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Opened 4 weeks ago
Closed 4 weeks ago
#19306 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-15.6.1-arm64-arm-64bit
ChimeraX Version: 1.10 (2025-06-26 08:57:52 UTC)
Description
trying to record a spin movie
Log:
UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
> open /Users/sphulera/Library/CloudStorage/OneDrive-
> TheScrippsResearchInstitute/EM/Clinical_trial_samples/C101/VRC01_class_analysis/N276_displacement_C101_C107_VRC01class_SPcopy.cxs
Log from Thu Nov 6 11:40:33 2025UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
> open /Users/sphulera/Library/CloudStorage/OneDrive-
> TheScrippsResearchInstitute/EM/Clinical_trial_samples/C101/VRC01_class_analysis/N276_displacement_C101_C107_VRC01class.cxs
Log from Wed Nov 5 13:21:24 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/gozorows/OneDrive - The Scripps Research
> Institute/TSRI/EM/Clinical_trial_samples/C101/VRC01_class_analysis/N276_displacement_C101_C107_VRC01class.cxs"
> format session
Log from Wed Nov 5 09:39:56 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/gozorows/Scripps Research Dropbox/Ward
> Lab/Manuscripts/Gabe/PUBLISHED/2024_C101trial/figures/N276_displacement_figure.cxs"
Log from Mon Feb 24 15:16:39 2025UCSF ChimeraX version: 1.9rc202412032254
(2024-12-03)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/gozorows/Scripps Research Dropbox/Ward
> Lab/Manuscripts/Gabe/2024_C101trial/figures/N276_displacement_figure.cxs"
Log from Tue Jan 7 12:51:49 2025UCSF ChimeraX version: 1.9rc202412032254
(2024-12-03)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/gozorows/Scripps Research Dropbox/Ward
> Lab/Manuscripts/Gabe/2024_C101trial/figures/N276_displacement_figure.cxs"
Log from Fri Dec 13 00:29:23 2024UCSF ChimeraX version: 1.9rc202412032254
(2024-12-03)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/gozorows/Scripps Research Dropbox/Ward
> Lab/Manuscripts/Gabe/2024_C101trial/figures/CDRL1_N276.cxs"
Log from Tue Oct 1 23:07:50 2024UCSF ChimeraX version: 1.8rc202405202242
(2024-05-20)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/gozorows/Scripps Research Dropbox/Gabriel
> Ozorowski/EMCC/Clinical_Trials/IAVI_C101/May_CCVIMC_SAB_presentation/colored_maps.cxs"
Opened 206-3G08_GT1.mrc as #7, grid size 400,400,400, pixel 1.03, shown at
level 0.276, step 1, values float32
Opened 206-9C09_GT1.mrc as #8, grid size 400,400,400, pixel 1.03, shown at
level 0.289, step 1, values float32
Opened 253_7A03_BG505_P455_J152_007_volume_map_sharp_C1_3.3.mrc as #9, grid
size 400,400,400, pixel 1.03, shown at level 0.18, step 1, values float32
Opened 273-4D01_BG505_RM20A3_P455_J315_C1_3.9.mrc as #10, grid size
400,400,400, pixel 1.03, shown at level 0.155, step 1, values float32
Opened 61-12A01_GT1.mrc as #11, grid size 400,400,400, pixel 1.03, shown at
level 0.237, step 1, values float32
Log from Fri May 3 15:29:01 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/gozorows/Dropbox (Scripps
> Research)/EMCC/Clinical_Trials/IAVI_C101/May_CCVIMC_SAB_presentation/C101_mAbs_cryoEM_compare_May2024.cxs"
Log from Fri May 3 10:57:15 2024 Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle
> graphics silhouettes true
> lighting soft
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/gozorows/Dropbox (Scripps
> Research)/TSRI/EM/C101/206-3G08_GT1-1_RM20A3/C101_3G08_GT11_SOSIP_RM20A3_real_space_refined_037.pdb"
Chain information for C101_3G08_GT11_SOSIP_RM20A3_real_space_refined_037.pdb
#1
---
Chain | Description
A C E | No description available
B D F | No description available
G J O | No description available
H K P | No description available
I M Q | No description available
L N R | No description available
> hide atoms
> show cartoons
> open 6v8x
6v8x title:
VRC01 Bound BG505 F14 HIV-1 SOSIP Envelope Trimer Structure [more info...]
Chain information for 6v8x #2
---
Chain | Description | UniProt
A E I | Envelope glycoprotein gp120 | Q2N0S6_9HIV1 33-505
B F J | Envelope glycoprotein gp41 | Q2N0S9_9HIV1 520-664
C G K | VRC01 Fab Heavy Chain | Q6N095_HUMAN 115-216
D H L | VRC01 Fab Light Chain | Q6PIL8_HUMAN 107-216
Non-standard residues in 6v8x #2
---
BMA — beta-D-mannopyranose
MAN — alpha-D-mannopyranose
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose
> hide atoms
> show cartoons
> mmaker #2/A to #1/A
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 C101_3G08_GT11_SOSIP_RM20A3_real_space_refined_037.pdb, chain A
(#1) with 6v8x, chain A (#2), sequence alignment score = 2060.5
RMSD between 408 pruned atom pairs is 1.080 angstroms; (across all 437 pairs:
1.791)
> select #1/A
3728 atoms, 3830 bonds, 2 pseudobonds, 460 residues, 2 models selected
> select #2/A:276
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel cartoons
> show sel atoms
> style sel stick
Changed 8 atom styles
> select #2/A:MAN:NAG:BMA
56 atoms, 56 bonds, 4 residues, 1 model selected
> show sel atoms
> hide sel atoms
> select #2/MAN:NAG:BMA
Nothing selected
> select #2:MAN:NAG:BMA
1416 atoms, 1470 bonds, 105 residues, 1 model selected
> show sel atoms
> hide sel atoms
> select #2/Q:1
14 atoms, 14 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/Q
39 atoms, 41 bonds, 3 residues, 1 model selected
> show sel atoms
> select clear
> open
> /Users/gozorows/coot_sessions/C101_coot/61-12A01_GT1-1_RM20A3/C101_12A01_Gt11_SOSIP_12A01-coot-0.pdb
Summary of feedback from opening
/Users/gozorows/coot_sessions/C101_coot/61-12A01_GT1-1_RM20A3/C101_12A01_Gt11_SOSIP_12A01-coot-0.pdb
---
warnings | Start residue of secondary structure not found: HELIX 7 7 PRO L 96 ASP L 98 1 3
Start residue of secondary structure not found: SHEET 29 2929 THR H 122 VAL H
126 0
Start residue of secondary structure not found: SHEET 33 3333 ALA L 40 GLN L
44 0
Start residue of secondary structure not found: SHEET 34 3434 ARG L 51 ILE L
54 0
Start residue of secondary structure not found: SHEET 35 3535 PHE L 76 SER L
83 0
3 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (104 )
Chain information for C101_12A01_Gt11_SOSIP_12A01-coot-0.pdb #3
---
Chain | Description
A C E | No description available
B D F | No description available
G J O | No description available
H K P | No description available
I M Q | No description available
L N R | No description available
> mmaker #3/A to #1/A
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 C101_3G08_GT11_SOSIP_RM20A3_real_space_refined_037.pdb, chain A
(#1) with C101_12A01_Gt11_SOSIP_12A01-coot-0.pdb, chain A (#3), sequence
alignment score = 2326
RMSD between 443 pruned atom pairs is 0.280 angstroms; (across all 443 pairs:
0.280)
> hide atoms
> hide #!2 models
> open
> /Users/gozorows/coot_sessions/C101_coot/253-7A03_BG505_RM20A3/253-7A03_BG505_RM20A3-coot-14.pdb
Summary of feedback from opening
/Users/gozorows/coot_sessions/C101_coot/253-7A03_BG505_RM20A3/253-7A03_BG505_RM20A3-coot-14.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK ANTIBODY STRUCTURE MODELLED USING ABODYBUILDER2
Ignored bad PDB record found on line 2
REMARK STRUCTURE REFINED USING OPENMM 8.0, 2024-04-23
Start residue of secondary structure not found: HELIX 15 15 THR I 28 PHE I 32
1 5
Start residue of secondary structure not found: HELIX 16 16 ASP I 61 LYS I 64
1 4
Start residue of secondary structure not found: HELIX 17 17 ARG I 83 THR I 87
1 5
Start residue of secondary structure not found: HELIX 18 18 GLN M 79 GLU M 83
1 5
Start residue of secondary structure not found: HELIX 19 19 ASN J 98 SER J 115
1 18
157 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (22 )
Cannot find LINK/SSBOND residue CYS (23 )
Cannot find LINK/SSBOND residue CYS (119 )
Cannot find LINK/SSBOND residue CYS (126 )
Cannot find LINK/SSBOND residue CYS (131 )
21 messages similar to the above omitted
Chain information for 253-7A03_BG505_RM20A3-coot-14.pdb #4
---
Chain | Description
A C E | No description available
B D F | No description available
G J M | No description available
H | No description available
I K N | No description available
L | No description available
> mmaker #4/A to #1/A
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 C101_3G08_GT11_SOSIP_RM20A3_real_space_refined_037.pdb, chain A
(#1) with 253-7A03_BG505_RM20A3-coot-14.pdb, chain A (#4), sequence alignment
score = 1785.2
RMSD between 432 pruned atom pairs is 0.525 angstroms; (across all 436 pairs:
0.603)
> hide #!1,3-4 atoms
> show #!1,3-4 cartoons
> hide #!3 models
> hide #!1 models
> select #4/A:276
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> select #4/A:276,629
22 atoms, 21 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 22 atom styles
> show #!2 models
> select #2/Q
39 atoms, 41 bonds, 3 residues, 1 model selected
> show sel atoms
> hide #!4 models
> show #!4 models
> hide #!4 models
> hide #!2 models
> show #!2 models
> save "/Users/gozorows/Dropbox (Scripps
> Research)/EMCC/Clinical_Trials/IAVI_C101/May_CCVIMC_SAB_presentation/C101_mAbs_cryoEM_compare_May2024.cxs"
——— End of log from Fri May 3 10:57:15 2024 ———
opened ChimeraX session
> open
> /Users/gozorows/coot_sessions/C101_coot/206-9C09_GT1-1_RM20A3/C101_9C09_GT11SOSIP_RM20A3_real_space_refined_007-coot-0.pdb
Chain information for
C101_9C09_GT11SOSIP_RM20A3_real_space_refined_007-coot-0.pdb #5
---
Chain | Description
A C E | No description available
B D F | No description available
G J O | No description available
H K P | No description available
I M Q | No description available
L N R | No description available
> open
> /Users/gozorows/coot_sessions/C101_coot/253-7A03_BG505_RM20A3/253-7A03_BG505_RM20A3_J152_real_space_refined_031-coot-0.pdb
Chain information for
253-7A03_BG505_RM20A3_J152_real_space_refined_031-coot-0.pdb #6
---
Chain | Description
A | No description available
B F | No description available
C | No description available
D | No description available
E | No description available
G J M | No description available
H | No description available
I K N | No description available
L | No description available
> close #4
> open
> /Users/gozorows/coot_sessions/C101_coot/273-4D01_BG505_RM20A3/273-4D01_BG505_RM20A3_J315_real_space_refined_032-coot-0.pdb
Chain information for
273-4D01_BG505_RM20A3_J315_real_space_refined_032-coot-0.pdb #4
---
Chain | Description
A | No description available
B F | No description available
C | No description available
D | No description available
E | No description available
G J M | No description available
H | No description available
I K N | No description available
L | No description available
> close #3
> open
> /Users/gozorows/coot_sessions/C101_coot/61-12A01_GT1-1_RM20A3/C101_12A01_GT11SISIP_RM20A3_real_space_refined_003-coot-1.pdb
Chain information for
C101_12A01_GT11SISIP_RM20A3_real_space_refined_003-coot-1.pdb #3
---
Chain | Description
A C E | No description available
B D F | No description available
G J O | No description available
H K P | No description available
I M Q | No description available
L N R | No description available
> show #!1 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> show #!2 models
> hide #!2 models
> show #!3 models
> select #3
24807 atoms, 25449 bonds, 9 pseudobonds, 3135 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> mmaker #3/A on #1/A
> matchmaker #3/A on #1/A
Expected a keyword
> mmaker #3/A to #1/A
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 C101_3G08_GT11_SOSIP_RM20A3_real_space_refined_037.pdb, chain A
(#1) with C101_12A01_GT11SISIP_RM20A3_real_space_refined_003-coot-1.pdb, chain
A (#3), sequence alignment score = 2311.6
RMSD between 439 pruned atom pairs is 0.302 angstroms; (across all 443 pairs:
0.393)
> hide #!3 models
> show #!4 models
> select #4
21020 atoms, 21545 bonds, 14 pseudobonds, 2652 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> mmaker #4/A to #1/A
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 C101_3G08_GT11_SOSIP_RM20A3_real_space_refined_037.pdb, chain A
(#1) with 273-4D01_BG505_RM20A3_J315_real_space_refined_032-coot-0.pdb, chain
A (#4), sequence alignment score = 2060.8
RMSD between 430 pruned atom pairs is 0.569 angstroms; (across all 437 pairs:
0.797)
> hide #!4 models
> show #!5 models
> select #5
24822 atoms, 25455 bonds, 9 pseudobonds, 3135 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> mmaker #5/A to #1/A
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 C101_3G08_GT11_SOSIP_RM20A3_real_space_refined_037.pdb, chain A
(#1) with C101_9C09_GT11SOSIP_RM20A3_real_space_refined_007-coot-0.pdb, chain
A (#5), sequence alignment score = 2305.6
RMSD between 439 pruned atom pairs is 0.255 angstroms; (across all 443 pairs:
0.428)
> hide #!5 models
> show #!6 models
> select #6
20990 atoms, 21509 bonds, 14 pseudobonds, 2648 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> mmaker #6/A to #1/A
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 C101_3G08_GT11_SOSIP_RM20A3_real_space_refined_037.pdb, chain A
(#1) with 253-7A03_BG505_RM20A3_J152_real_space_refined_031-coot-0.pdb, chain
A (#6), sequence alignment score = 1918.7
RMSD between 431 pruned atom pairs is 0.488 angstroms; (across all 436 pairs:
0.733)
> hide #!6 models
> save "/Users/gozorows/Dropbox (Scripps
> Research)/EMCC/Clinical_Trials/IAVI_C101/May_CCVIMC_SAB_presentation/C101_mAbs_cryoEM_compare_May2024.cxs"
> hide #!1 models
> open
> /Users/gozorows/coot_sessions/C101_coot/206-3G08_GT1-1_RM20A3/cryosparc_P455_J360_008_volume_map_sharp.mrc
Opened cryosparc_P455_J360_008_volume_map_sharp.mrc as #7, grid size
400,400,400, pixel 1.03, shown at level 0.077, step 2, values float32
> volume #7 level 0.1981
> volume #7 step 1
> volume #7 level 0.1921
> surface dust #7 size 10.3
> show #!1 models
> select #1/H,L
1713 atoms, 1760 bonds, 224 residues, 1 model selected
> hide #!1 models
> show #!1 models
> hide #!7 models
> select #1/H,L,K,N
3426 atoms, 3520 bonds, 448 residues, 1 model selected
> select #1/H,L,K,N,R,P
5139 atoms, 5280 bonds, 672 residues, 1 model selected
> select #1/H,L,N
2469 atoms, 2535 bonds, 327 residues, 1 model selected
> select #1/H
957 atoms, 985 bonds, 121 residues, 1 model selected
> select #1/H,K
1914 atoms, 1970 bonds, 242 residues, 1 model selected
> select #1/H,K,P
2871 atoms, 2955 bonds, 363 residues, 1 model selected
> select #1/H,L,K,N,R,P
5139 atoms, 5280 bonds, 672 residues, 1 model selected
> color sel red
> show #!7 models
> ui tool show "Surface Color"
> ui tool show "Color Zone"
> color zone #7 near sel distance 6.2
> color zone #7 near sel distance 6.53
> color zone #7 near sel distance 13.95
[Repeated 2 time(s)]
> color zone #7 near sel distance 25.92
> color zone #7 near sel distance 27.57
> color zone #7 near sel distance 16.53
> color zone #7 near sel distance 10
[Repeated 1 time(s)]
> volume #7 level 0.1869
> hide #!1 models
> set bgColor white
> lighting simple
> lighting soft
> lighting full
> lighting soft
> color zone #7 near sel distance 9.77
> color zone #7 near sel distance 10.08
> volume #7 level 0.2658
> volume #7 level 0.2395
> save "/Users/gozorows/Dropbox (Scripps
> Research)/EMCC/Clinical_Trials/IAVI_C101/May_CCVIMC_SAB_presentation/206-3G08_colored.png"
> width 2000 height 2097 supersample 3 transparentBackground true
> open
> /Users/gozorows/coot_sessions/C101_coot/206-9C09_GT1-1_RM20A3/cryosparc_P455_J387_008_volume_map_sharp.mrc
Opened cryosparc_P455_J387_008_volume_map_sharp.mrc as #8, grid size
400,400,400, pixel 1.03, shown at level 0.0813, step 2, values float32
> volume #8 level 0.4176
> volume #8 step 1
> volume #8 level 0.5128
> fitmap #8 inMap #7
Fit map cryosparc_P455_J387_008_volume_map_sharp.mrc in map
cryosparc_P455_J360_008_volume_map_sharp.mrc using 51232 points
correlation = 0.2058, correlation about mean = 0.02977, overlap = 2095
steps = 72, shift = 2.48, angle = 1.39 degrees
Position of cryosparc_P455_J387_008_volume_map_sharp.mrc (#8) relative to
cryosparc_P455_J360_008_volume_map_sharp.mrc (#7) coordinates:
Matrix rotation and translation
0.99983154 0.00366015 0.01798613 -5.74449561
-0.00337678 0.99987010 -0.01575992 4.04075291
-0.01804148 0.01569653 0.99971402 2.67400953
Axis 0.65069724 0.74525456 -0.14556356
Axis point 134.76935498 0.00000000 280.28073414
Rotation angle (degrees) 1.38505113
Shift along axis -1.11577622
> select #8
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.84354,0.53089,0.081226,-95.64,-0.53507,0.84377,0.04185,131.87,-0.046318,-0.078764,0.99582,28.635
> fitmap #8 inMap #7
Fit map cryosparc_P455_J387_008_volume_map_sharp.mrc in map
cryosparc_P455_J360_008_volume_map_sharp.mrc using 51232 points
correlation = 0.969, correlation about mean = 0.7646, overlap = 2.51e+04
steps = 108, shift = 4.27, angle = 7.97 degrees
Position of cryosparc_P455_J387_008_volume_map_sharp.mrc (#8) relative to
cryosparc_P455_J360_008_volume_map_sharp.mrc (#7) coordinates:
Matrix rotation and translation
0.78494241 0.61956873 -0.00006005 -83.63331882
-0.61956873 0.78494240 -0.00012257 172.61367122
-0.00002881 0.00013341 0.99999999 -1.45924376
Axis 0.00020658 -0.00002521 -0.99999998
Axis point 206.82834451 206.77870785 0.00000000
Rotation angle (degrees) 38.28464867
Shift along axis 1.43761524
> ui mousemode right select
> hide #!7 models
> color #8 gray
> color #8 lightgray
> select clear
> select #8
2 models selected
> surface dust #8 size 10.3
> show #!5 models
> volume #8 level 0.2524
> select clear
> select #5/H,L,K,N,R,P
5301 atoms, 5436 bonds, 678 residues, 1 model selected
> color sel purple
> color zone #8 near sel distance 6.2
> select clear
> hide #!5 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> rename #7 c206-3G08_GT1.mrc
> rename #8 206-9C09_GT1.mrc
> rename #7 206-3G08_GT1.mrc
> open
> /Users/gozorows/coot_sessions/C101_coot/253-7A03_BG505_RM20A3/253_7A03_BG505_P455_J152_007_volume_map_sharp_C1_3.3.mrc
Opened 253_7A03_BG505_P455_J152_007_volume_map_sharp_C1_3.3.mrc as #9, grid
size 400,400,400, pixel 1.03, shown at level 0.0518, step 2, values float32
> volume #9 level 0.1394
> volume #9 step 1
> fitmap #9 inMap #7
Fit map 253_7A03_BG505_P455_J152_007_volume_map_sharp_C1_3.3.mrc in map
206-3G08_GT1.mrc using 118509 points
correlation = 0.2078, correlation about mean = 0.01378, overlap = 1697
steps = 52, shift = 1.61, angle = 1.1 degrees
Position of 253_7A03_BG505_P455_J152_007_volume_map_sharp_C1_3.3.mrc (#9)
relative to 206-3G08_GT1.mrc (#7) coordinates:
Matrix rotation and translation
0.99981835 -0.01864194 -0.00396811 4.81770888
0.01865328 0.99982198 0.00283959 -4.24380239
0.00391447 -0.00291309 0.99998810 1.37292283
Axis -0.14922360 -0.20447286 0.96743122
Axis point 213.87814915 268.17303767 0.00000000
Rotation angle (degrees) 1.10446671
Shift along axis 1.47703497
> select #9
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #9,0.99347,0.05655,0.099096,-31.53,-0.066928,0.99225,0.10474,-5.5151,-0.092405,-0.11069,0.98955,47.438
> fitmap #9 inMap #7
Fit map 253_7A03_BG505_P455_J152_007_volume_map_sharp_C1_3.3.mrc in map
206-3G08_GT1.mrc using 118509 points
correlation = 0.2175, correlation about mean = 0.03955, overlap = 1829
steps = 220, shift = 5.78, angle = 9.01 degrees
Position of 253_7A03_BG505_P455_J152_007_volume_map_sharp_C1_3.3.mrc (#9)
relative to 206-3G08_GT1.mrc (#7) coordinates:
Matrix rotation and translation
0.96693216 0.19881785 0.15972999 -72.34957030
-0.21505077 0.97229884 0.09158672 35.27890625
-0.13709621 -0.12290820 0.98290295 57.15902682
Axis -0.38813404 0.53711456 -0.74890581
Axis point 105.42942018 373.18904160 0.00000000
Rotation angle (degrees) 16.04042679
Shift along axis 4.22341743
> ui mousemode right select
> ui mousemode right "translate selected models"
> view matrix models
> #9,0.96693,0.19882,0.15973,-75.756,-0.21505,0.9723,0.091587,28.326,-0.1371,-0.12291,0.9829,40.73
> ui mousemode right select
> fitmap #9 inMap #7
Fit map 253_7A03_BG505_P455_J152_007_volume_map_sharp_C1_3.3.mrc in map
206-3G08_GT1.mrc using 118509 points
correlation = 0.302, correlation about mean = 0.06687, overlap = 3065
steps = 276, shift = 7.44, angle = 13.4 degrees
Position of 253_7A03_BG505_P455_J152_007_volume_map_sharp_C1_3.3.mrc (#9)
relative to 206-3G08_GT1.mrc (#7) coordinates:
Matrix rotation and translation
0.99680963 0.07952189 -0.00684338 -14.90978555
-0.07955820 0.99681662 -0.00520735 18.30883011
0.00640750 0.00573519 0.99996303 -22.77742129
Axis 0.06838849 -0.08281508 -0.99421561
Axis point 242.48083125 214.51534158 0.00000000
Rotation angle (degrees) 4.58872741
Shift along axis 20.10976271
> show #!6 models
> ui mousemode right "rotate selected models"
> view matrix models
> #9,-0.71263,0.69196,-0.11554,244.84,-0.68979,-0.72114,-0.064366,530.79,-0.12786,0.03383,0.99122,1.9613
> ui mousemode right "translate selected models"
> view matrix models
> #9,-0.71263,0.69196,-0.11554,240.8,-0.68979,-0.72114,-0.064366,518.14,-0.12786,0.03383,0.99122,1.1206
> ui mousemode right select
> fitmap #9 inMap #7
Fit map 253_7A03_BG505_P455_J152_007_volume_map_sharp_C1_3.3.mrc in map
206-3G08_GT1.mrc using 118509 points
correlation = 0.8854, correlation about mean = 0.7068, overlap = 1.338e+04
steps = 156, shift = 8.86, angle = 12.4 degrees
Position of 253_7A03_BG505_P455_J152_007_volume_map_sharp_C1_3.3.mrc (#9)
relative to 206-3G08_GT1.mrc (#7) coordinates:
Matrix rotation and translation
-0.59510938 0.80364088 0.00248293 163.33159804
-0.80361339 -0.59511062 0.00698966 494.72140620
0.00709479 0.00216429 0.99997249 -17.07062895
Axis -0.00300221 -0.00286938 -0.99999138
Axis point 206.32544102 206.22959582 0.00000000
Rotation angle (degrees) 126.52145508
Shift along axis 15.16058201
> volume #9 level 0.1803
> select #6/H,L
1654 atoms, 1695 bonds, 217 residues, 1 model selected
> color sel forest green
> color #9 lightgray
> select #6/H,L
1654 atoms, 1695 bonds, 217 residues, 1 model selected
> select #9
2 models selected
> surface dust #9 size 10.3
> select #6/H,L
1654 atoms, 1695 bonds, 217 residues, 1 model selected
> color zone #9 near sel distance 6.2
> select clear
> hide #!9 models
> show #!9 models
> hide #!6 models
> open
> /Users/gozorows/coot_sessions/C101_coot/273-4D01_BG505_RM20A3/273-4D01_BG505_RM20A3_P455_J315_C1_3.9.mrc
Opened 273-4D01_BG505_RM20A3_P455_J315_C1_3.9.mrc as #10, grid size
400,400,400, pixel 1.03, shown at level 0.0436, step 2, values float32
> volume #10 level 0.09009
> volume #10 step 1
> volume #10 level 0.1217
> select #10
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #10,0.30665,-0.14812,-0.94023,374.39,-0.84327,-0.5004,-0.1962,552.11,-0.44143,0.85303,-0.27835,168.94
> view matrix models
> #10,0.99933,-0.019887,-0.030596,10.906,-0.017538,-0.99701,0.075205,431.72,-0.032001,-0.074618,-0.9967,437.55
> ui mousemode right "translate selected models"
> view matrix models
> #10,0.99933,-0.019887,-0.030596,11.615,-0.017538,-0.99701,0.075205,411,-0.032001,-0.074618,-0.9967,440.84
> ui mousemode right select
> ui mousemode right "translate selected models"
> view matrix models
> #10,0.99933,-0.019887,-0.030596,7.8777,-0.017538,-0.99701,0.075205,404.78,-0.032001,-0.074618,-0.9967,422.31
> fitmap #10 inMap #7
Fit map 273-4D01_BG505_RM20A3_P455_J315_C1_3.9.mrc in map 206-3G08_GT1.mrc
using 127916 points
correlation = 0.6727, correlation about mean = 0.4498, overlap = 6916
steps = 88, shift = 4.7, angle = 5.16 degrees
Position of 273-4D01_BG505_RM20A3_P455_J315_C1_3.9.mrc (#10) relative to
206-3G08_GT1.mrc (#7) coordinates:
Matrix rotation and translation
0.99981743 0.01907420 -0.00113637 -3.53035374
0.01907322 -0.99981771 -0.00087201 409.80193629
-0.00115280 0.00085017 -0.99999897 398.15238142
Axis 0.99995435 0.00953781 -0.00057222
Axis point 0.00000000 204.83208560 199.16340757
Rotation angle (degrees) 179.95066085
Shift along axis 0.15059048
> ui mousemode right rotate
> ui mousemode right select
> hide #!9 models
> volume #10 level 0.1424
> surface dust #10 size 10.3
> color #10 lightgray
> show #!4 models
> select #4/H,L
1712 atoms, 1753 bonds, 223 residues, 1 model selected
> ui tool show "Color Actions"
> color sel goldenrod
> color zone #10 near sel distance 6.2
> color zone #10 near sel distance 5.97
> color zone #10 near sel distance 6.35
> color zone #10 near sel distance 6.54
> color zone #10 near sel distance 7.74
> color zone #10 near sel distance 8.1
> color zone #10 near sel distance 8.75
> select clear
> hide #!4 models
> volume #10 level 0.1548
> hide #!10 models
> open
> /Users/gozorows/coot_sessions/C101_coot/61-12A01_GT1-1_RM20A3/cryosparc_P455_J363_008_volume_map_sharp.mrc
Opened cryosparc_P455_J363_008_volume_map_sharp.mrc as #11, grid size
400,400,400, pixel 1.03, shown at level 0.0749, step 2, values float32
> volume #11 level 0.3529
> volume #11 step 1
> volume #11 level 0.4692
> select #11
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #11,0.49225,0.87031,0.015907,-82.235,-0.86956,0.49083,0.054321,272.5,0.039468,-0.040571,0.9984,0.79486
> fitmap #11 inMap #7
Fit map cryosparc_P455_J363_008_volume_map_sharp.mrc in map 206-3G08_GT1.mrc
using 52819 points
correlation = 0.9316, correlation about mean = 0.6305, overlap = 2.326e+04
steps = 152, shift = 4.43, angle = 15 degrees
Position of cryosparc_P455_J363_008_volume_map_sharp.mrc (#11) relative to
206-3G08_GT1.mrc (#7) coordinates:
Matrix rotation and translation
0.69561667 0.71841314 -0.00010442 -85.59624410
-0.71841315 0.69561666 -0.00013735 211.52813954
-0.00002604 0.00017056 0.99999998 -0.77076995
Axis 0.00021430 -0.00005455 -0.99999998
Axis point 206.82884392 206.77747549 0.00000000
Rotation angle (degrees) 45.92362295
Shift along axis 0.74088854
> ui mousemode right select
> volume #11 level 0.3787
> surface dust #11 size 10.3
> color #11 lightgray
> show #!3 models
> select #3/H,L,K,N,R,P
5286 atoms, 5430 bonds, 678 residues, 1 model selected
> color sel cornflower blue
> volume #11 level 0.2367
> color zone #11 near sel distance 6.2
> hide #!3 models
> select clear
> rename #11 61-12A01_GT1.mrc
> save "/Users/gozorows/Dropbox (Scripps
> Research)/EMCC/Clinical_Trials/IAVI_C101/May_CCVIMC_SAB_presentation/61-12A01_map_segmented.png"
> width 2000 height 1920 supersample 3 transparentBackground true
> hide #!11 models
> show #!10 models
> save "/Users/gozorows/Dropbox (Scripps
> Research)/EMCC/Clinical_Trials/IAVI_C101/May_CCVIMC_SAB_presentation/61_12A01_map_segmented.png"
> width 2000 height 1920 supersample 3 transparentBackground true
> hide #!10 models
> show #!9 models
> save "/Users/gozorows/Dropbox (Scripps
> Research)/EMCC/Clinical_Trials/IAVI_C101/May_CCVIMC_SAB_presentation/253_7A03_map_segmented.png"
> width 2000 height 1920 supersample 3 transparentBackground true
> hide #!9 models
> show #!8 models
> volume #8 level 0.2894
> save "/Users/gozorows/Dropbox (Scripps
> Research)/EMCC/Clinical_Trials/IAVI_C101/May_CCVIMC_SAB_presentation/206_9C09_map_segmented.png"
> width 2000 height 1920 supersample 3 transparentBackground true
> hide #!8 models
> show #!7 models
> volume #7 level 0.2762
> save "/Users/gozorows/Dropbox (Scripps
> Research)/EMCC/Clinical_Trials/IAVI_C101/May_CCVIMC_SAB_presentation/206-3G08_segmented.png"
> width 2000 height 1920 supersample 3 transparentBackground true
> save "/Users/gozorows/Dropbox (Scripps
> Research)/EMCC/Clinical_Trials/IAVI_C101/May_CCVIMC_SAB_presentation/colored_maps.cxs"
——— End of log from Fri May 3 15:29:01 2024 ———
opened ChimeraX session
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> hide #!7 models
> show #!8 models
> show #!7 models
> hide #!8 models
> show #!8 models
> hide #!7 models
> show #!7 models
> hide #!8 models
> show #!5 models
> hide #!7 models
> show #!8 models
> hide #!8 models
> hide #!5 models
> show #!1 models
> color gray #1/A,C,E
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color #1/A,C,E gray
> color #1/A,C,E,B,D,F gray
> select clear
> select #1
24660 atoms, 25299 bonds, 9 pseudobonds, 3129 residues, 2 models selected
> show #!7 models
> ui tool show "Color Zone"
> color zone #7 near #1 distance 1.03
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> color zone #7 near #1 distance 1.03
> color zone #7 near #1 distance 1.07
> color zone #7 near #1 distance 24.03
> hide #!1 models
> select clear
> color #1/A,C,E,B,D,F light gray
> color zone #7 near #1 distance 24.03
[Repeated 2 time(s)]
> save "/Users/gozorows/Scripps Research Dropbox/Ward
> Lab/Manuscripts/Gabe/2024_C101trial/figures/segmented_maps_colored_models.cxs"
> save "/Users/gozorows/Scripps Research Dropbox/Ward
> Lab/Manuscripts/Gabe/2024_C101trial/figures/206-3G08_GT1_segmented_top.png"
> width 2000 height 1978 supersample 3 transparentBackground true
> hide #!7 models
> show #!8 models
> show #!5 models
> hide #!5 models
> color #5/A,C,E,B,D,F light gray
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> color zone #8 near #5 distance 6.2
> show #!5 models
> hide #!8 models
> hide #!5 models
> show #!11 models
> hide #!11 models
> show #!10 models
> hide #!10 models
> show #!8 models
> save "/Users/gozorows/Scripps Research Dropbox/Ward
> Lab/Manuscripts/Gabe/2024_C101trial/figures/206-9C09_GT1_segmented_top.png"
> width 2000 height 2087 supersample 3
> hide #!8 models
> show #!11 models
> show #!3 models
> hide #!3 models
> color #3/A,C,E,B,D,F light gray
> color zone #11 near #3 distance 6.2
> show #!5 models
> hide #!5 models
> show #!3 models
> hide #!11 models
> show #!11 models
> hide #!3 models
> save "/Users/gozorows/Scripps Research Dropbox/Ward
> Lab/Manuscripts/Gabe/2024_C101trial/figures/61-12A01_GT1_segmented_top.png"
> width 2000 height 2087 supersample 3
> hide #!11 models
> show #!9 models
> show #!6 models
> color #6/A,C,E,B,D,F light gray
> color zone #9 near #6 distance 6.2
> hide #!6 models
> save "/Users/gozorows/Scripps Research Dropbox/Ward
> Lab/Manuscripts/Gabe/2024_C101trial/figures/253-7A03_BG505_segmented_top.png"
> width 2000 height 3378 supersample 3
> hide #!9 models
> show #!10 models
> show #!4 models
> color #4/A,C,E,B,D,F light gray
> color zone #10 near #4 distance 8.75
> hide #!4 models
> save "/Users/gozorows/Scripps Research Dropbox/Ward
> Lab/Manuscripts/Gabe/2024_C101trial/figures/273-4D01_BG505_segmented_top.png"
> width 2000 height 3378 supersample 3
> show #!4 models
> hide #!10 models
> turn x 90
[Repeated 2 time(s)]
> cartoon style protein modeHelix default arrows false xsection oval width 1
> thickness 1
> hide #4.1 models
> select #4/L
781 atoms, 798 bonds, 103 residues, 1 model selected
> select #4/H
931 atoms, 955 bonds, 120 residues, 1 model selected
> ui tool show "Color Actions"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> color sel sienna
> select #4/L
781 atoms, 798 bonds, 103 residues, 1 model selected
> color sel gold
> select clear
> select #4/L
781 atoms, 798 bonds, 103 residues, 1 model selected
> color sel goldenrod
> select clear
> select #4/G,I
1754 atoms, 1795 bonds, 233 residues, 1 model selected
> select #4/G,I,J,K,M
4451 atoms, 4554 bonds, 590 residues, 1 model selected
> select #4/G,I,J,K,M,N
5262 atoms, 5385 bonds, 699 residues, 1 model selected
> select #4/G,I,J,K,M,N,O
5262 atoms, 5385 bonds, 699 residues, 1 model selected
> color sel dim gray
> select clear
> select #4/A,B,C,D,E,F
14046 atoms, 14407 bonds, 14 pseudobonds, 1730 residues, 2 models selected
> show sel surfaces
> hide sel cartoons
> select clear
> save "/Users/gozorows/Scripps Research Dropbox/Ward
> Lab/Manuscripts/Gabe/2024_C101trial/figures/segmented_maps_colored_models.cxs"
> save "/Users/gozorows/Scripps Research Dropbox/Ward
> Lab/Manuscripts/Gabe/2024_C101trial/figures/273-4D01_BG505_model_side.png"
> width 2000 height 1846 supersample 3
> hide #!4 models
> show #!6 models
> select #6/A,B,C,D,E,F
14074 atoms, 14429 bonds, 14 pseudobonds, 1732 residues, 2 models selected
> hide sel cartoons
> show sel surfaces
> select #6/G,I,J,K,M,N
5262 atoms, 5385 bonds, 699 residues, 1 model selected
> color sel dim gray
> select #6/H
937 atoms, 962 bonds, 119 residues, 1 model selected
> color sel forest green
> select #6/L
717 atoms, 733 bonds, 98 residues, 1 model selected
> color sel lime green
> select clear
> save "/Users/gozorows/Scripps Research Dropbox/Ward
> Lab/Manuscripts/Gabe/2024_C101trial/figures/253-7A03_BG505_model_side.png"
> width 2000 height 1846 supersample 3
> hide #!6 models
> show #!1 models
> select #1/A,B,C,D,E,F
14301 atoms, 14676 bonds, 9 pseudobonds, 1764 residues, 2 models selected
> hide sel cartoons
> show sel surfaces
> hide sel surfaces
> show sel surfaces
> select clear
> select #6/G,I,J,K,M,N
5262 atoms, 5385 bonds, 699 residues, 1 model selected
> select #1/G,I,J,K,M,N
5193 atoms, 5322 bonds, 686 residues, 1 model selected
> select clear
> select #1/J,M,G,I,O,Q
5220 atoms, 5343 bonds, 693 residues, 1 model selected
> color sel dim gray
> select #1/H
957 atoms, 985 bonds, 121 residues, 1 model selected
> select #1/H,K,P
2871 atoms, 2955 bonds, 363 residues, 1 model selected
> color sel dark red
> color sel red
> color sel fire brick
> color sel crimson
> select #1/L,N,R
2268 atoms, 2325 bonds, 309 residues, 1 model selected
> color sel dark salmon
> color sel light coral
> color sel light pink
> color sel pale violet red
> color sel tomato
> select clear
> select #1/L,N,R
2268 atoms, 2325 bonds, 309 residues, 1 model selected
> color sel salmon
> select clear
[Repeated 1 time(s)]
> save "/Users/gozorows/Scripps Research Dropbox/Ward
> Lab/Manuscripts/Gabe/2024_C101trial/figures/206-3G08_GT1_model_side.png"
> width 2000 height 1846 supersample 3 transparentBackground true
> hide #!1 models
> show #!3 models
> select #3/J,M,G,I,O,Q
5220 atoms, 5343 bonds, 693 residues, 1 model selected
> color sel dim gray
> select #3/A,B,C,D,E,F
14301 atoms, 14676 bonds, 9 pseudobonds, 1764 residues, 2 models selected
> hide sel cartoons
> show sel surfaces
> select #3/H,K,P
2922 atoms, 3012 bonds, 366 residues, 1 model selected
> color sel royal blue
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select clear
> select #3/L,N,R
2364 atoms, 2418 bonds, 312 residues, 1 model selected
> color sel cornflower blue
> select clear
> select #3/L,N,R
2364 atoms, 2418 bonds, 312 residues, 1 model selected
> color sel sky blue
> select clear
> save "/Users/gozorows/Scripps Research Dropbox/Ward
> Lab/Manuscripts/Gabe/2024_C101trial/figures/61-12A01_GT1_model_side.png"
> width 2000 height 1846 supersample 3 transparentBackground true
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!5 models
> show #!3 models
> hide #!3 models
> select #5/A,B,C,D,E,F
14301 atoms, 14676 bonds, 9 pseudobonds, 1764 residues, 2 models selected
> hide sel cartoons
> show sel surfaces
> select #5/J,M,G,I,O,Q
5220 atoms, 5343 bonds, 693 residues, 1 model selected
> color sel dim gray
> select #5/H,K,P
2907 atoms, 2988 bonds, 369 residues, 1 model selected
> color sel purple
> select #5/L,N,R
2394 atoms, 2448 bonds, 309 residues, 1 model selected
> color sel medium purple
> color sel plum
> select clear
> save "/Users/gozorows/Scripps Research Dropbox/Ward
> Lab/Manuscripts/Gabe/2024_C101trial/figures/206-9C09_GT1_model_side.png"
> width 2000 height 1846 supersample 3 transparentBackground true
> select #5/A,B,C,D,E,F
14301 atoms, 14676 bonds, 9 pseudobonds, 1764 residues, 2 models selected
> color sel light gray
> color sel white
> select clear
> lighting simple
> lighting soft
> lighting full
> lighting flat
> lighting shadows true intensity 0.5
> lighting simple
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting soft
> save "/Users/gozorows/Scripps Research Dropbox/Ward
> Lab/Manuscripts/Gabe/2024_C101trial/figures/206-9C09_GT1_model_side.png"
> width 2000 height 1846 supersample 3 transparentBackground true
> lighting soft
> lighting simple
> lighting shadows true
> lighting shadows false
> lighting flat
[Repeated 1 time(s)]
> lighting simple
> select #5/A,B,C,D,E,F
14301 atoms, 14676 bonds, 9 pseudobonds, 1764 residues, 2 models selected
> color sel light gray
> select clear
> save "/Users/gozorows/Scripps Research Dropbox/Ward
> Lab/Manuscripts/Gabe/2024_C101trial/figures/206-9C09_GT1_model_side.png"
> width 2000 height 1846 supersample 3 transparentBackground true
> select #5/A,B,C,D,E,F
14301 atoms, 14676 bonds, 9 pseudobonds, 1764 residues, 2 models selected
> hide sel surfaces
> show sel cartoons
> select clear
> select #5/A,B,C,D,E,F
14301 atoms, 14676 bonds, 9 pseudobonds, 1764 residues, 2 models selected
> hide sel cartoons
> show sel surfaces
> select clear
> lighting soft
> cartoon style protein modeHelix default arrows false xsection oval width 1
> thickness 2
> select #5/A,B,C,D,E,F
14301 atoms, 14676 bonds, 9 pseudobonds, 1764 residues, 2 models selected
> color sel light gray
> select clear
> save "/Users/gozorows/Scripps Research Dropbox/Ward
> Lab/Manuscripts/Gabe/2024_C101trial/figures/206-9C09_GT1_model_side.png"
> width 2000 height 1846 supersample 3 transparentBackground true
> select #5/A,B,C,D,E,F
14301 atoms, 14676 bonds, 9 pseudobonds, 1764 residues, 2 models selected
> color sel white
> select clear
> save "/Users/gozorows/Scripps Research Dropbox/Ward
> Lab/Manuscripts/Gabe/2024_C101trial/figures/206-9C09_GT1_model_side.png"
> width 2000 height 1846 supersample 3 transparentBackground true
> select #5/A,B,C,D,E,F
14301 atoms, 14676 bonds, 9 pseudobonds, 1764 residues, 2 models selected
> color sel light gray
> select clear
> save "/Users/gozorows/Scripps Research Dropbox/Ward
> Lab/Manuscripts/Gabe/2024_C101trial/figures/206-9C09_GT1_model_side.png"
> width 2000 height 1846 supersample 3 transparentBackground true
> turn x 90
> show #!8 models
> hide #!5 models
> save "/Users/gozorows/Scripps Research Dropbox/Ward
> Lab/Manuscripts/Gabe/2024_C101trial/figures/206-9C09_GT1_segmented_top.png"
> width 2000 height 1846 supersample 3 transparentBackground true
> hide #!8 models
> show #!7 models
> hide #!7 models
> show #!6 models
> hide #!6 models
> show #!11 models
> save "/Users/gozorows/Scripps Research Dropbox/Ward
> Lab/Manuscripts/Gabe/2024_C101trial/figures/61-12A01_GT1_segmented_top.png"
> width 2000 height 1846 supersample 3 transparentBackground true
> turn x -90
> hide #!11 models
> show #!3 models
> save "/Users/gozorows/Scripps Research Dropbox/Ward
> Lab/Manuscripts/Gabe/2024_C101trial/figures/segmented_maps_colored_models.cxs"
> save "/Users/gozorows/Scripps Research Dropbox/Ward
> Lab/Manuscripts/Gabe/2024_C101trial/figures/61-12A01_GT1_model_side.png"
> width 2000 height 1846 supersample 3 transparentBackground true
> turn x 90
> hide #!3 models
> show #!1 models
> hide #!1 models
> show #!7 models
> save "/Users/gozorows/Scripps Research Dropbox/Ward
> Lab/Manuscripts/Gabe/2024_C101trial/figures/206-3G08_GT1_segmented_top.png"
> width 2000 height 1846 supersample 3 transparentBackground true
> turn x -90
> hide #!7 models
> show #!1 models
> save "/Users/gozorows/Scripps Research Dropbox/Ward
> Lab/Manuscripts/Gabe/2024_C101trial/figures/206-3G08_GT1_model_side.png"
> width 2000 height 1846 supersample 3 transparentBackground true
> hide #!1 models
> show #!7 models
> hide #!7 models
> show #!9 models
> show #!6 models
> hide #!9 models
> save "/Users/gozorows/Scripps Research Dropbox/Ward
> Lab/Manuscripts/Gabe/2024_C101trial/figures/253-7A03_BG505_model_side.png"
> width 2000 height 1846 supersample 3 transparentBackground true
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!4 models
> save "/Users/gozorows/Scripps Research Dropbox/Ward
> Lab/Manuscripts/Gabe/2024_C101trial/figures/273-4D01_BG505_model_side.png"
> width 2000 height 1846 supersample 3 transparentBackground true
> turn x 90
> hide #!4 models
> show #!10 models
> save "/Users/gozorows/Scripps Research Dropbox/Ward
> Lab/Manuscripts/Gabe/2024_C101trial/figures/273-4D01_BG505_segmented_top.png"
> width 2000 height 1846 supersample 3 transparentBackground true
> hide #!10 models
> show #!9 models
> save "/Users/gozorows/Scripps Research Dropbox/Ward
> Lab/Manuscripts/Gabe/2024_C101trial/figures/253-7A03_BG505_segmented_top.png"
> width 2000 height 1846 supersample 3 transparentBackground true
> hide #!9 models
> show #!1 models
> hide #!1 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!7 models
> hide #!7 models
> show #!10 models
> hide #!10 models
> show #!9 models
> hide #!9 models
> show #!10 models
> ui tool show "Color Zone"
> color zone #10 near #1 distance 1.03
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
[Repeated 1 time(s)]
> color zone #10 near #4 distance 4.51
[Repeated 1 time(s)]
> color #4/L sienna
> color zone #10 near #4 distance 4.51
> save "/Users/gozorows/Scripps Research Dropbox/Ward
> Lab/Manuscripts/Gabe/2024_C101trial/figures/273-4D01_BG505_segmented_top.png"
> width 2000 height 2851 supersample 3 transparentBackground true
> save "/Users/gozorows/Scripps Research Dropbox/Ward
> Lab/Manuscripts/Gabe/2024_C101trial/figures/segmented_maps_colored_models.cxs"
> open "/Users/gozorows/Scripps Research Dropbox/Gabriel
> Ozorowski/TSRI/EM/C101/61-12A01_GT1-1_RM20A3/61-12A01_GT1-1_RM20A3_real_space_refined_054.pdb"
Chain information for 61-12A01_GT1-1_RM20A3_real_space_refined_054.pdb #12
---
Chain | Description
A C E | No description available
B D F | No description available
G J O | No description available
H K P | No description available
I M Q | No description available
L N R | No description available
> hide #!10 models
> close #7-8
> close #10-11
> close #9
> close #3
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> rename #1 206-3G08_GT11_SOSIP_RM20A3_real_space_refined_037.pdb
> close #5
> open "/Users/gozorows/Scripps Research Dropbox/Gabriel
> Ozorowski/TSRI/EM/C101/206-9C09_GT1-1_RM20A3/206-9C09_GT1-1_RM20A3_real_space_refined_047.pdb"
Chain information for 206-9C09_GT1-1_RM20A3_real_space_refined_047.pdb #3
---
Chain | Description
A C E | No description available
B D F | No description available
G J O | No description available
H K P | No description available
I M Q | No description available
L N R | No description available
> hide #!3 models
> open "/Users/gozorows/Scripps Research Dropbox/Gabriel
> Ozorowski/TSRI/EM/C101/273-4D01_BG505_RM20A3/C101_273-4D01_BG505_RM20A3_real_space_refined_041.pdb"
Chain information for C101_273-4D01_BG505_RM20A3_real_space_refined_041.pdb #5
---
Chain | Description
A | No description available
B F | No description available
C | No description available
D | No description available
E | No description available
G J M | No description available
H | No description available
I K N | No description available
L | No description available
> close #4
> close #6
> open "/Users/gozorows/Scripps Research Dropbox/Gabriel
> Ozorowski/TSRI/EM/C101/253-7A03_BG505/253-7A03_BG505_RM20A3_real_space_refined_033.pdb"
Chain information for 253-7A03_BG505_RM20A3_real_space_refined_033.pdb #4
---
Chain | Description
A | No description available
B F | No description available
C | No description available
D | No description available
E | No description available
G J M | No description available
H | No description available
I K N | No description available
L | No description available
> hide #!4 models
> hide #!5 models
> hide #!12 models
> show #!5 models
> hide #!5 models
> show #!4 models
> hide #!4 models
> show #!3 models
> hide #!3 models
> show #!2 models
> hide #!2 models
> show #!1 models
> select #1
24660 atoms, 25299 bonds, 9 pseudobonds, 3129 residues, 2 models selected
> hide sel surfaces
> hide sel cartoons
> select #1/A,H,L
5441 atoms, 5590 bonds, 2 pseudobonds, 684 residues, 2 models selected
> show sel atoms
> hide sel atoms
> show sel cartoons
> hide #1.1 models
> cartoon style protein modeHelix default arrows false xsection oval width 1
> thickness 1
> select clear
> mmaker #3/A to #1/A
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 206-3G08_GT11_SOSIP_RM20A3_real_space_refined_037.pdb, chain A (#1)
with 206-9C09_GT1-1_RM20A3_real_space_refined_047.pdb, chain A (#3), sequence
alignment score = 2248.2
RMSD between 434 pruned atom pairs is 0.318 angstroms; (across all 439 pairs:
0.512)
> mmaker #4/A to #1/A
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 206-3G08_GT11_SOSIP_RM20A3_real_space_refined_037.pdb, chain A (#1)
with 253-7A03_BG505_RM20A3_real_space_refined_033.pdb, chain A (#4), sequence
alignment score = 2138.9
RMSD between 432 pruned atom pairs is 0.469 angstroms; (across all 436 pairs:
0.712)
> mmaker #45A to #1/A
> matchmaker #45A to #1/A
Missing or invalid "matchAtoms" argument: invalid atoms specifier
> mmaker #5/A to #1/A
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 206-3G08_GT11_SOSIP_RM20A3_real_space_refined_037.pdb, chain A (#1)
with C101_273-4D01_BG505_RM20A3_real_space_refined_041.pdb, chain A (#5),
sequence alignment score = 2049.8
RMSD between 421 pruned atom pairs is 0.603 angstroms; (across all 431 pairs:
0.874)
> mmaker #12/A to #1/A
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 206-3G08_GT11_SOSIP_RM20A3_real_space_refined_037.pdb, chain A (#1)
with 61-12A01_GT1-1_RM20A3_real_space_refined_054.pdb, chain A (#12), sequence
alignment score = 2234.6
RMSD between 437 pruned atom pairs is 0.460 angstroms; (across all 443 pairs:
0.555)
> hide #!1 models
> show #!2 models
> select #2/H
1615 atoms, 1654 bonds, 208 residues, 1 model selected
> select #2/H,L
3230 atoms, 3308 bonds, 416 residues, 1 model selected
> select #2/A
3509 atoms, 3593 bonds, 4 pseudobonds, 443 residues, 2 models selected
> select #2/B
1039 atoms, 1059 bonds, 1 pseudobond, 129 residues, 2 models selected
> select #2/B,E
4548 atoms, 4652 bonds, 5 pseudobonds, 572 residues, 2 models selected
> select #2/B,E,F
5587 atoms, 5712 bonds, 6 pseudobonds, 701 residues, 2 models selected
> select #2/B,E,F,G
7297 atoms, 7470 bonds, 6 pseudobonds, 925 residues, 2 models selected
> select #2/B,E,F,G,H
8912 atoms, 9125 bonds, 6 pseudobonds, 1133 residues, 2 models selected
> select #2/B,E,F,G,H,I
12421 atoms, 12718 bonds, 10 pseudobonds, 1576 residues, 2 models selected
> select #2/B,E,F,G,H,I,J
13460 atoms, 13778 bonds, 11 pseudobonds, 1705 residues, 2 models selected
> select #2/B,E,F,G,H,I,J,K
15170 atoms, 15536 bonds, 11 pseudobonds, 1929 residues, 2 models selected
> select #2/B,E,F,G,H,I,J,K,L
16785 atoms, 17191 bonds, 11 pseudobonds, 2137 residues, 2 models selected
> delete atoms (#!2 & sel)
> delete bonds (#!2 & sel)
> hide #!2 models
> show #!2 models
> hide #2.1 models
> select #2/H:113-9999
Nothing selected
> select #2/C:113-9999
749 atoms, 769 bonds, 104 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #2/L:110-9999
Nothing selected
> select #2/D:110-9999
832 atoms, 849 bonds, 107 residues, 1 model selected
> select #2/D:108-9999
849 atoms, 866 bonds, 109 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #2/Q
39 atoms, 41 bonds, 3 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> show #!1 models
> mmaker #2/A to #1/A
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 206-3G08_GT11_SOSIP_RM20A3_real_space_refined_037.pdb, chain A (#1)
with 6v8x, chain A (#2), sequence alignment score = 2060.5
RMSD between 408 pruned atom pairs is 1.080 angstroms; (across all 437 pairs:
1.791)
> save "/Users/gozorows/Scripps Research Dropbox/Ward
> Lab/Manuscripts/Gabe/2024_C101trial/figures/Contacts_maintextfigure_N279-N280.cxs"
> color #2 white
> transparency #2 50
> transparency #2 50 target c
> transparency #2 80 target c
> hide #!2 models
> select #1/A:279,280
16 atoms, 15 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 16 atom styles
> color (#!1 & sel) byhetero
> select clear
> select #1/H:100
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/H:51
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1
24660 atoms, 25299 bonds, 9 pseudobonds, 3129 residues, 2 models selected
> hide sel cartoons
> select #1/H:100B
14 atoms, 15 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 14 atom styles
> color sel byhetero
> select #1/H:99-100B
37 atoms, 38 bonds, 4 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 37 atom styles
> color sel byhetero
> select clear
> open "/Users/gozorows/Scripps Research Dropbox/Gabriel
> Ozorowski/TSRI/EM/C101/206-3G08_GT1-1_RM20A3/206-3G08_GT1-1_RM20A3_real_space_refined_037-coot-0.pdb"
Chain information for 206-3G08_GT1-1_RM20A3_real_space_refined_037-coot-0.pdb
#6
---
Chain | Description
A C E | No description available
B D F | No description available
G J O | No description available
H K P | No description available
I M Q | No description available
L N R | No description available
> close #1
> select #6/A,H,L
5441 atoms, 5590 bonds, 2 pseudobonds, 684 residues, 2 models selected
> select ~sel & ##selected
19219 atoms, 19709 bonds, 7 pseudobonds, 2445 residues, 2 models selected
> delete atoms (#!6 & sel)
> delete bonds (#!6 & sel)
> color #6/A light gray
> color #6/H crimson
> color #6/L salmon
> select #6
5441 atoms, 5590 bonds, 2 pseudobonds, 684 residues, 2 models selected
> hide sel atoms
> hide sel cartoons
> select #6/A:279-280
16 atoms, 15 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 16 atom styles
> color sel byhetero
> select #6/H:99-100B
37 atoms, 38 bonds, 4 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 37 atom styles
> color sel byhetero
> select #6/H:50
14 atoms, 15 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 14 atom styles
> color sel byhetero
> select clear
> hide #!6 models
> show #!12 models
> select #12
25044 atoms, 25599 bonds, 6 pseudobonds, 3162 residues, 2 models selected
> hide sel atoms
> select #12/A:279-280
16 atoms, 15 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 16 atom styles
> color #12/A:279-280 light gray
> color sel byhetero
> color #12/H:96-100D
> select #12/H:96-100D
86 atoms, 90 bonds, 9 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 86 atom styles
> color #12/H royal blue
> color sel byhetero
> select clear
> select #12/H:96
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #12/H:96-100
46 atoms, 47 bonds, 5 residues, 1 model selected
> hide sel surfaces
> hide sel atoms
> color #12/L sky blue
> select #12/L:91-96
21 atoms, 21 bonds, 2 residues, 1 model selected
> select #12/L:96
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> color sel byhetero
> select clear
> show #!3 models
> hide #!3 models
> show #!2 models
> select #2/C:100B
14 atoms, 15 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 14 atom styles
> select #2/A:279
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> select #2/A:280
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> select #2/D:96
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!6 models
> select #6/L:96
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> color sel byhetero
> select clear
> select #12/H:50
14 atoms, 15 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 14 atom styles
> color sel byhetero
> select clear
> show #!3 models
> hide #!6 models
> hide #!12 models
> select #3
25266 atoms, 25809 bonds, 12 pseudobonds, 3171 residues, 2 models selected
> hide sel atoms
> color #3/A light gray
> color #3/H purple
> color #3/L plum
> select #3/H:100-100D
51 atoms, 52 bonds, 7 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 51 atom styles
> color sel byhetero
> select clear
> select #3/H:50
14 atoms, 15 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 14 atom styles
> color sel byhetero
> select #3/L:96
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> show sel cartoons
> hide sel cartoons
> style sel stick
Changed 9 atom styles
> color sel byhetero
> select #3/A:279-280
16 atoms, 15 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 16 atom styles
> color sel byhetero
> select clear
[Repeated 1 time(s)]
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
6 atoms, 5 bonds, 1 residue, 1 model selected
> ui tool show Rotamers
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> swapaa interactive sel SER rotLib Dunbrack
206-9C09_GT1-1_RM20A3_real_space_refined_047.pdb #3/H SER 100B: phi -68.4, psi
150.6 trans
Changed 9 bond radii
> swapaa #!3/H:100B SER criteria 3 rotLib Dunbrack retain false
Using Dunbrack library
206-9C09_GT1-1_RM20A3_real_space_refined_047.pdb #!3/H SER 100B: phi -68.4,
psi 150.6 trans
Applying SER rotamer (chi angles: 176.0) to
206-9C09_GT1-1_RM20A3_real_space_refined_047.pdb #!3/H SER 100B
> select clear
> show #!6 models
> show #!12 models
> hide #!12 models
> hide #!6 models
> hide #!3 models
> show #!12 models
> hide #!12 models
> show #!5 models
> select #5
20955 atoms, 21478 bonds, 14 pseudobonds, 2643 residues, 2 models selected
> hide sel atoms
> color #5/A light gray
> color #5/H sienna
> color #5/L goldenrod
> color #5/A:279-280
> show sel atoms
> style sel stick
Changed 20955 atom styles
> hide sel atoms
> select #5/A:279-280
16 atoms, 15 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 16 atom styles
> color sel byhetero
> select clear
> select #5/L:96
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> color sel byhetero
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui tool show Rotamers
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> swapaa interactive sel GLU rotLib Dunbrack
C101_273-4D01_BG505_RM20A3_real_space_refined_041.pdb #5/L GLU 96: phi -91.9,
psi 45.8 trans
Changed 324 bond radii
> swapaa #!5/L:96 GLU criteria 24 rotLib Dunbrack retain false
Using Dunbrack library
C101_273-4D01_BG505_RM20A3_real_space_refined_041.pdb #!5/L GLU 96: phi -91.9,
psi 45.8 trans
Applying GLU rotamer (chi angles: 67.3 -84.4 17.7) to
C101_273-4D01_BG505_RM20A3_real_space_refined_041.pdb #!5/L GLU 96
> select clear
> select #5/H:100-100d
31 atoms, 31 bonds, 4 residues, 1 model selected
> select #5/H:100-100D
31 atoms, 31 bonds, 4 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 31 atom styles
> color sel byhetero
> select clear
> select #5/L:32
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 12 atom styles
> style sel stick
Changed 12 atom styles
> color sel byhetero
> select clear
> hide #!5 models
> show #!4 models
> select #4
20957 atoms, 21480 bonds, 15 pseudobonds, 2645 residues, 2 models selected
> hide sel atoms
> color #4/A light gray
> color #4/H forest green
> color #4/L lime
> select #4/A:279-280
16 atoms, 15 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 16 atom styles
> color sel byhetero
> select clear
> select #4/L:96
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> color sel byhetero
> select clear
> select #4/H:100-100D
27 atoms, 28 bonds, 3 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 27 atom styles
> color sel byhetero
> select clear
> select #4/H:50
14 atoms, 15 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 14 atom styles
> color sel byhetero
> select clear
> hide #!4 models
> show #!5 models
> select #5/H:50
14 atoms, 15 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> hide #!5 models
> show #!3 models
> hide #!3 models
> show #!6 models
> ui tool show "Side View"
> save "/Users/gozorows/Scripps Research Dropbox/Ward
> Lab/Manuscripts/Gabe/2024_C101trial/figures/206-3G08_279-280.cxs"
> save "/Users/gozorows/Scripps Research Dropbox/Ward
> Lab/Manuscripts/Gabe/2024_C101trial/figures/206-3G08_279-280.png" width 2000
> height 1770 supersample 3 transparentBackground true
> hide #!6 models
> show #!12 models
> save "/Users/gozorows/Scripps Research Dropbox/Ward
> Lab/Manuscripts/Gabe/2024_C101trial/figures/61-12A01_279-280.cxs"
> save "/Users/gozorows/Scripps Research Dropbox/Ward
> Lab/Manuscripts/Gabe/2024_C101trial/figures/61-12A01_279-280.png" width 2000
> height 1770 supersample 3 transparentBackground true
> hide #!12 models
> show #!3 models
> save "/Users/gozorows/Scripps Research Dropbox/Ward
> Lab/Manuscripts/Gabe/2024_C101trial/figures/206-9C09_279-280.cxs"
> save "/Users/gozorows/Scripps Research Dropbox/Ward
> Lab/Manuscripts/Gabe/2024_C101trial/figures/206-9C09_279-280.png" width 2000
> height 1770 supersample 3 transparentBackground true
> hide #!3 models
> show #!4 models
> save "/Users/gozorows/Scripps Research Dropbox/Ward
> Lab/Manuscripts/Gabe/2024_C101trial/figures/253-7A03_279-280.cxs"
> save "/Users/gozorows/Scripps Research Dropbox/Ward
> Lab/Manuscripts/Gabe/2024_C101trial/figures/253-7A03_279-280.png" width 2000
> height 1770 supersample 3 transparentBackground true
> hide #!4 models
> show #!5 models
> save "/Users/gozorows/Scripps Research Dropbox/Ward
> Lab/Manuscripts/Gabe/2024_C101trial/figures/273-4D01_279-280.png" width 2000
> height 1770 supersample 3 transparentBackground true
> show #!2 models
> hide #!2 models
> select #5/A:274-280
54 atoms, 53 bonds, 7 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> select #5/A:276
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> select #5/A:MAN,NAG,BMA
305 atoms, 311 bonds, 22 residues, 1 model selected
> show sel atoms
> hide sel cartoons
> hide sel atoms
> select #5/A:621
14 atoms, 14 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> select #5/A:273-285
103 atoms, 102 bonds, 13 residues, 1 model selected
> show sel cartoons
> select clear
> select #5/H
921 atoms, 946 bonds, 118 residues, 1 model selected
> select #5/H,L
1694 atoms, 1736 bonds, 220 residues, 1 model selected
> hide sel atoms
> select #5/L:29-35
61 atoms, 63 bonds, 7 residues, 1 model selected
> show sel cartoons
> ui tool show "Show Sequence Viewer"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> sequence chain #5/L
Alignment identifier is 5/L
> select #5/L:27-35
74 atoms, 76 bonds, 9 residues, 1 model selected
> select #5/L:27-33
55 atoms, 55 bonds, 7 residues, 1 model selected
> select #5/L
773 atoms, 790 bonds, 102 residues, 1 model selected
> show sel cartoons
> select clear
> select #5/L:27
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/L:27-32
47 atoms, 47 bonds, 6 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> select #5/A:278
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select #5/L
773 atoms, 790 bonds, 102 residues, 1 model selected
> hide sel cartoons
> select #5/27-35
Nothing selected
> select #5/L:27-35
74 atoms, 76 bonds, 9 residues, 1 model selected
> show sel cartoons
> select clear
> show #!4 models
> select #4
20957 atoms, 21480 bonds, 15 pseudobonds, 2645 residues, 2 models selected
> hide sel atoms
> select #4/A:273-285
103 atoms, 102 bonds, 13 residues, 1 model selected
> show sel cartoons
> select #4/A:276,278
15 atoms, 13 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 15 atom styles
> color sel byhetero
> select clear
> select #4/L:27-35
55 atoms, 56 bonds, 7 residues, 1 model selected
> show sel cartoons
> ui tool show "Show Sequence Viewer"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> sequence chain #4/L
Alignment identifier is 4/L
> select #4/L:27
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #4/L:27-33
35 atoms, 34 bonds, 5 residues, 1 model selected
> select #4/L:27
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #4/L:27-32
28 atoms, 27 bonds, 4 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 28 atom styles
> color sel byhetero
> select #4/L:23-35
80 atoms, 81 bonds, 11 residues, 1 model selected
> show sel cartoons
> select #5/L:23-35
102 atoms, 104 bonds, 13 residues, 1 model selected
> show sel cartoons
> select clear
> select #4/A:621
Nothing selected
> hide #!5 models
> select #4/A:MAN:NAG:BMA
305 atoms, 311 bonds, 22 residues, 1 model selected
> show sel atoms
> hide sel atoms
> select #4/A:629
14 atoms, 14 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> show #!3 models
> hide #!3 models
> show #!6 models
> hide #!6 models
> show #!12 models
> hide #!12 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!5 models
> hide #!5 models
> hide #!4 models
> show #!3 models
> select #3
25266 atoms, 25809 bonds, 12 pseudobonds, 3171 residues, 2 models selected
> hide sel atoms
> select #3/A:273-285
107 atoms, 106 bonds, 13 residues, 1 model selected
> show sel cartoons
> select #3/A:276,278
19 atoms, 17 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 19 atom styles
> color sel byhetero
> select clear
> show #!2 models
> select #2
6442 atoms, 6640 bonds, 4 pseudobonds, 752 residues, 2 models selected
> hide sel cartoons
> hide sel atoms
> select #2/Q
39 atoms, 41 bonds, 3 residues, 1 model selected
> show sel atoms
> select clear
> transparency #2 50 target a
> transparency #2 80 target a
> select clear
[Repeated 1 time(s)]
> select #3/L:23-35
107 atoms, 109 bonds, 13 residues, 1 model selected
> show sel cartoons
> select clear
> ui tool show "Show Sequence Viewer"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> sequence chain #3/L
Alignment identifier is 3/L
> select #3/L:27
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/L:27-32
51 atoms, 51 bonds, 6 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 51 atom styles
> color sel byhetero
> select clear
> transparency #2 80 target a
> transparency #2 90 target a
> select #2/Q
39 atoms, 41 bonds, 3 residues, 1 model selected
> ui tool show "Color Actions"
> color sel black
> select clear
> select #2/Q
39 atoms, 41 bonds, 3 residues, 1 model selected
> color sel khaki
> select clear
> select #2/Q
39 atoms, 41 bonds, 3 residues, 1 model selected
> color sel yellow
> select clear
> hide #!3 models
> show #!6 models
> select #6
5441 atoms, 5590 bonds, 2 pseudobonds, 684 residues, 2 models selected
> hide sel atoms
> select #6/L:23-35
119 atoms, 122 bonds, 16 residues, 1 model selected
> show sel cartoons
> select clear
> ui tool show "Show Sequence Viewer"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> sequence chain #6/L
Alignment identifier is 6/L
> select #6/L:27-27A
27 atoms, 26 bonds, 4 residues, 1 model selected
> select #6/L:27-32
68 atoms, 69 bonds, 9 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 68 atom styles
> color sel byhetero
> select clear
> select #6/A:273-285
107 atoms, 106 bonds, 13 residues, 1 model selected
> show sel cartoons
> select clear
> select #6/A:276,278
19 atoms, 17 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 19 atom styles
> color sel byhetero
> select clear
> select #2/A:276
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> color sel yellow
> select clear
> hide #!6 models
> show #!5 models
> hide #!5 models
> show #!4 models
> hide #!4 models
> show #!6 models
> hide #!6 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!6 models
> hide #!6 models
> show #!12 models
> select #12
25044 atoms, 25599 bonds, 6 pseudobonds, 3162 residues, 2 models selected
> hide sel atoms
> select #12/A:273-285
107 atoms, 106 bonds, 13 residues, 1 model selected
> show sel cartoons
> select #12/A:276,278
19 atoms, 17 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 19 atom styles
> color sel byhetero
> select clear
> select #12/L:23-35
106 atoms, 108 bonds, 14 residues, 1 model selected
> show sel cartoons
> select clear
> select #12/A
3807 atoms, 3889 bonds, 1 pseudobond, 469 residues, 2 models selected
> color (#!12 & sel) light gray
> color (#!12 & sel) byhetero
> select clear
> ui tool show "Show Sequence Viewer"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> sequence chain #12/L
Alignment identifier is 12/L
> select #12/L:27
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #12/L:27-32
51 atoms, 51 bonds, 7 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 51 atom styles
> color sel byhetero
> select clear
> hide #!12 models
> show #!6 models
> hide #!6 models
> show #!5 models
> hide #!5 models
> show #!4 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!6 models
> show #!2 models
> hide #!2 models
> hide #!4 models
> show #!4 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> save "/Users/gozorows/Scripps Research Dropbox/Ward
> Lab/Manuscripts/Gabe/2024_C101trial/figures/CDRL1_N276.cxs"
> cartoon style protein modeHelix default arrows false xsection oval width 1
> thickness 1
[Repeated 1 time(s)]
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> save "/Users/gozorows/Scripps Research Dropbox/Ward
> Lab/Manuscripts/Gabe/2024_C101trial/figures/253-7A03_CDRL1_N276.png" width
> 2000 height 1770 supersample 3 transparentBackground true
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
[Repeated 4 time(s)]
> show #!5 models
> hide #!4 models
> save "/Users/gozorows/Scripps Research Dropbox/Ward
> Lab/Manuscripts/Gabe/2024_C101trial/figures/273-4D01_CDRL1_N276.png" width
> 2000 height 1770 supersample 3 transparentBackground true
> hide #!5 models
> show #!4 models
> hide #!4 models
> show #!3 models
> show #!2 models
> hide #!2 models
> show #!2 models
> save "/Users/gozorows/Scripps Research Dropbox/Ward
> Lab/Manuscripts/Gabe/2024_C101trial/figures/206-9C09_CDRL1_N276.png" width
> 2000 height 1770 supersample 3 transparentBackground true
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!6 models
> hide #!6 models
> show #!12 models
> save "/Users/gozorows/Scripps Research Dropbox/Ward
> Lab/Manuscripts/Gabe/2024_C101trial/figures/61-12A01_CDRL1_N276.png" width
> 2000 height 1770 supersample 3 transparentBackground true
> hide #!12 models
> show #!6 models
> save "/Users/gozorows/Scripps Research Dropbox/Ward
> Lab/Manuscripts/Gabe/2024_C101trial/figures/206-3G08_LCDR1_N276.png" width
> 2000 height 1770 supersample 3 transparentBackground true
> save "/Users/gozorows/Scripps Research Dropbox/Ward
> Lab/Manuscripts/Gabe/2024_C101trial/figures/CDRL1_N276.cxs"
——— End of log from Tue Oct 1 23:07:50 2024 ———
opened ChimeraX session
> hide #!6 models
> show #!4 models
> select #4/A:629@O4
1 atom, 1 residue, 1 model selected
> select add #2/Q:1@C4
2 atoms, 2 residues, 2 models selected
> select add #4/A:276
10 atoms, 7 bonds, 3 residues, 2 models selected
> select down
10 atoms, 7 bonds, 3 residues, 2 models selected
> select up
36 atoms, 36 bonds, 3 residues, 2 models selected
> select down
10 atoms, 7 bonds, 3 residues, 2 models selected
> select #4/A:276@ca
1 atom, 1 residue, 1 model selected
> select #4/A:629@O4:#4/A:276@ca
Expected an objects specifier or a keyword
> select #4/A:629@O4,#4/A:276@ca
Expected an objects specifier or a keyword
> select #4/A:629@O4 #4/A:276@ca
2 atoms, 2 residues, 1 model selected
> select #4/A:629@O4 #4/A:276@ca #2/Q:1@O4
3 atoms, 3 residues, 2 models selected
> ui tool show Angles/Torsions
> select #4/A:276@ca #4/A:629@O4 #2/Q:1@O4
3 atoms, 3 residues, 2 models selected
> angle #4/A:276@ca #4/A:629@O4 #2/Q:1@O4
Angle between 253-7A03_BG505_RM20A3_real_space_refined_033.pdb #4/A ASN 276
CA, 253-7A03_BG505_RM20A3_real_space_refined_033.pdb #4/A NAG 629 O4, and 6v8x
#2/Q NAG 1 O4: 72.026
> angle #4/A:629@O4 #4/A:276@ca #2/Q:1@O4
Angle between 253-7A03_BG505_RM20A3_real_space_refined_033.pdb #4/A NAG 629
O4, 253-7A03_BG505_RM20A3_real_space_refined_033.pdb #4/A ASN 276 CA, and 6v8x
#2/Q NAG 1 O4: 49.116
> select #4/A,C,E
11032 atoms, 11328 bonds, 12 pseudobonds, 1356 residues, 2 models selected
> show sel cartoons
> hide sel cartoons
> show sel surfaces
> select #4/A,C,E,B,D,F
14041 atoms, 14400 bonds, 15 pseudobonds, 1729 residues, 2 models selected
> show sel surfaces
> color (#!4 & sel) light gray
> select #4/A:475@CB
1 atom, 1 residue, 1 model selected
> select clear
> select #4/A
3733 atoms, 3835 bonds, 3 pseudobonds, 458 residues, 2 models selected
> hide sel surfaces
> show sel cartoons
> select clear
> hide #4.1 models
> hide #4.2 models
> show #4.2 models
> select #4/L
717 atoms, 733 bonds, 98 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> select clear
> select #2Q
Expected an objects specifier or a keyword
> select #2/Q
39 atoms, 41 bonds, 3 residues, 1 model selected
> color sel black
> transparency sel 0
> transparency #2,a 0
Missing or invalid "percent" argument: Expected a number
> transparency 0 #2/r
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> transparency #2/Q 0
> transparency #2/Q 0 a
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> transparency #2/Q 0 atoms
> select clear
> transparency #2/A 0 atoms
> transparency #2/Q
Missing or invalid "percent" argument: Expected a number
> select #2/Q
39 atoms, 41 bonds, 3 residues, 1 model selected
> color sel cyan
> color sel byhetero
> select #2/A:276
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel cyan
> color sel byhetero
> show sel cartoons
> hide sel cartoons
> select #4/A
3733 atoms, 3835 bonds, 3 pseudobonds, 458 residues, 2 models selected
> select #4/A:276
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/A:276,629
22 atoms, 22 bonds, 2 residues, 1 model selected
> color (#!4 & sel) forest green
> color (#!4 & sel) magenta
> color (#!4 & sel) purple
> color (#!4 & sel) orange red
> color (#!4 & sel) orange
> color (#!4 & sel) byhetero
> select clear
> save "/Users/gozorows/Scripps Research Dropbox/Ward
> Lab/Manuscripts/Gabe/2024_C101trial/figures/253-7A03_VRC01_N276.png" width
> 2000 height 1624 supersample 3 transparentBackground true
> angle #4/A:629@O4 #4/A:276@ca #2/Q:1@O4
Angle between 253-7A03_BG505_RM20A3_real_space_refined_033.pdb #4/A NAG 629
O4, 253-7A03_BG505_RM20A3_real_space_refined_033.pdb #4/A ASN 276 CA, and 6v8x
#2/Q NAG 1 O4: 49.116
> select #4/H,L
1654 atoms, 1695 bonds, 217 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> select #4/A
3733 atoms, 3835 bonds, 3 pseudobonds, 458 residues, 2 models selected
> hide sel cartoons
> show sel surfaces
> select clear
> select #4/A
3733 atoms, 3835 bonds, 3 pseudobonds, 458 residues, 2 models selected
> color (#!4 & sel) light gray
> select #4/A:629
14 atoms, 14 bonds, 1 residue, 1 model selected
> color sel orange
> color sel byhetero
> select clear
> select #4/A:629
14 atoms, 14 bonds, 1 residue, 1 model selected
> style sel sphere
Changed 14 atom styles
> select #2/Q
39 atoms, 41 bonds, 3 residues, 1 model selected
> style sel sphere
Changed 39 atom styles
> select clear
> select #2/Q
39 atoms, 41 bonds, 3 residues, 1 model selected
> color sel cyan
> select #4/A:629
14 atoms, 14 bonds, 1 residue, 1 model selected
> color sel orange
> select clear
> save "/Users/gozorows/Scripps Research Dropbox/Ward
> Lab/Manuscripts/Gabe/2024_C101trial/figures/253-7A03_VRC01_N276_fulltrimer.png"
> width 2000 height 1624 supersample 3 transparentBackground true
> select #4/A
3733 atoms, 3835 bonds, 3 pseudobonds, 458 residues, 2 models selected
> hide sel surfaces
> show sel cartoons
> select #4/A:629
14 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 14 atom styles
> select #2/Q
39 atoms, 41 bonds, 3 residues, 1 model selected
> style sel stick
Changed 39 atom styles
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> color (#!4 & sel) orange
> select clear
> show #!5 models
> select #5/H,L
1694 atoms, 1736 bonds, 220 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> select #5/A:629
Nothing selected
> select #5/A:621
14 atoms, 14 bonds, 1 residue, 1 model selected
> select ~sel & ##selected
20941 atoms, 21464 bonds, 14 pseudobonds, 2642 residues, 2 models selected
> select #5/A:621,276
22 atoms, 22 bonds, 2 residues, 1 model selected
> color sel purple
> select #2/A:276@CG
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
76 atoms, 75 bonds, 10 residues, 1 model selected
> select down
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
76 atoms, 75 bonds, 10 residues, 1 model selected
> color sel cyan
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
7 atoms, 6 bonds, 1 residue, 2 models selected
> hide sel atoms
> select #5/A:278@CB
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> angle #5/A:621@O4 #5/A:276@ca #2/Q:1@O4
Angle between C101_273-4D01_BG505_RM20A3_real_space_refined_041.pdb #5/A NAG
621 O4, C101_273-4D01_BG505_RM20A3_real_space_refined_041.pdb #5/A ASN 276 CA,
and 6v8x #2/Q NAG 1 O4: 42.431
> select clear
> save "/Users/gozorows/Scripps Research Dropbox/Ward
> Lab/Manuscripts/Gabe/2024_C101trial/figures/273-4D01_253-7A03_VRC01_276displacement.png"
> width 2000 height 1624 supersample 3 transparentBackground true
> save "/Users/gozorows/Scripps Research Dropbox/Ward
> Lab/Manuscripts/Gabe/2024_C101trial/figures/N276_displacement_figure.cxs"
——— End of log from Fri Dec 13 00:29:23 2024 ———
opened ChimeraX session
> open 6v0r
6v0r title:
BG505 SOSIP.664 Trimer [more info...]
Chain information for 6v0r #1
---
Chain | Description | UniProt
A C D | BG505 SOSIPv5.2 gp120 | Q2N0S6_9HIV1 31-507
B E F | BG505 SOSIPv5.2 gp41 | Q2N0S6_9HIV1 512-664
Non-standard residues in 6v0r #1
---
BMA — beta-D-mannopyranose
FUC — alpha-L-fucopyranose
MAN — alpha-D-mannopyranose
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose
> select #1
14910 atoms, 15330 bonds, 12 pseudobonds, 1812 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> mmaker #1/A to #2/A
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 6v8x, chain A (#2) with 6v0r, chain A (#1), sequence alignment
score = 2210.9
RMSD between 408 pruned atom pairs is 0.928 angstroms; (across all 433 pairs:
1.286)
> select #1
14910 atoms, 15330 bonds, 12 pseudobonds, 1812 residues, 2 models selected
> hide sel cartoons
> select #1/A:276
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> color sel white
> color sel gray
> color sel light gray
> select clear
> select #1/A:276@O
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #1/A:276@N
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #1/A:NAG
126 atoms, 126 bonds, 9 residues, 1 model selected
> show sel atoms
> hide sel atoms
> select #1:NAG
1176 atoms, 1200 bonds, 84 residues, 1 model selected
> show sel atoms
> select #1:NAG:MAN
1275 atoms, 1302 bonds, 93 residues, 1 model selected
> show sel atoms
> hide sel atoms
> select #1/H
28 atoms, 29 bonds, 2 residues, 1 model selected
> show sel atoms
> color sel light gray
> select clear
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!4 models
> show #!4 models
> hide #!3 models
> show #!3 models
> select #3/H,L
1758 atoms, 1801 bonds, 225 residues, 1 model selected
> show sel cartoons
> hide #!3 models
> select clear
> save "/Users/gozorows/Scripps Research Dropbox/Ward
> Lab/Manuscripts/Gabe/2024_C101trial/figures/N276_displacement_figure.cxs"
——— End of log from Tue Jan 7 12:51:49 2025 ———
opened ChimeraX session
> save "/Users/gozorows/Scripps Research Dropbox/Ward
> Lab/Manuscripts/Gabe/2024_C101trial/figures/N276_displacement_apo_compare_v2.png"
> width 2000 height 2206 supersample 3 transparentBackground true
> ui tool show Angles/Torsions
> select #2/Q:1@O4
1 atom, 1 residue, 1 model selected
> select #2/Q:1@O4, #2/A:276@ca
Expected an objects specifier or a keyword
> select #2/Q:1@O4: #2/A:276@ca
Expected an objects specifier or a keyword
> select #2/Q:1@O4, #2/A:276@ca
Expected an objects specifier or a keyword
> select #2/Q:1@O4:#2/A:276@ca
Expected an objects specifier or a keyword
> select #2/Q:1@O4 & #2/A:276@ca
Nothing selected
> select #2/Q:1@O4 :. #2/A:276@ca
Expected a keyword
> select #2/Q:1@O4/#2/A:276@ca
Expected an objects specifier or a keyword
> select #2/Q:1@O4
1 atom, 1 residue, 1 model selected
> select #2/Q:1@O4 & #2/A
Nothing selected
> select #2/Q:1@O4 & #2/A:276@ca
Nothing selected
> select #2/Q:1@O4 & (#2/A:276@ca)
Nothing selected
> select #2/Q:1@O4 | #2/A:276@ca
2 atoms, 2 residues, 1 model selected
> select #2/Q:1@O4 | #2/A:276@ca | #4/A:629@O4
3 atoms, 3 residues, 2 models selected
> select #2/A:276@ca | #2/Q:1@O4 | #4/A:629@O4
3 atoms, 3 residues, 2 models selected
> angle #2/Q:1@O4 | #2/A:276@ca | #4/A:629@O4
Angle between 6v8x #2/Q NAG 1 O4, 6v8x #2/A ASN 276 CA, and
253-7A03_BG505_RM20A3_real_space_refined_033.pdb #4/A NAG 629 O4: 50.929
> angle #1/H:1@O4 | #1/A:276@ca | #2/Q:1@O4
Angle between 6v0r #1/H NAG 1 O4, 6v0r #1/A ASN 276 CA, and 6v8x #2/Q NAG 1
O4: 33.774
> angle #1/H:1@O4 | #1/A:276@ca | #5/A:621@O4
Angle between 6v0r #1/H NAG 1 O4, 6v0r #1/A ASN 276 CA, and
C101_273-4D01_BG505_RM20A3_real_space_refined_041.pdb #5/A NAG 621 O4: 64.719
> angle #1/H:1@O4 | #1/A:276@ca | #4/A:629@O4
Angle between 6v0r #1/H NAG 1 O4, 6v0r #1/A ASN 276 CA, and
253-7A03_BG505_RM20A3_real_space_refined_033.pdb #4/A NAG 629 O4: 71.473
> save "/Users/gozorows/Scripps Research Dropbox/Ward
> Lab/Manuscripts/Gabe/2024_C101trial/figures/N276_displacement_figure.cxs"
——— End of log from Mon Feb 24 15:16:39 2025 ———
opened ChimeraX session
> select clear
> open /Users/gozorows/Library/CloudStorage/OneDrive-
> TheScrippsResearchInstitute/TSRI/EM/Clinical_trial_samples/C101/Sashank/October_2025_Sashank_C107_C101_xray/273_5G10_Q23gp120_refine_014.pdb
Chain information for 273_5G10_Q23gp120_refine_014.pdb #7
---
Chain | Description
C | No description available
H | No description available
L | No description available
Computing secondary structure
> hide #!1 models
> show #!1 models
> mmaker #7/C to #4/A
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 253-7A03_BG505_RM20A3_real_space_refined_033.pdb, chain A (#4) with
273_5G10_Q23gp120_refine_014.pdb, chain C (#7), sequence alignment score =
1073
RMSD between 261 pruned atom pairs is 0.855 angstroms; (across all 281 pairs:
2.108)
> select #7/C:276,506
22 atoms, 22 bonds, 2 residues, 1 model selected
> select ~sel & ##selected
5710 atoms, 5852 bonds, 5 pseudobonds, 730 residues, 2 models selected
> hide sel atoms
> hide sel cartoons
> select #7/C:276,506
22 atoms, 22 bonds, 2 residues, 1 model selected
> color sel lime
> select clear
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> close #12
> hide #!2 models
> show #!2 models
> show #!3 models
> close #3
> close #6
> open /Users/gozorows/Library/CloudStorage/OneDrive-
> TheScrippsResearchInstitute/TSRI/EM/Clinical_trial_samples/C101/Sashank/October_2025_Sashank_C107_C101_xray/187_6H10_Q23gp120_refine_018.pdb
Chain information for 187_6H10_Q23gp120_refine_018.pdb #3
---
Chain | Description
C | No description available
H | No description available
L | No description available
Computing secondary structure
> mmaker #3/C to #4/A
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 253-7A03_BG505_RM20A3_real_space_refined_033.pdb, chain A (#4) with
187_6H10_Q23gp120_refine_018.pdb, chain C (#3), sequence alignment score =
1048.3
RMSD between 255 pruned atom pairs is 0.868 angstroms; (across all 278 pairs:
2.053)
> select #3/C:507,276
22 atoms, 22 bonds, 2 residues, 1 model selected
> select ~sel & ##selected
5677 atoms, 5820 bonds, 6 pseudobonds, 724 residues, 2 models selected
> hide sel atoms
> hide sel cartoons
> select #3/C:507,276
22 atoms, 22 bonds, 2 residues, 1 model selected
> ui tool show "Color Actions"
> color sel tomato
> color sel saddle brown
> color sel chocolate
> color sel orange red
> color sel red
> color sel orange red
> color sel blue
> select clear
> select #3/C:507,276
22 atoms, 22 bonds, 2 residues, 1 model selected
> color sel pale violet red
> color sel deep pink
> select clear
> select #3/C:507,276
22 atoms, 22 bonds, 2 residues, 1 model selected
> color sel royal blue
> color sel dark blue
> select clear
> select #3/C:507,276
22 atoms, 22 bonds, 2 residues, 1 model selected
> color sel green
> color sel forest green
> color sel dark orange
> color sel brown
> color sel fire brick
> color sel crimson
> color sel red
> color sel orange red
> color sel red
> select clear
> open /Users/gozorows/Library/CloudStorage/OneDrive-
> TheScrippsResearchInstitute/TSRI/EM/Clinical_trial_samples/C101/Sashank/October_2025_Sashank_C107_C101_xray/61_2A05_Q23gp120_refine_023.pdb
Chain information for 61_2A05_Q23gp120_refine_023.pdb #6
---
Chain | Description
C | No description available
H | No description available
L | No description available
Computing secondary structure
> hide #!6 models
> show #!6 models
> mmaker #6/C to #4/A
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 253-7A03_BG505_RM20A3_real_space_refined_033.pdb, chain A (#4) with
61_2A05_Q23gp120_refine_023.pdb, chain C (#6), sequence alignment score =
1067.9
RMSD between 268 pruned atom pairs is 0.833 angstroms; (across all 280 pairs:
2.285)
> select #6/C:276,506
22 atoms, 22 bonds, 2 residues, 1 model selected
> select ~sel & ##selected
5752 atoms, 5897 bonds, 5 pseudobonds, 737 residues, 2 models selected
> hide sel atoms
> hide sel cartoons
> select #6/C:276,506
22 atoms, 22 bonds, 2 residues, 1 model selected
> color sel blue
> select clear
> save "/Users/gozorows/OneDrive - The Scripps Research
> Institute/TSRI/EM/Clinical_trial_samples/C101/VRC01_class_analysis/N276_displacement_C101_C107_VRC01class.cxs"
> view name N276
> save "/Users/gozorows/OneDrive - The Scripps Research
> Institute/TSRI/EM/Clinical_trial_samples/C101/VRC01_class_analysis/N276_displacement_C101_C107_VRC01class.cxs"
> save "/Users/gozorows/OneDrive - The Scripps Research
> Institute/TSRI/EM/Clinical_trial_samples/C101/VRC01_class_analysis/N276_all_C101_C107.png"
> width 2000 height 2102 supersample 3 transparentBackground true
> hide #!3 models
> hide #!2 models
> save "/Users/gozorows/OneDrive - The Scripps Research
> Institute/TSRI/EM/Clinical_trial_samples/C101/VRC01_class_analysis/N276_noVRC01_no187-6H10.png"
> width 2000 height 2102 supersample 3 transparentBackground true
> show #!2 models
> show #!3 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> hide #!7 models
> show #!4 models
> hide #!4 models
> show #!5 models
> show #!4 models
> show #!6 models
> show #!7 models
> hide #!1 models
> show #!1 models
> select #1/A
3588 atoms, 3680 bonds, 3 pseudobonds, 448 residues, 2 models selected
> show sel cartoons
> Display cartoons as licorice: car style protein modeh default arrows f xsect
> oval width 1 thick 1
Unknown command: Display cartoons as licorice: car style protein modeh default
arrows f xsect oval width 1 thick 1
> cartoon style protein modeHelix default arrows false xsection oval width 1
> thickness 1
> color (#!1 & sel) light gray
> select clear
> select #4,5/A
7424 atoms, 7626 bonds, 6 pseudobonds, 911 residues, 4 models selected
> hide sel cartoons
> select clear
> hide #!7 models
> hide #!6 models
> hide #!5 models
> hide #!4 models
> hide #!3 models
> hide #!2 models
> hide #!1 models
> show #!2 models
> show #!1 models
> select #2/A:276@CB
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
76 atoms, 75 bonds, 10 residues, 1 model selected
> select down
8 atoms, 7 bonds, 1 residue, 1 model selected
> select sideonly
36680 atoms, 29200 bonds, 8921 residues, 7 models selected
> select #2/A:276
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #2/A:276 sideonly
Expected a keyword
> select #2/A:276:sideonly
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select #2/A:276@O
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #2/A:276@N
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #2/A:276@C
1 atom, 1 residue, 1 model selected
> hide sel atoms
> hide #1.1 models
> show #!3 models
> select #3/C:276@CG
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #3/C:276@N
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #3/C:276@O
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #3/C:276@C
1 atom, 1 residue, 1 model selected
> hide sel atoms
> hide #!3 models
> show #!3 models
> show #!4 models
> select #4/A:276@O
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #4/A:276@N
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #4/A:276@C
1 atom, 1 residue, 1 model selected
> hide sel atoms
> show #!5 models
> select #5/A:276@O
1 atom, 1 residue, 1 model selected
> hide sel atoms
> hide #!1 models
> select #5/A:276@C
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #5/A:276@N
1 atom, 1 residue, 1 model selected
> hide sel atoms
> show #!6 models
> select #6/C:276
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
76 atoms, 75 bonds, 10 residues, 1 model selected
> hide sel cartoons
> select clear
> select #6/C:276@O
1 atom, 1 residue, 1 model selected
> hide sel cartoons
> hide sel atoms
> select #6/C:276@C
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #6/C:276@N
1 atom, 1 residue, 1 model selected
> hide sel atoms
> show #!7 models
> select #7/C:276
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
70 atoms, 69 bonds, 9 residues, 1 model selected
> select down
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select clear
> select #7/C:276@O
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #7/C:276@N
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #7/C:276@C
1 atom, 1 residue, 1 model selected
> hide sel atoms
> show #!1 models
> view N276
> save "/Users/gozorows/OneDrive - The Scripps Research
> Institute/TSRI/EM/Clinical_trial_samples/C101/VRC01_class_analysis/N276_all_C101_C107.png"
> width 2000 height 2102 supersample 3 transparentBackground true
> hide #!3 models
> hide #!2 models
> save "/Users/gozorows/OneDrive - The Scripps Research
> Institute/TSRI/EM/Clinical_trial_samples/C101/VRC01_class_analysis/N276_noVRC01_no187-6H10.png"
> width 2000 height 2102 supersample 3 transparentBackground true
> show #!2 models
> show #!3 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> hide #!7 models
> save "/Users/gozorows/OneDrive - The Scripps Research
> Institute/TSRI/EM/Clinical_trial_samples/C101/VRC01_class_analysis/N276_VRC01_187-6H10.png"
> width 2000 height 2102 supersample 3 transparentBackground true
> angle #1/H:1@O4 #1/A:276:@ca #3/C:507@O4
Unknown command: measure angle #1/H:1@O4 #1/A:276:@ca #3/C:507@O4
> angle #1/H:1@O4 #1/A:276:@ca #3/C:507@O4
Expected a number or a keyword
> angle #1/H:1@O4 #1/A:276:@ca #3/C:507@O4
Unknown command: measure angle #1/H:1@O4 #1/A:276:@ca #3/C:507@O4
> save "/Users/gozorows/OneDrive - The Scripps Research
> Institute/TSRI/EM/Clinical_trial_samples/C101/VRC01_class_analysis/N276_displacement_C101_C107_VRC01class.cxs"
——— End of log from Wed Nov 5 09:39:56 2025 ———
opened ChimeraX session
> view N276
> show #!4 models
> show #!5 models
> show #!6 models
> show #!7 models
> select #1-7
80469 atoms, 82563 bonds, 61 pseudobonds, 10049 residues, 14 models selected
> hide sel surfaces
> select clear
> save "/Users/gozorows/OneDrive - The Scripps Research
> Institute/TSRI/EM/Clinical_trial_samples/C101/VRC01_class_analysis/N276_displacement_C101_C107_VRC01class.cxs"
——— End of log from Wed Nov 5 13:21:24 2025 ———
> view name session-start
opened ChimeraX session
> save "/Users/sphulera/OneDrive - The Scripps Research
> Institute/EM/Clinical_trial_samples/C101/VRC01_class_analysis/N276_displacement_C101_C107_VRC01class_SPcopy.cxs"
> includeMaps true
——— End of log from Thu Nov 6 11:40:33 2025 ———
> view name session-start
opened ChimeraX session
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/sphulera/Desktop/movie1.mp4
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/toolbar/tool.py", line 185, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 397, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1419, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/__init__.py", line 66, in run_provider
shortcuts.run_provider(session, name)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 1394, in run_provider
keyboard_shortcuts(session).try_shortcut(name)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 403, in try_shortcut
self.run_shortcut(keys)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 421, in run_shortcut
sc.run(self.session, status = self._enabled)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 340, in run
f(s)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 1312, in save_spin_movie
run(session, cmd)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 537, in run
run_command(session, command, **kw)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3221, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/movie/moviecmd.py", line 202, in movie_encode
encode_op(session, output[-1], format, quality, qscale, bitrate,
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/movie/moviecmd.py", line 260, in encode_op
movie.start_encoding(output, f['ffmpeg_name'], output_size, f['ffmpeg_codec'],
"yuv420p", f['size_restriction'],
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/movie/movie.py", line 324, in start_encoding
self.encoder.run(Status_Reporter())
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/movie/encode.py", line 232, in run
p = Popen(self.arg_list, stdin=DEVNULL, stdout=PIPE, stderr=PIPE)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/subprocess.py",
line 1026, in __init__
self._execute_child(args, executable, preexec_fn, close_fds,
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/subprocess.py",
line 1950, in _execute_child
raise child_exception_type(errno_num, err_msg, err_filename)
PermissionError: [Errno 13] Permission denied:
'/Applications/ChimeraX-1.10.app/Contents/bin/ffmpeg'
PermissionError: [Errno 13] Permission denied:
'/Applications/ChimeraX-1.10.app/Contents/bin/ffmpeg'
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/subprocess.py",
line 1950, in _execute_child
raise child_exception_type(errno_num, err_msg, err_filename)
See log for complete Python traceback.
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M3
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 Air
Model Identifier: Mac15,12
Model Number: Z1B600163LL/A
Chip: Apple M3
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 11881.140.96
OS Loader Version: 11881.140.96
Software:
System Software Overview:
System Version: macOS 15.6.1 (24G90)
Kernel Version: Darwin 24.6.0
Time since boot: 4 days, 22 hours, 22 minutes
Graphics/Displays:
Apple M3:
Chipset Model: Apple M3
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina Display
Resolution: 2560 x 1664 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
LG HDR 4K:
Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
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 , 4 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 , 4 weeks ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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Hi Swastik,
--Eric