![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 5 weeks ago
Closed 5 weeks ago
#19034 closed defect (duplicate)
ffmpeg: Permission Denied
| Reported by: | Owned by: | Zach Pearson | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Build System | Version: | |
| Keywords: | Cc: | Eric Pettersen | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-15.5-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/BTX/CIRA_T/LAG3/Structure/Analysis/LAG3_VHH_Fc.cxs
Log from Sun Oct 5 04:44:23 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/BTX/CIRA_T/LAG3/Structure/Analysis/Oligomerizationwith VHH_Fc.cxs"
Log from Thu Oct 2 18:38:13 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/BTX/CIRA_T/LAG3/Structure/Analysis/Oligomerizationwith VHH.cxs"
Log from Wed Aug 13 17:38:39 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/BTX/LAG3/Structure/Analysis/PD1_VHH.cxs
Log from Tue Aug 12 17:31:29 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/BTX/LAG3/Structure/Analysis/PD1_VHH.cxs
Log from Tue Aug 12 16:35:49 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/asharma6/Library/CloudStorage/OneDrive-
> Moderna/BTX/LAG3/Structure/LAG3_refmac5 (1).pdb"
LAG3_refmac5 (1).pdb title:
MOLREP --- /Vers 11.9.02; 28.02.2022/ [more info...]
Chain information for LAG3_refmac5 (1).pdb #1
---
Chain | Description
A | No description available
B | No description available
Non-standard residues in LAG3_refmac5 (1).pdb #1
---
NAG — (NAG)
Computing secondary structure
> set bgColor white
> lighting soft
> graphics silhouettes true
> select /A:212
7 atoms, 7 bonds, 1 residue, 1 model selected
> select up
21 atoms, 21 bonds, 3 residues, 1 model selected
> select up
431 atoms, 445 bonds, 55 residues, 1 model selected
> select up
1581 atoms, 1626 bonds, 200 residues, 1 model selected
> rainbow sel
> open /Users/asharma6/Downloads/8so3.cif
8so3.cif title:
CryoEM structure of a therapeutic antibody (favezelimab) bound to human LAG3
[more info...]
Chain information for 8so3.cif #2
---
Chain | Description | UniProt
D X | Lymphocyte activation gene 3 protein | LAG3_HUMAN 1-525
H Y | favezelimab Fab heavy chain |
L Z | favezelimab Fab light chain |
Non-standard residues in 8so3.cif #2
---
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> 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 LAG3_refmac5 (1).pdb, chain A (#1) with 8so3.cif, chain X (#2),
sequence alignment score = 731.9
RMSD between 137 pruned atom pairs is 0.985 angstroms; (across all 165 pairs:
2.133)
> hide #!1 models
> show #!2 cartoons
> hide #!2 atoms
Drag select of 307 residues, 3 pseudobonds
> select up
4883 atoms, 4935 bonds, 3 pseudobonds, 347 residues, 2 models selected
> select up
8339 atoms, 8456 bonds, 3 pseudobonds, 604 residues, 2 models selected
> delete atoms (#!2 & sel)
> delete bonds (#!2 & sel)
> show #!1 models
Drag select of 81 residues, 2 pseudobonds
Drag select of 22 residues
> select up
1290 atoms, 1313 bonds, 2 pseudobonds, 139 residues, 3 models selected
> select up
3811 atoms, 3896 bonds, 2 pseudobonds, 365 residues, 3 models selected
> ui tool show Matchmaker
> matchmaker #!2 & sel to #1 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker LAG3_refmac5 (1).pdb, chain A (#1) with 8so3.cif, chain D (#2),
sequence alignment score = 638.8
RMSD between 137 pruned atom pairs is 1.089 angstroms; (across all 165 pairs:
2.206)
> select clear
> save "/Users/asharma6/OneDrive -
> Moderna/BTX/LAG3/Structure/Analysis/PD1_VHH.cxs"
Drag select of 95 residues, 1 pseudobonds
> delete atoms (#!2 & sel)
> delete bonds (#!2 & sel)
Drag select of 106 residues
> delete atoms sel
> delete bonds sel
Drag select of 116 residues
> select up
2120 atoms, 2138 bonds, 151 residues, 1 model selected
> select up
3232 atoms, 3273 bonds, 227 residues, 1 model selected
> open 7TZG
Summary of feedback from opening 7TZG fetched from pdb
---
note | Fetching compressed mmCIF 7tzg from http://files.rcsb.org/download/7tzg.cif
7tzg title:
Structure of human LAG3 in complex with antibody single-chain variable
fragment [more info...]
Chain information for 7tzg #3
---
Chain | Description | UniProt
A B | scFvF7 |
C D | Lymphocyte activation gene 3 protein | LAG3_HUMAN 23-430
Non-standard residues in 7tzg #3
---
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> mmaker #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 LAG3_refmac5 (1).pdb, chain A (#1) with 7tzg, chain C (#3),
sequence alignment score = 800
RMSD between 86 pruned atom pairs is 0.880 angstroms; (across all 171 pairs:
5.358)
> hide #!1 models
> hide #!2 models
Drag select of 152 residues
Drag select of 19 atoms, 147 residues, 2 pseudobonds, 19 bonds
> select up
2133 atoms, 2168 bonds, 2 pseudobonds, 300 residues, 2 models selected
> select up
3028 atoms, 3100 bonds, 2 pseudobonds, 430 residues, 2 models selected
> select up
4375 atoms, 4486 bonds, 2 pseudobonds, 610 residues, 2 models selected
> hide sel cartoons
> hide sel atoms
> delete atoms (#!3 & sel)
> delete bonds (#!3 & sel)
> show #!1 models
> open 9BF9
Summary of feedback from opening 9BF9 fetched from pdb
---
note | Fetching compressed mmCIF 9bf9 from http://files.rcsb.org/download/9bf9.cif
9bf9 title:
Human LAG-3-HLA-DR1 complex [more info...]
Chain information for 9bf9 #4
---
Chain | Description | UniProt
A | HLA class II histocompatibility antigen, DR alpha chain | DRA_HUMAN 5-181
B | HLA class II histocompatibility antigen DR beta chain | D7RIG0_HUMAN 0-198
D | Lymphocyte activation gene 3 protein | LAG3_HUMAN 1-407
G | Membrane protein | VME1_SARS2 1-13
Non-standard residues in 9bf9 #4
---
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)
MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose)
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
PEG — di(hydroxyethyl)ether
SO4 — sulfate ion
9bf9 mmCIF Assemblies
---
1| author_defined_assembly
> mmaker #4 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 LAG3_refmac5 (1).pdb, chain A (#1) with 9bf9, chain D (#4),
sequence alignment score = 872.9
RMSD between 149 pruned atom pairs is 1.026 angstroms; (across all 192 pairs:
3.175)
> rename #4 9bf9_MHC_boundLAG3
> rename #3 7tzg_scFv_boundLAG3
> rename #2 8so3_therapeutcAb_Favezelimab.cif
> open 7tzg
7tzg title:
Structure of human LAG3 in complex with antibody single-chain variable
fragment [more info...]
Chain information for 7tzg #5
---
Chain | Description | UniProt
A B | scFvF7 |
C D | Lymphocyte activation gene 3 protein | LAG3_HUMAN 23-430
Non-standard residues in 7tzg #5
---
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> close #3
> rename #5 7tzg_LAG3_scfv
> rename #5 7tzg_DIMER_LAG3_scfv
> mmaker #5 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 LAG3_refmac5 (1).pdb, chain A (#1) with 7tzg_DIMER_LAG3_scfv, chain
C (#5), sequence alignment score = 800
RMSD between 86 pruned atom pairs is 0.880 angstroms; (across all 171 pairs:
5.358)
> save "/Users/asharma6/OneDrive -
> Moderna/BTX/LAG3/Structure/Analysis/PD1_VHH.cxs"
> hide #!5 models
> hide #!4 models
> show #!5 models
> hide #!1 models
> select #5/C:167
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #5 /C:1-167
597 atoms, 606 bonds, 1 pseudobond, 91 residues, 2 models selected
> ui tool show "Color Actions"
> color sel light sky blue
> select #5 /C-D:1-167
1269 atoms, 1287 bonds, 3 pseudobonds, 204 residues, 2 models selected
> color sel light sky blue
> select #5/C:261
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #5 /C-D:168-261
1385 atoms, 1434 bonds, 188 residues, 1 model selected
> color sel dodger blue
> select #5/C:351
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #5/C:350
16 atoms, 14 bonds, 2 residues, 1 model selected
> select add #5/C:352
23 atoms, 20 bonds, 3 residues, 1 model selected
> select add #5/C:353
30 atoms, 26 bonds, 4 residues, 1 model selected
> select add #5/C:354
37 atoms, 32 bonds, 5 residues, 1 model selected
> select #5/C:355
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/C:356
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5 /C-D:262-356
1388 atoms, 1421 bonds, 190 residues, 1 model selected
> color sel cyan
> color sel turquoise
> color sel royal blue
> color sel medium slate blue
> color sel slate blue
> select #5 /C-D:357-440
1113 atoms, 1146 bonds, 145 residues, 1 model selected
> color sel rebecca purple
> select #5 /C-D:262-356
1388 atoms, 1421 bonds, 190 residues, 1 model selected
> color sel medium purple
Drag select of 77 residues, 1 pseudobonds
> select up
964 atoms, 980 bonds, 1 pseudobond, 130 residues, 2 models selected
> select up
1734 atoms, 1773 bonds, 1 pseudobond, 234 residues, 2 models selected
> color sel goldenrod
Drag select of 86 residues, 1 pseudobonds
> select up
1129 atoms, 1151 bonds, 1 pseudobond, 154 residues, 2 models selected
> select up
1729 atoms, 1768 bonds, 1 pseudobond, 234 residues, 2 models selected
> color sel goldenrod
> select clear
Drag select of 86 residues, 1 pseudobonds
Drag select of 55 residues
> select up
2094 atoms, 2132 bonds, 1 pseudobond, 280 residues, 2 models selected
> select up
3463 atoms, 3541 bonds, 1 pseudobond, 468 residues, 2 models selected
> hide sel cartoons
> hide pseudobonds
> select ::name="NAG"
276 atoms, 277 bonds, 16 residues, 4 models selected
> style sel & #!5 ball
Changed 98 atom styles
> color sel light gray
> color sel byhetero
> select clear
> show #!2 models
> show #!4 models
> show #!1 models
> hide #!2 models
> hide #!4 models
> hide #!5 models
Drag select of 4 atoms, 65 residues, 3 bonds
> ui tool show Matchmaker
> matchmaker #!2,4-5 to #1 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker LAG3_refmac5 (1).pdb, chain A (#1) with
8so3_therapeutcAb_Favezelimab.cif, chain D (#2), sequence alignment score =
220.2
RMSD between 54 pruned atom pairs is 1.017 angstroms; (across all 62 pairs:
2.564)
Matchmaker LAG3_refmac5 (1).pdb, chain A (#1) with 9bf9_MHC_boundLAG3, chain D
(#4), sequence alignment score = 277.2
RMSD between 51 pruned atom pairs is 0.757 angstroms; (across all 62 pairs:
2.774)
Matchmaker LAG3_refmac5 (1).pdb, chain A (#1) with 7tzg_DIMER_LAG3_scfv, chain
D (#5), sequence alignment score = 284.1
RMSD between 61 pruned atom pairs is 0.850 angstroms; (across all 65 pairs:
2.448)
> show #!2 models
> show #!4 models
> show #!5 models
> hide #!5 models
> hide #!4 models
Drag select of 128 residues
> select up
2769 atoms, 2827 bonds, 280 residues, 2 models selected
> select down
1912 atoms, 3 bonds, 193 residues, 2 models selected
> select clear
Drag select of 158 residues
> ui tool show Matchmaker
> matchmaker #!4 & sel to #1 & sel
No molecules/chains to match specified
> show #!4 models
> hide #!2 models
> matchmaker #!2 & sel to #1 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker LAG3_refmac5 (1).pdb, chain A (#1) with
8so3_therapeutcAb_Favezelimab.cif, chain D (#2), sequence alignment score =
140
RMSD between 61 pruned atom pairs is 1.018 angstroms; (across all 65 pairs:
1.236)
> show #!2 models
> hide #!2 models
Drag select of 83 residues
> matchmaker #!4 & sel to #1 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker LAG3_refmac5 (1).pdb, chain A (#1) with 9bf9_MHC_boundLAG3, chain D
(#4), sequence alignment score = 130.7
RMSD between 34 pruned atom pairs is 0.517 angstroms; (across all 34 pairs:
0.517)
> show #!5 models
> hide #!4 models
> hide #!1 models
Drag select of 89 residues
> show #!2 models
> hide #!5 models
Drag select of 72 residues
> hide #!2 models
> show #!4 models
Drag select of 71 residues
> show #!5 models
> show #!2 models
> matchmaker #!4 & sel to #5 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7tzg_DIMER_LAG3_scfv, chain D (#5) with 9bf9_MHC_boundLAG3, chain D
(#4), sequence alignment score = 191
RMSD between 35 pruned atom pairs is 0.812 angstroms; (across all 51 pairs:
4.134)
> matchmaker #!2 & sel to #5 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7tzg_DIMER_LAG3_scfv, chain D (#5) with
8so3_therapeutcAb_Favezelimab.cif, chain D (#2), sequence alignment score =
168.5
RMSD between 38 pruned atom pairs is 1.000 angstroms; (across all 48 pairs:
4.186)
> hide #!2 models
> hide #!4 models
Drag select of 27 atoms, 79 residues, 24 bonds
> show #!1 models
> hide #!5 models
Drag select of 17 atoms, 76 residues, 14 bonds
> show #!5 models
> matchmaker #!1 & sel to #5 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7tzg_DIMER_LAG3_scfv, chain D (#5) with LAG3_refmac5 (1).pdb, chain
A (#1), sequence alignment score = 302.8
RMSD between 65 pruned atom pairs is 0.837 angstroms; (across all 68 pairs:
1.172)
> select clear
> hide #!1 models
Drag select of 146 residues
> select up
1295 atoms, 1313 bonds, 209 residues, 1 model selected
> select up
5253 atoms, 5399 bonds, 734 residues, 1 model selected
> show sel surfaces
> select #5 /C-D:262-356
1388 atoms, 1421 bonds, 190 residues, 1 model selected
> color sel medium purple
> select #5 /C-D:357-440
1113 atoms, 1146 bonds, 145 residues, 1 model selected
> color sel dark violet
> color sel dark slate blue
> select #5 /C-D:262-356
1388 atoms, 1421 bonds, 190 residues, 1 model selected
> select #5 /C-D:168-261
1385 atoms, 1434 bonds, 188 residues, 1 model selected
> select #5 /C-D:1-167
1269 atoms, 1287 bonds, 3 pseudobonds, 204 residues, 2 models selected
> color sel sky blue
> color sel light sky blue
> select clear
> save "/Users/asharma6/OneDrive -
> Moderna/BTX/LAG3/Structure/Analysis/PD1_VHH.cxs"
——— End of log from Tue Aug 12 16:35:49 2025 ———
> view name session-start
opened ChimeraX session
Drag select of 7tzg_DIMER_LAG3_scfv_C SES surface, 7tzg_DIMER_LAG3_scfv_D SES
surface, 168 atoms, 727 residues, 163 bonds
Drag select of 7tzg_DIMER_LAG3_scfv_C SES surface, 310699 of 375252 triangles,
41 atoms, 307 residues, 40 bonds
> select up
2456 atoms, 2522 bonds, 340 residues, 2 models selected
> select up
2607 atoms, 2681 bonds, 358 residues, 2 models selected
> transparency (#!5 & sel) 50
> show #!1 models
> hide #!5 models
Drag select of 17 atoms, 190 residues, 13 bonds
> select up
1494 atoms, 1528 bonds, 192 residues, 1 model selected
> select up
1515 atoms, 1551 bonds, 192 residues, 1 model selected
> select up
1558 atoms, 1601 bonds, 197 residues, 1 model selected
> select up
1581 atoms, 1626 bonds, 200 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
Drag select of 19 atoms, 122 residues, 16 bonds
> ui tool show "Color Actions"
> color sel crimson
> hide sel atoms
> select clear
> show #!5 models
> select add #1
2596 atoms, 2591 bonds, 6 pseudobonds, 394 residues, 2 models selected
> save "/Users/asharma6/OneDrive -
> Moderna/BTX/LAG3/Structure/Analysis/Figures/VHH_at_dimer_Interface.png"
> width 1025 height 1045 supersample 3 transparentBackground true
> hide #!5 models
> select clear
> show #!1 cartoons
> select #1 /A:1-167
832 atoms, 852 bonds, 5 pseudobonds, 106 residues, 2 models selected
> color sel sky blue
> select #1 /A:168-300
721 atoms, 745 bonds, 1 pseudobond, 92 residues, 2 models selected
> color sel royal blue
> color sel cornflower blue
> color sel dodger blue
> select clear
> select ::name="NAG"
276 atoms, 277 bonds, 16 residues, 4 models selected
> show sel & #!1 atoms
> style sel & #!1 ball
Changed 28 atom styles
> select clear
> save "/Users/asharma6/OneDrive -
> Moderna/BTX/LAG3/Structure/Analysis/Figures/VHH_at_dimer_Interface_justCrystal.png"
> width 1025 height 1045 supersample 3 transparentBackground true
> show #!5 models
> select #5/C:390@O
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> select up
68 atoms, 68 bonds, 9 residues, 2 models selected
> select up
2354 atoms, 2423 bonds, 315 residues, 2 models selected
> hide sel cartoons
> hide sel surfaces
> select up
2387 atoms, 2455 bonds, 321 residues, 2 models selected
> select up
2607 atoms, 2681 bonds, 358 residues, 2 models selected
> hide sel atoms
> hide sel cartoons
> hide sel surfaces
> hide #!5 models
Drag select of 160 residues
Drag select of 14 atoms, 2 residues, 16 bonds
> select up
33 atoms, 31 bonds, 4 residues, 1 model selected
> select up
43 atoms, 42 bonds, 4 residues, 1 model selected
> select up
459 atoms, 473 bonds, 57 residues, 1 model selected
> select up
1581 atoms, 1626 bonds, 200 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> show #!5 models
> save "/Users/asharma6/OneDrive -
> Moderna/BTX/LAG3/Structure/Analysis/Figures/VHH_at_dimer_Interface_2.png"
> width 1025 height 1045 supersample 3 transparentBackground true
> save "/Users/asharma6/OneDrive -
> Moderna/BTX/LAG3/Structure/Analysis/PD1_VHH.cxs"
——— End of log from Tue Aug 12 17:31:29 2025 ———
> view name session-start
opened ChimeraX session
> hide #!1 models
> show #!5 cartoons
> show #!5 atoms
> hide #!5 surfaces
Drag select of 428 atoms, 114 residues, 359 bonds
Drag select of 149 atoms, 40 residues, 128 bonds
> select up
1213 atoms, 1213 bonds, 169 residues, 1 model selected
> select up
1301 atoms, 1311 bonds, 169 residues, 1 model selected
> select up
2253 atoms, 2293 bonds, 300 residues, 1 model selected
> select up
3463 atoms, 3541 bonds, 468 residues, 1 model selected
> hide sel cartoons
[Repeated 2 time(s)]
> hide sel atoms
[Repeated 1 time(s)]
> select clear
> hide #!5 atoms
> show #!1 models
> open 7TZG
7tzg title:
Structure of human LAG3 in complex with antibody single-chain variable
fragment [more info...]
Chain information for 7tzg #3
---
Chain | Description | UniProt
A B | scFvF7 |
C D | Lymphocyte activation gene 3 protein | LAG3_HUMAN 23-430
Non-standard residues in 7tzg #3
---
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> ui tool show Matchmaker
> matchmaker #!3 to #5
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 7tzg_DIMER_LAG3_scfv, chain D (#5) with 7tzg, chain D (#3),
sequence alignment score = 2047.5
RMSD between 373 pruned atom pairs is 0.000 angstroms; (across all 373 pairs:
0.000)
Drag select of 183 residues, 1 pseudobonds
Drag select of 65 residues, 1 pseudobonds
> select up
2484 atoms, 2528 bonds, 2 pseudobonds, 329 residues, 2 models selected
> select up
3463 atoms, 3541 bonds, 2 pseudobonds, 468 residues, 2 models selected
> delete atoms (#!3 & sel)
> delete bonds (#!3 & sel)
> hide #!5 models
Drag select of 52 atoms, 266 residues, 1 pseudobonds, 49 bonds
> select up
1891 atoms, 1933 bonds, 1 pseudobond, 269 residues, 2 models selected
> select up
2497 atoms, 2562 bonds, 1 pseudobond, 357 residues, 2 models selected
> select up
2646 atoms, 2718 bonds, 1 pseudobond, 376 residues, 2 models selected
> select up
5253 atoms, 5399 bonds, 3 pseudobonds, 734 residues, 2 models selected
> select down
2646 atoms, 2718 bonds, 1 pseudobond, 376 residues, 2 models selected
> delete atoms (#!3 & sel)
> delete bonds (#!3 & sel)
> show #!5 models
> ui mousemode right "translate selected models"
> select add #3
2607 atoms, 2681 bonds, 1 pseudobond, 358 residues, 3 models selected
> view matrix models
> #3,-0.81356,-0.14361,-0.56346,38.856,-0.32403,0.91659,0.23425,-51.658,0.48283,0.37315,-0.79223,54.325
> select clear
> open "/Users/asharma6/Library/CloudStorage/OneDrive-
> Moderna/BTX/LAG3/Structure/LAG3_refmac5 (1).pdb"
LAG3_refmac5 (1).pdb title:
MOLREP --- /Vers 11.9.02; 28.02.2022/ [more info...]
Chain information for LAG3_refmac5 (1).pdb #6
---
Chain | Description
A | No description available
B | No description available
Non-standard residues in LAG3_refmac5 (1).pdb #6
---
NAG — (NAG)
Computing secondary structure
Drag select of 57 atoms, 178 residues, 1 pseudobonds, 57 bonds
Drag select of 53 atoms, 102 residues, 52 bonds
> matchmaker #!6 to #3 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7tzg, chain C (#3) with LAG3_refmac5 (1).pdb, chain A (#6),
sequence alignment score = 396.4
RMSD between 77 pruned atom pairs is 0.823 angstroms; (across all 86 pairs:
1.726)
> select add #3
2607 atoms, 2681 bonds, 1 pseudobond, 358 residues, 3 models selected
> view matrix models
> #3,-0.81356,-0.14361,-0.56346,32.089,-0.32403,0.91659,0.23425,-60.745,0.48283,0.37315,-0.79223,60.994
> matchmaker #!6 to #3 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7tzg, chain C (#3) with LAG3_refmac5 (1).pdb, chain A (#6),
sequence alignment score = 800
RMSD between 86 pruned atom pairs is 0.880 angstroms; (across all 171 pairs:
5.358)
> view matrix models
> #3,-0.81356,-0.14361,-0.56346,31.158,-0.32403,0.91659,0.23425,-68.688,0.48283,0.37315,-0.79223,35.099
> matchmaker #!6 to #3 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7tzg, chain C (#3) with LAG3_refmac5 (1).pdb, chain A (#6),
sequence alignment score = 800
RMSD between 86 pruned atom pairs is 0.880 angstroms; (across all 171 pairs:
5.358)
> view matrix models
> #3,-0.81356,-0.14361,-0.56346,28.267,-0.32403,0.91659,0.23425,-67.524,0.48283,0.37315,-0.79223,34.894
> view matrix models
> #3,-0.81356,-0.14361,-0.56346,26.29,-0.32403,0.91659,0.23425,-67.475,0.48283,0.37315,-0.79223,26.802
> matchmaker #!6 to #3 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7tzg, chain C (#3) with LAG3_refmac5 (1).pdb, chain A (#6),
sequence alignment score = 800
RMSD between 86 pruned atom pairs is 0.880 angstroms; (across all 171 pairs:
5.358)
> view matrix models
> #3,-0.81356,-0.14361,-0.56346,19.439,-0.32403,0.91659,0.23425,-65.259,0.48283,0.37315,-0.79223,23.329
> matchmaker #!6 to #3 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7tzg, chain C (#3) with LAG3_refmac5 (1).pdb, chain A (#6),
sequence alignment score = 800
RMSD between 86 pruned atom pairs is 0.880 angstroms; (across all 171 pairs:
5.358)
> view matrix models
> #3,-0.81356,-0.14361,-0.56346,17.235,-0.32403,0.91659,0.23425,-65.72,0.48283,0.37315,-0.79223,30.799
> matchmaker #!6 to #3 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7tzg, chain C (#3) with LAG3_refmac5 (1).pdb, chain A (#6),
sequence alignment score = 800
RMSD between 86 pruned atom pairs is 0.880 angstroms; (across all 171 pairs:
5.358)
> view matrix models
> #3,-0.81356,-0.14361,-0.56346,15.082,-0.32403,0.91659,0.23425,-68.01,0.48283,0.37315,-0.79223,34.062
> matchmaker #!6 to #3 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7tzg, chain C (#3) with LAG3_refmac5 (1).pdb, chain A (#6),
sequence alignment score = 800
RMSD between 86 pruned atom pairs is 0.880 angstroms; (across all 171 pairs:
5.358)
> view matrix models
> #3,-0.81356,-0.14361,-0.56346,17.187,-0.32403,0.91659,0.23425,-70.696,0.48283,0.37315,-0.79223,34.653
> matchmaker #!6 to #3 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7tzg, chain C (#3) with LAG3_refmac5 (1).pdb, chain A (#6),
sequence alignment score = 800
RMSD between 86 pruned atom pairs is 0.880 angstroms; (across all 171 pairs:
5.358)
> hide #!1 models
> hide #!3 models
Drag select of 153 residues, 6 pseudobonds
> select up
1395 atoms, 1432 bonds, 6 pseudobonds, 179 residues, 2 models selected
> select up
1553 atoms, 1598 bonds, 6 pseudobonds, 198 residues, 2 models selected
> select up
1581 atoms, 1626 bonds, 6 pseudobonds, 200 residues, 2 models selected
> delete atoms (#!6 & sel)
> delete bonds (#!6 & sel)
> show #!4 models
> hide #!4 models
> close #4
> close #2
> show #!3 models
> show #!1 models
> select #3 /C:168-300
972 atoms, 1006 bonds, 133 residues, 1 model selected
> save "/Users/asharma6/OneDrive -
> Moderna/BTX/LAG3/Structure/Analysis/Oligomerizationwith VHH.cxs"
> select #3 /A:168-300
Nothing selected
> select #3 /C:168-300
972 atoms, 1006 bonds, 133 residues, 1 model selected
> select #3 /C-D:262-356
693 atoms, 709 bonds, 95 residues, 1 model selected
> ui tool show "Color Actions"
> color sel medium purple
> select #3 /C: 357-700
627 atoms, 644 bonds, 78 residues, 1 model selected
> select #3 /C: 357-500
571 atoms, 588 bonds, 74 residues, 1 model selected
> color sel indigo
> color sel dark slate blue
> select #3/C:167
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #3 /C: 1-167
597 atoms, 606 bonds, 1 pseudobond, 91 residues, 2 models selected
> color sel sky blue
> select #3 /C: 168-261
690 atoms, 715 bonds, 94 residues, 1 model selected
> color sel cornflower blue
> color sel dodger blue
Drag select of 101 residues
> select up
860 atoms, 876 bonds, 111 residues, 1 model selected
> select up
943 atoms, 965 bonds, 122 residues, 1 model selected
> color sel crimson
> select clear
> hide #!1 models
> hide #!5 models
> show #!5 models
> hide #!6 models
> hide #!3 models
> show #!5 surfaces
> select clear
Drag select of 7tzg_DIMER_LAG3_scfv_A SES surface, 77453 of 188248 triangles
Drag select of 7tzg_DIMER_LAG3_scfv_A SES surface, 6723 of 188248 triangles
Drag select of 7tzg_DIMER_LAG3_scfv_C SES surface, 15217 of 375252 triangles,
7tzg_DIMER_LAG3_scfv_B SES surface, 26984 of 182632 triangles, 16 residues
> select #5/B:198@CA
1 atom, 1 residue, 1 model selected
> select add #5/A:197@O
2 atoms, 2 residues, 2 models selected
> select up
14 atoms, 13 bonds, 2 residues, 3 models selected
> select up
143 atoms, 144 bonds, 20 residues, 3 models selected
> select up
1659 atoms, 1701 bonds, 223 residues, 3 models selected
> select up
1687 atoms, 1727 bonds, 228 residues, 3 models selected
> select up
3463 atoms, 3541 bonds, 468 residues, 3 models selected
> hide sel surfaces
> delete atoms (#!5 & sel)
> delete bonds (#!5 & sel)
> transparency #5 0
> show #!3 models
Drag select of 76 atoms, 354 residues, 1 pseudobonds, 76 bonds
> show sel surfaces
> select #3 /C: 1-167
597 atoms, 606 bonds, 1 pseudobond, 91 residues, 2 models selected
> color sel sky blue
> select #3 /C: 357-500
571 atoms, 588 bonds, 74 residues, 1 model selected
> color sel rebecca purple
> color sel dark slate blue
> select #3 /C-D:262-356
693 atoms, 709 bonds, 95 residues, 1 model selected
> color sel medium purple
> select clear
> hide psedobond
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide pseudobonds
> ui tool show "Side View"
> show #!6 models
> show #!1 models
Drag select of 7tzg_DIMER_LAG3_scfv_C SES surface, 75459 of 375252 triangles,
97 residues
> select up
936 atoms, 953 bonds, 125 residues, 2 models selected
> select up
2354 atoms, 2423 bonds, 315 residues, 2 models selected
> select up
2387 atoms, 2455 bonds, 321 residues, 2 models selected
> select up
2607 atoms, 2681 bonds, 358 residues, 2 models selected
> hide sel cartoons
> hide sel atoms
> hide sel surfaces
> select #1/B:124
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #6/B:124
12 atoms, 10 bonds, 2 residues, 2 models selected
> style sel stick
Changed 12 atom styles
> show sel atoms
> style sel sphere
Changed 12 atom styles
> select clear
> save "/Users/asharma6/OneDrive -
> Moderna/BTX/LAG3/Structure/Analysis/Oligomerizationwith VHH.cxs"
——— End of log from Wed Aug 13 17:38:39 2025 ———
> view name session-start
opened ChimeraX session
> open 1IGY
Summary of feedback from opening 1IGY fetched from pdb
---
notes | Fetching compressed mmCIF 1igy from http://files.rcsb.org/download/1igy.cif
Fetching CCD FUL from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/L/FUL/FUL.cif
1igy title:
Structure of immunoglobulin [more info...]
Chain information for 1igy #2
---
Chain | Description
A C | IGG1 INTACT ANTIBODY MAB61.1.3
B D | IGG1 INTACT ANTIBODY MAB61.1.3
Non-standard residues in 1igy #2
---
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)
FUC — alpha-L-fucopyranose (alpha-L-fucose; 6-deoxy-alpha-L-galactopyranose;
L-fucose; fucose)
FUL — beta-L-fucopyranose (beta-L-fucose; 6-deoxy-beta-L-galactopyranose;
L-fucose; fucose; 6-DEOXY-BETA-L-GALACTOSE)
GAL — beta-D-galactopyranose (beta-D-galactose; D-galactose; galactose)
MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose)
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
NDG — 2-acetamido-2-deoxy-alpha-D-glucopyranose (N-acetyl-alpha-D-glucosamine;
2-acetamido-2-deoxy-alpha-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE)
> select add #2
12750 atoms, 13044 bonds, 1312 residues, 1 model selected
Drag select of 23 residues
> select up
451 atoms, 453 bonds, 48 residues, 1 model selected
> select up
2043 atoms, 2082 bonds, 213 residues, 1 model selected
> select up
12750 atoms, 13044 bonds, 1312 residues, 1 model selected
> select down
2043 atoms, 2082 bonds, 213 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #2/A:184
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
56 atoms, 56 bonds, 5 residues, 1 model selected
> select up
2043 atoms, 2082 bonds, 213 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #2/D:228
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #2/D:227
7 atoms, 7 bonds, 1 residue, 1 model selected
> open 1HZH
Summary of feedback from opening 1HZH fetched from pdb
---
note | Fetching compressed mmCIF 1hzh from http://files.rcsb.org/download/1hzh.cif
1hzh title:
Crystal structure of the intact human igg B12 with broad and potent activity
against primary hiv-1 isolates: A template for hiv vaccine design [more
info...]
Chain information for 1hzh #4
---
Chain | Description | UniProt
H K | IMMUNOGLOBULIN HEAVY CHAIN | IGG1_HUMAN 111-478
L M | IMMUNOGLOBULIN LIGHT CHAIN,Uncharacterized protein | Q8TCD0_HUMAN 107-214
Non-standard residues in 1hzh #4
---
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)
FUC — alpha-L-fucopyranose (alpha-L-fucose; 6-deoxy-alpha-L-galactopyranose;
L-fucose; fucose)
GAL — beta-D-galactopyranose (beta-D-galactose; D-galactose; galactose)
MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose)
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> select add #2
8664 atoms, 8878 bonds, 886 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.41195,-0.84303,-0.34584,31.247,0.63275,0.0084531,-0.77431,25.036,0.65569,-0.5378,0.52994,11.983
> ui mousemode right translate
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.41195,-0.84303,-0.34584,11.755,0.63275,0.0084531,-0.77431,20.56,0.65569,-0.5378,0.52994,15.122
> view matrix models
> #2,-0.41195,-0.84303,-0.34584,4.747,0.63275,0.0084531,-0.77431,18.263,0.65569,-0.5378,0.52994,17.38
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.31655,-0.70862,0.6306,-38.894,-0.19246,0.69894,0.6888,-34.859,-0.92885,0.096676,-0.35763,76.034
> view matrix models
> #2,-0.31533,-0.67633,0.66569,-40.405,-0.18839,0.73213,0.65459,-33.377,-0.9301,0.081,-0.35827,76.06
> view matrix models
> #2,-0.3131,-0.62451,0.71551,-42.549,-0.1824,0.77891,0.60003,-31.014,-0.93204,0.05736,-0.35779,76.035
> ui tool show Matchmaker
> matchmaker #!4 to #2
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 1igy, chain D (#2) with 1hzh, chain H (#4), sequence alignment
score = 1318
RMSD between 75 pruned atom pairs is 0.845 angstroms; (across all 432 pairs:
48.017)
> close #2
> select #4/L:209
11 atoms, 11 bonds, 1 residue, 1 model selected
> select up
48 atoms, 48 bonds, 6 residues, 1 model selected
> select up
1668 atoms, 1706 bonds, 215 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #4/K:197
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
33 atoms, 33 bonds, 5 residues, 1 model selected
> select up
620 atoms, 635 bonds, 84 residues, 1 model selected
> select up
749 atoms, 770 bonds, 103 residues, 1 model selected
> select #4/M:138
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
74 atoms, 74 bonds, 10 residues, 1 model selected
> select up
1668 atoms, 1706 bonds, 215 residues, 1 model selected
> select up
1680 atoms, 1706 bonds, 227 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select add #4
7299 atoms, 7463 bonds, 2 pseudobonds, 978 residues, 3 models selected
> view matrix models
> #4,0.4169,-0.90091,-0.12062,87.973,-0.030258,0.11887,-0.99245,127.72,0.90845,0.4174,0.022298,-52.229
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.4169,-0.90091,-0.12062,84.795,-0.030258,0.11887,-0.99245,113.25,0.90845,0.4174,0.022298,-48.455
> view matrix models
> #4,0.4169,-0.90091,-0.12062,92.078,-0.030258,0.11887,-0.99245,92.462,0.90845,0.4174,0.022298,-81.925
> ui mousemode right translate
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.4169,-0.90091,-0.12062,80.983,-0.030258,0.11887,-0.99245,108.46,0.90845,0.4174,0.022298,-86.293
> view matrix models
> #4,0.4169,-0.90091,-0.12062,81.747,-0.030258,0.11887,-0.99245,110.48,0.90845,0.4174,0.022298,-87.566
> select clear
> ui tool show "Side View"
> save "/Users/asharma6/OneDrive - Moderna/OneDrive -
> Moderna/BTX/CIRA_T/LAG3/Structure/Analysis/Oligomerizationwith VHH_Fc.cxs"
——— End of log from Thu Oct 2 18:38:13 2025 ———
> view name session-start
opened ChimeraX session
> select #4/K:230
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> select #4/H:232
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #4/H:235
17 atoms, 15 bonds, 2 residues, 1 model selected
> select add #4/H:236
24 atoms, 21 bonds, 3 residues, 1 model selected
> select #4/H:230
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel sphere
Changed 6 atom styles
> select clear
[Repeated 1 time(s)]
> select #4/K:230@CA
1 atom, 1 residue, 1 model selected
> style sel sphere
Changed 1 atom style
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!4 models
> show #!4 models
> hide #!5 models
> show #!5 models
> hide #!6 models
> show #!6 models
> select add #6
1016 atoms, 965 bonds, 195 residues, 2 models selected
> select add #4
8314 atoms, 8428 bonds, 2 pseudobonds, 1172 residues, 4 models selected
> select subtract #4
1015 atoms, 965 bonds, 194 residues, 1 model selected
> select add #3
3622 atoms, 3646 bonds, 1 pseudobond, 552 residues, 4 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.81356,-0.14361,-0.56346,12.726,-0.32403,0.91659,0.23425,-73.138,0.48283,0.37315,-0.79223,37.987,#6,0.12471,-0.98947,-0.073429,-27.604,-0.96461,-0.13824,0.22453,-39.537,-0.23232,0.042828,-0.9717,56.973
> view matrix models
> #3,-0.81356,-0.14361,-0.56346,10.074,-0.32403,0.91659,0.23425,-72.3,0.48283,0.37315,-0.79223,37.38,#6,0.12471,-0.98947,-0.073429,-30.256,-0.96461,-0.13824,0.22453,-38.698,-0.23232,0.042828,-0.9717,56.365
> select #4/H: 1-230
1753 atoms, 1803 bonds, 230 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> delete atoms sel
> delete bonds sel
> select add #1
2596 atoms, 2591 bonds, 6 pseudobonds, 394 residues, 2 models selected
> select add #5
7849 atoms, 7990 bonds, 9 pseudobonds, 1128 residues, 5 models selected
> view matrix models
> #1,0.99997,-7.5661e-05,0.0081444,2.5324,4.1244e-05,0.99999,0.0042259,-2.4671,-0.0081446,-0.0042255,0.99996,3.0815,#5,-0.81356,-0.14361,-0.56346,69.125,-0.32403,0.91659,0.23425,-13.923,0.48283,0.37315,-0.79223,23.859
> view matrix models
> #1,0.99997,-7.5661e-05,0.0081444,1.7146,4.1244e-05,0.99999,0.0042259,4.6161,-0.0081446,-0.0042255,0.99996,8.5408,#5,-0.81356,-0.14361,-0.56346,68.307,-0.32403,0.91659,0.23425,-6.8393,0.48283,0.37315,-0.79223,29.319
> ui tool show "Side View"
> select clear
> select #4/K: 1-230
1711 atoms, 1760 bonds, 1 pseudobond, 223 residues, 2 models selected
> delete atoms (#!4 & sel)
> delete bonds (#!4 & sel)
Drag select of 60 residues
> select up
580 atoms, 585 bonds, 78 residues, 1 model selected
> select up
943 atoms, 965 bonds, 122 residues, 1 model selected
> select up
1015 atoms, 965 bonds, 194 residues, 1 model selected
> select clear
[Repeated 1 time(s)]
> select #4/H:236
7 atoms, 6 bonds, 1 residue, 1 model selected
Drag select of 57 residues
> select up
704 atoms, 715 bonds, 90 residues, 1 model selected
> select up
943 atoms, 965 bonds, 122 residues, 1 model selected
> ui tool show "Change Chain IDs"
> changechains sel H
Chain IDs of 122 residues changed
Drag select of 20 residues
> select up
278 atoms, 278 bonds, 40 residues, 1 model selected
> select up
943 atoms, 965 bonds, 122 residues, 1 model selected
> changechains sel K
Chain IDs of 122 residues changed
> changechains sel K
Chain IDs of 0 residues changed
Drag select of 291 atoms, 286 residues, 1 pseudobonds, 286 bonds
> select up
3133 atoms, 2748 bonds, 1 pseudobond, 400 residues, 4 models selected
> select up
3173 atoms, 3246 bonds, 1 pseudobond, 400 residues, 4 models selected
> select up
3922 atoms, 4018 bonds, 1 pseudobond, 496 residues, 4 models selected
> select up
5664 atoms, 5828 bonds, 1 pseudobond, 712 residues, 4 models selected
> select up
5715 atoms, 5828 bonds, 1 pseudobond, 763 residues, 4 models selected
> select up
7446 atoms, 7454 bonds, 1 pseudobond, 1113 residues, 4 models selected
> save "/Users/asharma6/OneDrive -
> Moderna/BTX/CIRA_T/LAG3/Structure/Analysis/VHH_Fc.pdb" selectedOnly true
> save "/Users/asharma6/OneDrive -
> Moderna/BTX/CIRA_T/LAG3/Structure/Analysis/LAG3_VHH_Fc.cxs"
——— End of log from Sun Oct 5 04:44:23 2025 ———
> view name session-start
opened ChimeraX session
> hide #!3 models
> show #!3 models
> hide #!4 models
> show #!4 models
> open /Users/asharma6/Library/CloudStorage/OneDrive-
> Moderna/BTX/CIRA_T/LAG3/Structure/Analysis/VHH_Fc.pdb
Chain information for VHH_Fc.pdb #2
---
Chain | Description
H | No description available
K | No description available
> hide #!5 models
> show #!5 models
> hide #!4 models
> close #4
> hide #!5 models
> show #!5 models
> hide #!6 models
> show #!6 models
> close #6
> hide #!1 models
> show #!1 models
> close #1
> select #2/H:93
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
59 atoms, 60 bonds, 8 residues, 1 model selected
> select up
2743 atoms, 2819 bonds, 349 residues, 1 model selected
> select up
5662 atoms, 5828 bonds, 710 residues, 1 model selected
> select down
2743 atoms, 2819 bonds, 349 residues, 1 model selected
> ui tool show "Color Actions"
> color sel crimson
> select #2/K:90
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
24 atoms, 24 bonds, 3 residues, 1 model selected
> select up
960 atoms, 982 bonds, 124 residues, 1 model selected
> select up
1045 atoms, 1071 bonds, 137 residues, 1 model selected
> select up
2698 atoms, 2772 bonds, 343 residues, 1 model selected
> color sel brown
> select clear
Drag select of 6 atoms, 33 residues, 5 bonds
> select #2/K:132
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #2/H:135
12 atoms, 10 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel sphere
Changed 12 atom styles
> color sel byhetero
> select #2/K:135
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #2/H:132
12 atoms, 10 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel sphere
Changed 12 atom styles
> color sel byhetero
> select #2/K:135@CB
1 atom, 1 residue, 1 model selected
> select add #2/H:135@CA
2 atoms, 2 residues, 1 model selected
> select up
12 atoms, 10 bonds, 2 residues, 1 model selected
> hide sel atoms
Drag select of 30 atoms, 35 bonds
> select up
49 atoms, 45 bonds, 7 residues, 1 model selected
> select up
73 atoms, 74 bonds, 7 residues, 1 model selected
> select up
341 atoms, 352 bonds, 46 residues, 1 model selected
Drag select of 26 atoms, 32 bonds
> select up
33 atoms, 33 bonds, 4 residues, 1 model selected
> select up
50 atoms, 52 bonds, 4 residues, 1 model selected
> select up
221 atoms, 237 bonds, 18 residues, 1 model selected
> color sel dim gray
> style sel sphere
Changed 221 atom styles
> color sel light gray
> color sel byhetero
> select clear
> save "/Users/asharma6/OneDrive -
> Moderna/BTX/CIRA_T/LAG3/Structure/Analysis/Lag3_VHH_Fc_2.cxs"
> select #2/H:102
10 atoms, 10 bonds, 1 residue, 1 model selected
> select add #2/K:33
22 atoms, 22 bonds, 2 residues, 1 model selected
> show sel atoms
> ui tool show Distances
> select #2/K:33@CB
1 atom, 1 residue, 1 model selected
> select add #2/H:102@ND1
2 atoms, 2 residues, 1 model selected
> distance #2/K:33@CB #2/H:102@ND1
Distance between VHH_Fc.pdb #2/K TYR 33 CB and /H HIS 102 ND1: 96.767Å
> select clear
> select ::name="NAG"
266 atoms, 268 bonds, 19 residues, 3 models selected
> style sel sphere
Changed 266 atom styles
> color sel light gray
> color sel byhetero
> select clear
> distance style decimalPlaces 2
[Repeated 2 time(s)]
> distance style decimalPlaces 1
[Repeated 2 time(s)]
> distance style decimalPlaces 0
[Repeated 2 time(s)]
> distance style radius 0.4
[Repeated 2 time(s)]
> distance style color #faed45
[Repeated 2 time(s)]
> distance style color #faed44
[Repeated 2 time(s)]
> distance style color #faee44
[Repeated 2 time(s)]
> distance style color #faef45
[Repeated 2 time(s)]
> distance style color #faf84b
[Repeated 2 time(s)]
> distance style color #c3fa4b
[Repeated 2 time(s)]
> distance style color #b6fa46
[Repeated 2 time(s)]
> distance style color #a8fa41
[Repeated 2 time(s)]
> distance style color #a1fa3e
[Repeated 2 time(s)]
> distance style color #93fa3a
[Repeated 2 time(s)]
> distance style color #86fa35
[Repeated 2 time(s)]
> distance style color #4afa22
[Repeated 2 time(s)]
> distance style color #44fa20
[Repeated 2 time(s)]
> distance style color #41fa1f
[Repeated 2 time(s)]
> distance style color #3dfa1d
[Repeated 2 time(s)]
> distance style color #39fa1c
[Repeated 2 time(s)]
> distance style color #37fa1b
[Repeated 2 time(s)]
> distance style color #1ffa13
[Repeated 2 time(s)]
> distance style color #19fa11
[Repeated 2 time(s)]
> distance style color #16fa10
[Repeated 2 time(s)]
> distance style color #13fa0f
[Repeated 2 time(s)]
> distance style color #06fa1c
[Repeated 2 time(s)]
> distance style color #05fa1d
[Repeated 2 time(s)]
> distance style color #04fa1e
[Repeated 2 time(s)]
> distance style color #03fa20
[Repeated 2 time(s)]
> distance style color #00fa28
[Repeated 2 time(s)]
> distance style color #00fa25
[Repeated 2 time(s)]
> distance style color #00fa2f
[Repeated 2 time(s)]
> distance style color #00fa32
[Repeated 2 time(s)]
> distance style color #00fa34
[Repeated 2 time(s)]
> distance style color #01fa36
[Repeated 2 time(s)]
> distance style color #00fa34
[Repeated 2 time(s)]
> distance style dashes 10
[Repeated 2 time(s)]
> distance style dashes 11
[Repeated 2 time(s)]
> distance style dashes 12
[Repeated 2 time(s)]
> distance style dashes 13
[Repeated 2 time(s)]
> distance style dashes 14
[Repeated 2 time(s)]
> distance style dashes 15
[Repeated 2 time(s)]
> distance style dashes 16
[Repeated 2 time(s)]
> distance style radius 0.5
[Repeated 2 time(s)]
> save "/Users/asharma6/OneDrive -
> Moderna/BTX/CIRA_T/LAG3/Structure/Analysis/Lag3_VHH_Fc_2.cxs"
> ui tool show "Basic Actions"
> ui tool show Distances
Exactly two atoms must be selected!
> ui mousemode right "move label"
[Repeated 3 time(s)]
> ui mousemode right distance
[Repeated 1 time(s)]
> ui mousemode right label
> ui mousemode right "move label"
> ui mousemode right "tape measure"
[Repeated 1 time(s)]
> setattr pb label_height 28
Unknown attribute target: 'pb'
> setattr pb label_height 28
Unknown attribute target: 'pb'
> help help:user/tools/distances.html
> ui mousemode right "tape measure"
> ui mousemode right translate
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/asharma6/Desktop/movie4.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: 11881.121.1
Software:
System Software Overview:
System Version: macOS 15.5 (24F74)
Kernel Version: Darwin 24.5.0
Time since boot: 10 days, 12 hours, 33 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-Clipper: 0.25.2
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-ISOLDE: 1.10.1
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 weeks ago
| Cc: | added |
|---|---|
| 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 weeks ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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Hi Arvind,
--Eric