ffmpeg: Permission denied

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-15.6-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:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.10 (2025-06-26)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/nolivero/Library/CloudStorage/OneDrive-
> St.JudeChildren'sResearchHospital/Lyms proyect/Alpha fold
> structures/fold_lymb.zip"

Unrecognized file suffix '.zip'  

> open "/Users/nolivero/Library/CloudStorage/OneDrive-
> St.JudeChildren'sResearchHospital/Lyms proyect/Alpha fold
> structures/fold_lymb/fold_lymb_model_0.cif"

Chain information for fold_lymb_model_0.cif #1  
---  
Chain | Description  
A | .  
  
Computing secondary structure  

> ui tool show "Show Sequence Viewer"

> sequence chain /A

Alignment identifier is 1/A  

> select /A:1

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

> select /A:1-18

135 atoms, 136 bonds, 18 residues, 1 model selected  

> select /A:24

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

> select /A:1-24

178 atoms, 179 bonds, 24 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel dark magenta

> select /A:32

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

> select /A:32-129

741 atoms, 745 bonds, 98 residues, 1 model selected  

> select /A:134

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

> select /A:32-134

780 atoms, 784 bonds, 103 residues, 1 model selected  

> color sel light sea green

> set bgColor white

> set bgColor #ffffff00

> select sequence
> DYAGLAVAKSENAGLQPQTAAFKEEIANLFGITSFSGYRPGDSGDHGKGLAIDFMVPERSELGDKIAEYAIQNMASRGISYIIWKQRFYAPFDSKYGPANTWNPMPDRGSVTENHYDHVHVS

951 atoms, 978 bonds, 122 residues, 1 model selected  

> color sel orange red

> save "/Users/nolivero/Library/CloudStorage/OneDrive-
> St.JudeChildren'sResearchHospital/Lyms proyect/Alpha fold structures/LymB
> domains.png" width 936 height 689 supersample 3

> select clear

> save "/Users/nolivero/Library/CloudStorage/OneDrive-
> St.JudeChildren'sResearchHospital/Lyms proyect/Alpha fold structures/LymB
> domains.png" width 936 height 689 supersample 3

> close session

> open "/Users/nolivero/Library/CloudStorage/OneDrive-
> St.JudeChildren'sResearchHospital/Lyms proyect/Alpha fold
> structures/fold_lyma (1)/fold_lyma_full_data_1.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/nolivero/Library/CloudStorage/OneDrive-
St.JudeChildren'sResearchHospital/Lyms proyect/Alpha fold structures/fold_lyma
(1)/fold_lyma_full_data_1.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/nolivero/Library/CloudStorage/OneDrive-
> St.JudeChildren'sResearchHospital/Lyms proyect/Alpha fold
> structures/fold_lyma (1)/fold_lyma_model_0.cif"

Chain information for fold_lyma_model_0.cif #1  
---  
Chain | Description  
A | .  
  
Computing secondary structure  

> open "/Users/nolivero/Library/CloudStorage/OneDrive-
> St.JudeChildren'sResearchHospital/Lyms proyect/Alpha fold structures/Crystal
> structures/Resucitation factor E mycobacterium.cif"

Resucitation factor E mycobacterium.cif title:  
Crystal structure of Mycobacterium tuberculosis Resuscitation promoting factor
E [more info...]  
  
Chain information for Resucitation factor E mycobacterium.cif #2  
---  
Chain | Description | UniProt  
A B C D E F | RESUSCITATION-PROMOTING FACTOR RPFE | RPFE_MYCTU 98-172  
  
Resucitation factor E mycobacterium.cif mmCIF Assemblies  
---  
1| software_defined_assembly  
2| software_defined_assembly  
3| software_defined_assembly  
4| software_defined_assembly  
5| software_defined_assembly  
6| software_defined_assembly  
  

> style stick

Changed 4720 atom styles  

> style sphere

Changed 4720 atom styles  

> style ball

Changed 4720 atom styles  

> style stick

Changed 4720 atom styles  

> show cartoons

> style stick

Changed 4720 atom styles  

> show cartoons

[Repeated 1 time(s)]

> hide cartoons

> show cartoons

> hide #1 models

> close

> open "/Users/nolivero/Library/CloudStorage/OneDrive-
> St.JudeChildren'sResearchHospital/Lyms proyect/Alpha fold
> structures/fold_lyma (1)/fold_lyma_model_0.cif" format mmcif

Chain information for fold_lyma_model_0.cif #1  
---  
Chain | Description  
A | .  
  
Computing secondary structure  

> close session

> open "/Users/nolivero/Library/CloudStorage/OneDrive-
> St.JudeChildren'sResearchHospital/Lyms proyect/Alpha fold structures/Crystal
> structures/Resucitation factor E mycobacterium.cif" format mmcif

Resucitation factor E mycobacterium.cif title:  
Crystal structure of Mycobacterium tuberculosis Resuscitation promoting factor
E [more info...]  
  
Chain information for Resucitation factor E mycobacterium.cif #1  
---  
Chain | Description | UniProt  
A B C D E F | RESUSCITATION-PROMOTING FACTOR RPFE | RPFE_MYCTU 98-172  
  
Resucitation factor E mycobacterium.cif mmCIF Assemblies  
---  
1| software_defined_assembly  
2| software_defined_assembly  
3| software_defined_assembly  
4| software_defined_assembly  
5| software_defined_assembly  
6| software_defined_assembly  
  

> show cartoons

> hide atoms

> ui tool show "Show Sequence Viewer"

> sequence chain /A /B /C /D /E /F

Alignment identifier is 1  

> close session

> open "/Users/nolivero/Library/CloudStorage/OneDrive-
> St.JudeChildren'sResearchHospital/Lyms proyect/Alpha fold structures/Crystal
> structures/Resucitation factor E mycobacterium biological assembly 1"

'/Users/nolivero/Library/CloudStorage/OneDrive-
St.JudeChildren'sResearchHospital/Lyms proyect/Alpha fold structures/Crystal
structures/Resucitation factor E mycobacterium biological assembly 1' has no
suffix  

> open "/Users/nolivero/Library/CloudStorage/OneDrive-
> St.JudeChildren'sResearchHospital/Lyms proyect/Alpha fold
> structures/fold_lyma (1)/fold_lyma_model_0.cif" format mmcif

Chain information for fold_lyma_model_0.cif #1  
---  
Chain | Description  
A | .  
  
Computing secondary structure  

> open "/Users/nolivero/Library/CloudStorage/OneDrive-
> St.JudeChildren'sResearchHospital/Lyms proyect/Alpha fold structures/Crystal
> structures/Resucitation factor E mycobacterium biological assembly 1.pdb"

Summary of feedback from opening
/Users/nolivero/Library/CloudStorage/OneDrive-
St.JudeChildren'sResearchHospital/Lyms proyect/Alpha fold structures/Crystal
structures/Resucitation factor E mycobacterium biological assembly 1.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 5 5 ASN B 100 SER B 109 1 10  
Start residue of secondary structure not found: HELIX 6 6 GLY B 130 ASN B 135
1 6  
Start residue of secondary structure not found: HELIX 7 7 SER B 145 GLN B 160
1 16  
Start residue of secondary structure not found: HELIX 8 8 GLY B 161 TRP B 165
5 5  
Start residue of secondary structure not found: HELIX 9 9 VAL B 167 GLY B 172
5 6  
26 messages similar to the above omitted  
Cannot find LINK/SSBOND residue CYS (107 )  
Cannot find LINK/SSBOND residue CYS (107 )  
Cannot find LINK/SSBOND residue CYS (107 )  
Cannot find LINK/SSBOND residue CYS (107 )  
  
Resucitation factor E mycobacterium biological assembly 1.pdb title:  
Crystal structure of mycobacterium tuberculosis resuscitation promoting factor
E [more info...]  
  
Chain information for Resucitation factor E mycobacterium biological assembly
1.pdb #2  
---  
Chain | Description  
A | No description available  
  

> ui tool show Matchmaker

> matchmaker #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 fold_lyma_model_0.cif, chain A (#1) with Resucitation factor E
mycobacterium biological assembly 1.pdb, chain A (#2), sequence alignment
score = 87.1  
RMSD between 31 pruned atom pairs is 1.079 angstroms; (across all 59 pairs:
3.561)  
  

> ui tool show Matchmaker

> matchmaker #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 fold_lyma_model_0.cif, chain A (#1) with Resucitation factor E
mycobacterium biological assembly 1.pdb, chain A (#2), sequence alignment
score = 87.1  
RMSD between 31 pruned atom pairs is 1.079 angstroms; (across all 59 pairs:
3.561)  
  

> save "/Users/nolivero/Library/CloudStorage/OneDrive-
> St.JudeChildren'sResearchHospital/Lyms proyect/Alpha fold structures/LymA
> c-term resusitation factor.cxs"

> close session

> open "/Users/nolivero/Library/CloudStorage/OneDrive-
> St.JudeChildren'sResearchHospital/Lyms proyect/Alpha fold
> structures/fold_lyma (1)/fold_lyma_model_0.cif" format mmcif

Chain information for fold_lyma_model_0.cif #1  
---  
Chain | Description  
A | .  
  
Computing secondary structure  

> select sequence SSTYTVKEGDTLSEIAETHNTTVEKLAENNHIDNIHLIYVDQELVI

365 atoms, 369 bonds, 46 residues, 1 model selected  

> color sel light sea green

> select sequence MKSITKKIKATLAGVAALFAVFAPSFVSA

208 atoms, 211 bonds, 29 residues, 1 model selected  

> ui tool show "Color Actions"

[Repeated 2 time(s)]

> color sel dark magenta

> select clear

> select sequence
> VSGSEAEAKEWIAQKESGGSYTATNGRYIGRYQLTDSYLNGDYSAENQERVADAYVAGRYGSWTAAKNFWLN

566 atoms, 579 bonds, 72 residues, 1 model selected  

> color sel orange red

> select clear

> save "/Users/nolivero/Library/CloudStorage/OneDrive-
> St.JudeChildren'sResearchHospital/Lyms proyect/Alpha fold structures/LymA
> domains.cxs"

> open "/Users/nolivero/Library/CloudStorage/OneDrive-
> St.JudeChildren'sResearchHospital/Lyms proyect/Alpha fold structures/LysM
> containing protein enterococcus faecium.pdb"

Summary of feedback from opening
/Users/nolivero/Library/CloudStorage/OneDrive-
St.JudeChildren'sResearchHospital/Lyms proyect/Alpha fold structures/LysM
containing protein enterococcus faecium.pdb  
---  
warning | Ignored bad PDB record found on line 38  
DBREF XXXX A 1 207 UNP A0A133CPE7 A0A133CPE7_ENTFC 1 207  
  
LysM containing protein enterococcus faecium.pdb title:  
Alphafold monomer V2.0 prediction for lysm peptidoglycan-binding domain-
containing protein (A0A133CPE7) [more info...]  
  
Chain information for LysM containing protein enterococcus faecium.pdb #2  
---  
Chain | Description  
A | lysm peptidoglycan-binding domain-containing protein  
  
Computing secondary structure  

> ui tool show "Show Sequence Viewer"

> sequence chain #2/A

Alignment identifier is 2/A  

> select #2/A:1

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

> select #2/A

1551 atoms, 1582 bonds, 207 residues, 1 model selected  

> color sel blue

> ui tool show Matchmaker

> matchmaker #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 fold_lyma_model_0.cif, chain A (#1) with LysM containing protein
enterococcus faecium.pdb, chain A (#2), sequence alignment score = 559.3  
RMSD between 71 pruned atom pairs is 0.310 angstroms; (across all 190 pairs:
23.762)  
  

> select clear

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/nolivero/Desktop/movie1.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 - 89.4
OpenGL renderer: Apple M3 Pro
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: Mac15,6
      Model Number: MRX63LL/A
      Chip: Apple M3 Pro
      Total Number of Cores: 11 (5 performance and 6 efficiency)
      Memory: 18 GB
      System Firmware Version: 11881.140.96
      OS Loader Version: 11881.140.96

Software:

    System Software Overview:

      System Version: macOS 15.6 (24G84)
      Kernel Version: Darwin 24.6.0
      Time since boot: 10 days, 18 hours, 26 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