![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 16 months ago
Last modified 16 months ago
#15615 closed defect
Crash changing display configuration on Mac — at Version 1
| 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",
"parentPid" : 1,
"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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"sip" : "enabled",
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"exception" : {"codes":"0x0000000000000001, 0x0000000000000000","rawCodes":[1,0],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000000"},
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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 (1)
comment:1 by , 16 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 |
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