pyKVFinder.egg-info/PKG-INFO
writing dependency_links to pyKVFinder.egg-info/dependency_links.txt
writing entry points to pyKVFinder.egg-info/entry_points.txt
writing requirements to pyKVFinder.egg-info/requires.txt
writing top-level names to pyKVFinder.egg-info/top_level.txt
reading manifest file 'pyKVFinder.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching 'requirements.txt'
adding license file 'LICENSE'
writing manifest file 'pyKVFinder.egg-info/SOURCES.txt'
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/WimleyWhite.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/EisenbergWeiss.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/ZhaoLondon.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/RadzickaWolfenden.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/MoonFleming.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/KyteDoolittle.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/HessaHeijne.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/vdw.dat ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/ADN.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/C1.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/PKI.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/1FMO.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/1FMO.KVFinder.output.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/ClO4.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/1FMO.xyz ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/custom-box.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/ADN.xyz ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/residues-box.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
running build_ext
building 'pyKVFinder._pyKVFinder' extension
swigging C/pyKVFinder.i to C/pyKVFinder_wrap.c
swig -python -o C/pyKVFinder_wrap.c C/pyKVFinder.i
creating build/temp.macosx-10.9-universal2-cpython-311/C
clang -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g
-fwrapv -O3 -Wall -arch arm64 -arch x86_64 -g
-I/private/var/folders/gd/ww67f0hx1mg613mfry6rddqsxqlhrx/T/pip-build-
env-n89hc9s1/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/Applications/ChimeraX-1.12.app/Contents/include/python3.11 -c
C/pyKVFinder.c -o build/temp.macosx-10.9-universal2-cpython-311/C/pyKVFinder.o
-Xpreprocessor -fopenmp=libomp -O3 -ffast-math
error: unknown argument: '-fopenmp=libomp'
error: command '/usr/bin/clang' failed with exit code 1
[end of output]
note: This error originates from a subprocess, and is likely not a problem
with pip.
ERROR: Failed building wheel for pyKVFinder
error: failed-wheel-build-for-install
× Failed to build installable wheels for some pyproject.toml based projects
╰─> pyKVFinder
File
"/Applications/ChimeraX-1.12.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 - 88.1
OpenGL renderer: Apple M3 Pro
OpenGL vendor: Apple
Python: 3.11.9
Locale: UTF-8
Qt version: PyQt6 6.10.2, Qt 6.10.0
Qt runtime version: 6.10.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac15,6
Model Number: Z1AX0029VLL/A
Chip: Apple M3 Pro
Total Number of Cores: 12 (6 performance and 6 efficiency)
Memory: 36 GB
System Firmware Version: mBoot-18000.101.7
OS Loader Version: 10151.140.19.701.1
Software:
System Software Overview:
System Version: macOS 14.8.5 (23J423)
Kernel Version: Darwin 23.6.0
Time since boot: 6 hours, 19 minutes
Graphics/Displays:
Apple M3 Pro:
Chipset Model: Apple M3 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 18
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
accessible-pygments: 0.0.5
aiohappyeyeballs: 2.6.2
aiohttp: 3.13.4
aiosignal: 1.4.0
alabaster: 1.0.0
annotated-types: 0.7.0
anyio: 4.13.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.1
attrs: 26.1.0
babel: 2.18.0
beautifulsoup4: 4.13.5
blockdiag: 3.0.0
blosc2: 4.4.3
bs4: 0.0.2
build: 1.3.0
certifi: 2025.7.14
cftime: 1.6.5
charset-normalizer: 3.4.7
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.2.8
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.2
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.2
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: 1.67.1
ChimeraX-AtomicLibrary: 14.4
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: 1.4.1
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.4
ChimeraX-Cluster: 1.0
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3.1
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.12
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: 1.2.2
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: 1.8.2
ChimeraX-Label: 1.5
ChimeraX-LightingGUI: 1.0
ChimeraX-ListInfo: 1.3.1
ChimeraX-Log: 1.2.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.3
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-MatchAlign: 1.2
ChimeraX-MatchMaker: 2.4.1
ChimeraX-MCopy: 1.0
ChimeraX-MCPServer: 0.2.0
ChimeraX-MDcrds: 2.19
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.3.9
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.23
ChimeraX-ModelPanel: 1.6.1
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: 1.0.1
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: 1.15.4
ChimeraX-OpenFold: 1.0
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.13
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: 1.6
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.8.2
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: 3.5.12
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.18
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-SNFG: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.3
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: 2.5.3
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.4
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.50.8
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.6.2
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: 8.4.1
colorama: 0.4.6
comm: 0.2.3
contourpy: 1.3.3
coverage: 7.14.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.2.4
debugpy: 1.8.21
decorator: 5.3.1
docutils: 0.21.2
executing: 2.2.1
filelock: 3.19.1
fonttools: 4.63.0
frozenlist: 1.8.0
funcparserlib: 2.0.0a0
glfw: 2.10.0
grako: 3.16.5
h11: 0.16.0
h5py: 3.16.0
html2text: 2025.4.15
httpcore: 1.0.9
httpx: 0.28.1
httpx-sse: 0.4.3
idna: 3.18
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 2.0.0
iniconfig: 2.3.0
ipykernel: 7.1.0
ipython: 9.9.0
ipython_pygments_lexers: 1.1.1
jedi: 0.19.2
Jinja2: 3.1.6
jsonschema: 4.26.0
jsonschema-specifications: 2025.9.1
jupyter_client: 8.8.0
jupyter_core: 5.9.1
kiwisolver: 1.5.0
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: 0.2.2
mcp: 1.18.0
msgpack: 1.1.1
multidict: 6.7.1
narwhals: 2.22.1
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: 8.4.0
openvr: 1.26.701
packaging: 25.0
ParmEd: 4.2.2
parso: 0.8.7
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: 4.10.0
plotly: 6.8.0
pluggy: 1.6.0
prompt_toolkit: 3.0.52
propcache: 0.5.2
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: 2.13.4
pydantic-settings: 2.14.1
pydantic_core: 2.46.4
pydata-sphinx-theme: 0.18.0
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.5.1
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: 6.10.2
PyQt6-Qt6: 6.10.2
PyQt6-WebEngine-commercial: 6.10.0
PyQt6-WebEngine-Qt6: 6.10.2
PyQt6_sip: 13.10.3
pytest: 9.0.3
pytest-cov: 7.1.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.2
python-multipart: 0.0.32
pyzmq: 27.1.0
qtconsole: 5.7.0
QtPy: 2.4.3
qtshim: 1.2.2
RandomWords: 0.4.0
referencing: 0.37.0
requests: 2.32.5
roman-numerals: 4.1.0
rpds-py: 2026.5.1
scipy: 1.14.0
setuptools: 80.9.0
sfftk-rw: 0.8.1
six: 1.17.0
snowballstemmer: 3.1.1
sortedcontainers: 2.4.0
soupsieve: 2.8.4
Sphinx: 9.0.4
sphinx-autodoc-typehints: 3.6.1
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: 3.4.4
stack-data: 0.6.3
starlette: 1.3.0
superqt: 0.7.6
tables: 3.10.2
tcia_utils: 3.2.1
threadpoolctl: 3.6.0
tifffile: 2025.3.13
tinyarray: 1.2.5
tornado: 6.5.7
tqdm: 4.68.2
traitlets: 5.14.3
typing-inspection: 0.4.2
typing_extensions: 4.15.0
Unidecode: 1.4.0
urllib3: 2.7.0
uvicorn: 0.49.0
wcwidth: 0.8.1
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
yarl: 1.24.2
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