ffmpeg: Permission denied

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-14.5-arm64-arm-64bit
ChimeraX Version: 1.10 (2025-06-26 08:57:52 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
UCSF ChimeraX version: 1.10 (2025-06-26)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open /Users/karim/Documents/Bristol/R2TP-DNAAFs-project/AlphaFold_PDBs-
> DNAAFs/DNAAF13-domains-coloured-BIS.cxs format session

Log from Sat Oct 26 18:55:53 2024UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open /Users/karim/Documents/Bristol/R2TP-DNAAFs-project/AlphaFold_PDBs-
> DNAAFs/DNAAF13-domains-coloured-BIS.cxs format session

Log from Sun Oct 13 03:05:51 2024UCSF ChimeraX version: 1.7rc202312120032
(2023-12-12)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open /Users/karim/Documents/Bristol/R2TP-DNAAFs-project/AlphaFold_PDBs-
> DNAAFs/DNAAF13-domains-coloured.cxs format session

Log from Sat Jan 6 22:54:50 2024UCSF ChimeraX version: 1.7rc202312120032
(2023-12-12)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/karim/Documents/Bristol/Data for Shulin Arl3
> paper/AlphaFold_PDBs/DNAAF13_AF-Q07617-F1-model_v1.pdb" format pdb

No such file/path: /Users/karim/Documents/Bristol/Data for Shulin Arl3
paper/AlphaFold_PDBs/DNAAF13_AF-Q07617-F1-model_v1.pdb  

> open "/Users/karim/Documents/Bristol/Data for Shulin Arl3
> paper/AlphaFold_PDBs/DNAAF16.cxs" format session

No such file/path: /Users/karim/Documents/Bristol/Data for Shulin Arl3
paper/AlphaFold_PDBs/DNAAF16.cxs  

> open /Users/karim/Documents/Bristol/R2TP-DNAAFs-project/7ole.pdb format pdb

7ole.pdb title:  
Cryo-em structure of the TELO2-TTI1-TTI2-RUVBL1-RUVBL2 complex [more info...]  
  
Chain information for 7ole.pdb #1  
---  
Chain | Description | UniProt  
A C E | ruvb-like 1 | RUVB1_HUMAN 1-456 99-554  
B D F | ruvb-like 2 | RUVB2_HUMAN 1-463  
H | protein SMG10 | TTI1_HUMAN 1050-38  
J | TELO2-interacting protein 2,TELO2-interacting protein 2, TTI2 | TTI2_HUMAN -464-43  
K | telomere length regulation protein TEL2 homolog | TELO2_HUMAN 1-38 48-66 74-138 156-444  
  
Non-standard residues in 7ole.pdb #1  
---  
ADP — adenosine-5'-diphosphate  
  

> open /Users/karim/Documents/Bristol/R2TP-DNAAFs-project/AlphaFold_PDBs-
> DNAAFs/DNAAF13_AF-Q07617-F1-model_v1.pdb

DNAAF13_AF-Q07617-F1-model_v1.pdb title:  
Alphafold V2.0 prediction for sperm-associated antigen 1 (Q07617) [more
info...]  
  
Chain information for DNAAF13_AF-Q07617-F1-model_v1.pdb #2  
---  
Chain | Description | UniProt  
A | sperm-associated antigen 1 | SPAG1_HUMAN 1-926  
  

> set bgColor white

> hide #!1 models

> show #!1 models

> hide #2 models

> close

> open /Users/karim/Documents/Bristol/R2TP-DNAAFs-project/AlphaFold_PDBs-
> DNAAFs/DNAAF13_AF-Q07617-F1-model_v1.pdb format pdb

DNAAF13_AF-Q07617-F1-model_v1.pdb title:  
Alphafold V2.0 prediction for sperm-associated antigen 1 (Q07617) [more
info...]  
  
Chain information for DNAAF13_AF-Q07617-F1-model_v1.pdb #1  
---  
Chain | Description | UniProt  
A | sperm-associated antigen 1 | SPAG1_HUMAN 1-926  
  
Alignment identifier is 1/A  

> select /A:777

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:777-861

647 atoms, 657 bonds, 85 residues, 1 model selected  

> select /A:777

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:777-878

791 atoms, 805 bonds, 102 residues, 1 model selected  

> select /A:925

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:925-926

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

> select /A:878

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:806-878

581 atoms, 591 bonds, 73 residues, 1 model selected  

> select /A:869-870

19 atoms, 19 bonds, 2 residues, 1 model selected  

> select /A:777-869

709 atoms, 720 bonds, 93 residues, 1 model selected  

> select clear

> ui tool show "Color Actions"

> color sandy brown

> lighting soft

> lighting simple

> lighting soft

> lighting full

> lighting flat

> lighting shadows true intensity 0.5

> graphics silhouettes false

> lighting soft

> lighting simple

> lighting soft

> width 3

Unknown command: width 3  

> cartoon style coil width 1 thickness 1

> cartoon style coil width 2 thickness 2

> cartoon style coil width 3 thickness 3

> cartoon style coil width 1 thickness 3

> cartoon style coil width 1 thickness 2

> cartoon style coil width 1.5 thickness 1.5

> cartoon style helix xsection round width 3

> cartoon style helix xsection round width 1.5

> cartoon style helix xsection round width 2

> cartoon style helix xsection round width 3

> cartoon style helix xsection round width 2

> cartoon style helix xsection round width 3

> cartoon style helix xsection round width 5

> cartoon style helix xsection round width 6

> cartoon style helix xsection round width 3

> cartoon style helix xsection round width 2

> cartoon style helix xsection round width 2.5

> cartoon style coil width 1 thickness 1

> cartoon style helix xsection round width 3

> cartoon style helix xsection round width 2

> cartoon style helix xsection round width 2.5

> cartoon style helix xsection round width 3

> cartoon style coil width 1 thickness 1

> cartoon style coil width 2 thickness 2

> save /Users/karim/Documents/Bristol/R2TP-DNAAFs-project/AlphaFold_PDBs-
> DNAAFs/DNAAF13.cxs

> cartoon style coil width 3 thickness 3

> lighting soft

> cartoon style coil width 2 thickness 2

> open /Users/karim/Downloads/Protein-20240106143443.xml

Opened Protein-20240106143443.xml  

> select /A:202

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:202-331

1043 atoms, 1056 bonds, 130 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel teal

> ui tool show "Color Actions"

> color sel light sea green

> select clear

> select /A:336

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select /A:202-336

1079 atoms, 1092 bonds, 135 residues, 1 model selected  

> color sel light sea green

> select clear

> select /A:202-203

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

> select /A:202-336

1079 atoms, 1092 bonds, 135 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel dark turquoise

> color sel cadet blue

[Repeated 1 time(s)]

> select clear

> select /A:430

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select /A:430-432

13 atoms, 12 bonds, 3 residues, 1 model selected  

> select /A:538-539

13 atoms, 12 bonds, 2 residues, 1 model selected  

> select /A:430-539

808 atoms, 822 bonds, 110 residues, 1 model selected  

> select /A:430

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select /A:430-549

892 atoms, 908 bonds, 120 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel cadet blue

> select /A:606-607

9 atoms, 8 bonds, 2 residues, 1 model selected  

> select /A:606-669

507 atoms, 512 bonds, 64 residues, 1 model selected  

> select /A:672-673

20 atoms, 20 bonds, 2 residues, 1 model selected  

> select /A:606-673

541 atoms, 547 bonds, 68 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel cadet blue

> select clear

> select /A:776-777

14 atoms, 13 bonds, 2 residues, 1 model selected  

> select /A:777-861

647 atoms, 657 bonds, 85 residues, 1 model selected  

> select /A:869-870

19 atoms, 19 bonds, 2 residues, 1 model selected  

> select /A:777-869

709 atoms, 720 bonds, 93 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel cornflower blue

> color sel dodger blue

> ui tool show "Color Actions"

> color sel cornflower blue

> select clear

> save /Users/karim/Documents/Bristol/R2TP-DNAAFs-project/AlphaFold_PDBs-
> DNAAFs/DNAAF13-domains-coloured.cxs

——— End of log from Sat Jan 6 22:54:50 2024 ———

opened ChimeraX session  

> select /A:788

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select /A:781-788

52 atoms, 51 bonds, 8 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel dodger blue

> color sel steel blue

> select clear

> select /A:622

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select /A:622

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select /A:611

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select /A:611

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select /A:743-744

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

> select /A:611-744

1080 atoms, 1091 bonds, 134 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel teal

> color sel cadet blue

> select clear

> select /A:868

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:868

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:869

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select /A:869

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select /A:870-871

21 atoms, 21 bonds, 2 residues, 1 model selected  

> select /A:870-926

484 atoms, 492 bonds, 57 residues, 1 model selected  

> color sel cornflower blue

> select clear

> select /A:777

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:777

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:780

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:777-780

26 atoms, 25 bonds, 4 residues, 1 model selected  

> color sel orange

> select clear

> undo

> ui tool show "Color Actions"

> color sel sandy brown

> select clear

> select /A:787-789

21 atoms, 20 bonds, 3 residues, 1 model selected  

> select /A:789-805

132 atoms, 135 bonds, 17 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel sandy brown

> select clear

> save /Users/karim/Documents/Bristol/R2TP-DNAAFs-project/AlphaFold_PDBs-
> DNAAFs/DNAAF13-domains-coloured-BIS.cxs

——— End of log from Sun Oct 13 03:05:51 2024 ———

opened ChimeraX session  

> lighting flat

> lighting soft

> select /A:550

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:550-573

182 atoms, 181 bonds, 24 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel lime

> color sel teal

> select clear

> select /A:550

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:550-573

182 atoms, 181 bonds, 24 residues, 1 model selected  

> color sel cadet blue

> select clear

> save /Users/karim/Documents/Bristol/R2TP-DNAAFs-project/AlphaFold_PDBs-
> DNAAFs/DNAAF14-domains-coloured-BIS.cxs

——— End of log from Sat Oct 26 18:55:53 2024 ———

> view name session-start

opened ChimeraX session  

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/karim/Desktop/movie6.mp4

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/toolbar/tool.py", line 185, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 397, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1419, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/__init__.py", line 66, in run_provider  
shortcuts.run_provider(session, name)  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 1394, in run_provider  
keyboard_shortcuts(session).try_shortcut(name)  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 403, in try_shortcut  
self.run_shortcut(keys)  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 421, in run_shortcut  
sc.run(self.session, status = self._enabled)  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 340, in run  
f(s)  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 1312, in save_spin_movie  
run(session, cmd)  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 537, in run  
run_command(session, command, **kw)  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3221, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/movie/moviecmd.py", line 202, in movie_encode  
encode_op(session, output[-1], format, quality, qscale, bitrate,  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/movie/moviecmd.py", line 260, in encode_op  
movie.start_encoding(output, f['ffmpeg_name'], output_size, f['ffmpeg_codec'],
"yuv420p", f['size_restriction'],  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/movie/movie.py", line 324, in start_encoding  
self.encoder.run(Status_Reporter())  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/movie/encode.py", line 232, in run  
p = Popen(self.arg_list, stdin=DEVNULL, stdout=PIPE, stderr=PIPE)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/subprocess.py",
line 1026, in __init__  
self._execute_child(args, executable, preexec_fn, close_fds,  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/subprocess.py",
line 1950, in _execute_child  
raise child_exception_type(errno_num, err_msg, err_filename)  
PermissionError: [Errno 13] Permission denied:
'/Applications/ChimeraX-1.10.app/Contents/bin/ffmpeg'  
  
PermissionError: [Errno 13] Permission denied:
'/Applications/ChimeraX-1.10.app/Contents/bin/ffmpeg'  
  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/subprocess.py",
line 1950, in _execute_child  
raise child_exception_type(errno_num, err_msg, err_filename)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M3 Pro
OpenGL vendor: Apple

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

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: Mac15,6
      Model Number: MRX33B/A
      Chip: Apple M3 Pro
      Total Number of Cores: 11 (5 performance and 6 efficiency)
      Memory: 18 GB
      System Firmware Version: 10151.121.1
      OS Loader Version: 10151.121.1

Software:

    System Software Overview:

      System Version: macOS 14.5 (23F79)
      Kernel Version: Darwin 23.5.0
      Time since boot: 193 days, 6 hours, 3 minutes

Graphics/Displays:

    Apple M3 Pro:

      Chipset Model: Apple M3 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 14
      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:
    alabaster: 1.0.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    auditwheel: 6.4.0
    babel: 2.17.0
    beautifulsoup4: 4.13.3
    blockdiag: 3.0.0
    blosc2: 3.5.0
    build: 1.2.2.post1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.2
    ChimeraX-AddCharge: 1.5.19
    ChimeraX-AddH: 2.2.7
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.20.2
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Aniso: 1.1.4
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60.7
    ChimeraX-AtomicLibrary: 14.1.18
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.3
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-Boltz: 1.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.5.1
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.10
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.5
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.4
    ChimeraX-Dicom: 1.2.7
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.4
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.4.1
    ChimeraX-Hbonds: 2.5.1
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.6.2
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.2.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.10.1
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.19
    ChimeraX-ModelPanel: 1.5.1
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14.1
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.10
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.3
    ChimeraX-ProfileGrids: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.3
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.7
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17.1
    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.19.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.45.2
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.5
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.2
    coverage: 7.9.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.12
    debugpy: 1.8.14
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.0
    filelock: 3.18.0
    fonttools: 4.58.4
    funcparserlib: 2.0.0a0
    glfw: 2.9.0
    grako: 3.16.5
    h5py: 3.14.0
    html2text: 2024.2.26
    idna: 3.10
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.1.0
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.7
    jedi: 0.19.1
    Jinja2: 3.1.6
    jupyter_client: 8.6.3
    jupyter_core: 5.8.1
    jupyterlab_widgets: 3.0.15
    kiwisolver: 1.4.8
    line_profiler: 4.2.0
    lxml: 5.3.1
    lz4: 4.4.4
    MarkupSafe: 3.0.2
    matplotlib: 3.10.1
    matplotlib-inline: 0.1.7
    msgpack: 1.1.0
    ndindex: 1.10.0
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.11.0
    numpy: 1.26.4
    OpenMM: 8.2.0
    openvr: 1.26.701
    packaging: 24.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 10.4.0
    pip: 25.0.1
    pkginfo: 1.11.1
    platformdirs: 4.3.8
    pluggy: 1.6.0
    prompt_toolkit: 3.0.51
    psutil: 7.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.32
    Pygments: 2.18.0
    pynmrstar: 3.3.5
    pynrrd: 1.0.0
    PyOpenGL: 3.1.9
    PyOpenGL-accelerate: 3.1.9
    pyopenxr: 1.1.4501
    pyparsing: 3.2.3
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.8.1
    PyQt6-Qt6: 6.8.2
    PyQt6-WebEngine-commercial: 6.8.0
    PyQt6-WebEngine-Qt6: 6.8.2
    PyQt6_sip: 13.10.0
    pytest: 8.4.1
    pytest-cov: 6.2.1
    python-dateutil: 2.9.0.post0
    pytz: 2025.2
    pyzmq: 27.0.0
    qtconsole: 5.5.2
    QtPy: 2.4.3
    qtshim: 1.1
    RandomWords: 0.4.0
    requests: 2.32.3
    roman-numerals-py: 3.1.0
    scipy: 1.14.0
    setuptools: 78.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 3.0.1
    sortedcontainers: 2.4.0
    soupsieve: 2.7
    Sphinx: 8.2.3
    sphinx-autodoc-typehints: 3.1.0
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.7.1
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.4
    tornado: 6.5.1
    traitlets: 5.14.3
    typing_extensions: 4.14.0
    tzdata: 2025.2
    urllib3: 2.5.0
    wcwidth: 0.2.13
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.14