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Opened 5 days ago
Closed 5 days ago
#19121 closed defect (duplicate)
ffmpeg: Permission Denied
| Reported by: | Owned by: | Zach Pearson | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Build System | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-13.7.7-x86_64-i386-64bit
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/boskostojanovski/Documents/Manuscripts/CryoEM/DesF1Mz-fXa-
> fXa/pre-EDC/Movies for paper/movie#7.cxs"
Log from Tue Oct 7 09:53:47 2025UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
> open /Users/boskostojanovski/Desktop/movie#5.cxs
Log from Wed Oct 1 16:46:57 2025UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
> open /Users/boskostojanovski/Desktop/movie#4.cxs
Log from Wed Oct 1 16:38:33 2025UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/boskostojanovski/Desktop/MOVIE 3 COMP.cxs"
Log from Wed Oct 1 14:27:54 2025UCSF 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/boskostojanovski/Desktop/DES_PTse_COOT/W19/Movies/PDB For
> Movies/7tpp.pdb"
7tpp.pdb title:
Cryo-em structure of human prothrombin:prothrombinase At 4.1 angstrom
resolution [more info...]
Chain information for 7tpp.pdb #1
---
Chain | Description | UniProt
A | factor X light chain | FA10_HUMAN 1-139
B | activated factor xa heavy chain | FA10_HUMAN 195-448
C | coagulation factor va | FA5_HUMAN 1-709
D | coagulation factor va | FA5_HUMAN 1546-2196
E | coagulation factor II | THRB_HUMAN 1-579
> open "/Users/boskostojanovski/Desktop/DES_PTse_COOT/W19/Movies/PDB For
> Movies/W19-090525.pdb"
Summary of feedback from opening
/Users/boskostojanovski/Desktop/DES_PTse_COOT/W19/Movies/PDB For
Movies/W19-090525.pdb
---
warnings | Cannot find LINK/SSBOND residue CYS (170 )
Cannot find LINK/SSBOND residue CYS (50 )
Cannot find LINK/SSBOND residue CYS (55 )
Cannot find LINK/SSBOND residue CYS (72 )
Chain information for W19-090525.pdb #2
---
Chain | Description
B | No description available
D | No description available
E | No description available
H | No description available
L | No description available
> hide atoms
> show cartoons
> lighting simple
> color #1 #fffc79ff
> color #2 #7a81ffff
> 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 7tpp.pdb, chain C (#1) with W19-090525.pdb, chain B (#2), sequence
alignment score = 2808
RMSD between 275 pruned atom pairs is 1.366 angstroms; (across all 699 pairs:
15.961)
> ui tool show Matchmaker
> hide #!2 models
> show #!2 models
> ui tool show Matchmaker
> matchmaker #2/B to #1/C pairing ss
Parameters
---
Chain pairing | ss
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 7tpp.pdb, chain C (#1) with W19-090525.pdb, chain B (#2), sequence
alignment score = 2808
RMSD between 275 pruned atom pairs is 1.366 angstroms; (across all 699 pairs:
15.961)
> matchmaker #2/B to #1/C pairing ss
Parameters
---
Chain pairing | ss
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 7tpp.pdb, chain C (#1) with W19-090525.pdb, chain B (#2), sequence
alignment score = 2808
RMSD between 275 pruned atom pairs is 1.366 angstroms; (across all 699 pairs:
15.961)
> matchmaker #2/B to #1/C pairing ss
Parameters
---
Chain pairing | ss
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 7tpp.pdb, chain C (#1) with W19-090525.pdb, chain B (#2), sequence
alignment score = 2808
RMSD between 275 pruned atom pairs is 1.366 angstroms; (across all 699 pairs:
15.961)
> save "/Users/boskostojanovski/Desktop/For movie.cxs" includeMaps true
> select #2/E
380 atoms, 387 bonds, 3 pseudobonds, 50 residues, 2 models selected
> delete atoms (#!2 & sel)
> delete bonds (#!2 & sel)
> select #1/A
1089 atoms, 1113 bonds, 139 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #1/D
5217 atoms, 5361 bonds, 641 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> ui tool show "Show Sequence Viewer"
> sequence chain #1/C
Alignment identifier is 1/C
> select #1/C:1
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/C:1-316
2496 atoms, 2564 bonds, 316 residues, 1 model selected
> select #1/C:1-2
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #1/C:1-313
2467 atoms, 2535 bonds, 313 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> ui tool show "Show Sequence Viewer"
> sequence chain #2/B
Alignment identifier is 2/B
> select #2/B:1-2
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #2/B:1-313
2460 atoms, 2527 bonds, 1 pseudobond, 312 residues, 2 models selected
> delete atoms (#!2 & sel)
> delete bonds (#!2 & sel)
> select #2/B:1546
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/B:1546-2196
5141 atoms, 5278 bonds, 6 pseudobonds, 631 residues, 2 models selected
> delete atoms (#!2 & sel)
> delete bonds (#!2 & sel)
> hide #!1 models
> show #!1 models
> hide #!2 models
> ui tool show "Show Sequence Viewer"
> sequence chain #1/E
Alignment identifier is 1/E
> ui tool show "Show Sequence Viewer"
> sequence chain #2/L
Alignment identifier is 2/L
> select #1/E:1
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/E:1-157
1228 atoms, 1259 bonds, 157 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> show #!2 models
> save "/Users/boskostojanovski/Desktop/For movie.cxs" includeMaps true
> save /Users/boskostojanovski/Desktop/7tpp-mo.pdb models #1
> hide #!1 models
> close #1
> ui tool show "Change Chain IDs"
> changechains H,L K,K
Chain IDs of 343 residues changed
Must select one or more chain IDs from the list on the left
> select /K
2760 atoms, 2816 bonds, 22 pseudobonds, 343 residues, 2 models selected
> ui tool show "Change Chain IDs"
> save /Users/boskostojanovski/Desktop/W19-MO.pdb
> close #2
> open /Users/boskostojanovski/Desktop/W19-MO.pdb
Chain information for W19-MO.pdb #1
---
Chain | Description
B | No description available
D | No description available
K | No description available
> open /Users/boskostojanovski/Desktop/7tpp-mo.pdb
7tpp-mo.pdb title:
Cryo-em structure of human prothrombin:prothrombinase At 4.1 angstrom
resolution [more info...]
Chain information for 7tpp-mo.pdb #2
---
Chain | Description | UniProt
B | activated factor xa heavy chain | FA10_HUMAN 195-448
C | coagulation factor va | FA5_HUMAN 1-709
E | coagulation factor II | THRB_HUMAN 1-579
> morph #1,2 wrap true frames 60
Computed 121 frame morph #3
> coordset #3 1,121
> hide #!3 models
> show #!3 models
> show #2 models
> close #3
> show #!1 models
> ui tool show "Show Sequence Viewer"
> sequence chain #1/B
Alignment identifier is 1/B
> ui tool show "Show Sequence Viewer"
> sequence chain #2/C
Alignment identifier is 2/C
> select #2/C:675
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/C:675-709
284 atoms, 287 bonds, 35 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> ui tool show "Show Sequence Viewer"
> sequence chain #2/B
Alignment identifier is 2/B
> select #2/B:429
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/B:429-448
148 atoms, 151 bonds, 20 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> morph #1,2 wrap true frames 60
Computed 121 frame morph #3
> coordset #3 1,121
> show #2 models
> show #!1 models
> hide #!3 models
> morph #1,2 wrap true frames 200
Computed 401 frame morph #4
> coordset #4 1,401
> show #!3 models
> hide #!4 models
> show #!4 models
> close #3
> close #4
> show #!1 models
> show #2 models
> morph #1,2 wrap true frames 10
Computed 21 frame morph #3
> coordset #3 1,21
> show #!1 models
> show #2 models
> hide #!3 models
> ui tool show Matchmaker
> matchmaker #2#!3 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 W19-MO.pdb, chain B (#1) with 7tpp-mo.pdb, chain C (#2), sequence
alignment score = 1486.6
RMSD between 132 pruned atom pairs is 1.327 angstroms; (across all 352 pairs:
7.163)
Matchmaker W19-MO.pdb, chain K (#1) with Morph - W19-MO.pdb, chain K (#3),
sequence alignment score = 1774.4
RMSD between 343 pruned atom pairs is 0.000 angstroms; (across all 343 pairs:
0.000)
> matchmaker #2#!3 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 W19-MO.pdb, chain B (#1) with 7tpp-mo.pdb, chain C (#2), sequence
alignment score = 1486.6
RMSD between 132 pruned atom pairs is 1.327 angstroms; (across all 352 pairs:
7.163)
Matchmaker W19-MO.pdb, chain K (#1) with Morph - W19-MO.pdb, chain K (#3),
sequence alignment score = 1774.4
RMSD between 343 pruned atom pairs is 0.000 angstroms; (across all 343 pairs:
0.000)
> morph #1,2 wrap true frames 60
Computed 121 frame morph #4
> coordset #4 1,121
> movie record
> movie encode /Users/boskostojanovski/Desktop/movie1.mp4 framerate 25.0
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/core/triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/slider.py", line 164, in next_value_cb
self.stop()
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/slider.py", line 148, in stop
self.record_cb()
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/slider.py", line 211, in record_cb
run(ses, f'movie encode %s framerate %.1f'
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'
Error processing trigger "new frame":
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.
> close #3
> close #4
> show #!1 models
> show #2 models
> save /Users/boskostojanovski/Desktop/MOVIE.pdb
> morph #1,2
Computed 51 frame morph #3
> coordset #3 1,51
> morph #2,1
Computed 51 frame morph #4
> coordset #4 1,51
> hide #!3 models
> movie record
> movie encode /Users/boskostojanovski/Desktop/movie1.mp4 framerate 25.0
Error processing trigger "new frame":
Currently encoding a movie
> show #!1 models
> show #2 models
> close #3
> close #4
> close #1
> close
> open "/Users/boskostojanovski/Desktop/DES_PTse_COOT/W19/Movies/PDB For
> Movies/7tpp.pdb"
7tpp.pdb title:
Cryo-em structure of human prothrombin:prothrombinase At 4.1 angstrom
resolution [more info...]
Chain information for 7tpp.pdb #1
---
Chain | Description | UniProt
A | factor X light chain | FA10_HUMAN 1-139
B | activated factor xa heavy chain | FA10_HUMAN 195-448
C | coagulation factor va | FA5_HUMAN 1-709
D | coagulation factor va | FA5_HUMAN 1546-2196
E | coagulation factor II | THRB_HUMAN 1-579
> close #1
> open /Users/boskostojanovski/Desktop/7tpp-mo.pdb
7tpp-mo.pdb title:
Cryo-em structure of human prothrombin:prothrombinase At 4.1 angstrom
resolution [more info...]
Chain information for 7tpp-mo.pdb #1
---
Chain | Description | UniProt
B | activated factor xa heavy chain | FA10_HUMAN 195-448
C | coagulation factor va | FA5_HUMAN 1-709
E | coagulation factor II | THRB_HUMAN 1-579
> ui tool show "Change Chain IDs"
[Repeated 1 time(s)]
> changechains B,C,E D,B,K
Chain IDs of 1059 residues changed
> changechains B D
No residues specified
> ui tool show "Change Chain IDs"
[Repeated 1 time(s)]
> close
> open /Users/boskostojanovski/Desktop/7tpp-mo.pdb
7tpp-mo.pdb title:
Cryo-em structure of human prothrombin:prothrombinase At 4.1 angstrom
resolution [more info...]
Chain information for 7tpp-mo.pdb #1
---
Chain | Description | UniProt
B | activated factor xa heavy chain | FA10_HUMAN 195-448
C | coagulation factor va | FA5_HUMAN 1-709
E | coagulation factor II | THRB_HUMAN 1-579
> ui tool show "Change Chain IDs"
> changechains B,C,E D,B,K
Chain IDs of 1059 residues changed
> changechains B D
No residues specified
> save /Users/boskostojanovski/Desktop/7tpp-mo2.pdb
> close
> open /Users/boskostojanovski/Desktop/7tpp-mo2.pdb
7tpp-mo2.pdb title:
Cryo-em structure of human prothrombin:prothrombinase At 4.1 angstrom
resolution [more info...]
Chain information for 7tpp-mo2.pdb #1
---
Chain | Description | UniProt
B | activated factor xa heavy chain | FA10_HUMAN 195-448
D | coagulation factor va | FA5_HUMAN 1546-2196
K | No description available |
> open /Users/boskostojanovski/Desktop/W19-MO.pdb
Chain information for W19-MO.pdb #2
---
Chain | Description
B | No description available
D | No description available
K | No description available
> morph #1,2 wrap true frames 60
Computed 121 frame morph #3
> coordset #3 1,121
> show #1 models
> hide #!3 models
> select #2/B
2899 atoms, 2972 bonds, 4 pseudobonds, 352 residues, 2 models selected
> show #!2 models
> color (#!2 & sel) #009193ff
> close #3
> select #2/K
2760 atoms, 2816 bonds, 22 pseudobonds, 343 residues, 2 models selected
> hide #1 models
> show #1 models
> hide #!2 models
> select add #2
7503 atoms, 7674 bonds, 26 pseudobonds, 928 residues, 2 models selected
> select subtract #2
Nothing selected
> select #1/D
1999 atoms, 2045 bonds, 254 residues, 1 model selected
> select #1/D
1999 atoms, 2045 bonds, 254 residues, 1 model selected
> show #!2 models
> select add #1
8512 atoms, 8724 bonds, 1059 residues, 1 model selected
> hide #!2 models
> select subtract #1
Nothing selected
> select #1/B
3248 atoms, 3328 bonds, 396 residues, 1 model selected
> color sel #00fdffff
> color sel #009193ff
> select #1/D
1999 atoms, 2045 bonds, 254 residues, 1 model selected
> color sel #fffc79ff
> select #1/K
3265 atoms, 3351 bonds, 409 residues, 1 model selected
> color sel #7a81ffff
> set bgColor white
> set bgColor #ffffff00
> select clear
> show #!2 models
> hide #1 models
> select #2/D
1844 atoms, 1886 bonds, 233 residues, 1 model selected
> color sel #fffc79ff
> select clear
> select #2/K
2760 atoms, 2816 bonds, 22 pseudobonds, 343 residues, 2 models selected
> color (#!2 & sel) #7a81ffff
> select clear
> show #1 models
> morph #1,2 wrap true frames 60
Computed 121 frame morph #3
> coordset #3 1,121
> show #!2 models
> show #1 models
> hide #!3 models
> hide #!2 models
> hide #1 models
> show #!3 models
> save "/Users/boskostojanovski/Desktop/MOVIE 3 COMP.cxs" includeMaps true
——— End of log from Wed Oct 1 14:27:54 2025 ———
> view name session-start
opened ChimeraX session
> show #1 models
> show #!2 models
> hide #1 models
> hide #!2 models
> show #1 models
> hide #1 models
> ui tool show "Show Sequence Viewer"
> sequence chain #2/K
Alignment identifier is 2/K
> show #1 models
> hide #1 models
> hide #!3 models
> show #!2 models
> select #2/K:271
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/K:271
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel sphere
Changed 11 atom styles
> color sel byhetero
> show #!3 models
> hide #!2 models
> select add #2
7503 atoms, 7674 bonds, 26 pseudobonds, 928 residues, 2 models selected
> select subtract #2
Nothing selected
> show #1 models
> show #!2 models
> hide #!2 models
> hide #!3 models
> ui tool show "Show Sequence Viewer"
> sequence chain #1/K
Alignment identifier is 1/K
> select #1/K:271
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/K:271
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> style sel sphere
Changed 11 atom styles
> color sel byhetero
> ui tool show "Show Sequence Viewer"
> sequence chain #2/D
Alignment identifier is 2/D
> select #2/D:189
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/D:189
8 atoms, 7 bonds, 1 residue, 1 model selected
> show #1 atoms
> hide #1 atoms
> show #!2 models
> hide #1 models
> show sel atoms
> style sel sphere
Changed 8 atom styles
> color sel byhetero
> hide #!2 models
> select add #2
7503 atoms, 7674 bonds, 26 pseudobonds, 928 residues, 2 models selected
> select subtract #2
Nothing selected
> show #1 models
> ui tool show "Show Sequence Viewer"
> sequence chain #1/D
Alignment identifier is 1/D
> select #1/D:373
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/D:373
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> style sel sphere
Changed 8 atom styles
> color sel byhetero
> ui tool show "Show Sequence Viewer"
> sequence chain #1/K
Alignment identifier is 1/K
> select #1/K:271
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/K:271
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> morph #1,2 wrap true frames 60
Computed 121 frame morph #4
> coordset #4 1,121
> show #!3 models
> hide #!3 models
> hide #!4 models
> show #!3 models
> show #!4 models
> hide #!3 models
> show #!2 models
> show #!3 models
> hide #!2 models
> hide #!3 models
> save /Users/boskostojanovski/Desktop/movie#3.cxs includeMaps true
> ui tool show "Show Sequence Viewer"
> show #1 models
> hide #!4 models
> ui tool show "Show Sequence Viewer"
> sequence chain #1/B
Alignment identifier is 1/B
> ui tool show "Show Sequence Viewer"
> sequence chain #2/B
Alignment identifier is 2/B
> select #2/B:337-338
14 atoms, 14 bonds, 2 residues, 1 model selected
> select #2/B:337-360
164 atoms, 166 bonds, 2 pseudobonds, 20 residues, 2 models selected
> select #2/B:337-338
14 atoms, 14 bonds, 2 residues, 1 model selected
> select #2/B:337-358
152 atoms, 154 bonds, 2 pseudobonds, 18 residues, 2 models selected
> show #!2 models
> delete atoms (#!2 & sel)
> delete bonds (#!2 & sel)
> select #1/B:337
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/B:337-358
182 atoms, 186 bonds, 22 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #1/B:474
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/B:474
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/B:423
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/B:423-446
190 atoms, 193 bonds, 24 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #2/B:423-424
18 atoms, 18 bonds, 2 residues, 1 model selected
> select #2/B:423-446
174 atoms, 176 bonds, 1 pseudobond, 22 residues, 2 models selected
> delete atoms (#!2 & sel)
> delete bonds (#!2 & sel)
> show #!4 models
> hide #!2 models
> hide #!4 models
> close #3
> close #4
> morph #1,2 wrap true frames 60
Computed 121 frame morph #3
> coordset #3 1,121
> hide label #2,B
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide label #2, B
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> label delete #3/B
> select #2/B:523
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/B:523-557
306 atoms, 314 bonds, 35 residues, 1 model selected
> show #!2 models
> delete atoms sel
> delete bonds sel
> select #1/B:523
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #1/B:523-557
306 atoms, 314 bonds, 35 residues, 1 model selected
> show #!1 models
> hide #!2 models
> hide #!3 models
> delete atoms sel
> delete bonds sel
> show #!3 models
> hide #!1 models
> close #3
> show #!2 models
> show #!1 models
> morph #1,2 wrap true frames 60
Computed 121 frame morph #3
> coordset #3 1,121
> label delete #3/B
> save /Users/boskostojanovski/Desktop/movie#4.cxs includeMaps true
——— End of log from Wed Oct 1 16:38:33 2025 ———
> view name session-start
opened ChimeraX session
> hide #3.1 models
> show #3.1 models
> movie record
> movie encode /Users/boskostojanovski/Desktop/movie1.mp4 framerate 25.0
Error processing trigger "new frame":
Currently encoding a movie
> save /Users/boskostojanovski/Desktop/movie#5.cxs
——— End of log from Wed Oct 1 16:46:57 2025 ———
> view name session-start
opened ChimeraX session
> cartoon style sel thickness 0.7
> select add #1
7834 atoms, 8025 bonds, 3 pseudobonds, 978 residues, 2 models selected
> select add #2
14705 atoms, 15049 bonds, 29 pseudobonds, 1831 residues, 4 models selected
> select add #3
21550 atoms, 22046 bonds, 56 pseudobonds, 2684 residues, 6 models selected
> cartoon style sel thickness 0.7
> select clear
> select add #2
6871 atoms, 7024 bonds, 26 pseudobonds, 853 residues, 2 models selected
> select add #3
13716 atoms, 14021 bonds, 53 pseudobonds, 1706 residues, 4 models selected
> select add #1
21550 atoms, 22046 bonds, 56 pseudobonds, 2684 residues, 6 models selected
> cartoon style sel thickness 0.8
> select clear
> select add #3
6845 atoms, 6997 bonds, 27 pseudobonds, 853 residues, 2 models selected
> select add #2
13716 atoms, 14021 bonds, 53 pseudobonds, 1706 residues, 4 models selected
> select add #1
21550 atoms, 22046 bonds, 56 pseudobonds, 2684 residues, 6 models selected
> cartoon style sel thickness 0.7
> select clear
> select add #3
6845 atoms, 6997 bonds, 27 pseudobonds, 853 residues, 2 models selected
> select add #2
13716 atoms, 14021 bonds, 53 pseudobonds, 1706 residues, 4 models selected
> select add #1
21550 atoms, 22046 bonds, 56 pseudobonds, 2684 residues, 6 models selected
> cartoon style sel thickness 0.6
> select subtract #3
14705 atoms, 15049 bonds, 29 pseudobonds, 1831 residues, 4 models selected
> select subtract #2
7834 atoms, 8025 bonds, 3 pseudobonds, 978 residues, 2 models selected
> select subtract #1
Nothing selected
> movie record
> movie encode /Users/boskostojanovski/Desktop/movie5.mp4 framerate 25.0
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/ui/widgets/slider.py", line 211, in record_cb
run(ses, f'movie encode %s framerate %.1f'
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.
> save /Users/boskostojanovski/Desktop/movie#7.cxs
——— End of log from Tue Oct 7 09:53:47 2025 ———
> view name session-start
opened ChimeraX session
> hide #!3 models
> show #!1 models
> show #!2 models
> ui tool show "Show Sequence Viewer"
> sequence chain #1/D
Alignment identifier is 1/D
> ui tool show "Show Sequence Viewer"
> sequence chain #1/D
Destroying pre-existing alignment with identifier 1/D
Alignment identifier is 1/D
> ui tool show "Show Sequence Viewer"
> sequence chain #1/K
Alignment identifier is 1/K
> ui tool show "Show Sequence Viewer"
> sequence chain #1/B
Alignment identifier is 1/B
> select #1/B:709
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/B:664-709
375 atoms, 382 bonds, 46 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> ui tool show "Show Sequence Viewer"
> sequence chain #2/B
Alignment identifier is 2/B
> select #2/B:674
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/B:664-674
92 atoms, 95 bonds, 11 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> hide #!2 models
> hide #!1 models
> show #!3 models
> ui tool show "Show Sequence Viewer"
> sequence chain #3/B
Alignment identifier is 3/B
> select #3/B:663
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/B:663-674
99 atoms, 102 bonds, 12 residues, 1 model selected
> select #3/B:664
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3/B:664-674
91 atoms, 94 bonds, 11 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #3/B:660-661
16 atoms, 15 bonds, 2 residues, 1 model selected
> select #3/B:660-663
33 atoms, 32 bonds, 4 residues, 1 model selected
> hide sel cartoons
> save "/Users/boskostojanovski/Documents/Manuscripts/CryoEM/DesF1Mz-fXa-
> fXa/pre-EDC/Movies for paper/movie_101325.cxs" includeMaps true
> ui tool show "Show Sequence Viewer"
> sequence chain #3/K
Alignment identifier is 3/K
> select #3/K:271
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #3/K:271
11 atoms, 10 bonds, 1 residue, 1 model selected
> color sel #ff85ffff
> color sel byhetero
> select clear
> movie record
> movie encode /Users/boskostojanovski/Desktop/movie6.mp4 framerate 25.0
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/ui/widgets/slider.py", line 211, in record_cb
run(ses, f'movie encode %s framerate %.1f'
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 ATI-4.14.4
OpenGL renderer: AMD Radeon Pro 575 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
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: iMac
Model Identifier: iMac18,3
Processor Name: Quad-Core Intel Core i5
Processor Speed: 3.5 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 256 KB
L3 Cache: 6 MB
Memory: 16 GB
System Firmware Version: 529.140.2.0.0
OS Loader Version: 577.140.2~30
SMC Version (system): 2.41f2
Software:
System Software Overview:
System Version: macOS 13.7.7 (22H722)
Kernel Version: Darwin 22.6.0
Time since boot: 4 days, 1 hour, 13 minutes
Graphics/Displays:
Radeon Pro 575:
Chipset Model: Radeon Pro 575
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 4 GB
Vendor: AMD (0x1002)
Device ID: 0x67df
Revision ID: 0x00c4
ROM Revision: 113-D000AA-931
VBIOS Version: 113-D0001A1P-025
EFI Driver Version: 01.00.931
Metal Support: Metal 2
Displays:
iMac:
Display Type: Built-In Retina LCD
Resolution: Retina 5K (5120 x 2880)
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
LG UltraFine:
Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: 201NTRLKF070
Mirror: Off
Online: Yes
Rotation: Supported
Automatically Adjust Brightness: Yes
Connection Type: Thunderbolt/DisplayPort
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
Change History (2)
comment:1 by , 5 days ago
| Component: | Unassigned → Build System |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → ffmpeg: Permission Denied |
comment:2 by , 5 days ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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