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#18452 closed defect (duplicate)

ffmpeg PermissionError: [Errno 13] Permission denied: '/Applications/ChimeraX-1.10.app/Contents/bin/ffmpeg'

Reported by:	chimerax-bug-report@…	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/Desktop/Movie for paper.cxs"

Log from Fri Aug 15 11:13:56 2025UCSF ChimeraX version: 1.10 (2025-06-26)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open
> /Users/boskostojanovski/Desktop/DES_PTse_COOT/W19/Movies/MzvPTfVafXa.cxs

Log from Fri Jul 18 11:26:37 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/boskostojanovski/Downloads/cryosparc_P2_J466_006_volume_map.mrc

Opened cryosparc_P2_J466_006_volume_map.mrc as #1, grid size 400,400,400,
pixel 0.776, shown at level 0.0116, step 2, values float32  

> volume #1 level 0.02717

> volume #1 level 0.05311

> volume #1 level 0.02976

> open /Users/boskostojanovski/Downloads/cryosparc_P2_J467_005_volume_map.mrc

Opened cryosparc_P2_J467_005_volume_map.mrc as #2, grid size 400,400,400,
pixel 0.776, shown at level 0.0116, step 2, values float32  

> volume #2 step 1

> volume #2 level 0.0246

> volume #2 level 0.04

> volume #2 level 0.02934

> volume #2 level 0.08502

> volume #2 level 0.02579

> close #1

> close #2

> open "/Users/boskostojanovski/Desktop/DES_PTse_COOT/W19/FInal W19
> PDB/W19-060325.pdb"

Summary of feedback from opening
/Users/boskostojanovski/Desktop/DES_PTse_COOT/W19/FInal W19 PDB/W19-060325.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 W19-060325.pdb #1  
---  
Chain | Description  
B | No description available  
D | No description available  
E | No description available  
H | No description available  
L | No description available  
  

> show atoms

> hide atoms

> show cartoons

> lighting simple

> open 7tpp

7tpp title:  
Cryo-em structure of human prothrombin:prothrombinase at 4.1 Angstrom
resolution [more info...]  
  
Chain information for 7tpp #2  
---  
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 | Prothrombin | THRB_HUMAN 1-579  
  

> hide atoms

> show cartoons

> lighting simple

> hide #!1 models

> ui tool show "Show Sequence Viewer"

> sequence chain #2/E

Alignment identifier is 2/E  

> select #2/E:1

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

> select #2/E:1-154

1202 atoms, 1233 bonds, 154 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> ui tool show "Show Sequence Viewer"

> sequence chain #2/A

Alignment identifier is 2/A  

> select #2/A:1-2

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

> select #2/A:1-83

664 atoms, 677 bonds, 83 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> show #!1 models

> ui tool show Matchmaker

> close #1

> save "/Users/boskostojanovski/Desktop/DES_PTse_COOT/W19/Alignments
> W19v7tpp/7tpp-delGlaK1EGF1.pdb" relModel #2

> ui tool show "Change Chain IDs"

[Repeated 1 time(s)]

> changechains C,D K,K

Chain IDs of 1350 residues changed  
Must select one or more chain IDs from the list on the left  

> save "/Users/boskostojanovski/Desktop/DES_PTse_COOT/W19/Alignments
> W19v7tpp/7tpp-delGlaK1EGF1.pdb" relModel #2

> close #2

> open "/Users/boskostojanovski/Desktop/DES_PTse_COOT/W19/FInal W19
> PDB/W19-060325.pdb"

Summary of feedback from opening
/Users/boskostojanovski/Desktop/DES_PTse_COOT/W19/FInal W19 PDB/W19-060325.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 W19-060325.pdb #1  
---  
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

> open "/Users/boskostojanovski/Desktop/DES_PTse_COOT/W19/Alignments
> W19v7tpp/7tpp-delGlaK1EGF1.pdb"

Summary of feedback from opening
/Users/boskostojanovski/Desktop/DES_PTse_COOT/W19/Alignments W19v7tpp/7tpp-
delGlaK1EGF1.pdb  
---  
warning | PDB SEQRES record for chain K is incomplete. Ignoring input sequence records as basis for sequence.  
  
Chain information for 7tpp-delGlaK1EGF1.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
E | No description available  
K | No description available  
  

> color #2 #ffd479ff

> ui tool show Matchmaker

> matchmaker #2/K#2/B#2/A to #1/B#1/D#1/E pairing ss

Computing secondary structure  
[Repeated 1 time(s)]  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 W19-060325.pdb, chain B (#1) with 7tpp-delGlaK1EGF1.pdb, chain K
(#2), sequence alignment score = 5440.1  
Matchmaker W19-060325.pdb, chain D (#1) with 7tpp-delGlaK1EGF1.pdb, chain B
(#2), sequence alignment score = 976.8  
Matchmaker W19-060325.pdb, chain E (#1) with 7tpp-delGlaK1EGF1.pdb, chain A
(#2), sequence alignment score = 241.6  
RMSD between 336 pruned atom pairs is 1.390 angstroms; (across all 1574 pairs:
7.005)  
  

> matchmaker #2/K#2/B#2/A to #1/B#1/D#1/E pairing ss

Computing secondary structure  
[Repeated 1 time(s)]  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 W19-060325.pdb, chain B (#1) with 7tpp-delGlaK1EGF1.pdb, chain K
(#2), sequence alignment score = 5440.1  
Matchmaker W19-060325.pdb, chain D (#1) with 7tpp-delGlaK1EGF1.pdb, chain B
(#2), sequence alignment score = 976.8  
Matchmaker W19-060325.pdb, chain E (#1) with 7tpp-delGlaK1EGF1.pdb, chain A
(#2), sequence alignment score = 241.6  
RMSD between 336 pruned atom pairs is 1.390 angstroms; (across all 1574 pairs:
7.005)  
  

> ui tool show "Show Sequence Viewer"

> sequence chain #1/B

Alignment identifier is 1/B  

> select #1/B:1

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

> select #1/B

10500 atoms, 10778 bonds, 12 pseudobonds, 1295 residues, 2 models selected  

> delete atoms (#!1 & sel)

> delete bonds (#!1 & sel)

> ui tool show "Show Sequence Viewer"

> sequence chain #2/K

Alignment identifier is 2/K  

> select #2/K:1

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

> select #2/K:1-2188

10865 atoms, 11155 bonds, 1342 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

Drag select of 8 residues  

> delete atoms sel

> delete bonds sel

> ui tool show "Show Sequence Viewer"

> sequence chain #2/A

Alignment identifier is 2/A  

> select clear

> select #2/A

425 atoms, 435 bonds, 56 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> ui tool show "Show Sequence Viewer"

> sequence chain #1/E

Alignment identifier is 1/E  

> select #1/E:84

11 atoms, 11 bonds, 1 residue, 1 model selected  

> select #1/E

380 atoms, 387 bonds, 3 pseudobonds, 50 residues, 2 models selected  

> delete atoms (#!1 & sel)

> delete bonds (#!1 & sel)

> morph #1,2 wrap true frames 60

models have different number of chains, 3 (Morph - W19-060325.pdb #/D,Morph -
W19-060325.pdb #/H,Morph - W19-060325.pdb #/L) and 2 (7tpp-delGlaK1EGF1.pdb
#2/B,7tpp-delGlaK1EGF1.pdb #2/E)  

> save "/Users/boskostojanovski/Desktop/DES_PTse_COOT/W19/Alignments
> W19v7tpp/Aligned_Mz v PT.pdb"

> close #1

> close #2

> open "/Users/boskostojanovski/Desktop/DES_PTse_COOT/W19/Alignments
> W19v7tpp/Aligned_Mz v PT.pdb"

Summary of feedback from opening
/Users/boskostojanovski/Desktop/DES_PTse_COOT/W19/Alignments
W19v7tpp/Aligned_Mz v PT.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 ALA D 56 TYR D 60 1 5  
Start residue of secondary structure not found: HELIX 2 2 ARG D 125 THR D 131
1 7  
Start residue of secondary structure not found: HELIX 3 3 ARG D 165 SER D 171
1 7  
Start residue of secondary structure not found: HELIX 4 4 VAL D 231 ALA D 233
1 3  
Start residue of secondary structure not found: HELIX 5 5 LEU D 235 SER D 241
1 7  
38 messages similar to the above omitted  
  
Chain information for Aligned_Mz v PT.pdb  
---  
Chain | Description  
1.2/B | No description available  
1.1/D | No description available  
1.2/E | No description available  
1.1/H | No description available  
1.1/L | No description available  
  
Computing secondary structure  

> hide #!1 models

> show #!1 models

> hide #!1.1 models

> hide #!1.2 models

> show #!1.2 models

> show #!1.1 models

> hide #!1 models

> show #!1 models

> hide #!1.1 models

> show #!1.1 models

> hide #!1.1 models

> show #!1.1 models

> color #1.1 #fffc79ff

> morph #1.1,1.2 wrap true frames 60

Require at least 2 structures for morph  

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1.1 models

> show #!1.1 models

> hide #!1.2 models

> save "/Users/boskostojanovski/Desktop/DES_PTse_COOT/W19/Alignments
> W19v7tpp/Mz for Aligning.pdb" models #1.1

> show #!1.2 models

> hide #!1.1 models

> hide #!1 models

> show #!1.1 models

> hide #!1.2 models

> show #!1.2 models

> hide #!1.1 models

> save "/Users/boskostojanovski/Desktop/DES_PTse_COOT/W19/Alignments
> W19v7tpp/PT for aligning.pdb" models #1.2

> close #1

> open "/Users/boskostojanovski/Desktop/DES_PTse_COOT/W19/Alignments
> W19v7tpp/Mz for Aligning.pdb"

Chain information for Mz for Aligning.pdb #1  
---  
Chain | Description  
D | No description available  
H | No description available  
L | No description available  
  

> open "/Users/boskostojanovski/Desktop/DES_PTse_COOT/W19/Alignments
> W19v7tpp/PT for aligning.pdb"

Chain information for PT for aligning.pdb #2  
---  
Chain | Description  
B | No description available  
E | No description available  
  

> morph #1,2 wrap true frames 60

models have different number of chains, 3 (Morph - Mz for Aligning.pdb
#/D,Morph - Mz for Aligning.pdb #/H,Morph - Mz for Aligning.pdb #/L) and 2 (PT
for aligning.pdb #2/B,PT for aligning.pdb #2/E)  

> hide #!1 models

> show #!1 models

> hide #!2 models

> close #2

> ui tool show "Change Chain IDs"

> changechains H,L M,M

Chain IDs of 353 residues changed  
Must select one or more chain IDs from the list on the left  

> save "/Users/boskostojanovski/Desktop/DES_PTse_COOT/W19/Alignments
> W19v7tpp/Mz for Aligning.pdb" relModel #1

> close #1

> open "/Users/boskostojanovski/Desktop/DES_PTse_COOT/W19/Alignments
> W19v7tpp/Mz for Aligning.pdb"

Chain information for Mz for Aligning.pdb #1  
---  
Chain | Description  
D | No description available  
M | No description available  
  

> open "/Users/boskostojanovski/Desktop/DES_PTse_COOT/W19/Alignments
> W19v7tpp/PT for aligning.pdb"

Chain information for PT for aligning.pdb #2  
---  
Chain | Description  
B | No description available  
E | No description available  
  

> 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

> show #!3 models

> hide #!2 models

> hide #!1 models

> show #!2 models

> show #!1 models

> color #3 #fffc79ff

> save "/Users/boskostojanovski/Desktop/DES_PTse_COOT/W19/Alignments
> W19v7tpp/Mz Transition.cxs"

> hide #!2 models

> hide #!1 models

> show #!2 models

> show #!1 models

> hide #!2 models

> hide #!1 models

> select add #3/M:271

11 atoms, 10 bonds, 1 residue, 1 model selected  

> show sel atoms

> style sel sphere

Changed 11 atom styles  

> style sel stick

Changed 11 atom styles  

> ui tool show "Show Sequence Viewer"

Drag select of 36 residues  

> color sel cornflower blue

Drag select of 13 residues  

> color sel cornflower blue

Drag select of 14 residues  

> color sel cornflower blue

Drag select of 85 residues  

> color sel cornflower blue

Drag select of 154 residues  

> color sel cornflower blue

Drag select of 29 residues  

> color sel cornflower blue

> select clear

> select add #3/M:271

11 atoms, 10 bonds, 1 residue, 1 model selected  

> color sel byhetero

> select clear

> select add #3/D:189

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

> show sel atoms

> color sel byhetero

> select clear

> show #!2 models

> hide #!3 models

> show #!3 models

> hide #!2 models

> movie record

> movie encode /Users/boskostojanovski/Desktop/movie1.mp4 framerate 25.0

Movie saved to /Users/boskostojanovski/Desktop/movie1.mp4  
  

> movie record

> movie encode /Users/boskostojanovski/Desktop/movie2.mp4 framerate 25.0

Movie saved to /Users/boskostojanovski/Desktop/movie2.mp4  
  

> movie record

> movie encode /Users/boskostojanovski/Desktop/movie3.mp4 framerate 25.0

Error processing trigger "new frame":  
Movie encoding failed because no images were recorded.  

> movie record

> movie encode /Users/boskostojanovski/Desktop/movie3.mp4 framerate 25.0

Movie saved to /Users/boskostojanovski/Desktop/movie3.mp4  
  

> movie record

> movie encode /Users/boskostojanovski/Desktop/movie4.mp4 framerate 25.0

Movie saved to /Users/boskostojanovski/Desktop/movie4.mp4  
  

> set bgColor white

> set bgColor #ffffff00

> movie record

> movie encode /Users/boskostojanovski/Desktop/movie4.mp4 framerate 25.0

Movie saved to /Users/boskostojanovski/Desktop/movie4.mp4  
  

> movie record

> movie encode /Users/boskostojanovski/Desktop/movie5.mp4 framerate 25.0

Movie saved to /Users/boskostojanovski/Desktop/movie5.mp4  
  

> movie record

> movie encode /Users/boskostojanovski/Desktop/movie6.mp4 framerate 25.0

Movie saved to /Users/boskostojanovski/Desktop/movie6.mp4  
  

> save /Users/boskostojanovski/Desktop/DES_PTse_COOT/W19/Movies/MzvPT.cxs

> show #!2 models

> show #!1 models

> hide #!2 models

> show #!2 models

> hide #!3 models

> open "/Users/boskostojanovski/Desktop/DES_PTse_COOT/W19/FInal W19
> PDB/W19-060325.pdb"

Summary of feedback from opening
/Users/boskostojanovski/Desktop/DES_PTse_COOT/W19/FInal W19 PDB/W19-060325.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 W19-060325.pdb #4  
---  
Chain | Description  
B | No description available  
D | No description available  
E | No description available  
H | No description available  
L | No description available  
  

> hide #!2 models

> hide #!1 models

> hide #!4 atoms

> show #!4 atoms

> hide #!4 atoms

> show #!4 cartoons

> show #!3 models

> hide #!3 models

> select #4/B

10500 atoms, 10778 bonds, 12 pseudobonds, 1295 residues, 2 models selected  

> select ~sel & ##selected

5055 atoms, 5170 bonds, 17 pseudobonds, 636 residues, 2 models selected  

> delete atoms (#!4 & sel)

> delete bonds (#!4 & sel)

> show #!3 models

> movie record

> movie encode /Users/boskostojanovski/Desktop/movie4.mp4 framerate 25.0

Movie saved to /Users/boskostojanovski/Desktop/movie4.mp4  
  

> save
> /Users/boskostojanovski/Desktop/DES_PTse_COOT/W19/Movies/MzvPTfVafXa.cxs

——— End of log from Fri Jul 18 11:26:37 2025 ———

> view name session-start

opened ChimeraX session  

> select #3/D

1844 atoms, 1886 bonds, 233 residues, 1 model selected  

> color sel #fffc79ff

> select clear

> select #1/M

2831 atoms, 2896 bonds, 14 pseudobonds, 353 residues, 2 models selected  

> select clear

> select #2/B#4/B

12499 atoms, 12823 bonds, 12 pseudobonds, 1549 residues, 3 models selected  

> select #1/M#3/M

5638 atoms, 5768 bonds, 28 pseudobonds, 706 residues, 4 models selected  

> color (#!3 & sel) #0433ffff

> color (#!3 & sel) #7a81ffff

> select clear

> select #1/M#3/M

5638 atoms, 5768 bonds, 28 pseudobonds, 706 residues, 4 models selected  

> color (#!3 & sel) #76d6ffff

> color (#!3 & sel) #d783ffff

> color (#!3 & sel) #9437ffff

> color (#!3 & sel) #7a81ffff

[Repeated 1 time(s)]

> color (#!3 & sel) #7a81fffd

> color (#!3 & sel) #7a81fff8

> color (#!3 & sel) #7a81fff7

> color (#!3 & sel) #7a81fff6

> color (#!3 & sel) #7a81fff4

> color (#!3 & sel) #7a81ffee

> color (#!3 & sel) #7a81ffeb

> color (#!3 & sel) #7a81ffea

[Repeated 1 time(s)]

> color (#!3 & sel) #7a81ffe9

> color (#!3 & sel) #7a81ffe8

> color (#!3 & sel) #7a81ffd3

> color (#!3 & sel) #7a81ffbf

> color (#!3 & sel) #7a81ffbd

[Repeated 1 time(s)]

> select clear

> select add #3/M:271@CG

1 atom, 1 bond, 1 residue, 1 model selected  

> select add #3/M:271@NH2

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

> color sel byhetero

> select clear

Drag select of 3 atoms, 4 bonds  
Drag select of 6 atoms, 5 bonds  

> color sel byhetero

> select clear

Drag select of 7 atoms, 6 bonds  

> style sel sphere

Changed 7 atom styles  

> select clear

> style #!3-4 stick

Changed 15151 atom styles  
Drag select of 3 atoms, 4 residues, 4 bonds  

> select clear

> color sel byhetero

> select clear

Drag select of 2 atoms, 2 bonds  

> color sel byhetero

Drag select of 1 atoms  

> color sel byhetero

> select clear

> hide #3.1 models

> hide #4.1 models

> show #3.1 models

> show #!3-4 atoms

> hide #!3-4 atoms

> ui tool show "Show Sequence Viewer"

> sequence chain #1/M #3/M

Alignment identifier is 1  

> select #1/M:271 #3/M:271

22 atoms, 20 bonds, 2 residues, 2 models selected  

> select #1/M:271 #3/M:271

22 atoms, 20 bonds, 2 residues, 2 models selected  
1 [ID: 1] region 2 chains [76] RMSD: 0.000  
  

> show sel & #!3 atoms

> color (#!3 & sel) byhetero

> select clear

> select #1/M#3/M

5638 atoms, 5768 bonds, 28 pseudobonds, 706 residues, 4 models selected  

> color (#!3 & sel) #ff85ffff

> color (#!3 & sel) #7a81ffff

> color (#!3 & sel) #76d6ffff

> color (#!3 & sel) #7a81ffff

> color (#!3 & sel) #d783ffff

> color (#!3 & sel) #9437ffff

> color (#!3 & sel) #ff40ffff

> color (#!3 & sel) #d783ffff

> color (#!3 & sel) #d783ff66

> color (#!3 & sel) #d783ff80

> select clear

> select #1/M#3/M

5638 atoms, 5768 bonds, 28 pseudobonds, 706 residues, 4 models selected  

> color (#!3 & sel) #7a81ffff

> color (#!3 & sel) #7a81ff66

> select clear

> select #1/M#3/M

5638 atoms, 5768 bonds, 28 pseudobonds, 706 residues, 4 models selected  

> color (#!3 & sel) #7a81ffff

> color (#!3 & sel) #7a81ff99

> color (#!3 & sel) #7a81ff80

> select clear

> select #1/M:271 #3/M:271

22 atoms, 20 bonds, 2 residues, 2 models selected  

> select #1/M:271 #3/M:271

22 atoms, 20 bonds, 2 residues, 2 models selected  
1 [ID: 1] region 2 chains [76] RMSD: 26.899  
  

> color (#!3 & sel) byhetero

> select clear

> ui tool show "Show Sequence Viewer"

> sequence chain #1/D #3/D

Alignment identifier is 2  

> select #1/D:189-190 #3/D:189-190

26 atoms, 24 bonds, 4 residues, 2 models selected  

> select #1/D:189-190 #3/D:189-190

26 atoms, 24 bonds, 4 residues, 2 models selected  
2 [ID: 2] region 2 chains [179-180] RMSD: 3.636  
  

> select #1/D:189 #3/D:189

16 atoms, 14 bonds, 2 residues, 2 models selected  

> select #1/D:189 #3/D:189

16 atoms, 14 bonds, 2 residues, 2 models selected  
2 [ID: 2] region 2 chains [179] RMSD: 3.437  
  

> show sel & #!3 atoms

> select clear

> ui mousemode right "mark plane"

[Repeated 1 time(s)]

> select add #3/M:271

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select clear

> close #5

> close #6

> style #!3-4 sphere

Changed 15151 atom styles  

> select clear

[Repeated 1 time(s)]

> hide #!4 models

> show #!4 models

> hide #!4 models

> select add #3/M:303

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

> hide sel atoms

> hide sel cartoons

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #4.1 models

> hide #4.1 models

> hide #!4 models

> select #1/M:171-172 #3/M:171-172

28 atoms, 28 bonds, 4 residues, 2 models selected  

> select #1/M #3/M

5638 atoms, 5768 bonds, 28 pseudobonds, 706 residues, 4 models selected  
1 [ID: 1] region 2 chains [1-353] RMSD: 16.641  
  

> show sel & #!3 cartoons

> select clear

> show #!4 models

> hide #!4 models

> select #1/D:16 #3/D:16

16 atoms, 14 bonds, 2 residues, 2 models selected  

> select #1/D:16-21 #3/D:16-21

82 atoms, 80 bonds, 12 residues, 2 models selected  
2 [ID: 2] region 2 chains [1-6] RMSD: 1.288  
  

> select #1/D:23 #3/D:23

18 atoms, 16 bonds, 2 residues, 2 models selected  

> select #1/D:16-23 #3/D:16-23

112 atoms, 110 bonds, 16 residues, 2 models selected  
2 [ID: 2] region 2 chains [1-8] RMSD: 1.168  
  

> hide sel & #!3 cartoons

> select #1/M#3/M

5638 atoms, 5768 bonds, 28 pseudobonds, 706 residues, 4 models selected  

> color (#!3 & sel) #d783ffff

> color (#!3 & sel) #d783ffcc

> color (#!3 & sel) #d783ffb3

> select clear

> select #1/M#3/M

5638 atoms, 5768 bonds, 28 pseudobonds, 706 residues, 4 models selected  

> color (#!3 & sel) #7a81ffff

> color (#!3 & sel) #7a81ff80

> color (#!3 & sel) #7a81ff99

> select clear

> select #1/M:272 #3/M:272

14 atoms, 12 bonds, 2 residues, 2 models selected  

> select #1/M:271-272 #3/M:271-272

36 atoms, 34 bonds, 4 residues, 2 models selected  
1 [ID: 1] region 2 chains [76-77] RMSD: 31.938  
  

> select #1/M:271 #3/M:271

22 atoms, 20 bonds, 2 residues, 2 models selected  

> select #1/M:271 #3/M:271

22 atoms, 20 bonds, 2 residues, 2 models selected  
1 [ID: 1] region 2 chains [76] RMSD: 30.783  
  

> color (#!3 & sel) byhetero

> select clear

> show #!4 models

> hide #!4 models

> select add #3/M:267

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

> select add #3/M:244

13 atoms, 11 bonds, 2 residues, 1 model selected  

> select clear

> select add #3/M:267

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

> select add #3/M:244

13 atoms, 11 bonds, 2 residues, 1 model selected  

> select add #3.1

13 atoms, 11 bonds, 14 pseudobonds, 2 residues, 2 models selected  

> select subtract #3.1

13 atoms, 11 bonds, 2 residues, 1 model selected  

> hide #3.1 models

> show #3.1 models

> hide #3.1 models

> show #3.1 models

> hide #3.1 models

> show #3.1 models

> select add #3.1

13 atoms, 11 bonds, 14 pseudobonds, 2 residues, 2 models selected  

> hide #3.1 models

> show #3.1 models

> select clear

> select add #3/M:267

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

> select clear

[Repeated 2 time(s)]

> hide #3.1 models

> show #3.1 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> select add #4

10500 atoms, 10778 bonds, 12 pseudobonds, 1295 residues, 2 models selected  

> hide #!4 models

> show #!4 models

> show sel surfaces

> color #4 #009193ff

> color #4 #00919333

> select clear

> select add #3/M:271@CA

1 atom, 1 residue, 1 model selected  

> select add #3/M:271@CD

2 atoms, 1 residue, 1 model selected  

> select add #3/M:271@NH1

3 atoms, 1 residue, 1 model selected  

> select #1/M:271 #3/M:271

22 atoms, 20 bonds, 2 residues, 2 models selected  

> select #1/M:271 #3/M:271

22 atoms, 20 bonds, 2 residues, 2 models selected  
1 [ID: 1] region 2 chains [76] RMSD: 29.337  
  

> color (#!3 & sel) #ff40ffff

> color (#!3 & sel) byhetero

> select clear

> ui tool show "Show Sequence Viewer"

> sequence chain #4/B

Alignment identifier is 4/B  

> select #4/B:662-663

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

> select #4/B:662-1546

115 atoms, 117 bonds, 1 pseudobond, 14 residues, 2 models selected  

> select #4/B:674

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

> select #4/B:660-674

125 atoms, 128 bonds, 15 residues, 1 model selected  

> hide sel surfaces

> hide sel cartoons

> select add #4

10500 atoms, 10778 bonds, 12 pseudobonds, 1295 residues, 3 models selected  

> hide sel cartoons

> show #4.1 models

> show sel surfaces

> hide sel surfaces

> show sel surfaces

> select #4/B:644

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

> select #4/B:644-646

24 atoms, 23 bonds, 3 residues, 1 model selected  

> select #4/B:674

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

> select #4/B:666-674

74 atoms, 76 bonds, 9 residues, 1 model selected  

> hide sel surfaces

> select #4/B:661-662

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

> select #4/B:661-665

43 atoms, 43 bonds, 5 residues, 1 model selected  

> hide sel surfaces

> select #4/B:659

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

> select #4/B:659-660

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

> hide sel surfaces

Drag select of 5 residues  

> select clear

> select add #3/M:303

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

> hide sel cartoons

> save /Users/boskostojanovski/Desktop/image40.png supersample 3

> save /Users/boskostojanovski/Desktop/image41.png supersample 3

> save /Users/boskostojanovski/Desktop/image42.png supersample 3

> save /Users/boskostojanovski/Desktop/image43.png supersample 3

> save /Users/boskostojanovski/Desktop/image44.png supersample 3

> save /Users/boskostojanovski/Desktop/image45.png supersample 3

> save "/Users/boskostojanovski/Desktop/Movie for paper.cxs" includeMaps true

——— End of log from Fri Aug 15 11:13:56 2025 ———

> view name session-start

opened ChimeraX session  

> hide #4.2 models

> show #4.2 models

> hide #!4 models

> show #!4 models

> select add #3

4651 atoms, 4758 bonds, 14 pseudobonds, 586 residues, 2 models selected  

> select subtract #3

Nothing selected  

> movie record

> movie encode /Users/boskostojanovski/Desktop/movie7.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.  
  




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: 2 days, 1 hour, 10 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 Tom Goddard, 3 months ago

Component:	Unassigned → Build System
Owner:	set to Zach Pearson
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → ffmpeg PermissionError: [Errno 13] Permission denied: '/Applications/ChimeraX-1.10.app/Contents/bin/ffmpeg'

comment:2 by Tom Goddard, 3 months ago

Resolution:	→ duplicate
Status:	assigned → closed

Fixed in 1.10.1 release.

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