ffmpeg: Permission Denied

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-15.6.1-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/johanneskullmann/Documents/AlphaFold3/HP1334_studies/HP1334_rae1_alignment.cxs
> format session

Log from Mon Sep 15 11:19:03 2025UCSF ChimeraX version: 1.10 (2025-06-26)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open /Users/johanneskullmann/Desktop/HP1334_dimer_2xMg2.cxs format session

Log from Sat Jul 26 18:44:45 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/johanneskullmann/Documents/AlphaFold3/HP1334_studies/fold_hp1334_dimer_2xmg2-2/fold_hp1334_dimer_2xmg2_model_0.cif

Chain information for fold_hp1334_dimer_2xmg2_model_0.cif #1  
---  
Chain | Description  
A B | .  
  
Computing secondary structure  

> select #1/A,B:152,177,179

48 atoms, 42 bonds, 6 residues, 1 model selected  

> show sel atoms

> select #1/A,B:152,177,179,10

64 atoms, 56 bonds, 8 residues, 1 model selected  

> show sel atoms

> select #1/A,B:152,177,179,10,148

82 atoms, 72 bonds, 10 residues, 1 model selected  

> select #1/A

1870 atoms, 1911 bonds, 224 residues, 1 model selected  

> select #1/B

1870 atoms, 1911 bonds, 224 residues, 1 model selected  

> hide sel atoms

> hide sel cartoons

> select #1/B,D

1871 atoms, 1911 bonds, 225 residues, 1 model selected  

> hide sel atoms

> select #1/A:152,177,179

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

> select #1/A:152,177,179,10

32 atoms, 28 bonds, 4 residues, 1 model selected  

> select #1/A:152,177,179,10,148

41 atoms, 36 bonds, 5 residues, 1 model selected  

> select #1/A

1870 atoms, 1911 bonds, 224 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel gray

> color sel dark gray

> color sel light gray

> set bgColor white

> color sel dark gray

> lighting soft

> graphics silhouettes true

> color sel dim gray

> color sel dark gray

> select #1/A:94:193

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

> select #1/A:94-193

809 atoms, 820 bonds, 100 residues, 1 model selected  

> color sel orange

> color sel dark orange

> select /z

Nothing selected  

> select /A:152,177,179

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

> select /A:152,177

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

> color sel magenta

> select /A:10,148,179

25 atoms, 22 bonds, 3 residues, 1 model selected  

> color sel blue

> color sel dark cyan

> color sel turquoise

> color sel medium turquoise

> color sel cornflower blue

> select /A:152,177

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

> color sel lime green

> color sel spring green

> color sel lime

> color sel green

> color sel chartreuse

> color sel medium sea green

> select /z177

Nothing selected  

> select /B

1870 atoms, 1911 bonds, 224 residues, 1 model selected  

> show sel cartoons

> color sel dark gray

[Repeated 1 time(s)]

> color sel dim gray

> color sel dark gray

> select /B:94-193

809 atoms, 820 bonds, 100 residues, 1 model selected  

> color sel dark orange

> select /z

Nothing selected  

> save /Users/johanneskullmann/Desktop/HP1334_dimer_2xMg2.cxs

——— End of log from Sat Jul 26 18:44:45 2025 ———

> view name session-start

opened ChimeraX session  

> select #1/B

1870 atoms, 1911 bonds, 224 residues, 1 model selected  

> hide sel cartoons

> hide sel atoms

> open /Users/johanneskullmann/Downloads/5mq8-assembly1.cif

5mq8-assembly1.cif title:  
Crystal structure of Rae1 (YacP) from Bacillus subtilis [more info...]  
  
Chain information for 5mq8-assembly1.cif #2  
---  
Chain | Description  
A D | Uncharacterized protein YacP  
  
Non-standard residues in 5mq8-assembly1.cif #2  
---  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
  

> select #1/A:94-193 #2:4-166

3475 atoms, 3524 bonds, 426 residues, 2 models selected  

> select #1/A:94-193 #2/A:4-166

2142 atoms, 2172 bonds, 263 residues, 2 models selected  

> ui tool show Matchmaker

> matchmaker #2 & sel to #1 & sel

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_hp1334_dimer_2xmg2_model_0.cif, chain A (#1) with
5mq8-assembly1.cif, chain A (#2), sequence alignment score = 33.5  
RMSD between 12 pruned atom pairs is 1.206 angstroms; (across all 72 pairs:
19.596)  
  

> select #1/B

1870 atoms, 1911 bonds, 224 residues, 1 model selected  

> select #1/D

1 atom, 1 residue, 1 model selected  

> select #2/D

1505 atoms, 1436 bonds, 262 residues, 1 model selected  

> hide sel atoms

> hide sel cartoons

> select #2/A

1487 atoms, 1423 bonds, 257 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel magenta

> color sel pale green

> color sel violet

> color sel light sea green

> color sel slate gray

> color sel light slate gray

> color sel gray

> color sel light cyan

> color sel aquamarine

> color sel light coral

> color sel deep pink

> color sel magenta

> color sel pale violet red

> select #2/A:4-166

1333 atoms, 1352 bonds, 163 residues, 1 model selected  

> color sel deep pink

> undo

> select #2/A

1487 atoms, 1423 bonds, 257 residues, 1 model selected  

> ui tool show "Show Sequence Viewer"

> sequence chain #1/A #1/B

Alignment identifier is 1  

> sequence chain #2/A #2/D

Alignment identifier is 2  

> select #2/A-D:8-20,22-45,79-91,109-114,120-166

1700 atoms, 1718 bonds, 206 residues, 1 model selected  

> select #1/A:152,177,179,10

32 atoms, 28 bonds, 4 residues, 1 model selected  

> hide sel atoms

> select #1/A:152,177,179,10,148

41 atoms, 36 bonds, 5 residues, 1 model selected  

> hide sel atoms

> select #1/A:152,177,179,10

32 atoms, 28 bonds, 4 residues, 1 model selected  

> show sel atoms

> color sel fire brick

> color sel gold

> color sel brown

> color sel fire brick

> select #1/A:148

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

> select #1/A:152,177,179,10

32 atoms, 28 bonds, 4 residues, 1 model selected  

> color sel orange red

> select #1/A:148

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

> color sel gold

> show sel atoms

> select #1/A:148

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

> select #1/z

Nothing selected  

> ui tool show "Show Sequence Viewer"

> select #1/z

Nothing selected  

> sequence chain #1/A #1/B

Alignment identifier is 1  

> sequence chain #2/A #2/D

Alignment identifier is 2  

> select #1/A-B:3-10,52-62,68-70,77-79,102-107,115-118,142-145,170-174,193-197

836 atoms, 840 bonds, 98 residues, 1 model selected  

> select clear

[Repeated 1 time(s)]

> select #2/A-D:1

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

> select #2/A-D:1-174

2808 atoms, 2846 bonds, 348 residues, 1 model selected  

> select #2/A-D:1-174

2808 atoms, 2846 bonds, 348 residues, 1 model selected  

> select #2/A-D:1-174

2808 atoms, 2846 bonds, 348 residues, 1 model selected  

> select #2/A-D:174

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

> select #2/A-D:174

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

> select #2/A-D:1

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

> select #2/A-D:1-174

2808 atoms, 2846 bonds, 348 residues, 1 model selected  

> select #2/A-D:167-168

24 atoms, 22 bonds, 4 residues, 1 model selected  

> select #2/A-D:167-170

56 atoms, 54 bonds, 8 residues, 1 model selected  

> select #2/A-D:168

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

> select #2/A-D:168-170

48 atoms, 46 bonds, 6 residues, 1 model selected  

> select #2/A:69,67

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

> select #2/A:169,167

12 atoms, 10 bonds, 2 residues, 1 model selected  

> select #2/A:168,166

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

> select #2/A:168,170

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

> show sel atoms

> color sel orange red

> color sel deep pink

> color sel blue violet

[Repeated 1 time(s)]

> select #2/A:7

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

> show sel atoms

> color sel dark violet

> color sel blue violet

> select #2/A:81

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

> show sel atoms

> color sel blue violet

> select #2/A:104

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

> show sel atoms

> color sel blue violet

> select #2/z

Nothing selected  

> select #2/A:107

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

> show sel atoms

> color sel pale violet red

[Repeated 1 time(s)]

> color sel purple

> color sel light coral

> color sel violet

> color sel cadet blue

> color sel dark orchid

> color sel dark magenta

> color sel blue

> select /z

Nothing selected  

> select #2/A-D:91-98

122 atoms, 120 bonds, 16 residues, 1 model selected  

> select #2/A-D:91-102

180 atoms, 180 bonds, 24 residues, 1 model selected  

> select /z

Nothing selected  

> movie record size 2560,1440

> turn y 2 180

> movie encode HP1334_raw1_spin.mp4 quality highest

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/cmd_line/tool.py", line 319, in execute  
cmd.run(cmd_text)  
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.  
  

> movie encode Desktop/HP1334_raw1_spin.mp4 quality highest

Currently encoding a movie  

> movie encode Desktop/HP1334_raw1_spin.mp4 quality highest

Currently encoding a movie  

> movie stop

Not currently recording  

> movie record size 2560,1440

> turn y 2 180

> movie reset

Attempted movie reset when encoding not finished.  

> save
> /Users/johanneskullmann/Documents/AlphaFold3/HP1334_studies/HP1334_rae1_alignment.cxs

——— End of log from Mon Sep 15 11:19:03 2025 ———

> view name session-start

opened ChimeraX session  

> movie record size 2560,1440

> turn y 2 180

> hide #1 models

> turn y 2 180

> hide #2 models

> show #1 models

> turn y 2 180

> show #2 models

> turn y 2 180

> movie encode quality highest

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/cmd_line/tool.py", line 319, in execute  
cmd.run(cmd_text)  
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 205, in movie_encode  
encode_op(session, output, 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 - 89.4
OpenGL renderer: Apple M3
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 Air
      Model Identifier: Mac15,12
      Model Number: Z1G50005RD/A
      Chip: Apple M3
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 16 GB
      System Firmware Version: 11881.140.96
      OS Loader Version: 11881.140.96

Software:

    System Software Overview:

      System Version: macOS 15.6.1 (24G90)
      Kernel Version: Darwin 24.6.0
      Time since boot: 12 days, 11 hours, 14 minutes

Graphics/Displays:

    Apple M3:

      Chipset Model: Apple M3
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 10
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina Display
          Resolution: 2560 x 1664 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        P27-8 TS Pro:
          Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
          UI Looks like: 2560 x 1440 @ 60.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported


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