ffmpeg: Permission denied

[angrish.arvind@…]

The following bug report has been submitted:
Platform:        macOS-15.4.1-arm64-arm-64bit
ChimeraX Version: 1.10 (2025-06-26 08:57:52 UTC)
Description
Replace this text with list of actions that caused this problem to occur

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

> open /Users/asharma6/Library/CloudStorage/OneDrive-
> Moderna/BACTERIOLOGY/GAS/SpnA/Sturcture/OB1_OB2_crystal_Structure/AF2_vs_Crystal_structure.cxs

Log from Tue Aug 12 14:59:00 2025UCSF ChimeraX version: 1.10 (2025-06-26)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open /Users/asharma6/Library/CloudStorage/OneDrive-
> Moderna/BACTERIOLOGY/GAS/SpnA/Sturcture/OB_domain_Comparison.cxs

Log from Wed Jan 29 11:40:59 2025UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open /Users/asharma6/Library/CloudStorage/OneDrive-
> Moderna/BACTERIOLOGY/GAS/SpnA/Sturcture/OB_domain_Comparison.cxs

Log from Tue Jan 14 14:44:39 2025UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open /Users/asharma6/Library/CloudStorage/OneDrive-
> Moderna/BACTERIOLOGY/GAS/SpnA/Sturcture/OB_domain_Comparison.cxs

Log from Tue Jan 14 14:05:48 2025UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open /Users/asharma6/Library/CloudStorage/OneDrive-
> Moderna/BACTERIOLOGY/GAS/SpnA/Sturcture/AF2_vs_Structure.cxs

Log from Tue Jan 14 13:32:56 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/asharma6/Library/CloudStorage/OneDrive-
> Moderna/BACTERIOLOGY/GAS/SpnA/AF2_Dan_SpnA_A0A455ZLU4.pdb

Chain information for AF2_Dan_SpnA_A0A455ZLU4.pdb #1  
---  
Chain | Description  
A | No description available  
  
Computing secondary structure  

> rainbow

> select /A:72

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

> open /Users/asharma6/Library/CloudStorage/OneDrive-
> Moderna/BACTERIOLOGY/GAS/SpnA/Sturcture/Refinements/J89_fitted_coot4_Iso5_woH.pdb

Chain information for J89_fitted_coot4_Iso5_woH.pdb #2  
---  
Chain | Description  
A | No description available  
  

> ui tool show Matchmaker

> matchmaker #1 to #2

Computing secondary structure  
[Repeated 1 time(s)]  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 J89_fitted_coot4_Iso5_woH.pdb, chain A (#2) with
AF2_Dan_SpnA_A0A455ZLU4.pdb, chain A (#1), sequence alignment score = 2761.9  
RMSD between 539 pruned atom pairs is 0.911 angstroms; (across all 565 pairs:
1.039)  
  

> lighting soft

> set bgColor white

> show sel atoms

> select clear

> show atoms

> select #1/A:1-23

172 atoms, 172 bonds, 23 residues, 1 model selected  

> hide sel atoms

> ui tool show "Color Actions"

> color sel lime

> ui tool show "Render/Select by Attribute"

No attribute chosen for rendering  
All 'worm_radius' values are 1  
[Repeated 2 time(s)]

> select #1/A:24-98

592 atoms, 602 bonds, 75 residues, 1 model selected  

> select #1/A:24-84

479 atoms, 488 bonds, 61 residues, 1 model selected  

> color sel dim gray

> hide sel atoms

> color sel black

> color sel dim gray

> select #1/A:175

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

> select #1/A:85-175

714 atoms, 729 bonds, 91 residues, 1 model selected  

> color sel lavender

> color sel thistle

> color sel byhetero

> hide sel atoms

> color sel orchid

> select #1/A:275

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

> select #1/A:175-2075

5673 atoms, 5767 bonds, 736 residues, 1 model selected  

> select #1/A:175-275

769 atoms, 776 bonds, 101 residues, 1 model selected  

> color sel violet

> color sel plum

> color sel hot pink

> color sel pale violet red

> color sel salmon

> select #1/A:85-174

708 atoms, 723 bonds, 90 residues, 1 model selected  

> color sel salmon

> color sel light salmon

> color sel tan

> color sel light coral

> color sel pink

> color sel light pink

> select #1/A:276@CB

1 atom, 1 residue, 1 model selected  

> select add #1/A:287

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

> select #1/A:276-287

85 atoms, 84 bonds, 12 residues, 1 model selected  

> color sel dim gray

> hide sel cartoons

> show sel cartoons

> hide sel atoms

> select clear

> hide #2 models

> select clear

> select #1/A:399

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

> select #1/A:288-399

850 atoms, 860 bonds, 112 residues, 1 model selected  

> color sel tomato

> hide sel atoms

> select clear

> hide #1 atoms

> select clear

> select add #1/A:854

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

> select add #1/A:853

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

> select #1/A:400-853

3542 atoms, 3614 bonds, 454 residues, 1 model selected  

> color sel cornflower blue

> select clear

> save "/Users/asharma6/OneDrive -
> Moderna/BACTERIOLOGY/GAS/SpnA/Sturcture/AF2_vs_Structure.cxs"

> ui tool show "Show Sequence Viewer"

> sequence chain #1/A

Alignment identifier is 1/A  

> ui tool show "Show Sequence Viewer"

> ui tool show "Selection Inspector"

[Repeated 1 time(s)]

> sequence chain #1/A

Destroying pre-existing alignment with identifier 1/A  
Alignment identifier is 1/A  

> select #1/A:877

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

> select #1/A:877-881

35 atoms, 35 bonds, 5 residues, 1 model selected  

> show sel atoms

> style sel sphere

Changed 35 atom styles  

> select clear

> graphics silhouettes true

> save "/Users/asharma6/OneDrive -
> Moderna/BACTERIOLOGY/GAS/SpnA/Sturcture/AF2_vs_Structure.cxs"

——— End of log from Tue Jan 14 13:32:56 2025 ———

opened ChimeraX session  

> select #1/A:167

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

> select add #1/A:275

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

> select #1/A:168

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

> select add #1/A:275

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

> select #1/A:167

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

> select clear

> select #1/A:168

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

> select add #1/A:169

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

> select add #1/A:170

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

> select add #1/A:171

31 atoms, 27 bonds, 4 residues, 1 model selected  

> select add #1/A:173

38 atoms, 34 bonds, 5 residues, 1 model selected  

> select add #1/A:174

45 atoms, 40 bonds, 6 residues, 1 model selected  

> select add #1/A:172

56 atoms, 51 bonds, 7 residues, 1 model selected  

> color sel dark gray

> select #1/A:175

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

> select add #1/A:84

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

> select #1/A:174

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

> select #1/A:174-176

20 atoms, 19 bonds, 3 residues, 1 model selected  

> select add #1/A:84

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

> select add #1/A:167

36 atoms, 33 bonds, 5 residues, 1 model selected  

> select clear

> select #1/A:287

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

> select add #1/A:286

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

> select add #1/A:399

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

> select clear

> select #1/A:276

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

> select add #1/A:173

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

> open /Users/asharma6/Library/CloudStorage/OneDrive-
> Moderna/BACTERIOLOGY/GAS/SpnA/AF2_Dan_SpnA_A0A455ZLU4.pdb

Chain information for AF2_Dan_SpnA_A0A455ZLU4.pdb #3  
---  
Chain | Description  
A | No description available  
  
Computing secondary structure  

> open /Users/asharma6/Library/CloudStorage/OneDrive-
> Moderna/BACTERIOLOGY/GAS/SpnA/AF2_Dan_SpnA_A0A455ZLU4.pdb

Chain information for AF2_Dan_SpnA_A0A455ZLU4.pdb #4  
---  
Chain | Description  
A | No description available  
  
Computing secondary structure  

> hide #4 models

> hide #3 models

> select #1/A:85-174

708 atoms, 723 bonds, 90 residues, 1 model selected  

> show #3 models

> hide #1 models

> select add #3

7740 atoms, 7876 bonds, 1000 residues, 2 models selected  

> show #1 models

> show #2 models

> ui tool show Matchmaker

> matchmaker #3 to #2

Computing secondary structure  
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 J89_fitted_coot4_Iso5_woH.pdb, chain A (#2) with
AF2_Dan_SpnA_A0A455ZLU4.pdb, chain A (#3), sequence alignment score = 2761.9  
RMSD between 539 pruned atom pairs is 0.911 angstroms; (across all 565 pairs:
1.039)  
  

> matchmaker #4 to #2

Computing secondary structure  
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 J89_fitted_coot4_Iso5_woH.pdb, chain A (#2) with
AF2_Dan_SpnA_A0A455ZLU4.pdb, chain A (#4), sequence alignment score = 2761.9  
RMSD between 539 pruned atom pairs is 0.911 angstroms; (across all 565 pairs:
1.039)  
  

> hide #2 models

> hide #1 models

> select #1/A:85-174

708 atoms, 723 bonds, 90 residues, 1 model selected  

> show #1 models

> hide #3 models

> ui tool show "Color Actions"

> color sel yellow

> select #1/A:175-275

769 atoms, 776 bonds, 101 residues, 1 model selected  

> color sel tomato

> color sel light salmon

> color sel orange

> select #1/A:288-399

850 atoms, 860 bonds, 112 residues, 1 model selected  

> color sel dark red

> color sel orange red

> select clear

> select #1/A:288-399

850 atoms, 860 bonds, 112 residues, 1 model selected  

> select ~sel & ##selected

6182 atoms, 6293 bonds, 798 residues, 1 model selected  

> hide sel cartoons

> hide sel atoms

> show #3 models

> select #2/A:175-275

Nothing selected  

> select #3/A:175-275

769 atoms, 776 bonds, 101 residues, 1 model selected  

> select #2/A:175-275, #1/A:288-399

Expected an objects specifier or a keyword  

> select #2/A:175-275 #1/A:288-399

850 atoms, 860 bonds, 112 residues, 1 model selected  

> select #3/A:175-275 #1/A:288-399

1619 atoms, 1636 bonds, 213 residues, 2 models selected  

> ui tool show Matchmaker

> matchmaker #3 & sel to #1 & sel

Computing secondary structure  
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 AF2_Dan_SpnA_A0A455ZLU4.pdb, chain A (#1) with
AF2_Dan_SpnA_A0A455ZLU4.pdb, chain A (#3), sequence alignment score = 58  
RMSD between 33 pruned atom pairs is 0.845 angstroms; (across all 79 pairs:
13.828)  
  

> select #3/A:175-275

769 atoms, 776 bonds, 101 residues, 1 model selected  

> select ~sel & ##selected

6263 atoms, 6377 bonds, 809 residues, 1 model selected  

> hide sel cartoons

> show #4 models

> hide #3 models

> select #1/A:85-174

708 atoms, 723 bonds, 90 residues, 1 model selected  

> select #4/A:85-174

708 atoms, 723 bonds, 90 residues, 1 model selected  

> select #4/A:85-174 #1/A:288-399

1558 atoms, 1583 bonds, 202 residues, 2 models selected  

> matchmaker #4 & sel to #1 & sel

Computing secondary structure  
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 AF2_Dan_SpnA_A0A455ZLU4.pdb, chain A (#1) with
AF2_Dan_SpnA_A0A455ZLU4.pdb, chain A (#4), sequence alignment score = 82.5  
RMSD between 51 pruned atom pairs is 0.852 angstroms; (across all 87 pairs:
3.365)  
  

> select #4/A:85-174

708 atoms, 723 bonds, 90 residues, 1 model selected  

> select ~sel & ##selected

6324 atoms, 6430 bonds, 820 residues, 1 model selected  

> hide sel cartoons

> show #3 models

> hide #1 models

> hide #3 models

Drag select of 90 residues  

> color sel yellow

> show #3 models

> hide #4 models

Drag select of 101 residues  

> color sel orange

> show #4 models

> show #1 models

> select clear

> select #3/A:175

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

> select add #3/A:176

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

> hide sel cartoons

> select #1/A:395

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

> select add #1/A:396

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

> select add #4/A:170

22 atoms, 19 bonds, 3 residues, 2 models selected  

> select add #4/A:171

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

> select add #4/A:172

39 atoms, 35 bonds, 5 residues, 2 models selected  

> select add #4/A:173

46 atoms, 42 bonds, 6 residues, 2 models selected  

> select add #4/A:174

53 atoms, 48 bonds, 7 residues, 2 models selected  

> select add #1/A:397

60 atoms, 54 bonds, 8 residues, 2 models selected  

> select add #1/A:398

67 atoms, 61 bonds, 9 residues, 2 models selected  

> select add #1/A:399

73 atoms, 66 bonds, 10 residues, 2 models selected  

> hide sel cartoons

> save "/Users/asharma6/OneDrive -
> Moderna/BACTERIOLOGY/GAS/SpnA/Sturcture/OB_domain_Comparison.cxs"

——— End of log from Tue Jan 14 14:05:48 2025 ———

opened ChimeraX session  

> open 5ODL

Summary of feedback from opening 5ODL fetched from pdb  
---  
notes | Fetching compressed mmCIF 5odl from http://files.rcsb.org/download/5odl.cif  
Fetching CCD NA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/NA/NA.cif  
  
5odl title:  
Single-stranded DNA-binding protein from bacteriophage Enc34 in complex with
ssDNA [more info...]  
  
Chain information for 5odl #5  
---  
Chain | Description | UniProt  
A | single-stranded DNA-binding protein | H6WYG2_9CAUD 1-178  
D | oligo(T) |   
  
Non-standard residues in 5odl #5  
---  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
NA — sodium ion  
  
47 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
Drag select of 291 residues  

> ui tool show Matchmaker

> matchmaker #!5 to #1 & sel

Computing secondary structure  
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 AF2_Dan_SpnA_A0A455ZLU4.pdb, chain A (#1) with 5odl, chain A (#5),
sequence alignment score = 12  
RMSD between 9 pruned atom pairs is 0.994 angstroms; (across all 47 pairs:
18.209)  
  

> ui tool show Matchmaker

> matchmaker #!5 to #3 & sel

Computing secondary structure  
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 AF2_Dan_SpnA_A0A455ZLU4.pdb, chain A (#3) with 5odl, chain A (#5),
sequence alignment score = 28.4  
RMSD between 14 pruned atom pairs is 0.900 angstroms; (across all 90 pairs:
15.000)  
  

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select up

164 atoms, 179 bonds, 9 residues, 1 model selected  

> select ~sel & ##selected

1559 atoms, 1447 bonds, 1 pseudobond, 319 residues, 2 models selected  

> hide sel cartoons

> hide sel atoms

Drag select of 17 atoms, 18 bonds  

> select up

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

> select up

40 atoms, 43 bonds, 2 residues, 1 model selected  

> select up

164 atoms, 179 bonds, 9 residues, 1 model selected  

> color sel forest green

> color sel byhetero

> select clear

> select #3/A:275

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

> select #1/A:394

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

> color sel red

> style sel sphere

Changed 7 atom styles  

> show sel atoms

> select #3/A:177

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

> show sel atoms

> style sel sphere

Changed 9 atom styles  

> hide sel atoms

> select #1/A:288

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

> show sel atoms

> style sel sphere

Changed 8 atom styles  

> color sel blue

> select clear

> matchmaker #!5 to #3 & sel

No 'to' model specified  

> hide #!5 models

> turn y 90

> show #!5 models

> hide #!5 models

> save "/Users/asharma6/OneDrive -
> Moderna/BACTERIOLOGY/GAS/SpnA/Sturcture/OB_domain_Comparison.cxs"

——— End of log from Tue Jan 14 14:44:39 2025 ———

opened ChimeraX session  

> open /Users/asharma6/Library/CloudStorage/OneDrive-
> Moderna/BACTERIOLOGY/GAS/SpnA/Sturcture/A_domain_SpnA.pdb

Chain information for A_domain_SpnA.pdb #6  
---  
Chain | Description  
A | No description available  
  

> ui tool show Matchmaker

> matchmaker #6 to #1

Computing secondary structure  
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 AF2_Dan_SpnA_A0A455ZLU4.pdb, chain A (#1) with A_domain_SpnA.pdb,
chain A (#6), sequence alignment score = 3429  
RMSD between 135 pruned atom pairs is 0.000 angstroms; (across all 135 pairs:
0.000)  
  
Drag select of 9 atoms, 304 residues  

> matchmaker #6 to #1 & sel

Computing secondary structure  
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 AF2_Dan_SpnA_A0A455ZLU4.pdb, chain A (#1) with A_domain_SpnA.pdb,
chain A (#6), sequence alignment score = 357  
Fewer than 3 residues aligned; cannot match AF2_Dan_SpnA_A0A455ZLU4.pdb, chain
A with A_domain_SpnA.pdb, chain A  

> select add #6

3230 atoms, 1052 bonds, 421 residues, 4 models selected  

> select clear

> select add #6

1031 atoms, 1052 bonds, 135 residues, 1 model selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #6,-0.86256,-0.50162,-0.066036,96.319,-0.50099,0.86503,-0.026989,104.58,0.070661,0.0098043,-0.99745,94.154

> view matrix models
> #6,0.14576,-0.93271,-0.32985,100.87,0.84629,0.29024,-0.44672,111.11,0.5124,-0.21404,0.83165,83.227

> view matrix models
> #6,0.56643,-0.70676,-0.42385,107.44,-0.21405,0.37049,-0.90384,106.66,0.79583,0.60268,0.058569,100.04

> view matrix models
> #6,0.45285,-0.89084,-0.036479,101.89,-0.32938,-0.12913,-0.93533,100.08,0.82852,0.43557,-0.3519,100.97

> view matrix models
> #6,0.45233,-0.88296,-0.12561,102.55,-0.24626,0.011714,-0.96913,102.6,0.85718,0.4693,-0.21214,100.69

> view matrix models
> #6,0.59515,-0.76199,0.25527,102.64,-0.37847,-0.54599,-0.74743,93.578,0.70891,0.34823,-0.61334,100.68

> view matrix models
> #6,0.90239,-0.088047,-0.42184,117.34,-0.41995,-0.39923,-0.81502,95.413,-0.096651,0.91261,-0.39724,99.602

> view matrix models
> #6,0.10421,0.86709,-0.48712,122.73,-0.99159,0.12838,0.016373,91.782,0.076732,0.48132,0.87318,87.719

> view matrix models
> #6,-0.86284,-0.30534,0.40284,95.61,0.36137,0.18463,0.91396,97.302,-0.35344,0.93417,-0.048962,95.598

> view matrix models
> #6,-0.92133,-0.13984,0.36275,97.356,0.36915,-0.021953,0.92911,94.835,-0.12197,0.98993,0.071849,97.296

> view matrix models
> #6,-0.88153,-0.44326,0.16256,95.386,0.24225,-0.12913,0.96158,92.368,-0.40524,0.88704,0.22121,92.899

> view matrix models
> #6,-0.92203,-0.27694,-0.27048,99.81,-0.34198,0.25532,0.90436,92.669,-0.18139,0.92634,-0.33012,98.666

> view matrix models
> #6,-0.93586,-0.3523,-0.006759,97.118,-0.21282,0.54983,0.80771,97.771,-0.28084,0.75734,-0.58954,97.565

> view matrix models
> #6,-0.93951,-0.34225,-0.013682,97.253,-0.21023,0.54466,0.81188,97.704,-0.27042,0.76565,-0.58366,97.707

> ui mousemode right "translate selected models"

> view matrix models
> #6,-0.93951,-0.34225,-0.013682,90.081,-0.21023,0.54466,0.81188,108.08,-0.27042,0.76565,-0.58366,90.068

> view matrix models
> #6,-0.93951,-0.34225,-0.013682,90.336,-0.21023,0.54466,0.81188,106.85,-0.27042,0.76565,-0.58366,85.711

> view matrix models
> #6,-0.93951,-0.34225,-0.013682,93.059,-0.21023,0.54466,0.81188,104.83,-0.27042,0.76565,-0.58366,85.403

> view matrix models
> #6,-0.93951,-0.34225,-0.013682,93.325,-0.21023,0.54466,0.81188,105.52,-0.27042,0.76565,-0.58366,85.261

> select #6/A:533

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

> select add #6/A:399

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

> show sel atoms

> style sel sphere

Changed 10 atom styles  

> select #6/A:399@CA

1 atom, 1 residue, 1 model selected  

> color sel blue

> select #6/A:533

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

> color sel red

> select clear

> save "/Users/asharma6/OneDrive -
> Moderna/BACTERIOLOGY/GAS/SpnA/Sturcture/Figures/OBdomains_cpmarison.png"
> width 1428 height 1172 supersample 3 transparentBackground true

> save "/Users/asharma6/OneDrive -
> Moderna/BACTERIOLOGY/GAS/SpnA/Sturcture/OB_domain_Comparison.cxs"

——— End of log from Wed Jan 29 11:40:59 2025 ———

> view name session-start

opened ChimeraX session  

> hide #1 models

> hide #6 models

> close #6

> show #!5 models

> close #5

> show #1 models

> close #1

> hide #4 models

> show #3 cartoons

> show #4 models

> close #4

> close #2

> select clear

> select /A:81

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

> select /A:280

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

> select #3 /A:1-79, 280-1000

5489 atoms, 5585 bonds, 710 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> save "/Users/asharma6/OneDrive -
> Moderna/BACTERIOLOGY/GAS/SpnA/Sturcture/OB1_OB2_crystal_Structure/AF2_vs_Crystal_structure.cxs"

> select /A:85

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

> select #3 /A:85-174

708 atoms, 723 bonds, 90 residues, 1 model selected  

> color sel yellow

> select clear

> save "/Users/asharma6/OneDrive -
> Moderna/BACTERIOLOGY/GAS/SpnA/Sturcture/OB1_OB2_crystal_Structure/AF2_vs_Crystal_structure.cxs"

> open "/Users/asharma6/Library/CloudStorage/OneDrive-
> Moderna/BACTERIOLOGY/GAS/SpnA/Sturcture/OB1_OB2_crystal_Structure/SPNA10_refmac5
> (1).pdb"

SPNA10_refmac5 (1).pdb title:  
MOLREP --- /Vers 11.9.02; 28.02.2022/ [more info...]  
  
Chain information for SPNA10_refmac5 (1).pdb #1  
---  
Chain | Description  
A | No description available  
  
Non-standard residues in SPNA10_refmac5 (1).pdb #1  
---  
CL — (CL)  
EDO — (EDO)  
MES — (MES)  
ZN — (ZN)  
  
18 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
Computing secondary structure  

> ui tool show Matchmaker

> matchmaker #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 SPNA10_refmac5 (1).pdb, chain A (#1) with
AF2_Dan_SpnA_A0A455ZLU4.pdb, chain A (#3), sequence alignment score = 948.9  
RMSD between 191 pruned atom pairs is 0.716 angstroms; (across all 196 pairs:
0.798)  
  

> view

> hide #3 models

> show #3 models

> select #1/A:174

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

> select #1/A:83

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

> select #1 /A:83-174

722 atoms, 737 bonds, 92 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel gold

> select #3 /A:83-174

722 atoms, 737 bonds, 92 residues, 1 model selected  

> color sel light gray

> select #3/A:82

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

> select add #3/A:81

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

> select add #3/A:80

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

> color sel saddle brown

> select clear

> select #1/A:275

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

> select #1/A:276

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

> select clear

> show atoms

> select #3/A:278

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

> select #1 /A:175-278

792 atoms, 799 bonds, 104 residues, 1 model selected  

> color sel orange

> select #3 /A:175-278

792 atoms, 799 bonds, 104 residues, 1 model selected  

> color sel dim gray

> select clear

> color byhetero

> select #3/A:279

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

> color sel sienna

> select clear

> color byhetero

> style stick

Changed 3216 atom styles  

> select #1/A:113

14 atoms, 15 bonds, 1 residue, 1 model selected  

> select #1/B:1@C8

1 atom, 1 residue, 1 model selected  

> select #1/B:1@C8

1 atom, 1 residue, 1 model selected  

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

12 atoms, 12 bonds, 1 residue, 1 model selected  

> style sel sphere

Changed 12 atom styles  

> color sel hot pink

> color sel byhetero

> color sel violet

> color sel byhetero

> select #1/F:1@CL

1 atom, 1 residue, 1 model selected  

> style sel sphere

Changed 1 atom style  

> select #1/D:1@ZN

1 atom, 1 residue, 1 model selected  

> style sel sphere

Changed 1 atom style  

> save "/Users/asharma6/OneDrive -
> Moderna/BACTERIOLOGY/GAS/SpnA/Sturcture/OB1_OB2_crystal_Structure/AF2_vs_Crystal_structure.cxs"

> select #3/A:279

6 atoms, 5 bonds, 1 residue, 1 model selected  
Drag select of 11 atoms, 3 residues, 9 bonds  

> select up

29 atoms, 27 bonds, 4 residues, 1 model selected  

> hide sel atoms

> color sel white

> select clear

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/asharma6/Desktop/movie6.mp4

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

> save "/Users/asharma6/OneDrive -
> Moderna/BACTERIOLOGY/GAS/SpnA/Sturcture/OB1_OB2_crystal_Structure/AF2_vs_Crystal_structure.cxs"

——— End of log from Tue Aug 12 14:59:00 2025 ———

> view name session-start

opened ChimeraX session  

> select #1/B:1@C6

1 atom, 1 residue, 1 model selected  

> select up

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select up

1673 atoms, 1558 bonds, 335 residues, 1 model selected  

> select down

12 atoms, 12 bonds, 1 residue, 1 model selected  

> ui tool show "Color Actions"

> color sel medium aquamarine

> color sel teal

> color sel medium aquamarine

> color sel medium turquoise

> color sel byhetero

> select clear

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/asharma6/Desktop/movie6.mp4

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




OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M1 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: MacBookPro18,3
      Model Number: Z15G001WALL/A
      Chip: Apple M1 Pro
      Total Number of Cores: 8 (6 performance and 2 efficiency)
      Memory: 32 GB
      System Firmware Version: 11881.140.96
      OS Loader Version: 11881.101.1

Software:

    System Software Overview:

      System Version: macOS 15.4.1 (24E263)
      Kernel Version: Darwin 24.4.0
      Time since boot: 4 days, 9 hours, 23 minutes

Graphics/Displays:

    Apple M1 Pro:

      Chipset Model: Apple M1 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

[Eric Pettersen]

Hi Arvind,

Thanks for reporting this problem. It is fixed in the 1.10.1 release, so if you upgrade to that then movie recording will work.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab