![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 15 months ago
Closed 15 months ago
#15615 closed defect (duplicate)
Crash changing display configuration on Mac
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: macOS-14.5-x86_64-i386-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
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{
"uptime" : 11000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "MacBookPro15,1",
"coalitionID" : 2463,
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"build" : "23F79",
"releaseType" : "User"
},
"captureTime" : "2024-07-16 11:16:06.0922 +0200",
"codeSigningMonitor" : 0,
"incident" : "4913C447-D3CB-410E-9E4B-38729633C12C",
"pid" : 4927,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-07-16 11:15:40.3096 +0200",
"procStartAbsTime" : 11896597222802,
"procExitAbsTime" : 11922377296471,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/Biology\/*\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
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"parentProc" : "launchd",
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"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "0D5DE8DA-3A8B-C1EA-D7CC-5AC7584FDF08",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
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"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
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Log:
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs"
Log from Mon Jul 15 16:59:09 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs"
Log from Mon Jul 15 16:48:15 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs"
Log from Mon Jul 15 14:11:54 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs"
Log from Sun Jul 14 15:37:22 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs"
Log from Sun Jul 14 15:13:35 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" format session
Log from Sun Jul 14 14:55:26 2024 Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/Jean/Desktop/3j0c.pdb1
3j0c.pdb1 title:
Models of E1, E2 and CP of venezuelan equine encephalitis virus Tc-83 strain
restrained by A near atomic resolution cryo-em map [more info...]
Chain information for 3j0c.pdb1
---
Chain | Description
1.1/A 1.2/A 1.3/A 1.4/A 1.5/A 1.6/A 1.7/A 1.8/A 1.9/A 1.10/A 1.11/A 1.12/A 1.13/A 1.14/A 1.15/A 1.16/A 1.17/A 1.18/A 1.19/A 1.20/A 1.21/A 1.22/A 1.23/A 1.24/A 1.25/A 1.26/A 1.27/A 1.28/A 1.29/A 1.30/A 1.31/A 1.32/A 1.33/A 1.34/A 1.35/A 1.36/A 1.37/A 1.38/A 1.39/A 1.40/A 1.41/A 1.42/A 1.43/A 1.44/A 1.45/A 1.46/A 1.47/A 1.48/A 1.49/A 1.50/A 1.51/A 1.52/A 1.53/A 1.54/A 1.55/A 1.56/A 1.57/A 1.58/A 1.59/A 1.60/A 1.1/D 1.2/D 1.3/D 1.4/D 1.5/D 1.6/D 1.7/D 1.8/D 1.9/D 1.10/D 1.11/D 1.12/D 1.13/D 1.14/D 1.15/D 1.16/D 1.17/D 1.18/D 1.19/D 1.20/D 1.21/D 1.22/D 1.23/D 1.24/D 1.25/D 1.26/D 1.27/D 1.28/D 1.29/D 1.30/D 1.31/D 1.32/D 1.33/D 1.34/D 1.35/D 1.36/D 1.37/D 1.38/D 1.39/D 1.40/D 1.41/D 1.42/D 1.43/D 1.44/D 1.45/D 1.46/D 1.47/D 1.48/D 1.49/D 1.50/D 1.51/D 1.52/D 1.53/D 1.54/D 1.55/D 1.56/D 1.57/D 1.58/D 1.59/D 1.60/D 1.1/G 1.2/G 1.3/G 1.4/G 1.5/G 1.6/G 1.7/G 1.8/G 1.9/G 1.10/G 1.11/G 1.12/G 1.13/G 1.14/G 1.15/G 1.16/G 1.17/G 1.18/G 1.19/G 1.20/G 1.21/G 1.22/G 1.23/G 1.24/G 1.25/G 1.26/G 1.27/G 1.28/G 1.29/G 1.30/G 1.31/G 1.32/G 1.33/G 1.34/G 1.35/G 1.36/G 1.37/G 1.38/G 1.39/G 1.40/G 1.41/G 1.42/G 1.43/G 1.44/G 1.45/G 1.46/G 1.47/G 1.48/G 1.49/G 1.50/G 1.51/G 1.52/G 1.53/G 1.54/G 1.55/G 1.56/G 1.57/G 1.58/G 1.59/G 1.60/G 1.1/J 1.2/J 1.3/J 1.4/J 1.5/J 1.6/J 1.7/J 1.8/J 1.9/J 1.10/J 1.11/J 1.12/J 1.13/J 1.14/J 1.15/J 1.16/J 1.17/J 1.18/J 1.19/J 1.20/J 1.21/J 1.22/J 1.23/J 1.24/J 1.25/J 1.26/J 1.27/J 1.28/J 1.29/J 1.30/J 1.31/J 1.32/J 1.33/J 1.34/J 1.35/J 1.36/J 1.37/J 1.38/J 1.39/J 1.40/J 1.41/J 1.42/J 1.43/J 1.44/J 1.45/J 1.46/J 1.47/J 1.48/J 1.49/J 1.50/J 1.51/J 1.52/J 1.53/J 1.54/J 1.55/J 1.56/J 1.57/J 1.58/J 1.59/J 1.60/J | No description available
1.1/B 1.2/B 1.3/B 1.4/B 1.5/B 1.6/B 1.7/B 1.8/B 1.9/B 1.10/B 1.11/B 1.12/B 1.13/B 1.14/B 1.15/B 1.16/B 1.17/B 1.18/B 1.19/B 1.20/B 1.21/B 1.22/B 1.23/B 1.24/B 1.25/B 1.26/B 1.27/B 1.28/B 1.29/B 1.30/B 1.31/B 1.32/B 1.33/B 1.34/B 1.35/B 1.36/B 1.37/B 1.38/B 1.39/B 1.40/B 1.41/B 1.42/B 1.43/B 1.44/B 1.45/B 1.46/B 1.47/B 1.48/B 1.49/B 1.50/B 1.51/B 1.52/B 1.53/B 1.54/B 1.55/B 1.56/B 1.57/B 1.58/B 1.59/B 1.60/B 1.1/E 1.2/E 1.3/E 1.4/E 1.5/E 1.6/E 1.7/E 1.8/E 1.9/E 1.10/E 1.11/E 1.12/E 1.13/E 1.14/E 1.15/E 1.16/E 1.17/E 1.18/E 1.19/E 1.20/E 1.21/E 1.22/E 1.23/E 1.24/E 1.25/E 1.26/E 1.27/E 1.28/E 1.29/E 1.30/E 1.31/E 1.32/E 1.33/E 1.34/E 1.35/E 1.36/E 1.37/E 1.38/E 1.39/E 1.40/E 1.41/E 1.42/E 1.43/E 1.44/E 1.45/E 1.46/E 1.47/E 1.48/E 1.49/E 1.50/E 1.51/E 1.52/E 1.53/E 1.54/E 1.55/E 1.56/E 1.57/E 1.58/E 1.59/E 1.60/E 1.1/H 1.2/H 1.3/H 1.4/H 1.5/H 1.6/H 1.7/H 1.8/H 1.9/H 1.10/H 1.11/H 1.12/H 1.13/H 1.14/H 1.15/H 1.16/H 1.17/H 1.18/H 1.19/H 1.20/H 1.21/H 1.22/H 1.23/H 1.24/H 1.25/H 1.26/H 1.27/H 1.28/H 1.29/H 1.30/H 1.31/H 1.32/H 1.33/H 1.34/H 1.35/H 1.36/H 1.37/H 1.38/H 1.39/H 1.40/H 1.41/H 1.42/H 1.43/H 1.44/H 1.45/H 1.46/H 1.47/H 1.48/H 1.49/H 1.50/H 1.51/H 1.52/H 1.53/H 1.54/H 1.55/H 1.56/H 1.57/H 1.58/H 1.59/H 1.60/H 1.1/K 1.2/K 1.3/K 1.4/K 1.5/K 1.6/K 1.7/K 1.8/K 1.9/K 1.10/K 1.11/K 1.12/K 1.13/K 1.14/K 1.15/K 1.16/K 1.17/K 1.18/K 1.19/K 1.20/K 1.21/K 1.22/K 1.23/K 1.24/K 1.25/K 1.26/K 1.27/K 1.28/K 1.29/K 1.30/K 1.31/K 1.32/K 1.33/K 1.34/K 1.35/K 1.36/K 1.37/K 1.38/K 1.39/K 1.40/K 1.41/K 1.42/K 1.43/K 1.44/K 1.45/K 1.46/K 1.47/K 1.48/K 1.49/K 1.50/K 1.51/K 1.52/K 1.53/K 1.54/K 1.55/K 1.56/K 1.57/K 1.58/K 1.59/K 1.60/K | No description available
1.1/C 1.2/C 1.3/C 1.4/C 1.5/C 1.6/C 1.7/C 1.8/C 1.9/C 1.10/C 1.11/C 1.12/C 1.13/C 1.14/C 1.15/C 1.16/C 1.17/C 1.18/C 1.19/C 1.20/C 1.21/C 1.22/C 1.23/C 1.24/C 1.25/C 1.26/C 1.27/C 1.28/C 1.29/C 1.30/C 1.31/C 1.32/C 1.33/C 1.34/C 1.35/C 1.36/C 1.37/C 1.38/C 1.39/C 1.40/C 1.41/C 1.42/C 1.43/C 1.44/C 1.45/C 1.46/C 1.47/C 1.48/C 1.49/C 1.50/C 1.51/C 1.52/C 1.53/C 1.54/C 1.55/C 1.56/C 1.57/C 1.58/C 1.59/C 1.60/C 1.1/F 1.2/F 1.3/F 1.4/F 1.5/F 1.6/F 1.7/F 1.8/F 1.9/F 1.10/F 1.11/F 1.12/F 1.13/F 1.14/F 1.15/F 1.16/F 1.17/F 1.18/F 1.19/F 1.20/F 1.21/F 1.22/F 1.23/F 1.24/F 1.25/F 1.26/F 1.27/F 1.28/F 1.29/F 1.30/F 1.31/F 1.32/F 1.33/F 1.34/F 1.35/F 1.36/F 1.37/F 1.38/F 1.39/F 1.40/F 1.41/F 1.42/F 1.43/F 1.44/F 1.45/F 1.46/F 1.47/F 1.48/F 1.49/F 1.50/F 1.51/F 1.52/F 1.53/F 1.54/F 1.55/F 1.56/F 1.57/F 1.58/F 1.59/F 1.60/F 1.1/I 1.2/I 1.3/I 1.4/I 1.5/I 1.6/I 1.7/I 1.8/I 1.9/I 1.10/I 1.11/I 1.12/I 1.13/I 1.14/I 1.15/I 1.16/I 1.17/I 1.18/I 1.19/I 1.20/I 1.21/I 1.22/I 1.23/I 1.24/I 1.25/I 1.26/I 1.27/I 1.28/I 1.29/I 1.30/I 1.31/I 1.32/I 1.33/I 1.34/I 1.35/I 1.36/I 1.37/I 1.38/I 1.39/I 1.40/I 1.41/I 1.42/I 1.43/I 1.44/I 1.45/I 1.46/I 1.47/I 1.48/I 1.49/I 1.50/I 1.51/I 1.52/I 1.53/I 1.54/I 1.55/I 1.56/I 1.57/I 1.58/I 1.59/I 1.60/I 1.1/L 1.2/L 1.3/L 1.4/L 1.5/L 1.6/L 1.7/L 1.8/L 1.9/L 1.10/L 1.11/L 1.12/L 1.13/L 1.14/L 1.15/L 1.16/L 1.17/L 1.18/L 1.19/L 1.20/L 1.21/L 1.22/L 1.23/L 1.24/L 1.25/L 1.26/L 1.27/L 1.28/L 1.29/L 1.30/L 1.31/L 1.32/L 1.33/L 1.34/L 1.35/L 1.36/L 1.37/L 1.38/L 1.39/L 1.40/L 1.41/L 1.42/L 1.43/L 1.44/L 1.45/L 1.46/L 1.47/L 1.48/L 1.49/L 1.50/L 1.51/L 1.52/L 1.53/L 1.54/L 1.55/L 1.56/L 1.57/L 1.58/L 1.59/L 1.60/L | No description available
> set bgColor white
> save /Users/Jean/Desktop/image1.png supersample 3
> save "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" includeMaps true
——— End of log from Sun Jul 14 14:55:26 2024 ———
opened ChimeraX session
> hide cartoons
> hide atoms
> select #1.1/A
3370 atoms, 3467 bonds, 442 residues, 1 model selected
> ui tool show Matchmaker
> show sel cartoons
> view sel
> open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
Chain information for AF3 E1 1-421.pdb #2
---
Chain | Description
A | No description available
> matchmaker #2 to #1.1 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain A (#1.1) with AF3 E1 1-421.pdb, chain A (#2),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
3.020)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #3
---
Chain | Description
A | No description available
> matchmaker #3 to #1.1 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain A (#1.1) with AF3 E1 422-461.pdb, chain A (#3),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.572 angstroms; (across all 38 pairs:
2.776)
> select #1.1/B
3304 atoms, 3400 bonds, 423 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
Chain information for AF3 E2 1-352.pdb #4
---
Chain | Description
B | No description available
> matchmaker #4 to #1.1 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain B (#1.1) with AF3 E2 1-352.pdb, chain B (#4),
sequence alignment score = 583.7
RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
5.933)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #5
---
Chain | Description
B | No description available
> matchmaker #5 to #1.1 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain B (#1.1) with AF3 E2 353-438.pdb, chain B (#5),
sequence alignment score = 333.4
RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
8.411)
> save "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" includeMaps true
——— End of log from Sun Jul 14 15:13:35 2024 ———
opened ChimeraX session
> select #1.1/C
1277 atoms, 1305 bonds, 162 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 CA.pdb"
Chain information for AF3 CA.pdb #6
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #6 to #1.1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain F (#1.1) with AF3 CA.pdb, chain A (#6), sequence
alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> matchmaker #6 to #1.1 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain C (#1.1) with AF3 CA.pdb, chain A (#6), sequence
alignment score = 328.1
RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
2.714)
> save "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" includeMaps true
——— End of log from Sun Jul 14 15:37:22 2024 ———
opened ChimeraX session
> color #2 dodgerblue
> color #3 dodgerblue
> color #4 #00b305ff
> color #5 #00b305ff
> color #6 #f15839ff
> select #1.1/A
3370 atoms, 3467 bonds, 442 residues, 1 model selected
> hide sel cartoons
> select #1.1/B
3304 atoms, 3400 bonds, 423 residues, 1 model selected
> hide sel cartoons
> select #1.1/C
1277 atoms, 1305 bonds, 162 residues, 1 model selected
> hide sel cartoons
> ui tool show Matchmaker
> open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
Chain information for AF3 E1 1-421.pdb #7
---
Chain | Description
A | No description available
> select #1.2/A
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> show sel cartoons
> matchmaker #7 to #1.2 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain A (#1.2) with AF3 E1 1-421.pdb, chain A (#7),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
3.020)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #8
---
Chain | Description
A | No description available
> matchmaker #8 to #1.2 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain A (#1.2) with AF3 E1 422-461.pdb, chain A (#8),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.572 angstroms; (across all 38 pairs:
2.775)
> select #1.2/B
3304 atoms, 3395 bonds, 423 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
Chain information for AF3 E2 1-352.pdb #9
---
Chain | Description
B | No description available
> matchmaker #9 to #1.2 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain B (#1.2) with AF3 E2 1-352.pdb, chain B (#9),
sequence alignment score = 583.7
RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
5.933)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #10
---
Chain | Description
B | No description available
> matchmaker #10 to #1.2 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain B (#1.2) with AF3 E2 353-438.pdb, chain B (#10),
sequence alignment score = 322.6
RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
8.411)
> select #1.3/A
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> select clear
> select #1.2/C
1277 atoms, 1305 bonds, 162 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 CA.pdb"
Chain information for AF3 CA.pdb #11
---
Chain | Description
A | No description available
> matchmaker #10 to #1.2 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain C (#1.2) with AF3 E2 353-438.pdb, chain B (#10),
sequence alignment score = 16.2
RMSD between 8 pruned atom pairs is 0.563 angstroms; (across all 28 pairs:
19.587)
> select #1.2/B
3304 atoms, 3395 bonds, 423 residues, 1 model selected
> matchmaker #10 to #1.2 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain B (#1.2) with AF3 E2 353-438.pdb, chain B (#10),
sequence alignment score = 322.6
RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
8.411)
> select #1.3/C
1277 atoms, 1305 bonds, 162 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> select #1.2/C
1277 atoms, 1305 bonds, 162 residues, 1 model selected
> show sel cartoons
> matchmaker #11 to #1.2 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain C (#1.2) with AF3 CA.pdb, chain A (#11), sequence
alignment score = 328.1
RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
2.714)
> hide sel cartoons
> select #1.2/A
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> hide sel cartoons
> select #1.2/B
3304 atoms, 3395 bonds, 423 residues, 1 model selected
> hide sel cartoons
> color #7 dodgerblue
> color #8 dodgerblue
> color #9 #00b305ff
> color #10 #00b305ff
> color #11 #f15839ff
> select #1.3/A
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> show sel cartoons
[Repeated 1 time(s)]
> select #1.3/A
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> select #1.3/A
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> show sel cartoons
> select #1.3/B
3304 atoms, 3395 bonds, 423 residues, 1 model selected
> show sel cartoons
> select #1.3/C
1277 atoms, 1305 bonds, 162 residues, 1 model selected
> show sel cartoons
> select #1.4/A
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> show sel cartoons
> save "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" includeMaps true
——— End of log from Mon Jul 15 14:11:54 2024 ———
opened ChimeraX session
> select #1.3/A
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> show sel cartoons
> view sel
> lighting soft
> set bgColor black
> lighting full
> lighting soft
> lighting simple
> lighting soft
> lighting full
> view sel
> view
> select #1.4/A
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> hide sel cartoons
> select #1.3/C
1277 atoms, 1305 bonds, 162 residues, 1 model selected
> hide sel cartoons
> show sel cartoons
> select #1.3/A
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
Chain information for AF3 E1 1-421.pdb #12
---
Chain | Description
A | No description available
> matchmaker #12 to #1.3
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 3j0c.pdb1, chain A (#1.3) with AF3 E1 1-421.pdb, chain A (#12),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
3.020)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #13
---
Chain | Description
A | No description available
> matchmaker #12 to #1.3
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 3j0c.pdb1, chain A (#1.3) with AF3 E1 1-421.pdb, chain A (#12),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
3.020)
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> matchmaker #13 to #1.3
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 3j0c.pdb1, chain A (#1.3) with AF3 E1 422-461.pdb, chain A (#13),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
2.775)
> select #1.3/B
3304 atoms, 3395 bonds, 423 residues, 1 model selected
> open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
Chain information for AF3 E2 1-352.pdb #14
---
Chain | Description
B | No description available
> matchmaker #14 to #1.3
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 3j0c.pdb1, chain E (#1.3) with AF3 E2 1-352.pdb, chain B (#14),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> matchmaker #14 to #1.3 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain B (#1.3) with AF3 E2 1-352.pdb, chain B (#14),
sequence alignment score = 583.7
RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
5.933)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #15
---
Chain | Description
B | No description available
> matchmaker #15 to #1.3 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain B (#1.3) with AF3 E2 353-438.pdb, chain B (#15),
sequence alignment score = 322.6
RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
8.411)
> hide sel cartoons
> select #1.3/C
1277 atoms, 1305 bonds, 162 residues, 1 model selected
> open "/Users/Jean/Desktop/AF3 CA.pdb"
Chain information for AF3 CA.pdb #16
---
Chain | Description
A | No description available
> matchmaker #16 to #1.3 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain C (#1.3) with AF3 CA.pdb, chain A (#16), sequence
alignment score = 328.1
RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
2.714)
> hide sel cartoons
> select #1.3/A
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> hide sel cartoons
> hide #12 models
> show #12 models
> color #12 dodgerblue
> color #13 dodgerblue
> color #14 #00b305ff
> color #15 #00b305ff
> color #16 #f15839ff
> select #1.4/A
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
Chain information for AF3 E1 1-421.pdb #17
---
Chain | Description
A | No description available
> matchmaker #17 to #1.4 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain A (#1.4) with AF3 E1 1-421.pdb, chain A (#17),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
3.020)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #18
---
Chain | Description
A | No description available
> matchmaker #18 to #1.4 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain A (#1.4) with AF3 E1 422-461.pdb, chain A (#18),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.572 angstroms; (across all 38 pairs:
2.775)
> hide sel cartoons
> select #1.4/B
3304 atoms, 3395 bonds, 423 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
Chain information for AF3 E2 1-352.pdb #19
---
Chain | Description
B | No description available
> matchmaker #19 to #1.4 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain B (#1.4) with AF3 E2 1-352.pdb, chain B (#19),
sequence alignment score = 583.7
RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
5.933)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #20
---
Chain | Description
B | No description available
> matchmaker #20 to #1.4 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain B (#1.4) with AF3 E2 353-438.pdb, chain B (#20),
sequence alignment score = 322.6
RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
8.411)
> select #1.4/C
1277 atoms, 1305 bonds, 162 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 CA.pdb"
Chain information for AF3 CA.pdb #21
---
Chain | Description
A | No description available
> matchmaker #21 to #1.4 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain C (#1.4) with AF3 CA.pdb, chain A (#21), sequence
alignment score = 328.1
RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
2.714)
> hide sel cartoons
> select #1.4/B
3304 atoms, 3395 bonds, 423 residues, 1 model selected
> hide sel cartoons
> color #17 dodgerblue
> color #18 dodgerblue
> color #19 #00b305ff
> color #20 #00b305ff
> color #21 #f15839ff
> select #1.5/A
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
Chain information for AF3 E1 1-421.pdb #22
---
Chain | Description
A | No description available
> matchmaker #22 to #1.5 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain A (#1.5) with AF3 E1 1-421.pdb, chain A (#22),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
3.020)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #23
---
Chain | Description
A | No description available
> matchmaker #23 to #1.5 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain A (#1.5) with AF3 E1 422-461.pdb, chain A (#23),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.572 angstroms; (across all 38 pairs:
2.776)
> select #1.5/B
3304 atoms, 3395 bonds, 423 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
Chain information for AF3 E2 1-352.pdb #24
---
Chain | Description
B | No description available
> matchmaker #24 to #1.5 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain B (#1.5) with AF3 E2 1-352.pdb, chain B (#24),
sequence alignment score = 583.7
RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
5.933)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #25
---
Chain | Description
B | No description available
> matchmaker #25 to #1.5 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain B (#1.5) with AF3 E2 353-438.pdb, chain B (#25),
sequence alignment score = 322.6
RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
8.411)
> hide sel cartoons
> select #1.5/A
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> hide sel cartoons
> select #1.5/C
1277 atoms, 1305 bonds, 162 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 CA.pdb"
Chain information for AF3 CA.pdb #26
---
Chain | Description
A | No description available
> matchmaker #26 to #1.5 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain C (#1.5) with AF3 CA.pdb, chain A (#26), sequence
alignment score = 328.1
RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
2.714)
> hide sel cartoons
> color #22 dodgerblue
> color #23 dodgerblue
> color #24 #00b305ff
> color #25 #00b305ff
> color #26 #f15839ff
> select #1.6/A
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
Chain information for AF3 E1 1-421.pdb #27
---
Chain | Description
A | No description available
> matchmaker #27 to #1.6 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain A (#1.6) with AF3 E1 1-421.pdb, chain A (#27),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
3.020)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #28
---
Chain | Description
A | No description available
> matchmaker #28 to #1.6 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain A (#1.6) with AF3 E1 422-461.pdb, chain A (#28),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
2.775)
> hide sel cartoons
> select #1.6/B
3304 atoms, 3395 bonds, 423 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
Chain information for AF3 E2 1-352.pdb #29
---
Chain | Description
B | No description available
> matchmaker #29 to #1.6 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain B (#1.6) with AF3 E2 1-352.pdb, chain B (#29),
sequence alignment score = 583.7
RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
5.933)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #30
---
Chain | Description
B | No description available
> matchmaker #30 to #1.6 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain B (#1.6) with AF3 E2 353-438.pdb, chain B (#30),
sequence alignment score = 333.4
RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
8.411)
> hide sel cartoons
> select #1.6/C
1277 atoms, 1305 bonds, 162 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 CA.pdb"
Chain information for AF3 CA.pdb #31
---
Chain | Description
A | No description available
> matchmaker #31 to #1.6 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain C (#1.6) with AF3 CA.pdb, chain A (#31), sequence
alignment score = 328.1
RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
2.714)
> hide sel cartoons
> color #27 dodgerblue
> color #28 dodgerblue
> color #29 #00b305ff
> color #30 #00b305ff
> color #31 #f15839ff
> select #1.7/A
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
Chain information for AF3 E1 1-421.pdb #32
---
Chain | Description
A | No description available
> matchmaker #32 to #1.7 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain A (#1.7) with AF3 E1 1-421.pdb, chain A (#32),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
3.020)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #33
---
Chain | Description
A | No description available
> matchmaker #33 to #1.7 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain A (#1.7) with AF3 E1 422-461.pdb, chain A (#33),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
2.775)
> hide sel cartoons
> select #1.7/B
3304 atoms, 3395 bonds, 423 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
Chain information for AF3 E2 1-352.pdb #34
---
Chain | Description
B | No description available
> matchmaker #34 to #1.7 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain B (#1.7) with AF3 E2 1-352.pdb, chain B (#34),
sequence alignment score = 583.7
RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
5.933)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #35
---
Chain | Description
B | No description available
> matchmaker #35 to #1.7 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain B (#1.7) with AF3 E2 353-438.pdb, chain B (#35),
sequence alignment score = 333.4
RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
8.411)
> hide sel cartoons
> select #1.7/C
1277 atoms, 1305 bonds, 162 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 CA.pdb"
Chain information for AF3 CA.pdb #36
---
Chain | Description
A | No description available
> matchmaker #36 to #1.7 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain C (#1.7) with AF3 CA.pdb, chain A (#36), sequence
alignment score = 328.1
RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
2.714)
> hide sel cartoons
> hide #32 models
> color #32 dodgerblue
> color #33 dodgerblue
> color #34 #00b305ff
> color #35 #00b305ff
> color #36 #f15839ff
> select #1.8/A
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
Chain information for AF3 E1 1-421.pdb #37
---
Chain | Description
A | No description available
> matchmaker #37 to #1.8 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain A (#1.8) with AF3 E1 1-421.pdb, chain A (#37),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
3.020)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #38
---
Chain | Description
A | No description available
> matchmaker #38 to #1.8 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain A (#1.8) with AF3 E1 422-461.pdb, chain A (#38),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.572 angstroms; (across all 38 pairs:
2.775)
> hide sel cartoons
> select #1.8/B
3304 atoms, 3395 bonds, 423 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
Chain information for AF3 E2 1-352.pdb #39
---
Chain | Description
B | No description available
> matchmaker #39 to #1.8 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain B (#1.8) with AF3 E2 1-352.pdb, chain B (#39),
sequence alignment score = 583.7
RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
5.933)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #40
---
Chain | Description
B | No description available
> matchmaker #40 to #1.8 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain B (#1.8) with AF3 E2 353-438.pdb, chain B (#40),
sequence alignment score = 333.4
RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
8.411)
> hide sel cartoons
[Repeated 1 time(s)]
> select #1.8/C
1277 atoms, 1305 bonds, 162 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 CA.pdb"
Chain information for AF3 CA.pdb #41
---
Chain | Description
A | No description available
> matchmaker #41 to #1.8 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain C (#1.8) with AF3 CA.pdb, chain A (#41), sequence
alignment score = 328.1
RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
2.714)
> hide sel cartoons
> show #32 models
> color #37 dodgerblue
> color #38 dodgerblue
> color #39 #00b305ff
> color #40 #00b305ff
> color #41 #f15839ff
> select #1.9/A
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
Chain information for AF3 E1 1-421.pdb #42
---
Chain | Description
A | No description available
> matchmaker #42 to #1.8 & sel
No 'to' model specified
> matchmaker #42 to #1.9 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain A (#1.9) with AF3 E1 1-421.pdb, chain A (#42),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
3.020)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #43
---
Chain | Description
A | No description available
> matchmaker #43 to #1.9 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain A (#1.9) with AF3 E1 422-461.pdb, chain A (#43),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.572 angstroms; (across all 38 pairs:
2.775)
> hide sel cartoons
> select #1.9/B
3304 atoms, 3395 bonds, 423 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
Chain information for AF3 E2 1-352.pdb #44
---
Chain | Description
B | No description available
> matchmaker #44 to #1.9 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain B (#1.9) with AF3 E2 1-352.pdb, chain B (#44),
sequence alignment score = 583.7
RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
5.933)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #45
---
Chain | Description
B | No description available
> matchmaker #45 to #1.9 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain B (#1.9) with AF3 E2 353-438.pdb, chain B (#45),
sequence alignment score = 322.6
RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
8.411)
> hide sel cartoons
> select #1.9/C
1277 atoms, 1305 bonds, 162 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 CA.pdb"
Chain information for AF3 CA.pdb #46
---
Chain | Description
A | No description available
> matchmaker #46 to #1.9 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain C (#1.9) with AF3 CA.pdb, chain A (#46), sequence
alignment score = 328.1
RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
2.714)
> hide sel cartoons
> hide #42 models
> show #42 models
> color #42 dodgerblue
> color #43 dodgerblue
> color #44 #00b305ff
> color #45 #00b305ff
> color #46 #f15839ff
> select #1.10/A
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
Chain information for AF3 E1 1-421.pdb #47
---
Chain | Description
A | No description available
> matchmaker #47 to #1.10 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain A (#1.10) with AF3 E1 1-421.pdb, chain A (#47),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
3.020)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #48
---
Chain | Description
A | No description available
> matchmaker #47 to #1.10 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain A (#1.10) with AF3 E1 1-421.pdb, chain A (#47),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
3.020)
> matchmaker #47 to #1.10 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain A (#1.10) with AF3 E1 1-421.pdb, chain A (#47),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
3.020)
> matchmaker #48 to #1.10 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain A (#1.10) with AF3 E1 422-461.pdb, chain A (#48),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.572 angstroms; (across all 38 pairs:
2.776)
> hide sel cartoons
> select #1.10/B
3304 atoms, 3395 bonds, 423 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
Chain information for AF3 E2 1-352.pdb #49
---
Chain | Description
B | No description available
> matchmaker #49 to #1.10 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain B (#1.10) with AF3 E2 1-352.pdb, chain B (#49),
sequence alignment score = 583.7
RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
5.933)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #50
---
Chain | Description
B | No description available
> matchmaker #50 to #1.10 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain B (#1.10) with AF3 E2 353-438.pdb, chain B (#50),
sequence alignment score = 322.6
RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
8.411)
> hide sel cartoons
> select #1.10/C
1277 atoms, 1305 bonds, 162 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 CA.pdb"
Chain information for AF3 CA.pdb #51
---
Chain | Description
A | No description available
> matchmaker #51 to #1.10 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain C (#1.10) with AF3 CA.pdb, chain A (#51), sequence
alignment score = 328.1
RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
2.714)
> hide sel cartoons
> color #47 dodgerblue
> color #48 dodgerblue
> color #49 #00b305ff
> color #50 #00b305ff
> color #51 #f15839ff
> save "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" includeMaps true
> select #1.11/A
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
Chain information for AF3 E1 1-421.pdb #52
---
Chain | Description
A | No description available
> matchmaker #52 to #1.11 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain A (#1.11) with AF3 E1 1-421.pdb, chain A (#52),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
3.020)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #53
---
Chain | Description
A | No description available
> matchmaker #53 to #1.11 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain A (#1.11) with AF3 E1 422-461.pdb, chain A (#53),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
2.776)
> hide sel cartoons
> select #1.11/B
3304 atoms, 3395 bonds, 423 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
Chain information for AF3 E2 1-352.pdb #54
---
Chain | Description
B | No description available
> matchmaker #54 to #1.11 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain B (#1.11) with AF3 E2 1-352.pdb, chain B (#54),
sequence alignment score = 583.7
RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
5.933)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #55
---
Chain | Description
B | No description available
> matchmaker #55 to #1.11 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain B (#1.11) with AF3 E2 353-438.pdb, chain B (#55),
sequence alignment score = 333.4
RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
8.411)
> hide sel cartoons
> select #1.11/C
1277 atoms, 1305 bonds, 162 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 CA.pdb"
Chain information for AF3 CA.pdb #56
---
Chain | Description
A | No description available
> matchmaker #56 to #1.11 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain C (#1.11) with AF3 CA.pdb, chain A (#56), sequence
alignment score = 328.1
RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
2.714)
[deleted to fit within ticket limits]
> hide sel cartoons
> select #1.52/C
1277 atoms, 1305 bonds, 162 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 CA.pdb"
Chain information for AF3 CA.pdb #261
---
Chain | Description
A | No description available
> matchmaker #261 to #1.52 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain C (#1.52) with AF3 CA.pdb, chain A (#261),
sequence alignment score = 328.1
RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
2.714)
> hide sel cartoons
[Repeated 1 time(s)]
> color #257 dodgerblue
> color #258 dodgerblue
> color #259 #00b305ff
> color #260 #00b305ff
> color #261 #f15839ff
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select
2325488 atoms, 2385760 bonds, 301652 residues, 321 models selected
> hide sel cartoons
> select up
2325488 atoms, 2385760 bonds, 301652 residues, 321 models selected
> show #176 target m
> show sel cartoons
> hide #!1 models
> select subtract #1
417248 atoms, 427076 bonds, 55172 residues, 260 models selected
> select clear
> hide #2 models
> hide #3 models
> hide #4 models
> hide #5 models
> hide #6 models
> hide #7 models
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> hide #10 models
> hide #11 models
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> show #16 models
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> hide #16 models
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> hide #30 models
> hide #31 models
> hide #32 models
> hide #33 models
> hide #34 models
> show #34 models
> hide #35 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> hide #37 target m
> hide #34 models
> hide #36 models
> hide #38 models
> hide #39 models
> hide #40 models
> hide #41 models
> hide #42 models
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> hide #49 models
> hide #50 models
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> hide #53 models
> hide #54 models
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> hide #208 models
> hide #209 models
> hide #210 models
> hide #211 models
> hide #212 models
> hide #213 models
> hide #214 models
> hide #215 models
> hide #216 models
> hide #217 models
> hide #218 models
> hide #219 models
> hide #220 models
> hide #221 models
> hide #222 models
> hide #223 models
> hide #224 models
> hide #225 models
> hide #226 models
> hide #227 models
> hide #228 models
> hide #229 models
> hide #230 models
> hide #231 models
> hide #232 models
> hide #233 models
> hide #234 models
> hide #235 models
> hide #236 models
> hide #237 models
> hide #238 models
> hide #239 models
> hide #240 models
> hide #241 models
> hide #242 models
> hide #243 models
> hide #244 models
> hide #245 models
> hide #246 models
> hide #247 models
> hide #248 models
> hide #249 models
> hide #250 models
> hide #251 models
> hide #252 models
> hide #253 models
> hide #254 models
> hide #255 models
> hide #256 models
> hide #257 models
> hide #258 models
> hide #259 models
> hide #260 models
> hide #261 models
> select #1.53/A
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> select #1.52/A
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> view sel
No displayed objects specified.
> show #!1 models
> select ~sel & ##selected
28434 atoms, 29183 bonds, 3666 residues, 1 model selected
> hide sel cartoons
> select
> #1.1/A#1.2/A#1.3/A#1.4/A#1.5/A#1.6/A#1.7/A#1.8/A#1.9/A#1.10/A#1.11/A#1.12/A#1.13/A#1.14/A#1.15/A#1.16/A#1.17/A#1.18/A#1.19/A#1.20/A#1.21/A#1.22/A#1.23/A#1.24/A#1.25/A#1.26/A#1.27/A#1.28/A#1.29/A#1.30/A#1.31/A#1.32/A#1.33/A#1.34/A#1.35/A#1.36/A#1.37/A#1.38/A#1.39/A#1.40/A#1.41/A#1.42/A#1.43/A#1.44/A#1.45/A#1.46/A#1.47/A#1.48/A#1.49/A#1.50/A#1.51/A#1.52/A#1.53/A#1.54/A#1.55/A#1.56/A#1.57/A#1.58/A#1.59/A#1.60/A#2/A#3/A#6/A#7/A#8/A#11/A#12/A#13/A#16/A#17/A#18/A#21/A#22/A#23/A#26/A#27/A#28/A#31/A#32/A#33/A#36/A#37/A#38/A#41/A#42/A#43/A#46/A#47/A#48/A#51/A#52/A#53/A#56/A#57/A#58/A#61/A#62/A#63/A#66/A#67/A#68/A#71/A#72/A#73/A#76/A#77/A#78/A#81/A#82/A#83/A#86/A#87/A#88/A#91/A#92/A#93/A#96/A#97/A#98/A#101/A#102/A#103/A#106/A#107/A#108/A#111/A#112/A#113/A#116/A#117/A#118/A#121/A#122/A#123/A#126/A#127/A#128/A#131/A#132/A#133/A#136/A#137/A#138/A#141/A#142/A#143/A#146/A#147/A#148/A#151/A#152/A#153/A#156/A#157/A#158/A#161/A#162/A#163/A#166/A#167/A#168/A#171/A#172/A#173/A#176/A#177/A#178/A#181/A#182/A#183/A#186/A#187/A#188/A#191/A#192/A#193/A#196/A#197/A#198/A#201/A#202/A#203/A#206/A#207/A#208/A#211/A#212/A#213/A#216/A#217/A#218/A#221/A#222/A#223/A#226/A#227/A#228/A#231/A#232/A#233/A#236/A#237/A#238/A#241/A#242/A#243/A#246/A#247/A#248/A#251/A#252/A#253/A#256/A#257/A#258/A#261/A
447224 atoms, 458514 bonds, 58916 residues, 216 models selected
> select
2325488 atoms, 2385760 bonds, 301652 residues, 321 models selected
> hide sel & #1.1-60 cartoons
> select #1.53/A
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
Chain information for AF3 E1 1-421.pdb #262
---
Chain | Description
A | No description available
> matchmaker #262 to #1.53 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain A (#1.53) with AF3 E1 1-421.pdb, chain A (#262),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
3.020)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #263
---
Chain | Description
A | No description available
> matchmaker #263 to #1.53 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain A (#1.53) with AF3 E1 422-461.pdb, chain A (#263),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
2.775)
> hide sel cartoons
> select #1.53/B
3304 atoms, 3395 bonds, 423 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
Chain information for AF3 E2 1-352.pdb #264
---
Chain | Description
B | No description available
> matchmaker #264 to #1.53 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain B (#1.53) with AF3 E2 1-352.pdb, chain B (#264),
sequence alignment score = 583.7
RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
5.933)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #265
---
Chain | Description
B | No description available
> matchmaker #265 to #1.53 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain B (#1.53) with AF3 E2 353-438.pdb, chain B (#265),
sequence alignment score = 333.4
RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
8.411)
> hide sel cartoons
> select #1.53/C
1277 atoms, 1305 bonds, 162 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 CA.pdb"
Chain information for AF3 CA.pdb #266
---
Chain | Description
A | No description available
> matchmaker #266 to #1.53 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain C (#1.53) with AF3 CA.pdb, chain A (#266),
sequence alignment score = 328.1
RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
2.714)
> hide sel cartoons
> select #1.54/A
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
Chain information for AF3 E1 1-421.pdb #267
---
Chain | Description
A | No description available
> matchmaker #267 to #1.54 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain A (#1.54) with AF3 E1 1-421.pdb, chain A (#267),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
3.020)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #268
---
Chain | Description
A | No description available
> matchmaker #268 to #1.54 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain A (#1.54) with AF3 E1 422-461.pdb, chain A (#268),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.572 angstroms; (across all 38 pairs:
2.776)
> matchmaker #268 to #1.54 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain A (#1.54) with AF3 E1 422-461.pdb, chain A (#268),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.572 angstroms; (across all 38 pairs:
2.776)
> hide sel cartoons
> select #1.54/B
3304 atoms, 3395 bonds, 423 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
Chain information for AF3 E2 1-352.pdb #269
---
Chain | Description
B | No description available
> matchmaker #269 to #1.54 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain B (#1.54) with AF3 E2 1-352.pdb, chain B (#269),
sequence alignment score = 583.7
RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
5.933)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #270
---
Chain | Description
B | No description available
> matchmaker #270 to #1.54 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain B (#1.54) with AF3 E2 353-438.pdb, chain B (#270),
sequence alignment score = 333.4
RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
8.411)
> hide sel cartoons
> select #1.54/C
1277 atoms, 1305 bonds, 162 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 CA.pdb"
Chain information for AF3 CA.pdb #271
---
Chain | Description
A | No description available
> matchmaker #271 to #1.54 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain C (#1.54) with AF3 CA.pdb, chain A (#271),
sequence alignment score = 328.1
RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
2.714)
> hide sel cartoons
> color #262 dodgerblue
> color #263 dodgerblue
> color #264 #00b305ff
> color #265 #00b305ff
> color #266 #f15839ff
> color #267 dodgerblue
> color #268 dodgerblue
> color #269 #00b305ff
> color #270 #00b305ff
> color #271 #f15839ff
> select #1.55/A
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
Chain information for AF3 E1 1-421.pdb #272
---
Chain | Description
A | No description available
> matchmaker #272 to #1.54 & sel
No 'to' model specified
> matchmaker #272 to #1.55 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain A (#1.55) with AF3 E1 1-421.pdb, chain A (#272),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
3.020)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #273
---
Chain | Description
A | No description available
> matchmaker #273 to #1.55 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain A (#1.55) with AF3 E1 422-461.pdb, chain A (#273),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.572 angstroms; (across all 38 pairs:
2.775)
> hide sel cartoons
> open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
Chain information for AF3 E2 1-352.pdb #274
---
Chain | Description
B | No description available
> select #1.55/B
3304 atoms, 3395 bonds, 423 residues, 1 model selected
> show sel cartoons
> matchmaker #274 to #1.55 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain B (#1.55) with AF3 E2 1-352.pdb, chain B (#274),
sequence alignment score = 583.7
RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
5.933)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #275
---
Chain | Description
B | No description available
> matchmaker #275 to #1.55 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain B (#1.55) with AF3 E2 353-438.pdb, chain B (#275),
sequence alignment score = 322.6
RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
8.411)
> hide sel cartoons
> select #1.55/C
1277 atoms, 1305 bonds, 162 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 CA.pdb"
Chain information for AF3 CA.pdb #276
---
Chain | Description
A | No description available
> matchmaker #276 to #1.55 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain C (#1.55) with AF3 CA.pdb, chain A (#276),
sequence alignment score = 328.1
RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
2.714)
> hide sel cartoons
> color #272 dodgerblue
> color #273 dodgerblue
> color #274 #00b305ff
> color #275 #00b305ff
> color #276 #f15839ff
> select #1.56/A
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
Chain information for AF3 E1 1-421.pdb #277
---
Chain | Description
A | No description available
> matchmaker #277 to #1.55 & sel
No 'to' model specified
> matchmaker #277 to #1.56 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain A (#1.56) with AF3 E1 1-421.pdb, chain A (#277),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
3.020)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #278
---
Chain | Description
A | No description available
> matchmaker #278 to #1.56 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain A (#1.56) with AF3 E1 422-461.pdb, chain A (#278),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.572 angstroms; (across all 38 pairs:
2.775)
> hide sel cartoons
> select #1.56/B
3304 atoms, 3395 bonds, 423 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
Chain information for AF3 E2 1-352.pdb #279
---
Chain | Description
B | No description available
> matchmaker #279 to #1.56 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain B (#1.56) with AF3 E2 1-352.pdb, chain B (#279),
sequence alignment score = 583.7
RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
5.933)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #280
---
Chain | Description
B | No description available
> matchmaker #280 to #1.56 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain B (#1.56) with AF3 E2 353-438.pdb, chain B (#280),
sequence alignment score = 333.4
RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
8.411)
> hide sel cartoons
> select #1.56/C
1277 atoms, 1305 bonds, 162 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 CA.pdb"
Chain information for AF3 CA.pdb #281
---
Chain | Description
A | No description available
> matchmaker #281 to #1.56 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain C (#1.56) with AF3 CA.pdb, chain A (#281),
sequence alignment score = 328.1
RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
2.714)
> hide sel cartoons
> color #277 dodgerblue
> color #278 dodgerblue
> color #279 #00b305ff
> color #280 #00b305ff
> color #281 #f15839ff
> select #1.57/A
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
Chain information for AF3 E1 1-421.pdb #282
---
Chain | Description
A | No description available
> matchmaker #282 to #1.56 & sel
No 'to' model specified
> matchmaker #282 to #1.57 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain A (#1.57) with AF3 E1 1-421.pdb, chain A (#282),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
3.020)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #283
---
Chain | Description
A | No description available
> matchmaker #283 to #1.57 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain A (#1.57) with AF3 E1 422-461.pdb, chain A (#283),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
2.776)
> hide sel cartoons
> select #1.57/B
3304 atoms, 3395 bonds, 423 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
Chain information for AF3 E2 1-352.pdb #284
---
Chain | Description
B | No description available
> matchmaker #284 to #1.57 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain B (#1.57) with AF3 E2 1-352.pdb, chain B (#284),
sequence alignment score = 583.7
RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
5.933)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #285
---
Chain | Description
B | No description available
> matchmaker #285 to #1.57 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain B (#1.57) with AF3 E2 353-438.pdb, chain B (#285),
sequence alignment score = 333.4
RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
8.411)
> hide sel cartoons
[Repeated 1 time(s)]
> select #1.57/C
1277 atoms, 1305 bonds, 162 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 CA.pdb"
Chain information for AF3 CA.pdb #286
---
Chain | Description
A | No description available
> matchmaker #286 to #1.57 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain C (#1.57) with AF3 CA.pdb, chain A (#286),
sequence alignment score = 328.1
RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
2.714)
> hide sel cartoons
> color #282 dodgerblue
> color #283 dodgerblue
> color #284 #00b305ff
> color #285 #00b305ff
> color #286 #f15839ff
> select #1.58/A
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
Chain information for AF3 E1 1-421.pdb #287
---
Chain | Description
A | No description available
> matchmaker #287 to #1.58 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain A (#1.58) with AF3 E1 1-421.pdb, chain A (#287),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
3.020)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #288
---
Chain | Description
A | No description available
> matchmaker #288 to #1.58 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain A (#1.58) with AF3 E1 422-461.pdb, chain A (#288),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
2.775)
> hide sel cartoons
> select #1.58/B
3304 atoms, 3395 bonds, 423 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
Chain information for AF3 E2 1-352.pdb #289
---
Chain | Description
B | No description available
> matchmaker #289 to #1.58 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain B (#1.58) with AF3 E2 1-352.pdb, chain B (#289),
sequence alignment score = 583.7
RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
5.933)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #290
---
Chain | Description
B | No description available
> matchmaker #290 to #1.58 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain B (#1.58) with AF3 E2 353-438.pdb, chain B (#290),
sequence alignment score = 322.6
RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
8.411)
> hide sel cartoons
> select #1.58/C
1277 atoms, 1305 bonds, 162 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 CA.pdb"
Chain information for AF3 CA.pdb #291
---
Chain | Description
A | No description available
> matchmaker #291 to #1.58 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain C (#1.58) with AF3 CA.pdb, chain A (#291),
sequence alignment score = 328.1
RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
2.714)
> hide sel cartoons
> color #287 dodgerblue
> color #288 dodgerblue
> color #289 #00b305ff
> color #290 #00b305ff
> color #291 #f15839ff
> select #1.59/A
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
Chain information for AF3 E1 1-421.pdb #292
---
Chain | Description
A | No description available
> matchmaker #291 to #1.59 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain A (#1.59) with AF3 CA.pdb, chain A (#291),
sequence alignment score = 32.6
RMSD between 11 pruned atom pairs is 1.204 angstroms; (across all 110 pairs:
22.675)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #293
---
Chain | Description
A | No description available
> matchmaker #291 to #1.58 & sel
No 'to' model specified
> select #1.58/C
1277 atoms, 1305 bonds, 162 residues, 1 model selected
> show sel cartoons
> matchmaker #291 to #1.58 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain C (#1.58) with AF3 CA.pdb, chain A (#291),
sequence alignment score = 328.1
RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
2.714)
> hide sel cartoons
> select #1.59/A
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> matchmaker #292 to #1.59 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain A (#1.59) with AF3 E1 1-421.pdb, chain A (#292),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
3.020)
> matchmaker #293 to #1.59 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain A (#1.59) with AF3 E1 422-461.pdb, chain A (#293),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
2.776)
> select #1.39/B
3304 atoms, 3395 bonds, 423 residues, 1 model selected
> select #1.59/A
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> hide sel cartoons
> select #1.59/B
3304 atoms, 3395 bonds, 423 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
Chain information for AF3 E2 1-352.pdb #294
---
Chain | Description
B | No description available
> matchmaker #294 to #1.59 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain B (#1.59) with AF3 E2 1-352.pdb, chain B (#294),
sequence alignment score = 583.7
RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
5.933)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #295
---
Chain | Description
B | No description available
> matchmaker #295 to #1.59 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain B (#1.59) with AF3 E2 353-438.pdb, chain B (#295),
sequence alignment score = 322.6
RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
8.411)
> hide sel cartoons
> select #1.59/C
1277 atoms, 1305 bonds, 162 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 CA.pdb"
Chain information for AF3 CA.pdb #296
---
Chain | Description
A | No description available
> matchmaker #296 to #1.59 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain C (#1.59) with AF3 CA.pdb, chain A (#296),
sequence alignment score = 328.1
RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
2.714)
> hide sel cartoons
> color #292 dodgerblue
> color #293 dodgerblue
> color #294 #00b305ff
> color #295 #00b305ff
> color #296 #f15839ff
> select #1.60/A
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
Chain information for AF3 E1 1-421.pdb #297
---
Chain | Description
A | No description available
> matchmaker #297 to #1.60 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain A (#1.60) with AF3 E1 1-421.pdb, chain A (#297),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
3.020)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #298
---
Chain | Description
A | No description available
> matchmaker #298 to #1.60 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain A (#1.60) with AF3 E1 422-461.pdb, chain A (#298),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
2.776)
> hide sel cartoons
> select #1.60/B
3304 atoms, 3395 bonds, 423 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
Chain information for AF3 E2 1-352.pdb #299
---
Chain | Description
B | No description available
> matchmaker #299 to #1.60 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain B (#1.60) with AF3 E2 1-352.pdb, chain B (#299),
sequence alignment score = 583.7
RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
5.933)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #300
---
Chain | Description
B | No description available
> matchmaker #300 to #1.60 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain B (#1.60) with AF3 E2 353-438.pdb, chain B (#300),
sequence alignment score = 333.4
RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
8.411)
> hide sel cartoons
> select #1.60/C
1277 atoms, 1305 bonds, 162 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 CA.pdb"
Chain information for AF3 CA.pdb #301
---
Chain | Description
A | No description available
> matchmaker #301 to #1.60 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain C (#1.60) with AF3 CA.pdb, chain A (#301),
sequence alignment score = 328.1
RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
2.714)
> hide sel cartoons
> color #297 dodgerblue
> color #298 dodgerblue
> color #299 #00b305ff
> color #300 #00b305ff
> color #301 #f15839ff
> save "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" includeMaps true
——— End of log from Mon Jul 15 16:48:15 2024 ———
opened ChimeraX session
> show #2 models
> show #3 models
> show #4 models
> show #5 models
> show #6 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
[Repeated 1 time(s)]
> hide #2-6,262-301#1.2-60 target m
> show #1.2 target m
> hide #1.1 target m
> hide #!1 models
> show #2 models
> show #3 models
> show #4 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> show #5 models
> show #6 models
> show #7 models
> show #8 models
> show #9 models
> show #10 models
> show #11 models
> show #12 models
> show #13 models
> show #14 models
> show #15 models
> show #16 models
> show #17 models
> show #18 models
> show #19 models
> show #20 models
> show #21 models
> show #22 models
> show #23 models
> show #24 models
> show #25 models
> show #26 models
> show #27 models
> show #28 models
> show #29 models
> show #30 models
> show #31 models
> show #32 models
> show #33 models
> show #34 models
> show #35 models
> show #36 models
> show #37 models
> show #38 models
> show #39 models
> show #40 models
> show #41 models
> show #42 models
> show #43 models
> show #44 models
> show #45 models
> show #46 models
> show #47 models
> show #48 models
> show #49 models
> show #50 models
> show #51 models
> show #52 models
> show #53 models
> show #54 models
> show #55 models
> show #56 models
> show #57 models
> show #58 models
> show #59 models
> show #60 models
> show #61 models
> show #62 models
> show #63 models
> show #64 models
> show #65 models
> show #66 models
> show #67 models
> show #68 models
> show #69 models
> show #70 models
> show #71 models
> show #72 models
> show #73 models
> show #74 models
> show #75 models
> show #76 models
> show #77 models
> show #78 models
> show #79 models
> show #80 models
> show #81 models
> show #82 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> show #82-301 models
> hide #2-301 models
> show #2-301 models
> save "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" includeMaps true
——— End of log from Mon Jul 15 16:59:09 2024 ———
opened ChimeraX session
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
OpenGL version: 4.1 ATI-5.5.17
OpenGL renderer: AMD Radeon Pro 560X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro15,1
Processor Name: 6-Core Intel Core i9
Processor Speed: 2.9 GHz
Number of Processors: 1
Total Number of Cores: 6
L2 Cache (per Core): 256 KB
L3 Cache: 12 MB
Hyper-Threading Technology: Enabled
Memory: 32 GB
System Firmware Version: 2022.100.22.0.0 (iBridge: 21.16.5077.0.0,0)
OS Loader Version: 580~2215
Software:
System Software Overview:
System Version: macOS 14.5 (23F79)
Kernel Version: Darwin 23.5.0
Time since boot: 3 hours, 31 minutes
Graphics/Displays:
Intel UHD Graphics 630:
Chipset Model: Intel UHD Graphics 630
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3e9b
Revision ID: 0x0000
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Support: Metal 3
Radeon Pro 560X:
Chipset Model: Radeon Pro 560X
Type: GPU
Bus: PCIe
PCIe Lane Width: x8
VRAM (Total): 4 GB
Vendor: AMD (0x1002)
Device ID: 0x67ef
Revision ID: 0x00c2
ROM Revision: 113-C980AL-075
VBIOS Version: 113-C97501U-005
EFI Driver Version: 01.A1.075
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Support: Metal 2
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2880 x 1800 Retina
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
DELL P2418D:
Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
UI Looks like: 2560 x 1440 @ 60.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: MY3ND77M013T
Mirror: Off
Online: Yes
Rotation: Supported
Connection Type: DVI or HDMI
Adapter Firmware Version: c.55
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
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: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
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: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
ChimeraX-ModelPanel: 1.5
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-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.5
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: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
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: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
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
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
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: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
Change History (2)
comment:1 by , 15 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash changing display configuration on Mac |
comment:2 by , 15 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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ChimeraX crashed unplugging or plugging in an external display. This is due to a bug in the Qt 6.6 window toolkit used by ChimeraX specific to Macs and especially common on old Intel Mac machines. Possibly it is fixed in Qt 6.7 which is being used in the ChimeraX daily build.
My only suggestion is to save your work as a ChimeraX session (.cxs file) before removing or adding an external display on a Mac or quit ChimeraX.