pyKVFinder: missing LC_LOAD_DYLIB (must link with at least libSystem.dylib)

[clmarino@…]

The following bug report has been submitted:
Platform:        macOS-15.4-arm64-arm-64bit
ChimeraX Version: 1.10.dev202504090046 (2025-04-09 00:46:27 UTC)
Description
I downloaded ChimeraX daily -> find cavities -> selected structure -> error

Log:
UCSF ChimeraX version: 1.10.dev202504090046 (2025-04-09)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open /Users/clmarino/Desktop/040825_GPG2_E3Ch.cxs format session

Log from Tue Apr 8 10:42:14 2025UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open
> /Users/clmarino/Downloads/fold_2025_02_03_relnmut_lrp63/040225_rlnmut_wnt3alrp6.cxs
> format session

Log from Wed Apr 2 16:38:25 2025UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open /Users/clmarino/Desktop/031925CTR-RLNmut-wnt3qlrp62.cxs format session

Log from Wed Mar 19 17:40:52 2025 Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/clmarino/Downloads/fold_2025_02_03_relnmutctrwnr3a_lrp6/fold_2025_02_03_relnmutctrwnr3a_lrp6_model_0.cif

Chain information for fold_2025_02_03_relnmutctrwnr3a_lrp6_model_0.cif #1  
---  
Chain | Description  
A | .  
B | .  
C | .  
  
Computing secondary structure  

> open
> /Users/clmarino/Downloads/fold_2025_02_03_relnmutctrwnr3a_lrp6/fold_2025_02_03_relnmutctrwnr3a_lrp6_model_1.cif

Chain information for fold_2025_02_03_relnmutctrwnr3a_lrp6_model_1.cif #2  
---  
Chain | Description  
A | .  
B | .  
C | .  
  

> open
> /Users/clmarino/Downloads/fold_2025_02_03_relnmutctrwnr3a_lrp6/fold_2025_02_03_relnmutctrwnr3a_lrp6_model_2.cif

Chain information for fold_2025_02_03_relnmutctrwnr3a_lrp6_model_2.cif #3  
---  
Chain | Description  
A | .  
B | .  
C | .  
  

> open
> /Users/clmarino/Downloads/fold_2025_02_03_relnmutctrwnr3a_lrp6/fold_2025_02_03_relnmutctrwnr3a_lrp6_model_3.cif

Chain information for fold_2025_02_03_relnmutctrwnr3a_lrp6_model_3.cif #4  
---  
Chain | Description  
A | .  
B | .  
C | .  
  

> open
> /Users/clmarino/Downloads/fold_2025_02_03_relnmutctrwnr3a_lrp6/fold_2025_02_03_relnmutctrwnr3a_lrp6_model_4.cif

Chain information for fold_2025_02_03_relnmutctrwnr3a_lrp6_model_4.cif #5  
---  
Chain | Description  
A | .  
B | .  
C | .  
  
Computing secondary structure  
[Repeated 3 time(s)]

> color bychain

> ui tool show Matchmaker

> matchmaker #1-4 to #5

Computing secondary structure  
[Repeated 4 time(s)]  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 fold_2025_02_03_relnmutctrwnr3a_lrp6_model_4.cif, chain B (#5) with
fold_2025_02_03_relnmutctrwnr3a_lrp6_model_0.cif, chain B (#1), sequence
alignment score = 8309.7  
RMSD between 629 pruned atom pairs is 0.526 angstroms; (across all 1613 pairs:
35.956)  
  
Matchmaker fold_2025_02_03_relnmutctrwnr3a_lrp6_model_4.cif, chain B (#5) with
fold_2025_02_03_relnmutctrwnr3a_lrp6_model_1.cif, chain B (#2), sequence
alignment score = 8323.5  
RMSD between 603 pruned atom pairs is 0.413 angstroms; (across all 1613 pairs:
26.069)  
  
Matchmaker fold_2025_02_03_relnmutctrwnr3a_lrp6_model_4.cif, chain B (#5) with
fold_2025_02_03_relnmutctrwnr3a_lrp6_model_2.cif, chain B (#3), sequence
alignment score = 8222.1  
RMSD between 719 pruned atom pairs is 0.877 angstroms; (across all 1613 pairs:
28.773)  
  
Matchmaker fold_2025_02_03_relnmutctrwnr3a_lrp6_model_4.cif, chain B (#5) with
fold_2025_02_03_relnmutctrwnr3a_lrp6_model_3.cif, chain B (#4), sequence
alignment score = 8344.5  
RMSD between 1048 pruned atom pairs is 1.092 angstroms; (across all 1613
pairs: 36.264)  
  

> hide #4 models

> hide #3 models

> hide #2 models

> hide #1 models

> save /Users/clmarino/Desktop/031925CTR-RLNmut-wnt3qlrp62.cxs

——— End of log from Wed Mar 19 17:40:52 2025 ———

opened ChimeraX session  

> ui tool show AlphaFold

> alphafold match #1/A

1 AlphaFold model found using sequence similarity searches: A0A6J2IBV3 (chain
A)  
AlphaFold prediction matching fold_2025_02_03_relnmutctrwnr3a_lrp6_model_0.cif  
---  
Chain| UniProt Id| UniProt Name| RMSD| Length| Seen| % Id  
A | A0A6J2IBV3 | A0A6J2IBV3_9PASS | 29.71 | 32 | 32 | 97   
  
Opened 1 AlphaFold model  

> alphafold match #1/B

1 AlphaFold model found using sequence similarity searches: O75581 (chain B)  
AlphaFold prediction matching fold_2025_02_03_relnmutctrwnr3a_lrp6_model_0.cif  
---  
Chain| UniProt Id| UniProt Name| RMSD| Length| Seen| % Id  
B | O75581 | LRP6_HUMAN | 37.13 | 1613 | 1613 | 100   
  
Opened 1 AlphaFold model  

> alphafold match #1/C

1 AlphaFold model found using sequence similarity searches: P56704 (chain C)  
AlphaFold prediction matching fold_2025_02_03_relnmutctrwnr3a_lrp6_model_0.cif  
---  
Chain| UniProt Id| UniProt Name| RMSD| Length| Seen| % Id  
C | P56704 | WNT3A_HUMAN | 3.55 | 352 | 352 | 100   
  
Opened 1 AlphaFold model  

Fetching PAE using AlphaFold database version 4  

> alphafold pae #8.1 uniprotId P56704 version 4

> color #8.1/C:351 lime

> color #8.1/C:349 magenta

> color #8.1/C:216-352 lime

> color #8.1/C:249 lime

> color #8.1/C:189 magenta

> color #8.1/C:225-350 lime

> color #8.1/C:102-168 magenta

> color #8.1/C:13-65 lime

> color #8.1/C:281-352 magenta

> color #8.1/C:285-343 lime

> color #8.1/C:73-123 magenta

> color #8.1/C:324 lime

> color #8.1/C:5 magenta

> hide #5 models

> hide #!6 models

> show #!6 models

> hide #6.1 models

> show #6.1 models

> hide #8.1 models

> show #8.1 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> hide #7.1 models

> show #7.1 models

> show #5 models

> hide #!6 models

> show #!6 models

> hide #6.1 models

> show #6.1 models

> hide #!7 models

> show #!7 models

> hide #5 models

> hide #7.1 models

> show #7.1 models

> show #5 models

> hide #5 models

> show #5 models

> hide #5 models

> save
> /Users/clmarino/Downloads/fold_2025_02_03_relnmut_lrp63/040225_rlnmut_wnt3alrp6.cxs

——— End of log from Wed Apr 2 16:38:25 2025 ———

opened ChimeraX session  

> color #6.1#7.1 bychain

> interfaces #6.1#7.1 & ~solvent

1 buried areas: #7.1/B #6.1/A 2236  
Ignoring fixed y limits to fulfill fixed data aspect with adjustable data
limits.  
Ignoring fixed x limits to fulfill fixed data aspect with adjustable data
limits.  

> ui tool show "Find Cavities"

> kvfinder #1

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/kvfinder/tool.py", line 67, in find_cavities  
run(self.session, "kvfinder %s" % concise_model_spec(self.session, structures,  
File
"/Applications/ChimeraX-1.9.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-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/kvfinder/cmd.py", line 52, in cmd_kvfinder  
num_cavities, cavity_matrix = pyKVFinder.detect(struct_input, vertices,
grid_spacing,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/clmarino/Library/Application
Support/ChimeraX/1.9/lib/python/site-packages/pyKVFinder/grid.py", line 820,
in detect  
from _pyKVFinder import _detect, _detect_ladj  
ImportError: dlopen(/Users/clmarino/Library/Application
Support/ChimeraX/1.9/lib/python/site-
packages/_pyKVFinder.cpython-311-darwin.so, 0x0002): tried:
'/Users/clmarino/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/_pyKVFinder.cpython-311-darwin.so' (missing LC_LOAD_DYLIB (must link
with at least libSystem.dylib)),
'/System/Volumes/Preboot/Cryptexes/OS/Users/clmarino/Library/Application
Support/ChimeraX/1.9/lib/python/site-
packages/_pyKVFinder.cpython-311-darwin.so' (no such file),
'/Users/clmarino/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/_pyKVFinder.cpython-311-darwin.so' (missing LC_LOAD_DYLIB (must link
with at least libSystem.dylib))  
  
ImportError: dlopen(/Users/clmarino/Library/Application
Support/ChimeraX/1.9/lib/python/site-
packages/_pyKVFinder.cpython-311-darwin.so, 0x0002): tried:
'/Users/clmarino/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/_pyKVFinder.cpython-311-darwin.so' (missing LC_LOAD_DYLIB (must link
with at least libSystem.dylib)),
'/System/Volumes/Preboot/Cryptexes/OS/Users/clmarino/Library/Application
Support/ChimeraX/1.9/lib/python/site-
packages/_pyKVFinder.cpython-311-darwin.so' (no such file),
'/Users/clmarino/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/_pyKVFinder.cpython-311-darwin.so' (missing LC_LOAD_DYLIB (must link
with at least libSystem.dylib))  
  
File "/Users/clmarino/Library/Application
Support/ChimeraX/1.9/lib/python/site-packages/pyKVFinder/grid.py", line 820,
in detect  
from _pyKVFinder import _detect, _detect_ladj  
  
See log for complete Python traceback.  
  

> close

> open
> /Users/clmarino/Downloads/fold_2025_04_gpc2_e3ch/fold_2025_04_gpc2_e3ch_model_0.cif

Chain information for fold_2025_04_gpc2_e3ch_model_0.cif #1  
---  
Chain | Description  
A | .  
B | .  
  
Computing secondary structure  

> open
> /Users/clmarino/Downloads/fold_2025_04_gpc2_e3ch/fold_2025_04_gpc2_e3ch_model_1.cif

Chain information for fold_2025_04_gpc2_e3ch_model_1.cif #2  
---  
Chain | Description  
A | .  
B | .  
  

> open
> /Users/clmarino/Downloads/fold_2025_04_gpc2_e3ch/fold_2025_04_gpc2_e3ch_model_2.cif

Chain information for fold_2025_04_gpc2_e3ch_model_2.cif #3  
---  
Chain | Description  
A | .  
B | .  
  

> open
> /Users/clmarino/Downloads/fold_2025_04_gpc2_e3ch/fold_2025_04_gpc2_e3ch_model_3.cif

Chain information for fold_2025_04_gpc2_e3ch_model_3.cif #4  
---  
Chain | Description  
A | .  
B | .  
  

> open
> /Users/clmarino/Downloads/fold_2025_04_gpc2_e3ch/fold_2025_04_gpc2_e3ch_model_4.cif

Chain information for fold_2025_04_gpc2_e3ch_model_4.cif #5  
---  
Chain | Description  
A | .  
B | .  
  
Computing secondary structure  
[Repeated 3 time(s)]

> ui tool show Matchmaker

> matchmaker #2-5 to #1

Computing secondary structure  
[Repeated 4 time(s)]  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 fold_2025_04_gpc2_e3ch_model_0.cif, chain A (#1) with
fold_2025_04_gpc2_e3ch_model_1.cif, chain A (#2), sequence alignment score =
2960.8  
RMSD between 460 pruned atom pairs is 0.420 angstroms; (across all 579 pairs:
22.051)  
  
Matchmaker fold_2025_04_gpc2_e3ch_model_0.cif, chain A (#1) with
fold_2025_04_gpc2_e3ch_model_2.cif, chain A (#3), sequence alignment score =
2960.8  
RMSD between 459 pruned atom pairs is 0.438 angstroms; (across all 579 pairs:
34.370)  
  
Matchmaker fold_2025_04_gpc2_e3ch_model_0.cif, chain A (#1) with
fold_2025_04_gpc2_e3ch_model_3.cif, chain A (#4), sequence alignment score =
2948.8  
RMSD between 446 pruned atom pairs is 0.611 angstroms; (across all 579 pairs:
33.139)  
  
Matchmaker fold_2025_04_gpc2_e3ch_model_0.cif, chain A (#1) with
fold_2025_04_gpc2_e3ch_model_4.cif, chain A (#5), sequence alignment score =
2971  
RMSD between 457 pruned atom pairs is 0.391 angstroms; (across all 579 pairs:
11.026)  
  

> color bychain

> hbonds reveal true

13085 hydrogen bonds found  

> undo

> color bychain

> ~hbonds

> hide #2 models

> hide #3 models

> hide #4 models

> hide #5 models

> ui tool show Contacts

> contacts intraModel false intraMol false ignoreHiddenModels true color
> #fbf342 reveal true

No contacts  

> contacts intraModel false intraMol false ignoreHiddenModels true color
> #fbf342 reveal true

No contacts  

> interfaces #1 & ~solvent

1 buried areas: A B 852  
Ignoring fixed y limits to fulfill fixed data aspect with adjustable data
limits.  
Ignoring fixed x limits to fulfill fixed data aspect with adjustable data
limits.  

> hbonds #1 reveal true

4575 hydrogen bonds found  

> save /Users/clmarino/Desktop/040825_GPG2_E3Ch.cxs

——— End of log from Tue Apr 8 10:42:14 2025 ———

> view name session-start

opened ChimeraX session  

> ui tool show "Find Cavities"

pyKVFinder module not installed; fetching from PyPi repository...  

Errors may have occurred when running pip:  

pip standard error:  
\---  
ERROR: pip's dependency resolver does not currently take into account all the
packages that are installed. This behaviour is the source of the following
dependency conflicts.  
chimerax-bundlebuilder 1.4.0 requires numpy==1.26.4, but you have numpy 2.2.4
which is incompatible.  
nptyping 2.5.0 requires numpy<2.0.0,>=1.20.0; python_version >= "3.8", but you
have numpy 2.2.4 which is incompatible.  
\---  

pip standard output:  
\---  
\---  

pyKVFinder module installed from PyPi repository.  

> kvfinder #3

Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/kvfinder/tool.py", line 136, in find_cavities  
run(self.session, cmd)  
File
"/Applications/ChimeraX_Daily.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_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3215, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/kvfinder/cmd.py", line 56, in cmd_kvfinder  
num_cavities, cavity_matrix = pyKVFinder.detect(struct_input, vertices,
grid_spacing,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/clmarino/Library/Application
Support/ChimeraX/1.10/lib/python/site-packages/pyKVFinder/grid.py", line 820,
in detect  
from _pyKVFinder import _detect, _detect_ladj  
ImportError: dlopen(/Users/clmarino/Library/Application
Support/ChimeraX/1.10/lib/python/site-
packages/_pyKVFinder.cpython-311-darwin.so, 0x0002): tried:
'/Users/clmarino/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/_pyKVFinder.cpython-311-darwin.so' (missing LC_LOAD_DYLIB (must link
with at least libSystem.dylib)),
'/System/Volumes/Preboot/Cryptexes/OS/Users/clmarino/Library/Application
Support/ChimeraX/1.10/lib/python/site-
packages/_pyKVFinder.cpython-311-darwin.so' (no such file),
'/Users/clmarino/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/_pyKVFinder.cpython-311-darwin.so' (missing LC_LOAD_DYLIB (must link
with at least libSystem.dylib))  
  
ImportError: dlopen(/Users/clmarino/Library/Application
Support/ChimeraX/1.10/lib/python/site-
packages/_pyKVFinder.cpython-311-darwin.so, 0x0002): tried:
'/Users/clmarino/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/_pyKVFinder.cpython-311-darwin.so' (missing LC_LOAD_DYLIB (must link
with at least libSystem.dylib)),
'/System/Volumes/Preboot/Cryptexes/OS/Users/clmarino/Library/Application
Support/ChimeraX/1.10/lib/python/site-
packages/_pyKVFinder.cpython-311-darwin.so' (no such file),
'/Users/clmarino/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/_pyKVFinder.cpython-311-darwin.so' (missing LC_LOAD_DYLIB (must link
with at least libSystem.dylib))  
  
File "/Users/clmarino/Library/Application
Support/ChimeraX/1.10/lib/python/site-packages/pyKVFinder/grid.py", line 820,
in detect  
from _pyKVFinder import _detect, _detect_ladj  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M4
OpenGL vendor: Apple

Python: 3.11.4
Locale: en_US.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: Mac16,1
      Model Number: MCX04LL/A
      Chip: Apple M4
      Total Number of Cores: 10 (4 performance and 6 efficiency)
      Memory: 24 GB
      System Firmware Version: 11881.101.1
      OS Loader Version: 11881.101.1

Software:

    System Software Overview:

      System Version: macOS 15.4 (24E248)
      Kernel Version: Darwin 24.4.0
      Time since boot: 5 days, 5 hours, 19 minutes

Graphics/Displays:

    Apple M4:

      Chipset Model: Apple M4
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 10
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        DELL P2425H:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 100.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3024 x 1964 Retina
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    auditwheel: 6.3.0
    babel: 2.17.0
    beautifulsoup4: 4.13.3
    blockdiag: 3.0.0
    blosc2: 3.3.0
    build: 1.2.2.post1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.1
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.7
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.20
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Aniso: 1.1.1
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60.5
    ChimeraX-AtomicLibrary: 14.1.14
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.3
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.10.dev202504090046
    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: 1.5.3
    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
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.8
    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: 1.5.18
    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: 2.7.7
    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: 1.1.2
    ChimeraX-ProfileGrids: 1.1.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.3
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.7
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17.1
    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.19.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.45.1
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.1
    coverage: 7.8.0
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.12
    debugpy: 1.8.13
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.0
    filelock: 3.18.0
    fonttools: 4.57.0
    funcparserlib: 2.0.0a0
    glfw: 2.8.0
    grako: 3.16.5
    h5py: 3.13.0
    html2text: 2024.2.26
    idna: 3.10
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.1.0
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jedi: 0.19.1
    Jinja2: 3.1.6
    jupyter_client: 8.6.3
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.8
    line_profiler: 4.2.0
    lxml: 5.3.1
    lz4: 4.4.4
    MarkupSafe: 3.0.2
    matplotlib: 3.10.1
    matplotlib-inline: 0.1.7
    msgpack: 1.1.0
    narwhals: 1.34.1
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    numpy: 2.2.4
    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: 4.3.7
    plotly: 6.0.1
    pluggy: 1.5.0
    prompt_toolkit: 3.0.50
    psutil: 7.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.32
    Pygments: 2.18.0
    pyKVFinder: 0.7.3
    pynmrstar: 3.3.5
    pynrrd: 1.0.0
    PyOpenGL: 3.1.9
    PyOpenGL-accelerate: 3.1.9
    pyopenxr: 1.1.4501
    pyparsing: 3.2.3
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.8.1
    PyQt6-Qt6: 6.8.2
    PyQt6-WebEngine-commercial: 6.8.0
    PyQt6-WebEngine-Qt6: 6.8.2
    PyQt6_sip: 13.10.0
    pytest: 8.3.5
    pytest-cov: 6.1.1
    python-dateutil: 2.9.0.post0
    pytz: 2025.2
    pyzmq: 26.4.0
    qtconsole: 5.5.2
    QtPy: 2.4.3
    qtshim: 1.1
    RandomWords: 0.4.0
    requests: 2.32.3
    roman-numerals-py: 3.1.0
    scipy: 1.14.0
    setuptools: 78.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    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
    toml: 0.10.2
    tornado: 6.4.2
    traitlets: 5.14.3
    typing_extensions: 4.13.1
    tzdata: 2025.2
    urllib3: 2.3.0
    wcwidth: 0.2.13
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.13

[pett]

Duplicate of #17304