![[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
ChimeraX bug report submission — at Initial Version
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
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,
"osVersion" : {
"train" : "macOS 14.5",
"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",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.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,
"bridgeVersion" : {"build":"21P5077","train":"8.5"},
"sip" : "enabled",
"vmRegionInfo" : "0 is not in any region. Bytes before following region: 4407644160\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 106b75000-106b79000 [ 16K] r-x\/r-x SM=COW \/Applications\/Biology\/*\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000000","rawCodes":[1,0],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000000"},
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"path" : "\/usr\/lib\/libc++.1.dylib",
"name" : "libc++.1.dylib"
}
],
"sharedCache" : {
"base" : 140703130492928,
"size" : 25769803776,
"uuid" : "b48cfc6b-b7ed-3343-97fb-f5187dc04df8"
},
"vmSummary" : "ReadOnly portion of Libraries: Total=1.2G resident=0K(0%) swapped_out_or_unallocated=1.2G(100%)\nWritable regions: Total=38.2G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=38.2G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 128K 1 \nActivity Tracing 256K 1 \nCG image 120K 8 \nColorSync 252K 31 \nCoreAnimation 820K 58 \nCoreGraphics 16K 3 \nCoreGraphics (reserved) 8K 1 reserved VM address space (unallocated)\nCoreServices 244K 1 \nCoreUI image data 3420K 23 \nFoundation 16K 1 \nIOKit 23.3M 3 \nKernel Alloc Once 8K 1 \nMALLOC 37.0G 172 \nMALLOC guard page 48K 12 \nMach message 16K 3 \nOpenGL GLSL 384K 4 \nSTACK GUARD 200K 50 \nStack 206.4M 51 \nStack Guard 56.0M 1 \nVM_ALLOCATE 873.7M 1361 \nVM_ALLOCATE (reserved) 96.0M 1 reserved VM address space (unallocated)\n__CTF 824 1 \n__DATA 44.1M 755 \n__DATA_CONST 61.6M 433 \n__DATA_DIRTY 1691K 221 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__LINKEDIT 212.2M 154 \n__OBJC_RO 71.8M 1 \n__OBJC_RW 2200K 2 \n__TEXT 1.0G 763 \ndyld private memory 552K 7 \nmapped file 211.9M 63 \nshared memory 2992K 28 \n=========== ======= ======= \nTOTAL 39.9G 4217 \nTOTAL, minus reserved VM space 39.8G 4217 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"logWritingSignature" : "9b32d37eed40f7db94dcf0c0e7f64901f98a5d9d",
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "648c94d4ebdf9e3e398fa708",
"factorPackIds" : {
"SIRI_UNDERSTANDING_NL_OVERRIDES" : "65a8104b6712a43e7922cab8"
},
"deploymentId" : 240000171
},
{
"rolloutId" : "639124e81d92412bfb4880b3",
"factorPackIds" : {
},
"deploymentId" : 240000012
}
],
"experiments" : [
{
"treatmentId" : "3dff9c91-a8fb-424e-a656-c8d6e6037574",
"experimentId" : "662152ede2d11d1408c4db33",
"deploymentId" : 400000014
},
{
"treatmentId" : "45f4e2a5-551b-4bc2-a2dc-19c244dda8f8",
"experimentId" : "6643969b3099cf28e049862f",
"deploymentId" : 400000003
}
]
}
}
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)
> hide sel cartoons
> color #52 dodgerblue
> color #53 dodgerblue
> color #54 #00b305ff
> color #55 #00b305ff
> color #56 #f15839ff
> select #1.12/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 #57
---
Chain | Description
A | No description available
> matchmaker #57 to #1.12 & 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 (#1.12) with AF3 E1 1-421.pdb, chain A (#57),
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 #58
---
Chain | Description
A | No description available
> matchmaker #58 to #1.12 & 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 (#1.12) with AF3 E1 422-461.pdb, chain A (#58),
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 #1.12/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 #59
---
Chain | Description
B | No description available
> matchmaker #59 to #1.12 & 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 (#1.12) with AF3 E2 1-352.pdb, chain B (#59),
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 #60
---
Chain | Description
B | No description available
> matchmaker #60 to #1.12 & 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 (#1.12) with AF3 E2 353-438.pdb, chain B (#60),
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 #1.12/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 #61
---
Chain | Description
A | No description available
> matchmaker #61 to #1.12 & 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 (#1.12) with AF3 CA.pdb, chain A (#61), 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 #57 models
> show #57 models
> color #57 dodgerblue
> color #58 dodgerblue
> color #59 #00b305ff
> color #60 #00b305ff
> color #61 #f15839ff
> select #1.13/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 #62
---
Chain | Description
A | No description available
> matchmaker #62 to #1.12 & sel
No 'to' model specified
> matchmaker #62 to #1.13 & 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 (#1.13) with AF3 E1 1-421.pdb, chain A (#62),
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 #63
---
Chain | Description
A | No description available
> matchmaker #63 to #1.13 & 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 (#1.13) with AF3 E1 422-461.pdb, chain A (#63),
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 #1.13/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 #64
---
Chain | Description
B | No description available
> matchmaker #64 to #1.13 & 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 (#1.13) with AF3 E2 1-352.pdb, chain B (#64),
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 #65
---
Chain | Description
B | No description available
> matchmaker #65 to #1.13 & 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 (#1.13) with AF3 E2 353-438.pdb, chain B (#65),
sequence alignment score = 322.6
RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
8.411)
> select #1.13/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 #66
---
Chain | Description
A | No description available
> matchmaker #66 to #1.13 & 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 (#1.13) with AF3 CA.pdb, chain A (#66), 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 #1.13/B
3304 atoms, 3395 bonds, 423 residues, 1 model selected
> hide sel cartoons
> color #62 dodgerblue
> color #63 dodgerblue
> color #64 #00b305ff
> color #65 #00b305ff
> color #66 #f15839ff
> select #1.14/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 #67
---
Chain | Description
A | No description available
> matchmaker #67 to #1.13 & sel
No 'to' model specified
> matchmaker #67 to #1.14 & 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 (#1.14) with AF3 E1 1-421.pdb, chain A (#67),
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 #68
---
Chain | Description
A | No description available
> matchmaker #68 to #1.14 & 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 (#1.14) with AF3 E1 422-461.pdb, chain A (#68),
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 #1.14/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 #69
---
Chain | Description
B | No description available
> matchmaker #69 to #1.14 & 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 (#1.14) with AF3 E2 1-352.pdb, chain B (#69),
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 #70
---
Chain | Description
B | No description available
> matchmaker #70 to #1.14 & 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 (#1.14) with AF3 E2 353-438.pdb, chain B (#70),
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 #1.14/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 #71
---
Chain | Description
A | No description available
> matchmaker #71 to #1.14 & 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 (#1.14) with AF3 CA.pdb, chain A (#71), 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 #67 dodgerblue
> color #68 dodgerblue
> color #69 #00b305ff
> color #70 #00b305ff
> color #71 #f15839ff
> select #1.15/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 #72
---
Chain | Description
A | No description available
> matchmaker #72 to #1.15 & 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 (#1.15) with AF3 E1 1-421.pdb, chain A (#72),
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 #73
---
Chain | Description
A | No description available
> matchmaker #73 to #1.15 & 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 (#1.15) with AF3 E1 422-461.pdb, chain A (#73),
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 #1.15/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 #74
---
Chain | Description
B | No description available
> matchmaker #74 to #1.15 & 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 (#1.15) with AF3 E2 1-352.pdb, chain B (#74),
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 #75
---
Chain | Description
B | No description available
> matchmaker #75 to #1.15 & 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 (#1.15) with AF3 E2 353-438.pdb, chain B (#75),
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 #1.15/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 #76
---
Chain | Description
A | No description available
> matchmaker #76 to #1.15 & 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 (#1.15) with AF3 CA.pdb, chain A (#76), 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 #72 dodgerblue
> color #73 dodgerblue
> color #74 #00b305ff
> color #75 #00b305ff
> color #76 #f15839ff
> select #1.16/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 #77
---
Chain | Description
A | No description available
> matchmaker #77 to #1.16 & 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 (#1.16) with AF3 E1 1-421.pdb, chain A (#77),
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 #78
---
Chain | Description
A | No description available
> matchmaker #78 to #1.16 & 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 (#1.16) with AF3 E1 422-461.pdb, chain A (#78),
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 #1.16/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 #79
---
Chain | Description
B | No description available
> matchmaker #79 to #1.16 & 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 (#1.16) with AF3 E2 1-352.pdb, chain B (#79),
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 #80
---
Chain | Description
B | No description available
> matchmaker #80 to #1.16 & 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 (#1.16) with AF3 E2 353-438.pdb, chain B (#80),
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 #1.16/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 #81
---
Chain | Description
A | No description available
> matchmaker #81 to #1.16 & 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 (#1.16) with AF3 CA.pdb, chain A (#81), 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 #77 dodgerblue
> color #78 dodgerblue
> color #79 #00b305ff
> color #80 #00b305ff
> color #81 #f15839ff
> select #1.17/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 #82
---
Chain | Description
A | No description available
> matchmaker #82 to #1.17 & 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 (#1.17) with AF3 E1 1-421.pdb, chain A (#82),
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 #83
---
Chain | Description
A | No description available
> matchmaker #83 to #1.17 & 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 (#1.17) with AF3 E1 422-461.pdb, chain A (#83),
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 #1.17/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 #84
---
Chain | Description
B | No description available
> matchmaker #84 to #1.17 & 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 (#1.17) with AF3 E2 1-352.pdb, chain B (#84),
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 #85
---
Chain | Description
B | No description available
> matchmaker #85 to #1.17 & 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 (#1.17) with AF3 E2 353-438.pdb, chain B (#85),
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 #1.17/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 #86
---
Chain | Description
A | No description available
> matchmaker #86 to #1.17 & 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 (#1.17) with AF3 CA.pdb, chain A (#86), 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 #82 dodgerblue
> color #83 dodgerblue
> color #84 #00b305ff
> color #85 #00b305ff
> color #86 #f15839ff
> select #1.18/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 #87
---
Chain | Description
A | No description available
> matchmaker #87 to #1.18 & 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 (#1.18) with AF3 E1 1-421.pdb, chain A (#87),
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 #88
---
Chain | Description
A | No description available
> matchmaker #88 to #1.18 & 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 (#1.18) with AF3 E1 422-461.pdb, chain A (#88),
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 #1.18/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 #89
---
Chain | Description
B | No description available
> matchmaker #89 to #1.18 & 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 (#1.18) with AF3 E2 1-352.pdb, chain B (#89),
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 #90
---
Chain | Description
B | No description available
> matchmaker #90 to #1.18 & 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 (#1.18) with AF3 E2 353-438.pdb, chain B (#90),
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 #1.18/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 #91
---
Chain | Description
A | No description available
> matchmaker #91 to #1.18 & 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 (#1.18) with AF3 CA.pdb, chain A (#91), 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 #87 dodgerblue
> color #88 dodgerblue
> color #89 #00b305ff
> color #90 #00b305ff
> color #91 #f15839ff
> select #1.19/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 #92
---
Chain | Description
A | No description available
> matchmaker #92 to #1.19 & 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 (#1.19) with AF3 E1 1-421.pdb, chain A (#92),
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 #93
---
Chain | Description
A | No description available
> matchmaker #93 to #1.19 & 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 (#1.19) with AF3 E1 422-461.pdb, chain A (#93),
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 #1.19/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 #94
---
Chain | Description
B | No description available
> matchmaker #94 to #1.19 & 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 (#1.19) with AF3 E2 1-352.pdb, chain B (#94),
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 #95
---
Chain | Description
B | No description available
> matchmaker #95 to #1.19 & 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 (#1.19) with AF3 E2 353-438.pdb, chain B (#95),
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 #1.19/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 #96
---
Chain | Description
A | No description available
> matchmaker #96 to #1.19 & 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 (#1.19) with AF3 CA.pdb, chain A (#96), 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 #92 dodgerblue
> color #93 dodgerblue
> color #94 dodgerblue
> color #94 #00b305ff
> color #95 #00b305ff
> color #96 #f15839ff
> select #1.20/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 #97
---
Chain | Description
A | No description available
> matchmaker #97 to #1.20 & 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 (#1.20) with AF3 E1 1-421.pdb, chain A (#97),
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 #98
---
Chain | Description
A | No description available
> matchmaker #98 to #1.20 & 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 (#1.20) with AF3 E1 422-461.pdb, chain A (#98),
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 #1.20/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 #99
---
Chain | Description
B | No description available
> matchmaker #99 to #1.20 & 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 (#1.20) with AF3 E2 1-352.pdb, chain B (#99),
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 #100
---
Chain | Description
B | No description available
> matchmaker #100 to #1.20 & 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 (#1.20) with AF3 E2 353-438.pdb, chain B (#100),
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 #1.20/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 #101
---
Chain | Description
A | No description available
> matchmaker #101 to #1.20 & 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 (#1.20) with AF3 CA.pdb, chain A (#101),
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 #97 dodgerblue
> color #98 dodgerblue
> color #99 #00b305ff
> color #100 #00b305ff
> color #101 #f15839ff
> save "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" includeMaps true
> select #1.21/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 #102
---
Chain | Description
A | No description available
> matchmaker #102 to #1.21 & 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 (#1.21) with AF3 E1 1-421.pdb, chain A (#102),
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 #103
---
Chain | Description
A | No description available
> matchmaker #103 to #1.21 & 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 (#1.21) with AF3 E1 422-461.pdb, chain A (#103),
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 #1.21/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 #104
---
Chain | Description
B | No description available
> matchmaker #104 to #1.21 & 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 (#1.21) with AF3 E2 1-352.pdb, chain B (#104),
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 #105
---
Chain | Description
B | No description available
> matchmaker #105 to #1.21 & 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 (#1.21) with AF3 E2 353-438.pdb, chain B (#105),
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 #1.21/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 #106
---
Chain | Description
A | No description available
> matchmaker #106 to #1.21 & 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 (#1.21) with AF3 CA.pdb, chain A (#106),
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 #102 dodgerblue
> color #103 dodgerblue
> color #104 #00b305ff
> color #105 #00b305ff
> color #106 #f15839ff
> select #1.22/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 #107
---
Chain | Description
A | No description available
> matchmaker #107 to #1.22 & 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 (#1.22) with AF3 E1 1-421.pdb, chain A (#107),
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 #108
---
Chain | Description
A | No description available
> matchmaker #108 to #1.22 & 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 (#1.22) with AF3 E1 422-461.pdb, chain A (#108),
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 #1.22/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 #109
---
Chain | Description
B | No description available
> matchmaker #109 to #1.22 & 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 (#1.22) with AF3 E2 1-352.pdb, chain B (#109),
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 #110
---
Chain | Description
B | No description available
> matchmaker #110 to #1.22 & 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 (#1.22) with AF3 E2 353-438.pdb, chain B (#110),
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 #1.22/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 #111
---
Chain | Description
A | No description available
> matchmaker #111 to #1.22 & 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 (#1.22) with AF3 CA.pdb, chain A (#111),
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 #107 dodgerblue
> color #108 dodgerblue
> color #109 #00b305ff
> color #110 #00b305ff
> color #111 #f15839ff
> select #1.23/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 #112
---
Chain | Description
A | No description available
> matchmaker #112 to #1.23 & 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 (#1.23) with AF3 E1 1-421.pdb, chain A (#112),
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 #113
---
Chain | Description
A | No description available
> matchmaker #113 to #1.23 & 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 (#1.23) with AF3 E1 422-461.pdb, chain A (#113),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
2.776)
> hide sel cartoons
[Repeated 1 time(s)]
> select #1.23/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 #114
---
Chain | Description
B | No description available
> matchmaker #114 to #1.23 & 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 (#1.23) with AF3 E2 1-352.pdb, chain B (#114),
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 #115
---
Chain | Description
B | No description available
> matchmaker #115 to #1.23 & 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 (#1.23) with AF3 E2 353-438.pdb, chain B (#115),
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 #1.23/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 #116
---
Chain | Description
A | No description available
> matchmaker #116 to #1.23 & 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 (#1.23) with AF3 CA.pdb, chain A (#116),
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 #112 dodgerblue
> color #113 dodgerblue
> color #114 #00b305ff
> color #115 #00b305ff
> color #116 #f15839ff
> select #1.24/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 #117
---
Chain | Description
A | No description available
> matchmaker #117 to #1.24 & 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 (#1.24) with AF3 E1 1-421.pdb, chain A (#117),
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 #118
---
Chain | Description
A | No description available
> matchmaker #118 to #1.24 & 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 (#1.24) with AF3 E1 422-461.pdb, chain A (#118),
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 #1.24/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 #119
---
Chain | Description
B | No description available
> matchmaker #119 to #1.24 & 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 (#1.24) with AF3 E2 1-352.pdb, chain B (#119),
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 #120
---
Chain | Description
B | No description available
> matchmaker #120 to #1.24 & 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 (#1.24) with AF3 E2 353-438.pdb, chain B (#120),
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 #1.24/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 #121
---
Chain | Description
A | No description available
> matchmaker #121 to #1.24 & 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 (#1.24) with AF3 CA.pdb, chain A (#121),
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 #117 dodgerblue
> color #118 dodgerblue
> color #119 #00b305ff
> color #120 #00b305ff
> color #121 #f15839ff
> select #1.25/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 #122
---
Chain | Description
A | No description available
> matchmaker #122 to #1.25 & 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 (#1.25) with AF3 E1 1-421.pdb, chain A (#122),
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 #123
---
Chain | Description
A | No description available
> matchmaker #123 to #1.25 & 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 (#1.25) with AF3 E1 422-461.pdb, chain A (#123),
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 #1.25/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 #124
---
Chain | Description
B | No description available
> matchmaker #124 to #1.25 & 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 (#1.25) with AF3 E2 1-352.pdb, chain B (#124),
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 #125
---
Chain | Description
B | No description available
> matchmaker #125 to #1.25 & 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 (#1.25) with AF3 E2 353-438.pdb, chain B (#125),
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 #1.25/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 #126
---
Chain | Description
A | No description available
> matchmaker #126 to #1.25 & 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 (#1.25) with AF3 CA.pdb, chain A (#126),
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 #122 dodgerblue
> color #123 dodgerblue
> color #124 #00b305ff
> color #125 #00b305ff
> color #126 #f15839ff
> select #1.26/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 #127
---
Chain | Description
A | No description available
> matchmaker #127 to #1.26 & 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 (#1.26) with AF3 E1 1-421.pdb, chain A (#127),
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 #128
---
Chain | Description
A | No description available
> matchmaker #128 to #1.26 & 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 (#1.26) with AF3 E1 422-461.pdb, chain A (#128),
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 #1.26/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 #129
---
Chain | Description
B | No description available
> matchmaker #129 to #1.26 & 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 (#1.26) with AF3 E2 1-352.pdb, chain B (#129),
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 #130
---
Chain | Description
B | No description available
> matchmaker #130 to #1.26 & 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 (#1.26) with AF3 E2 353-438.pdb, chain B (#130),
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 #1.26/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 #131
---
Chain | Description
A | No description available
> matchmaker #131 to #1.26 & 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 (#1.26) with AF3 CA.pdb, chain A (#131),
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 #127 dodgerblue
> color #128 dodgerblue
> color #129 #00b305ff
> color #130 #00b305ff
> color #131 #f15839ff
> select #1.27/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 #132
---
Chain | Description
A | No description available
> matchmaker #132 to #1.27 & 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 (#1.27) with AF3 E1 1-421.pdb, chain A (#132),
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 #133
---
Chain | Description
A | No description available
> matchmaker #133 to #1.27 & 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 (#1.27) with AF3 E1 422-461.pdb, chain A (#133),
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 #1.27/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 #134
---
Chain | Description
B | No description available
> matchmaker #134 to #1.27 & 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 (#1.27) with AF3 E2 1-352.pdb, chain B (#134),
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 #135
---
Chain | Description
B | No description available
> matchmaker #135 to #1.27 & 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 (#1.27) with AF3 E2 353-438.pdb, chain B (#135),
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 #1.27/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 #136
---
Chain | Description
A | No description available
> matchmaker #136 to #1.27 & 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 (#1.27) with AF3 CA.pdb, chain A (#136),
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 #132 dodgerblue
> color #133 dodgerblue
> color #134 #00b305ff
> color #135 #00b305ff
> color #136 #f15839ff
> select #1.28/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 #137
---
Chain | Description
A | No description available
> matchmaker #137 to #1.28 & 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 (#1.28) with AF3 E1 1-421.pdb, chain A (#137),
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 #138
---
Chain | Description
A | No description available
> matchmaker #138 to #1.28 & 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 (#1.28) with AF3 E1 422-461.pdb, chain A (#138),
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 #1.28/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 #139
---
Chain | Description
B | No description available
> matchmaker #139 to #1.28 & 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 (#1.28) with AF3 E2 1-352.pdb, chain B (#139),
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 #140
---
Chain | Description
B | No description available
> matchmaker #140 to #1.28 & 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 (#1.28) with AF3 E2 353-438.pdb, chain B (#140),
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 #1.28/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 #141
---
Chain | Description
A | No description available
> matchmaker #141 to #1.28 & 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 (#1.28) with AF3 CA.pdb, chain A (#141),
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 #137 dodgerblue
> color #138 dodgerblue
> color #139 #00b305ff
> color #140 #00b305ff
> color #141 #f15839ff
> select #1.29/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 #142
---
Chain | Description
A | No description available
> matchmaker #142 to #1.29 & 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 (#1.29) with AF3 E1 1-421.pdb, chain A (#142),
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 #143
---
Chain | Description
A | No description available
> matchmaker #143 to #1.29 & 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 (#1.29) with AF3 E1 422-461.pdb, chain A (#143),
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 #1.29/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 #144
---
Chain | Description
B | No description available
> matchmaker #144 to #1.29 & 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 (#1.29) with AF3 E2 1-352.pdb, chain B (#144),
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 #145
---
Chain | Description
B | No description available
> matchmaker #145 to #1.29 & 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 (#1.29) with AF3 E2 353-438.pdb, chain B (#145),
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 #1.29/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 #146
---
Chain | Description
A | No description available
> matchmaker #146 to #1.29 & 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 (#1.29) with AF3 CA.pdb, chain A (#146),
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 #142 dodgerblue
> color #143 dodgerblue
> color #144 #00b305ff
> color #145 #00b305ff
> color #146 #f15839ff
> select #1.30/A
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> show sel cartoons
> select #1.30/B
3304 atoms, 3395 bonds, 423 residues, 1 model selected
> select #1.30/A
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
Chain information for AF3 E1 1-421.pdb #147
---
Chain | Description
A | No description available
> matchmaker #147 to #1.30 & 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 (#1.30) with AF3 E1 1-421.pdb, chain A (#147),
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 #148
---
Chain | Description
A | No description available
> matchmaker #148 to #1.30 & 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 (#1.30) with AF3 E1 422-461.pdb, chain A (#148),
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 #1.30/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 #149
---
Chain | Description
B | No description available
> matchmaker #149 to #1.30 & 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 (#1.30) with AF3 E2 1-352.pdb, chain B (#149),
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 #150
---
Chain | Description
B | No description available
> matchmaker #150 to #1.30 & 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 (#1.30) with AF3 E2 353-438.pdb, chain B (#150),
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 #1.30/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 #151
---
Chain | Description
A | No description available
> matchmaker #151 to #1.30 & 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 (#1.30) with AF3 CA.pdb, chain A (#151),
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 #147 dodgerblue
> color #148 dodgerblue
> color #149 #00b305ff
> color #150 #00b305ff
> color #151 #f15839ff
> save "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" includeMaps true
> select #1.31/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 #152
---
Chain | Description
A | No description available
> matchmaker #152 to #1.31 & 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 (#1.31) with AF3 E1 1-421.pdb, chain A (#152),
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 #153
---
Chain | Description
A | No description available
> matchmaker #153 to #1.31 & 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 (#1.31) with AF3 E1 422-461.pdb, chain A (#153),
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 #1.31/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 #154
---
Chain | Description
B | No description available
> matchmaker #154 to #1.31 & 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 (#1.31) with AF3 E2 1-352.pdb, chain B (#154),
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 #155
---
Chain | Description
B | No description available
> matchmaker #155 to #1.31 & 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 (#1.31) with AF3 E2 353-438.pdb, chain B (#155),
sequence alignment score = 333.4
RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
8.411)
> select #1.31/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 #156
---
Chain | Description
A | No description available
> matchmaker #156 to #1.31 & 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 (#1.31) with AF3 CA.pdb, chain A (#156),
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 #1.31/B
3304 atoms, 3395 bonds, 423 residues, 1 model selected
> hide sel cartoons
> color #152 dodgerblue
> color #153 dodgerblue
> color #154 #00b305ff
> color #155 #00b305ff
> color #156 #f15839ff
> select #1.32/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 #157
---
Chain | Description
A | No description available
> matchmaker #157 to #1.32 & 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 (#1.32) with AF3 E1 1-421.pdb, chain A (#157),
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 #158
---
Chain | Description
A | No description available
> matchmaker #158 to #1.32 & 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 (#1.32) with AF3 E1 422-461.pdb, chain A (#158),
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 #1.32/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 #159
---
Chain | Description
B | No description available
> matchmaker #159 to #1.32 & 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 (#1.32) with AF3 E2 1-352.pdb, chain B (#159),
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 #160
---
Chain | Description
B | No description available
> matchmaker #160 to #1.32 & 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 (#1.32) with AF3 E2 353-438.pdb, chain B (#160),
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 #1.32/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 #161
---
Chain | Description
A | No description available
> matchmaker #161 to #1.32 & 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 (#1.32) with AF3 CA.pdb, chain A (#161),
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 #157 dodgerblue
> color #158 dodgerblue
> color #159 #00b305ff
> color #160 #00b305ff
> color #161 #f15839ff
> select #1.33/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 #162
---
Chain | Description
A | No description available
> matchmaker #162 to #1.33 & 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 (#1.33) with AF3 E1 1-421.pdb, chain A (#162),
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 #163
---
Chain | Description
A | No description available
> matchmaker #163 to #1.33 & 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 (#1.33) with AF3 E1 422-461.pdb, chain A (#163),
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 #1.33/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 #164
---
Chain | Description
B | No description available
> matchmaker #164 to #1.33 & 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 (#1.33) with AF3 E2 1-352.pdb, chain B (#164),
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 #165
---
Chain | Description
B | No description available
> matchmaker #165 to #1.33 & 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 (#1.33) with AF3 E2 353-438.pdb, chain B (#165),
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 #1.33/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 #166
---
Chain | Description
A | No description available
> matchmaker #166 to #1.33 & 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 (#1.33) with AF3 CA.pdb, chain A (#166),
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 #162 dodgerblue
> color #163 dodgerblue
> color #164 #00b305ff
> color #165 #00b305ff
> color #166 #f15839ff
> select #1.34/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 #167
---
Chain | Description
A | No description available
> matchmaker #167 to #1.34 & 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 (#1.34) with AF3 E1 1-421.pdb, chain A (#167),
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 #168
---
Chain | Description
A | No description available
> matchmaker #168 to #1.34 & 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 (#1.34) with AF3 E1 422-461.pdb, chain A (#168),
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 #1.34/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 #169
---
Chain | Description
B | No description available
> matchmaker #169 to #1.34 & 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 (#1.34) with AF3 E2 1-352.pdb, chain B (#169),
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 #170
---
Chain | Description
B | No description available
> matchmaker #170 to #1.34 & 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 (#1.34) with AF3 E2 353-438.pdb, chain B (#170),
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 #1.34/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 #171
---
Chain | Description
A | No description available
> matchmaker #171 to #1.34 & 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 (#1.34) with AF3 CA.pdb, chain A (#171),
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 #167 dodgerblue
> color #168 dodgerblue
> color #169 #00b305ff
> color #170 #00b305ff
> color #171 #f15839ff
> select #1.35/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 #172
---
Chain | Description
A | No description available
> matchmaker #172 to #1.35 & 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 (#1.35) with AF3 E1 1-421.pdb, chain A (#172),
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 #173
---
Chain | Description
A | No description available
> matchmaker #173 to #1.35 & 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 (#1.35) with AF3 E1 422-461.pdb, chain A (#173),
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 #1.35/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 #174
---
Chain | Description
B | No description available
> matchmaker #174 to #1.35 & 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 (#1.35) with AF3 E2 1-352.pdb, chain B (#174),
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 #175
---
Chain | Description
B | No description available
> matchmaker #175 to #1.35 & 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 (#1.35) with AF3 E2 353-438.pdb, chain B (#175),
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 #1.35/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 #176
---
Chain | Description
A | No description available
> matchmaker #176 to #1.35 & 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 (#1.35) with AF3 CA.pdb, chain A (#176),
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 #172 dodgerblue
> color #173 dodgerblue
> color #174 #00b305ff
> color #175 #00b305ff
> color #176 #f15839ff
> select #1.36/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 #177
---
Chain | Description
A | No description available
> matchmaker #177 to #1.36 & 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 (#1.36) with AF3 E1 1-421.pdb, chain A (#177),
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 #178
---
Chain | Description
A | No description available
> matchmaker #178 to #1.36 & 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 (#1.36) with AF3 E1 422-461.pdb, chain A (#178),
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 #1.36/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 #179
---
Chain | Description
B | No description available
> matchmaker #179 to #1.36 & 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 (#1.36) with AF3 E2 1-352.pdb, chain B (#179),
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 #180
---
Chain | Description
B | No description available
> matchmaker #180 to #1.36 & 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 (#1.36) with AF3 E2 353-438.pdb, chain B (#180),
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 #1.36/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 #181
---
Chain | Description
A | No description available
> matchmaker #181 to #1.36 & 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 (#1.36) with AF3 CA.pdb, chain A (#181),
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 #177 dodgerblue
> color #178 dodgerblue
> color #179 #00b305ff
> color #180 #00b305ff
> color #181 #f15839ff
> select #1.37/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 #182
---
Chain | Description
A | No description available
> matchmaker #182 to #1.37 & 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 (#1.37) with AF3 E1 1-421.pdb, chain A (#182),
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 #183
---
Chain | Description
A | No description available
> matchmaker #183 to #1.37 & 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 (#1.37) with AF3 E1 422-461.pdb, chain A (#183),
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 #1.37/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 #184
---
Chain | Description
B | No description available
> matchmaker #184 to #1.37 & 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 (#1.37) with AF3 E2 1-352.pdb, chain B (#184),
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 #185
---
Chain | Description
B | No description available
> matchmaker #185 to #1.37 & 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 (#1.37) with AF3 E2 353-438.pdb, chain B (#185),
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 #1.37/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 #186
---
Chain | Description
A | No description available
> matchmaker #186 to #1.37 & 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 (#1.37) with AF3 CA.pdb, chain A (#186),
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 #182 dodgerblue
> color #183 dodgerblue
> color #184 #00b305ff
> color #185 #00b305ff
> color #186 #f15839ff
> select #1.38/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 #187
---
Chain | Description
A | No description available
> matchmaker #187 to #1.38 & 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 (#1.38) with AF3 E1 1-421.pdb, chain A (#187),
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 #188
---
Chain | Description
A | No description available
> matchmaker #188 to #1.38 & 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 (#1.38) with AF3 E1 422-461.pdb, chain A (#188),
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 #1.38/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 #189
---
Chain | Description
B | No description available
> matchmaker #189 to #1.38 & 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 (#1.38) with AF3 E2 1-352.pdb, chain B (#189),
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 #190
---
Chain | Description
B | No description available
> matchmaker #190 to #1.38 & 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 (#1.38) with AF3 E2 353-438.pdb, chain B (#190),
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 #1.38/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 #191
---
Chain | Description
A | No description available
> matchmaker #191 to #1.38 & 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 (#1.38) with AF3 CA.pdb, chain A (#191),
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 #187 dodgerblue
> color #188 dodgerblue
> color #189 #00b305ff
> color #190 #00b305ff
> color #191 #f15839ff
> select #1.39/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 #192
---
Chain | Description
A | No description available
> matchmaker #192 to #1.39 & 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 (#1.39) with AF3 E1 1-421.pdb, chain A (#192),
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 #193
---
Chain | Description
A | No description available
> matchmaker #193 to #1.39 & 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 (#1.39) with AF3 E1 422-461.pdb, chain A (#193),
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 #1.39/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 #194
---
Chain | Description
B | No description available
> matchmaker #194 to #1.39 & 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 (#1.39) with AF3 E2 1-352.pdb, chain B (#194),
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 #195
---
Chain | Description
B | No description available
> matchmaker #195 to #1.39 & 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 (#1.39) with AF3 E2 353-438.pdb, chain B (#195),
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 #1.39/C
1277 atoms, 1305 bonds, 162 residues, 1 model selected
> show sel atoms
> hide sel atoms
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 CA.pdb"
Chain information for AF3 CA.pdb #196
---
Chain | Description
A | No description available
> matchmaker #196 to #1.39 & 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 (#1.39) with AF3 CA.pdb, chain A (#196),
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 #192 dodgerblue
> color #193 dodgerblue
> color #194 #00b305ff
> color #195 #00b305ff
> color #196 #f15839ff
> select #1.40/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 #197
---
Chain | Description
A | No description available
> matchmaker #197 to #1.40 & 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 (#1.40) with AF3 E1 1-421.pdb, chain A (#197),
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 #198
---
Chain | Description
A | No description available
> matchmaker #198 to #1.40 & 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 (#1.40) with AF3 E1 422-461.pdb, chain A (#198),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
2.775)
> hide sel cartoons
[Repeated 1 time(s)]
> select #1.40/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 #199
---
Chain | Description
B | No description available
> matchmaker #199 to #1.40 & 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 (#1.40) with AF3 E2 1-352.pdb, chain B (#199),
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 #200
---
Chain | Description
B | No description available
> matchmaker #200 to #1.40 & 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 (#1.40) with AF3 E2 353-438.pdb, chain B (#200),
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 #1.40/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 #201
---
Chain | Description
A | No description available
> matchmaker #201 to #1.40 & 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 (#1.40) with AF3 CA.pdb, chain A (#201),
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 #197 dodgerblue
> color #198 dodgerblue
> color #199 #00b305ff
> color #200 #00b305ff
> color #201 #f15839ff
> save "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" includeMaps true
> select #1.41/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 #202
---
Chain | Description
A | No description available
> matchmaker #202 to #1.41 & 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 (#1.41) with AF3 E1 1-421.pdb, chain A (#202),
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 #203
---
Chain | Description
A | No description available
> matchmaker #203 to #1.41 & 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 (#1.41) with AF3 E1 422-461.pdb, chain A (#203),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
2.776)
> hide sel cartoons
[Repeated 1 time(s)]
> select #1.41/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 #204
---
Chain | Description
B | No description available
> matchmaker #204 to #1.41 & 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 (#1.41) with AF3 E2 1-352.pdb, chain B (#204),
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 #205
---
Chain | Description
B | No description available
> matchmaker #205 to #1.41 & 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 (#1.41) with AF3 E2 353-438.pdb, chain B (#205),
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 #1.41/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 #206
---
Chain | Description
A | No description available
> matchmaker #206 to #1.41 & 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 (#1.41) with AF3 CA.pdb, chain A (#206),
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 #202 dodgerblue
> color #203 dodgerblue
> color #204 #00b305ff
> color #205 #00b305ff
> color #206 #f15839ff
> select #1.42/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 #207
---
Chain | Description
A | No description available
> matchmaker #207 to #1.42 & 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 (#1.42) with AF3 E1 1-421.pdb, chain A (#207),
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 #208
---
Chain | Description
A | No description available
> matchmaker #208 to #1.42 & 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 (#1.42) with AF3 E1 422-461.pdb, chain A (#208),
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 #1.42/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 #209
---
Chain | Description
B | No description available
> matchmaker #209 to #1.42 & 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 (#1.42) with AF3 E2 1-352.pdb, chain B (#209),
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 #210
---
Chain | Description
B | No description available
> matchmaker #210 to #1.42 & 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 (#1.42) with AF3 E2 353-438.pdb, chain B (#210),
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 #1.42/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 #211
---
Chain | Description
A | No description available
> matchmaker #211 to #1.42 & 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 (#1.42) with AF3 CA.pdb, chain A (#211),
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 #207 dodgerblue
> color #208 dodgerblue
> color #209 #00b305ff
> color #210 #00b305ff
> color #211 #f15839ff
> select #1.43/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 #212
---
Chain | Description
A | No description available
> matchmaker #212 to #1.43 & 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 (#1.43) with AF3 E1 1-421.pdb, chain A (#212),
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 #213
---
Chain | Description
A | No description available
> matchmaker #213 to #1.43 & 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 (#1.43) with AF3 E1 422-461.pdb, chain A (#213),
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 #1.43/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 #214
---
Chain | Description
B | No description available
> matchmaker #214 to #1.43 & 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 (#1.43) with AF3 E2 1-352.pdb, chain B (#214),
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 #215
---
Chain | Description
B | No description available
> matchmaker #215 to #1.43 & 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 (#1.43) with AF3 E2 353-438.pdb, chain B (#215),
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 #1.43/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 #216
---
Chain | Description
A | No description available
> matchmaker #216 to #1.43 & 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 (#1.43) with AF3 CA.pdb, chain A (#216),
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 #212 dodgerblue
> color #213 dodgerblue
> color #214 #00b305ff
> color #215 #00b305ff
> color #216 #f15839ff
> select #1.44/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 #217
---
Chain | Description
A | No description available
> matchmaker #217 to #1.43 & sel
No 'to' model specified
> matchmaker #217 to #1.44 & 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 (#1.44) with AF3 E1 1-421.pdb, chain A (#217),
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 #218
---
Chain | Description
A | No description available
> matchmaker #218 to #1.44 & 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 (#1.44) with AF3 E1 422-461.pdb, chain A (#218),
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 #1.44/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 #219
---
Chain | Description
B | No description available
> matchmaker #219 to #1.44 & 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 (#1.44) with AF3 E2 1-352.pdb, chain B (#219),
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 #220
---
Chain | Description
B | No description available
> matchmaker #220 to #1.44 & 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 (#1.44) with AF3 E2 353-438.pdb, chain B (#220),
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 #1.44/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 #221
---
Chain | Description
A | No description available
> matchmaker #221 to #1.44 & 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 (#1.44) with AF3 CA.pdb, chain A (#221),
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 #217 dodgerblue
> color #218 dodgerblue
> color #219 #00b305ff
> color #220 #00b305ff
> color #221 #f15839ff
> select #1.45/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 #222
---
Chain | Description
A | No description available
> matchmaker #222 to #1.45 & 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 (#1.45) with AF3 E1 1-421.pdb, chain A (#222),
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 #223
---
Chain | Description
A | No description available
> matchmaker #223 to #1.45 & 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 (#1.45) with AF3 E1 422-461.pdb, chain A (#223),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
2.775)
> hide sel cartoons
[Repeated 1 time(s)]
> select #1.45/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 #224
---
Chain | Description
B | No description available
> matchmaker #224 to #1.45 & 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 (#1.45) with AF3 E2 1-352.pdb, chain B (#224),
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 #225
---
Chain | Description
B | No description available
> matchmaker #225 to #1.45 & 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 (#1.45) with AF3 E2 353-438.pdb, chain B (#225),
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 #1.45/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 #226
---
Chain | Description
A | No description available
> matchmaker #226 to #1.45 & 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 (#1.45) with AF3 CA.pdb, chain A (#226),
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 #222 dodgerblue
> color #223 dodgerblue
> color #224 #00b305ff
> color #225 #00b305ff
> color #226 #f15839ff
> select #1.46/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 #227
---
Chain | Description
A | No description available
> matchmaker #227 to #1.46 & 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 (#1.46) with AF3 E1 1-421.pdb, chain A (#227),
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 #228
---
Chain | Description
A | No description available
> matchmaker #228 to #1.46 & 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 (#1.46) with AF3 E1 422-461.pdb, chain A (#228),
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 #1.46/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 #229
---
Chain | Description
B | No description available
> matchmaker #229 to #1.46 & 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 (#1.46) with AF3 E2 1-352.pdb, chain B (#229),
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 #230
---
Chain | Description
B | No description available
> matchmaker #230 to #1.46 & 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 (#1.46) with AF3 E2 353-438.pdb, chain B (#230),
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 #1.46/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 #231
---
Chain | Description
A | No description available
> matchmaker #231 to #1.46 & 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 (#1.46) with AF3 CA.pdb, chain A (#231),
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 #227 #408ca2ff
> color #227 dodgerblue
> color #228 dodgerblue
> color #229 #00b305ff
> color #230 #00b305ff
> color #231 #f15839ff
> view sel
No displayed objects specified.
> 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
418952 atoms, 429570 bonds, 55178 residues, 198 models selected
> view sel
> select clear
> select #1.47/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 #232
---
Chain | Description
A | No description available
> matchmaker #232 to #1.47 & 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 (#1.47) with AF3 E1 1-421.pdb, chain A (#232),
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 #233
---
Chain | Description
A | No description available
> matchmaker #233 to #1.47 & 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 (#1.47) with AF3 E1 422-461.pdb, chain A (#233),
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 #1.47/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 #234
---
Chain | Description
B | No description available
> matchmaker #234 to #1.47 & 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 (#1.47) with AF3 E2 1-352.pdb, chain B (#234),
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 #235
---
Chain | Description
B | No description available
> matchmaker #235 to #1.47 & 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 (#1.47) with AF3 E2 353-438.pdb, chain B (#235),
sequence alignment score = 322.6
RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
8.411)
> open "/Users/Jean/Desktop/AF3 CA.pdb"
Chain information for AF3 CA.pdb #236
---
Chain | Description
A | No description available
> hide sel cartoons
> select #1.47/C
1277 atoms, 1305 bonds, 162 residues, 1 model selected
> show sel cartoons
> matchmaker #236 to #1.47 & 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 (#1.47) with AF3 CA.pdb, chain A (#236),
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 #232 dodgerblue
> color #233 dodgerblue
> color #234 #00b305ff
> color #235 #00b305ff
> color #236 #f15839ff
> select #1.48/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 #237
---
Chain | Description
A | No description available
> matchmaker #237 to #1.48 & 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 (#1.48) with AF3 E1 1-421.pdb, chain A (#237),
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 #238
---
Chain | Description
A | No description available
> matchmaker #238 to #1.48 & 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 (#1.48) with AF3 E1 422-461.pdb, chain A (#238),
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 #1.48/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 #239
---
Chain | Description
B | No description available
> matchmaker #239 to #1.48 & 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 (#1.48) with AF3 E2 1-352.pdb, chain B (#239),
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 #240
---
Chain | Description
B | No description available
> matchmaker #240 to #1.48 & 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 (#1.48) with AF3 E2 353-438.pdb, chain B (#240),
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 #1.48/B
3304 atoms, 3395 bonds, 423 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> select #1.48/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 #241
---
Chain | Description
A | No description available
> matchmaker #241 to #1.48 & 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 (#1.48) with AF3 CA.pdb, chain A (#241),
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 #237 dodgerblue
> color #238 dodgerblue
> color #239 #00b305ff
> color #241 #f15839ff
> color #240 #00b305ff
> select #1.49/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 #242
---
Chain | Description
A | No description available
> matchmaker #242 to #1.49 & 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 (#1.49) with AF3 E1 1-421.pdb, chain A (#242),
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 #243
---
Chain | Description
A | No description available
> matchmaker #243 to #1.49 & 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 (#1.49) with AF3 E1 422-461.pdb, chain A (#243),
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 #1.49/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 #244
---
Chain | Description
B | No description available
> matchmaker #244 to #1.49 & 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 (#1.49) with AF3 E2 1-352.pdb, chain B (#244),
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 #245
---
Chain | Description
B | No description available
> matchmaker #245 to #1.49 & 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 (#1.49) with AF3 E2 353-438.pdb, chain B (#245),
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 #1.49/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 #246
---
Chain | Description
A | No description available
> matchmaker #246 to #1.49 & 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 (#1.49) with AF3 CA.pdb, chain A (#246),
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 #242 dodgerblue
> color #243 dodgerblue
> color #244 #00b305ff
> color #245 #00b305ff
> color #245 #f15839ff
> color #245 #00b305ff
> color #246 #f15839ff
> select #1.50/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 #247
---
Chain | Description
A | No description available
> matchmaker #247 to #1.49 & sel
No 'to' model specified
> matchmaker #247 to #1.50 & 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 (#1.50) with AF3 E1 1-421.pdb, chain A (#247),
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 #248
---
Chain | Description
A | No description available
> matchmaker #248 to #1.50 & 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 (#1.50) with AF3 E1 422-461.pdb, chain A (#248),
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 #1.50/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 #249
---
Chain | Description
B | No description available
> matchmaker #249 to #1.50 & 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 (#1.50) with AF3 E2 1-352.pdb, chain B (#249),
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 #250
---
Chain | Description
B | No description available
> matchmaker #250 to #1.50 & 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 (#1.50) with AF3 E2 353-438.pdb, chain B (#250),
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 #1.50/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 #251
---
Chain | Description
A | No description available
> matchmaker #251 to #1.50 & 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 (#1.50) with AF3 CA.pdb, chain A (#251),
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 #247 dodgerblue
> color #248 dodgerblue
> color #249 #00b305ff
> color #250 #00b305ff
> color #251 #f15839ff
> save "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" includeMaps true
> select #1.51/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 #252
---
Chain | Description
A | No description available
> matchmaker #252 to #1.51 & 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 (#1.51) with AF3 E1 1-421.pdb, chain A (#252),
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 #253
---
Chain | Description
A | No description available
> matchmaker #253 to #1.51 & 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 (#1.51) with AF3 E1 422-461.pdb, chain A (#253),
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 #1.51/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 #254
---
Chain | Description
B | No description available
> matchmaker #254 to #1.51 & 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 (#1.51) with AF3 E2 1-352.pdb, chain B (#254),
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 #255
---
Chain | Description
B | No description available
> matchmaker #255 to #1.51 & 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 (#1.51) with AF3 E2 353-438.pdb, chain B (#255),
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 #1.51/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 #256
---
Chain | Description
A | No description available
> matchmaker #256 to #1.51 & 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 (#1.51) with AF3 CA.pdb, chain A (#256),
sequence alignment score = 328.1
RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
2.714)
> matchmaker #256 to #1.51 & 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 (#1.51) with AF3 CA.pdb, chain A (#256),
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 #252 dodgerblue
> color #253 dodgerblue
> color #254 #00b305ff
> color #255 #00b305ff
> color #256 #f15839ff
> select #1.52/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 #257
---
Chain | Description
A | No description available
> matchmaker #257 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 A (#1.52) with AF3 E1 1-421.pdb, chain A (#257),
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 #258
---
Chain | Description
A | No description available
> matchmaker #258 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 A (#1.52) with AF3 E1 422-461.pdb, chain A (#258),
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 #1.52/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 #259
---
Chain | Description
B | No description available
> matchmaker #259 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 B (#1.52) with AF3 E2 1-352.pdb, chain B (#259),
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 #260
---
Chain | Description
B | No description available
> matchmaker #260 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 B (#1.52) with AF3 E2 353-438.pdb, chain B (#260),
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 #1.52/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
> hide #8 models
> hide #9 models
> hide #10 models
> hide #11 models
> hide #12 models
> hide #13 models
> hide #14 models
> hide #15 models
> hide #16 models
> hide #17 models
> show #16 models
> show #17 models
> hide #18 models
> hide #19 models
> hide #20 models
> hide #21 models
> hide #22 models
> hide #23 models
> hide #24 models
> hide #25 models
> hide #16 models
> hide #17 models
> hide #26 models
> hide #27 models
> hide #28 models
> hide #29 models
> 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
> hide #43 models
> hide #44 models
> hide #45 models
> hide #46 models
> hide #47 models
> hide #48 models
> hide #49 models
> hide #50 models
> hide #51 models
> hide #52 models
> hide #53 models
> hide #54 models
> hide #55 models
> hide #56 models
> hide #57 models
> hide #58 models
> hide #59 models
> hide #60 models
> hide #61 models
> hide #62 models
> hide #63 models
> hide #64 models
> hide #65 models
> hide #66 models
> hide #67 models
> hide #68 models
> hide #69 models
> hide #70 models
> hide #71 models
> hide #72 models
> hide #73 models
> hide #74 models
> hide #75 models
> hide #76 models
> hide #77 models
> hide #78 models
> hide #79 models
> hide #80 models
> hide #81 models
> hide #82 models
> hide #83 models
> hide #84 models
> hide #85 models
> hide #86 models
> hide #87 models
> hide #88 models
> hide #89 models
> hide #90 models
> hide #91 models
> hide #92 models
> hide #93 models
> hide #94 models
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> hide #96 models
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> hide #101 models
> hide #102 models
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> hide #110 models
> hide #111 models
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> hide #113 models
> hide #114 models
> hide #115 models
> hide #116 models
> hide #117 models
> hide #118 models
> hide #119 models
> hide #120 models
> hide #121 models
> hide #122 models
> hide #123 models
> hide #124 models
> hide #125 models
> hide #126 models
> hide #127 models
> hide #128 models
> hide #129 models
> hide #130 models
> hide #131 models
> hide #132 models
> hide #133 models
> hide #134 models
> hide #135 models
> hide #136 models
> hide #137 models
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> hide #141 models
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> hide #150 models
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> hide #158 models
> hide #159 models
> hide #160 models
> hide #161 models
> hide #162 models
> hide #163 models
> hide #164 models
> hide #165 models
> hide #166 models
> hide #167 models
> hide #168 models
> hide #169 models
> hide #170 models
> hide #171 models
> hide #172 models
> hide #173 models
> hide #174 models
> hide #175 models
> hide #176 models
> hide #177 models
> hide #178 models
> hide #179 models
> hide #180 models
> hide #181 models
> hide #182 models
> hide #183 models
> hide #184 models
> hide #185 models
> hide #186 models
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> hide #188 models
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> hide #190 models
> hide #191 models
> hide #192 models
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> hide #194 models
> hide #195 models
> hide #196 models
> hide #197 models
> hide #198 models
> hide #199 models
> hide #200 models
> hide #201 models
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> hide #234 models
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> hide #236 models
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> hide #246 models
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> 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
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