![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 17 months ago
Last modified 17 months ago
#15628 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.
Fatal Python error: Segmentation fault
Current thread 0x00007ff851ef2fc0 (most recent call first):
File "/Applications/Biology/Bio/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
File "/Applications/Biology/Bio/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
File "/Applications/Biology/Bio/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.pdb_lib._load_libs, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, chimerax.alignment_algs._sw (total: 59)
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{
"uptime" : 5400,
"procRole" : "Foreground",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "MacBookPro15,1",
"coalitionID" : 1165,
"osVersion" : {
"train" : "macOS 14.5",
"build" : "23F79",
"releaseType" : "User"
},
"captureTime" : "2024-07-18 09:26:01.9398 +0200",
"codeSigningMonitor" : 0,
"incident" : "1EDF5ADA-5B27-483B-9DDF-91AB08B884B0",
"pid" : 1059,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-07-18 08:01:23.0626 +0200",
"procStartAbsTime" : 356295690989,
"procExitAbsTime" : 5435149572380,
"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"},
"storeInfo" : {"deviceIdentifierForVendor":"29E949B5-C6C5-56AA-9663-9485431E4002","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "0D5DE8DA-3A8B-C1EA-D7CC-5AC7584FDF08",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"bridgeVersion" : {"build":"21P5077","train":"8.5"},
"sip" : "enabled",
"vmRegionInfo" : "0 is not in any region. Bytes before following region: 4376354816\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 104d9e000-104da2000 [ 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"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":1059},
"vmregioninfo" : "0 is not in any region. Bytes before following region: 4376354816\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 104d9e000-104da2000 [ 16K] r-x\/r-x SM=COW \/Applications\/Biology\/*\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
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"faultingThread" : 0,
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===== Log before crash start =====
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 Wed Jul 17 16:12:00 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 Wed Jul 17 13:58:06 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 Tue Jul 16 18:02:55 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 16:59:09 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
> hide #95 models
> hide #96 models
> hide #97 models
> hide #98 models
> hide #99 models
> hide #100 models
> hide #101 models
> hide #102 models
> hide #103 models
> hide #104 models
> hide #105 models
> hide #106 models
> hide #107 models
> hide #108 models
> hide #109 models
> hide #110 models
> hide #111 models
> hide #112 models
> 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
> hide #138 models
> hide #139 models
> hide #140 models
> hide #141 models
> hide #142 models
> hide #143 models
> hide #144 models
> hide #145 models
> hide #146 models
> hide #147 models
> hide #148 models
> hide #149 models
> hide #150 models
> hide #151 models
> hide #152 models
> hide #153 models
> hide #154 models
> hide #155 models
> hide #156 models
> hide #157 models
> 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
> hide #187 models
> hide #188 models
> hide #189 models
> hide #190 models
> hide #191 models
> hide #192 models
> hide #193 models
> hide #194 models
> hide #195 models
> hide #196 models
> hide #197 models
> hide #198 models
> hide #199 models
> hide #200 models
> hide #201 models
> hide #202 models
> hide #203 models
> hide #204 models
> hide #205 models
> hide #206 models
> hide #207 models
> hide #208 models
> hide #209 models
> hide #210 models
> hide #211 models
> hide #212 models
> hide #213 models
> hide #214 models
> hide #215 models
> hide #216 models
> hide #217 models
> hide #218 models
> hide #219 models
> hide #220 models
> hide #221 models
> hide #222 models
> hide #223 models
> hide #224 models
> hide #225 models
> hide #226 models
> hide #227 models
> hide #228 models
> hide #229 models
> hide #230 models
> hide #231 models
> hide #232 models
> hide #233 models
> hide #234 models
> hide #235 models
> hide #236 models
> hide #237 models
> hide #238 models
> hide #239 models
> hide #240 models
> hide #241 models
> hide #242 models
> hide #243 models
> hide #244 models
> hide #245 models
> hide #246 models
> hide #247 models
> hide #248 models
> hide #249 models
> hide #250 models
> hide #251 models
> hide #252 models
> hide #253 models
> hide #254 models
> hide #255 models
> hide #256 models
> hide #257 models
> hide #258 models
> hide #259 models
> hide #260 models
> hide #261 models
> select #1.53/A
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> select #1.52/A
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> view sel
No displayed objects specified.
> show #!1 models
> select ~sel & ##selected
28434 atoms, 29183 bonds, 3666 residues, 1 model selected
> hide sel cartoons
> select
> #1.1/A#1.2/A#1.3/A#1.4/A#1.5/A#1.6/A#1.7/A#1.8/A#1.9/A#1.10/A#1.11/A#1.12/A#1.13/A#1.14/A#1.15/A#1.16/A#1.17/A#1.18/A#1.19/A#1.20/A#1.21/A#1.22/A#1.23/A#1.24/A#1.25/A#1.26/A#1.27/A#1.28/A#1.29/A#1.30/A#1.31/A#1.32/A#1.33/A#1.34/A#1.35/A#1.36/A#1.37/A#1.38/A#1.39/A#1.40/A#1.41/A#1.42/A#1.43/A#1.44/A#1.45/A#1.46/A#1.47/A#1.48/A#1.49/A#1.50/A#1.51/A#1.52/A#1.53/A#1.54/A#1.55/A#1.56/A#1.57/A#1.58/A#1.59/A#1.60/A#2/A#3/A#6/A#7/A#8/A#11/A#12/A#13/A#16/A#17/A#18/A#21/A#22/A#23/A#26/A#27/A#28/A#31/A#32/A#33/A#36/A#37/A#38/A#41/A#42/A#43/A#46/A#47/A#48/A#51/A#52/A#53/A#56/A#57/A#58/A#61/A#62/A#63/A#66/A#67/A#68/A#71/A#72/A#73/A#76/A#77/A#78/A#81/A#82/A#83/A#86/A#87/A#88/A#91/A#92/A#93/A#96/A#97/A#98/A#101/A#102/A#103/A#106/A#107/A#108/A#111/A#112/A#113/A#116/A#117/A#118/A#121/A#122/A#123/A#126/A#127/A#128/A#131/A#132/A#133/A#136/A#137/A#138/A#141/A#142/A#143/A#146/A#147/A#148/A#151/A#152/A#153/A#156/A#157/A#158/A#161/A#162/A#163/A#166/A#167/A#168/A#171/A#172/A#173/A#176/A#177/A#178/A#181/A#182/A#183/A#186/A#187/A#188/A#191/A#192/A#193/A#196/A#197/A#198/A#201/A#202/A#203/A#206/A#207/A#208/A#211/A#212/A#213/A#216/A#217/A#218/A#221/A#222/A#223/A#226/A#227/A#228/A#231/A#232/A#233/A#236/A#237/A#238/A#241/A#242/A#243/A#246/A#247/A#248/A#251/A#252/A#253/A#256/A#257/A#258/A#261/A
447224 atoms, 458514 bonds, 58916 residues, 216 models selected
> select
2325488 atoms, 2385760 bonds, 301652 residues, 321 models selected
> hide sel & #1.1-60 cartoons
> select #1.53/A
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
Chain information for AF3 E1 1-421.pdb #262
---
Chain | Description
A | No description available
> matchmaker #262 to #1.53 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain A (#1.53) with AF3 E1 1-421.pdb, chain A (#262),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
3.020)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #263
---
Chain | Description
A | No description available
> matchmaker #263 to #1.53 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain A (#1.53) with AF3 E1 422-461.pdb, chain A (#263),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
2.775)
> hide sel cartoons
> select #1.53/B
3304 atoms, 3395 bonds, 423 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
Chain information for AF3 E2 1-352.pdb #264
---
Chain | Description
B | No description available
> matchmaker #264 to #1.53 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain B (#1.53) with AF3 E2 1-352.pdb, chain B (#264),
sequence alignment score = 583.7
RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
5.933)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #265
---
Chain | Description
B | No description available
> matchmaker #265 to #1.53 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain B (#1.53) with AF3 E2 353-438.pdb, chain B (#265),
sequence alignment score = 333.4
RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
8.411)
> hide sel cartoons
> select #1.53/C
1277 atoms, 1305 bonds, 162 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 CA.pdb"
Chain information for AF3 CA.pdb #266
---
Chain | Description
A | No description available
> matchmaker #266 to #1.53 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain C (#1.53) with AF3 CA.pdb, chain A (#266),
sequence alignment score = 328.1
RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
2.714)
> hide sel cartoons
> select #1.54/A
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
Chain information for AF3 E1 1-421.pdb #267
---
Chain | Description
A | No description available
> matchmaker #267 to #1.54 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain A (#1.54) with AF3 E1 1-421.pdb, chain A (#267),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
3.020)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #268
---
Chain | Description
A | No description available
> matchmaker #268 to #1.54 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain A (#1.54) with AF3 E1 422-461.pdb, chain A (#268),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.572 angstroms; (across all 38 pairs:
2.776)
> matchmaker #268 to #1.54 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain A (#1.54) with AF3 E1 422-461.pdb, chain A (#268),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.572 angstroms; (across all 38 pairs:
2.776)
> hide sel cartoons
> select #1.54/B
3304 atoms, 3395 bonds, 423 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
Chain information for AF3 E2 1-352.pdb #269
---
Chain | Description
B | No description available
> matchmaker #269 to #1.54 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain B (#1.54) with AF3 E2 1-352.pdb, chain B (#269),
sequence alignment score = 583.7
RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
5.933)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #270
---
Chain | Description
B | No description available
> matchmaker #270 to #1.54 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain B (#1.54) with AF3 E2 353-438.pdb, chain B (#270),
sequence alignment score = 333.4
RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
8.411)
> hide sel cartoons
> select #1.54/C
1277 atoms, 1305 bonds, 162 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 CA.pdb"
Chain information for AF3 CA.pdb #271
---
Chain | Description
A | No description available
> matchmaker #271 to #1.54 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain C (#1.54) with AF3 CA.pdb, chain A (#271),
sequence alignment score = 328.1
RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
2.714)
> hide sel cartoons
> color #262 dodgerblue
> color #263 dodgerblue
> color #264 #00b305ff
> color #265 #00b305ff
> color #266 #f15839ff
> color #267 dodgerblue
> color #268 dodgerblue
> color #269 #00b305ff
> color #270 #00b305ff
> color #271 #f15839ff
> select #1.55/A
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
Chain information for AF3 E1 1-421.pdb #272
---
Chain | Description
A | No description available
> matchmaker #272 to #1.54 & sel
No 'to' model specified
> matchmaker #272 to #1.55 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain A (#1.55) with AF3 E1 1-421.pdb, chain A (#272),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
3.020)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #273
---
Chain | Description
A | No description available
> matchmaker #273 to #1.55 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain A (#1.55) with AF3 E1 422-461.pdb, chain A (#273),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.572 angstroms; (across all 38 pairs:
2.775)
> hide sel cartoons
> open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
Chain information for AF3 E2 1-352.pdb #274
---
Chain | Description
B | No description available
> select #1.55/B
3304 atoms, 3395 bonds, 423 residues, 1 model selected
> show sel cartoons
> matchmaker #274 to #1.55 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain B (#1.55) with AF3 E2 1-352.pdb, chain B (#274),
sequence alignment score = 583.7
RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
5.933)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #275
---
Chain | Description
B | No description available
> matchmaker #275 to #1.55 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain B (#1.55) with AF3 E2 353-438.pdb, chain B (#275),
sequence alignment score = 322.6
RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
8.411)
> hide sel cartoons
> select #1.55/C
1277 atoms, 1305 bonds, 162 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 CA.pdb"
Chain information for AF3 CA.pdb #276
---
Chain | Description
A | No description available
> matchmaker #276 to #1.55 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain C (#1.55) with AF3 CA.pdb, chain A (#276),
sequence alignment score = 328.1
RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
2.714)
> hide sel cartoons
> color #272 dodgerblue
> color #273 dodgerblue
> color #274 #00b305ff
> color #275 #00b305ff
> color #276 #f15839ff
> select #1.56/A
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
Chain information for AF3 E1 1-421.pdb #277
---
Chain | Description
A | No description available
> matchmaker #277 to #1.55 & sel
No 'to' model specified
> matchmaker #277 to #1.56 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain A (#1.56) with AF3 E1 1-421.pdb, chain A (#277),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
3.020)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #278
---
Chain | Description
A | No description available
> matchmaker #278 to #1.56 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain A (#1.56) with AF3 E1 422-461.pdb, chain A (#278),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.572 angstroms; (across all 38 pairs:
2.775)
> hide sel cartoons
> select #1.56/B
3304 atoms, 3395 bonds, 423 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
Chain information for AF3 E2 1-352.pdb #279
---
Chain | Description
B | No description available
> matchmaker #279 to #1.56 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain B (#1.56) with AF3 E2 1-352.pdb, chain B (#279),
sequence alignment score = 583.7
RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
5.933)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #280
---
Chain | Description
B | No description available
> matchmaker #280 to #1.56 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain B (#1.56) with AF3 E2 353-438.pdb, chain B (#280),
sequence alignment score = 333.4
RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
8.411)
> hide sel cartoons
> select #1.56/C
1277 atoms, 1305 bonds, 162 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 CA.pdb"
Chain information for AF3 CA.pdb #281
---
Chain | Description
A | No description available
> matchmaker #281 to #1.56 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain C (#1.56) with AF3 CA.pdb, chain A (#281),
sequence alignment score = 328.1
RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
2.714)
> hide sel cartoons
> color #277 dodgerblue
> color #278 dodgerblue
> color #279 #00b305ff
> color #280 #00b305ff
> color #281 #f15839ff
> select #1.57/A
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
Chain information for AF3 E1 1-421.pdb #282
---
Chain | Description
A | No description available
> matchmaker #282 to #1.56 & sel
No 'to' model specified
> matchmaker #282 to #1.57 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain A (#1.57) with AF3 E1 1-421.pdb, chain A (#282),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
3.020)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #283
---
Chain | Description
A | No description available
> matchmaker #283 to #1.57 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain A (#1.57) with AF3 E1 422-461.pdb, chain A (#283),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
2.776)
> hide sel cartoons
> select #1.57/B
3304 atoms, 3395 bonds, 423 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
Chain information for AF3 E2 1-352.pdb #284
---
Chain | Description
B | No description available
> matchmaker #284 to #1.57 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain B (#1.57) with AF3 E2 1-352.pdb, chain B (#284),
sequence alignment score = 583.7
RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
5.933)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #285
---
Chain | Description
B | No description available
> matchmaker #285 to #1.57 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain B (#1.57) with AF3 E2 353-438.pdb, chain B (#285),
sequence alignment score = 333.4
RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
8.411)
> hide sel cartoons
[Repeated 1 time(s)]
> select #1.57/C
1277 atoms, 1305 bonds, 162 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 CA.pdb"
Chain information for AF3 CA.pdb #286
---
Chain | Description
A | No description available
> matchmaker #286 to #1.57 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain C (#1.57) with AF3 CA.pdb, chain A (#286),
sequence alignment score = 328.1
RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
2.714)
> hide sel cartoons
> color #282 dodgerblue
> color #283 dodgerblue
> color #284 #00b305ff
> color #285 #00b305ff
> color #286 #f15839ff
> select #1.58/A
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
Chain information for AF3 E1 1-421.pdb #287
---
Chain | Description
A | No description available
> matchmaker #287 to #1.58 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain A (#1.58) with AF3 E1 1-421.pdb, chain A (#287),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
3.020)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #288
---
Chain | Description
A | No description available
> matchmaker #288 to #1.58 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain A (#1.58) with AF3 E1 422-461.pdb, chain A (#288),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
2.775)
> hide sel cartoons
> select #1.58/B
3304 atoms, 3395 bonds, 423 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
Chain information for AF3 E2 1-352.pdb #289
---
Chain | Description
B | No description available
> matchmaker #289 to #1.58 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain B (#1.58) with AF3 E2 1-352.pdb, chain B (#289),
sequence alignment score = 583.7
RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
5.933)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #290
---
Chain | Description
B | No description available
> matchmaker #290 to #1.58 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain B (#1.58) with AF3 E2 353-438.pdb, chain B (#290),
sequence alignment score = 322.6
RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
8.411)
> hide sel cartoons
> select #1.58/C
1277 atoms, 1305 bonds, 162 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 CA.pdb"
Chain information for AF3 CA.pdb #291
---
Chain | Description
A | No description available
> matchmaker #291 to #1.58 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain C (#1.58) with AF3 CA.pdb, chain A (#291),
sequence alignment score = 328.1
RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
2.714)
> hide sel cartoons
> color #287 dodgerblue
> color #288 dodgerblue
> color #289 #00b305ff
> color #290 #00b305ff
> color #291 #f15839ff
> select #1.59/A
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
Chain information for AF3 E1 1-421.pdb #292
---
Chain | Description
A | No description available
> matchmaker #291 to #1.59 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain A (#1.59) with AF3 CA.pdb, chain A (#291),
sequence alignment score = 32.6
RMSD between 11 pruned atom pairs is 1.204 angstroms; (across all 110 pairs:
22.675)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #293
---
Chain | Description
A | No description available
> matchmaker #291 to #1.58 & sel
No 'to' model specified
> select #1.58/C
1277 atoms, 1305 bonds, 162 residues, 1 model selected
> show sel cartoons
> matchmaker #291 to #1.58 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain C (#1.58) with AF3 CA.pdb, chain A (#291),
sequence alignment score = 328.1
RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
2.714)
> hide sel cartoons
> select #1.59/A
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> matchmaker #292 to #1.59 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain A (#1.59) with AF3 E1 1-421.pdb, chain A (#292),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
3.020)
> matchmaker #293 to #1.59 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain A (#1.59) with AF3 E1 422-461.pdb, chain A (#293),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
2.776)
> select #1.39/B
3304 atoms, 3395 bonds, 423 residues, 1 model selected
> select #1.59/A
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> hide sel cartoons
> select #1.59/B
3304 atoms, 3395 bonds, 423 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
Chain information for AF3 E2 1-352.pdb #294
---
Chain | Description
B | No description available
> matchmaker #294 to #1.59 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain B (#1.59) with AF3 E2 1-352.pdb, chain B (#294),
sequence alignment score = 583.7
RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
5.933)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #295
---
Chain | Description
B | No description available
> matchmaker #295 to #1.59 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain B (#1.59) with AF3 E2 353-438.pdb, chain B (#295),
sequence alignment score = 322.6
RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
8.411)
> hide sel cartoons
> select #1.59/C
1277 atoms, 1305 bonds, 162 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 CA.pdb"
Chain information for AF3 CA.pdb #296
---
Chain | Description
A | No description available
> matchmaker #296 to #1.59 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain C (#1.59) with AF3 CA.pdb, chain A (#296),
sequence alignment score = 328.1
RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
2.714)
> hide sel cartoons
> color #292 dodgerblue
> color #293 dodgerblue
> color #294 #00b305ff
> color #295 #00b305ff
> color #296 #f15839ff
> select #1.60/A
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
Chain information for AF3 E1 1-421.pdb #297
---
Chain | Description
A | No description available
> matchmaker #297 to #1.60 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain A (#1.60) with AF3 E1 1-421.pdb, chain A (#297),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
3.020)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #298
---
Chain | Description
A | No description available
> matchmaker #298 to #1.60 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain A (#1.60) with AF3 E1 422-461.pdb, chain A (#298),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
2.776)
> hide sel cartoons
> select #1.60/B
3304 atoms, 3395 bonds, 423 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
Chain information for AF3 E2 1-352.pdb #299
---
Chain | Description
B | No description available
> matchmaker #299 to #1.60 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain B (#1.60) with AF3 E2 1-352.pdb, chain B (#299),
sequence alignment score = 583.7
RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
5.933)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #300
---
Chain | Description
B | No description available
> matchmaker #300 to #1.60 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain B (#1.60) with AF3 E2 353-438.pdb, chain B (#300),
sequence alignment score = 333.4
RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
8.411)
> hide sel cartoons
> select #1.60/C
1277 atoms, 1305 bonds, 162 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 CA.pdb"
Chain information for AF3 CA.pdb #301
---
Chain | Description
A | No description available
> matchmaker #301 to #1.60 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain C (#1.60) with AF3 CA.pdb, chain A (#301),
sequence alignment score = 328.1
RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
2.714)
> hide sel cartoons
> color #297 dodgerblue
> color #298 dodgerblue
> color #299 #00b305ff
> color #300 #00b305ff
> color #301 #f15839ff
> save "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" includeMaps true
——— End of log from Mon Jul 15 16:48:15 2024 ———
opened ChimeraX session
> show #2 models
> show #3 models
> show #4 models
> show #5 models
> show #6 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
[Repeated 1 time(s)]
> hide #2-6,262-301#1.2-60 target m
> show #1.2 target m
> hide #1.1 target m
> hide #!1 models
> show #2 models
> show #3 models
> show #4 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> show #5 models
> show #6 models
> show #7 models
> show #8 models
> show #9 models
> show #10 models
> show #11 models
> show #12 models
> show #13 models
> show #14 models
> show #15 models
> show #16 models
> show #17 models
> show #18 models
> show #19 models
> show #20 models
> show #21 models
> show #22 models
> show #23 models
> show #24 models
> show #25 models
> show #26 models
> show #27 models
> show #28 models
> show #29 models
> show #30 models
> show #31 models
> show #32 models
> show #33 models
> show #34 models
> show #35 models
> show #36 models
> show #37 models
> show #38 models
> show #39 models
> show #40 models
> show #41 models
> show #42 models
> show #43 models
> show #44 models
> show #45 models
> show #46 models
> show #47 models
> show #48 models
> show #49 models
> show #50 models
> show #51 models
> show #52 models
> show #53 models
> show #54 models
> show #55 models
> show #56 models
> show #57 models
> show #58 models
> show #59 models
> show #60 models
> show #61 models
> show #62 models
> show #63 models
> show #64 models
> show #65 models
> show #66 models
> show #67 models
> show #68 models
> show #69 models
> show #70 models
> show #71 models
> show #72 models
> show #73 models
> show #74 models
> show #75 models
> show #76 models
> show #77 models
> show #78 models
> show #79 models
> show #80 models
> show #81 models
> show #82 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> show #82-301 models
> hide #2-301 models
> show #2-301 models
> save "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" includeMaps true
——— End of log from Mon Jul 15 16:59:09 2024 ———
opened ChimeraX session
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select #1.1/D
3370 atoms, 3467 bonds, 442 residues, 1 model selected
> show #2-301 cartoons
> view sel
No displayed objects specified.
> select add #1
1908240 atoms, 1958684 bonds, 246480 residues, 61 models selected
> hide #1.2 models
> show #1.1 models
> hide #1.1 models
> show #1.1 models
> show sel & #1.1 cartoons
> hide #1.1 models
> hide #!1 models
> show #1.1 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select subtract #1
Nothing selected
> hide #!1 models
> hide #1.1 models
> show #1.1 models
> show #1.2 models
> show #1.3 models
> show #1.4 models
> select
2389680 atoms, 2451464 bonds, 310140 residues, 361 models selected
> show sel & #2-301#1.1-4 cartoons
> hide #!1 models
> show #!1 models
> show #1.5 models
> show #1.6 models
> show #1.7 models
> hide #1.7 models
> show #1.7 models
> show #1.8 models
> ui tool show "Selection Inspector"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
[Repeated 1 time(s)]
> setattr sel struct display true
Assigning display attribute to 360 items
> select #1.1/A
3370 atoms, 3467 bonds, 442 residues, 1 model selected
> select ~sel & ##selected
28434 atoms, 29221 bonds, 3666 residues, 1 model selected
> hide sel cartoons
> select
2389680 atoms, 2451464 bonds, 310140 residues, 361 models selected
> hide sel cartoons
> select #1.1/A
3370 atoms, 3467 bonds, 442 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> select #1.1/D
3370 atoms, 3467 bonds, 442 residues, 1 model selected
> show sel cartoons
> 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 #302
---
Chain | Description
A | No description available
> matchmaker #301 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 D (#1.1) with AF3 CA.pdb, chain A (#301), sequence
alignment score = 32.6
RMSD between 11 pruned atom pairs is 1.228 angstroms; (across all 110 pairs:
22.710)
> select #1.60/C
1277 atoms, 1305 bonds, 162 residues, 1 model selected
> show sel cartoons
> hide #301 models
> show #301 models
> select add #301
2536 atoms, 2591 bonds, 324 residues, 2 models selected
> hide #301 models
> show #301 models
> color #301 #f15839ff
> show sel cartoons
> select subtract #301
1277 atoms, 1305 bonds, 162 residues, 1 model selected
> 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
> hide #301 models
> select #1.1/D
3370 atoms, 3467 bonds, 442 residues, 1 model selected
> matchmaker #302 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 D (#1.1) with AF3 E1 1-421.pdb, chain A (#302),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #303
---
Chain | Description
A | No description available
> matchmaker #303 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 D (#1.1) with AF3 E1 422-461.pdb, chain A (#303),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> select #1.1/E
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 #304
---
Chain | Description
B | No description available
> matchmaker #304 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 E (#1.1) with AF3 E2 1-352.pdb, chain B (#304),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #305
---
Chain | Description
B | No description available
> matchmaker #305 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 E (#1.1) with AF3 E2 353-438.pdb, chain B (#305),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
8.673)
> select #1.1/F
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 #306
---
Chain | Description
A | No description available
> matchmaker #306 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 F (#1.1) with AF3 CA.pdb, chain A (#306), sequence
alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> select #1.1/F
1277 atoms, 1305 bonds, 162 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> select #1.1/E
3304 atoms, 3400 bonds, 423 residues, 1 model selected
> hide sel cartoons
> select #1.1/D
3370 atoms, 3467 bonds, 442 residues, 1 model selected
> hide sel cartoons
> color #302 dodgerblue
> color #303 dodgerblue
> color #304 #00b305ff
> color #305 #00b305ff
> color #306 #f15839ff
> select #1.2/D
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 #307
---
Chain | Description
A | No description available
> matchmaker #307 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 D (#1.2) with AF3 E1 1-421.pdb, chain A (#307),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #308
---
Chain | Description
A | No description available
> matchmaker #308 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 D (#1.2) with AF3 E1 422-461.pdb, chain A (#308),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
[Repeated 1 time(s)]
> select #1.2/E
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 #309
---
Chain | Description
B | No description available
> matchmaker #309 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 E (#1.2) with AF3 E2 1-352.pdb, chain B (#309),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #310
---
Chain | Description
B | No description available
> matchmaker #310 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 E (#1.2) with AF3 E2 353-438.pdb, chain B (#310),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.2/F
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 #311
---
Chain | Description
A | No description available
> matchmaker #311 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 F (#1.2) with AF3 CA.pdb, chain A (#311), sequence
alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #307 dodgerblue
> color #308 dodgerblue
> color #309 #00b305ff
> color #310 #00b305ff
> color #311 #f15839ff
> select #1.3/D
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 #312
---
Chain | Description
A | No description available
> matchmaker #312 to #1.2 & sel
No 'to' model specified
> matchmaker #312 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 D (#1.3) with AF3 E1 1-421.pdb, chain A (#312),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #313
---
Chain | Description
A | No description available
> matchmaker #313 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 D (#1.3) with AF3 E1 422-461.pdb, chain A (#313),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.3/B
3304 atoms, 3395 bonds, 423 residues, 1 model selected
> select #1.3/E
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 #314
---
Chain | Description
B | No description available
> matchmaker #314 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 E (#1.3) with AF3 E2 1-352.pdb, chain B (#314),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #315
---
Chain | Description
B | No description available
> matchmaker #315 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 E (#1.3) with AF3 E2 353-438.pdb, chain B (#315),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.3/F
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 #316
---
Chain | Description
A | No description available
> matchmaker #316 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 F (#1.3) with AF3 CA.pdb, chain A (#316), sequence
alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #312 dodgerblue
> color #313 dodgerblue
> color #314 #00b305ff
> color #315 #00b305ff
> color #316 #f15839ff
> select #1.4/D
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 #317
---
Chain | Description
A | No description available
> matchmaker #317 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 D (#1.4) with AF3 E1 1-421.pdb, chain A (#317),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #318
---
Chain | Description
A | No description available
> matchmaker #318 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 D (#1.4) with AF3 E1 422-461.pdb, chain A (#318),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.4/E
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 #319
---
Chain | Description
B | No description available
> matchmaker #319 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 E (#1.4) with AF3 E2 1-352.pdb, chain B (#319),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #320
---
Chain | Description
B | No description available
> matchmaker #320 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 E (#1.4) with AF3 E2 353-438.pdb, chain B (#320),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.4/F
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 #321
---
Chain | Description
A | No description available
> matchmaker #321 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 F (#1.4) with AF3 CA.pdb, chain A (#321), sequence
alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #317 dodgerblue
> color #318 dodgerblue
> color #319 #00b305ff
> color #320 #00b305ff
> color #321 #f15839ff
> select #1.5/D
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 #322
---
Chain | Description
A | No description available
> matchmaker #322 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 D (#1.5) with AF3 E1 1-421.pdb, chain A (#322),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #323
---
Chain | Description
A | No description available
> matchmaker #323 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 D (#1.5) with AF3 E1 422-461.pdb, chain A (#323),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.915)
> hide sel cartoons
> select #1.5/E
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 #324
---
Chain | Description
B | No description available
> matchmaker #324 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 E (#1.5) with AF3 E2 1-352.pdb, chain B (#324),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #325
---
Chain | Description
B | No description available
> matchmaker #325 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 E (#1.5) with AF3 E2 353-438.pdb, chain B (#325),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.5/F
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 #326
---
Chain | Description
A | No description available
> matchmaker #326 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 F (#1.5) with AF3 CA.pdb, chain A (#326), sequence
alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #322 dodgerblue
> color #323 dodgerblue
> color #324 #00b305ff
> color #325 #00b305ff
> color #326 #f15839ff
> select #1.6/D
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 #327
---
Chain | Description
A | No description available
> matchmaker #327 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 D (#1.6) with AF3 E1 1-421.pdb, chain A (#327),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #328
---
Chain | Description
A | No description available
> matchmaker #328 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 D (#1.6) with AF3 E1 422-461.pdb, chain A (#328),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.6/E
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 #329
---
Chain | Description
B | No description available
> matchmaker #329 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 E (#1.6) with AF3 E2 1-352.pdb, chain B (#329),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #330
---
Chain | Description
B | No description available
> matchmaker #330 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 E (#1.6) with AF3 E2 353-438.pdb, chain B (#330),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.6/F
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 #331
---
Chain | Description
A | No description available
> matchmaker #331 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 F (#1.6) with AF3 CA.pdb, chain A (#331), sequence
alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #327 dodgerblue
> color #328 dodgerblue
> color #329 #00b305ff
> color #330 #00b305ff
> color #331 #f15839ff
> select #1.7/D
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 #332
---
Chain | Description
A | No description available
> matchmaker #332 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 D (#1.7) with AF3 E1 1-421.pdb, chain A (#332),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #333
---
Chain | Description
A | No description available
> matchmaker #333 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 D (#1.7) with AF3 E1 422-461.pdb, chain A (#333),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.7/E
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 #334
---
Chain | Description
B | No description available
> matchmaker #334 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 E (#1.7) with AF3 E2 1-352.pdb, chain B (#334),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #335
---
Chain | Description
B | No description available
> matchmaker #335 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 E (#1.7) with AF3 E2 353-438.pdb, chain B (#335),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.7/F
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 #336
---
Chain | Description
A | No description available
> matchmaker #336 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 F (#1.7) with AF3 CA.pdb, chain A (#336), sequence
alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #332 dodgerblue
> color #333 dodgerblue
> color #334 #00b305ff
> color #335 #00b305ff
> color #336 #f15839ff
> select #1.8/D
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 #337
---
Chain | Description
A | No description available
> matchmaker #337 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 D (#1.8) with AF3 E1 1-421.pdb, chain A (#337),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #338
---
Chain | Description
A | No description available
> matchmaker #338 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 D (#1.8) with AF3 E1 422-461.pdb, chain A (#338),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.8/E
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 #339
---
Chain | Description
B | No description available
> matchmaker #339 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 E (#1.8) with AF3 E2 1-352.pdb, chain B (#339),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #340
---
Chain | Description
B | No description available
> matchmaker #340 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 E (#1.8) with AF3 E2 353-438.pdb, chain B (#340),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.8/F
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 #341
---
Chain | Description
A | No description available
> matchmaker #341 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 F (#1.8) with AF3 CA.pdb, chain A (#341), sequence
alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #337 dodgerblue
> color #338 dodgerblue
> color #339 #00b305ff
> color #340 #00b305ff
> color #341 #f15839ff
> select #1.9/D
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 #342
---
Chain | Description
A | No description available
> matchmaker #342 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 D (#1.9) with AF3 E1 1-421.pdb, chain A (#342),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #343
---
Chain | Description
A | No description available
> matchmaker #343 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 D (#1.9) with AF3 E1 422-461.pdb, chain A (#343),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.9/E
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 #344
---
Chain | Description
B | No description available
> matchmaker #344 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 E (#1.9) with AF3 E2 1-352.pdb, chain B (#344),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #345
---
Chain | Description
B | No description available
> matchmaker #345 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 E (#1.9) with AF3 E2 353-438.pdb, chain B (#345),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.9/F
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 #346
---
Chain | Description
A | No description available
> matchmaker #346 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 F (#1.9) with AF3 CA.pdb, chain A (#346), sequence
alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #342 dodgerblue
> color #343 dodgerblue
> color #344 #00b305ff
> color #345 #00b305ff
> color #346 #f15839ff
> save "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" includeMaps true
> hide #302-346 models
> select #1.10/D
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 #347
---
Chain | Description
A | No description available
> matchmaker #347 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 D (#1.10) with AF3 E1 1-421.pdb, chain A (#347),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #348
---
Chain | Description
A | No description available
> matchmaker #348 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 D (#1.10) with AF3 E1 422-461.pdb, chain A (#348),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.10/E
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 #349
---
Chain | Description
B | No description available
> matchmaker #349 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 E (#1.10) with AF3 E2 1-352.pdb, chain B (#349),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #350
---
Chain | Description
B | No description available
> matchmaker #350 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 E (#1.10) with AF3 E2 353-438.pdb, chain B (#350),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.10/F
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 #351
---
Chain | Description
A | No description available
> matchmaker #351 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 F (#1.10) with AF3 CA.pdb, chain A (#351),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #347 dodgerblue
> color #348 dodgerblue
> color #349 #00b305ff
> color #350 #00b305ff
> color #351 #f15839ff
> save "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" includeMaps true
> select #1.11/D
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 #352
---
Chain | Description
A | No description available
> matchmaker #352 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 D (#1.11) with AF3 E1 1-421.pdb, chain A (#352),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> view sel
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #353
---
Chain | Description
A | No description available
> matchmaker #353 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 D (#1.11) with AF3 E1 422-461.pdb, chain A (#353),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.11/E
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 #354
---
Chain | Description
B | No description available
> matchmaker #354 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 E (#1.11) with AF3 E2 1-352.pdb, chain B (#354),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #355
---
Chain | Description
B | No description available
> matchmaker #355 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 E (#1.11) with AF3 E2 353-438.pdb, chain B (#355),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.11/F
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 #356
---
Chain | Description
A | No description available
> matchmaker #356 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 F (#1.11) with AF3 CA.pdb, chain A (#356),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #352 dodgerblue
> color #353 dodgerblue
> color #354 #00b305ff
> color #355 #00b305ff
> color #356 #f15839ff
> select #1.12/D
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 #357
---
Chain | Description
A | No description available
> matchmaker #357 to #1.11 & sel
No 'to' model specified
> matchmaker #357 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 D (#1.12) with AF3 E1 1-421.pdb, chain A (#357),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #358
---
Chain | Description
A | No description available
> matchmaker #358 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 D (#1.12) with AF3 E1 422-461.pdb, chain A (#358),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.12/E
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 #359
---
Chain | Description
B | No description available
> matchmaker #359 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 E (#1.12) with AF3 E2 1-352.pdb, chain B (#359),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #360
---
Chain | Description
B | No description available
> matchmaker #360 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 E (#1.12) with AF3 E2 353-438.pdb, chain B (#360),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.12/F
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 #361
---
Chain | Description
A | No description available
> matchmaker #361 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 F (#1.12) with AF3 CA.pdb, chain A (#361),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #357 dodgerblue
> color #358 dodgerblue
> color #359 #00b305ff
> color #360 #00b305ff
> color #361 #f15839ff
> select #1.13/D
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> show sel cartoons
> lighting soft
> lighting full
> lighting simple
> lighting soft
[Repeated 1 time(s)]
> view
> open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
Chain information for AF3 E1 1-421.pdb #362
---
Chain | Description
A | No description available
> matchmaker #362 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 D (#1.13) with AF3 E1 1-421.pdb, chain A (#362),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #363
---
Chain | Description
A | No description available
> matchmaker #363 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 D (#1.13) with AF3 E1 422-461.pdb, chain A (#363),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> lighting simple
> select #1.13/E
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 #364
---
Chain | Description
B | No description available
> matchmaker #364 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 E (#1.13) with AF3 E2 1-352.pdb, chain B (#364),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #365
---
Chain | Description
B | No description available
> matchmaker #365 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 E (#1.13) with AF3 E2 353-438.pdb, chain B (#365),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.13/F
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 #366
---
Chain | Description
A | No description available
> matchmaker #366 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 F (#1.13) with AF3 CA.pdb, chain A (#366),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #362 dodgerblue
> color #363 dodgerblue
> color #364 #00b305ff
> color #365 #00b305ff
> color #366 #f15839ff
> select #1.14/D
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 #367
---
Chain | Description
A | No description available
> matchmaker #367 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 D (#1.14) with AF3 E1 1-421.pdb, chain A (#367),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #368
---
Chain | Description
A | No description available
> matchmaker #368 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 D (#1.14) with AF3 E1 422-461.pdb, chain A (#368),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.14/E
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 #369
---
Chain | Description
B | No description available
> matchmaker #369 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 E (#1.14) with AF3 E2 1-352.pdb, chain B (#369),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #370
---
Chain | Description
B | No description available
> matchmaker #370 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 E (#1.14) with AF3 E2 353-438.pdb, chain B (#370),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.14/F
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 #371
---
Chain | Description
A | No description available
> matchmaker #371 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 F (#1.14) with AF3 CA.pdb, chain A (#371),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #367 dodgerblue
> color #368 dodgerblue
> color #369 #00b305ff
> color #370 #00b305ff
> color #371 #f15839ff
> select #1.16/D
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 #372
---
Chain | Description
A | No description available
> hide sel cartoons
> select #1.15/D
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> show sel cartoons
> matchmaker #372 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 D (#1.15) with AF3 E1 1-421.pdb, chain A (#372),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #373
---
Chain | Description
A | No description available
> matchmaker #373 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 D (#1.15) with AF3 E1 422-461.pdb, chain A (#373),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.15/E
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 #374
---
Chain | Description
B | No description available
> matchmaker #374 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 E (#1.15) with AF3 E2 1-352.pdb, chain B (#374),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #375
---
Chain | Description
B | No description available
> matchmaker #375 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 E (#1.15) with AF3 E2 353-438.pdb, chain B (#375),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.15/F
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 #376
---
Chain | Description
A | No description available
> matchmaker #376 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 F (#1.15) with AF3 CA.pdb, chain A (#376),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #372 dodgerblue
> color #373 dodgerblue
> color #374 #00b305ff
> color #375 #00b305ff
> color #376 #f15839ff
> select #1.16/D
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 #377
---
Chain | Description
A | No description available
> matchmaker #377 to #1.15 & sel
No 'to' model specified
> matchmaker #377 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 D (#1.16) with AF3 E1 1-421.pdb, chain A (#377),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #378
---
Chain | Description
A | No description available
> matchmaker #378 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 D (#1.16) with AF3 E1 422-461.pdb, chain A (#378),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.16/E
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 #379
---
Chain | Description
B | No description available
> matchmaker #379 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 E (#1.16) with AF3 E2 1-352.pdb, chain B (#379),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #380
---
Chain | Description
B | No description available
> matchmaker #380 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 E (#1.16) with AF3 E2 353-438.pdb, chain B (#380),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.16/F
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 #381
---
Chain | Description
A | No description available
> matchmaker #381 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 F (#1.16) with AF3 CA.pdb, chain A (#381),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #377 dodgerblue
> color #378 dodgerblue
> color #379 #00b305ff
> color #380 #00b305ff
> color #381 #f15839ff
> select #1.17/D
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 #382
---
Chain | Description
A | No description available
> matchmaker #382 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 D (#1.17) with AF3 E1 1-421.pdb, chain A (#382),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #383
---
Chain | Description
A | No description available
> matchmaker #383 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 D (#1.17) with AF3 E1 422-461.pdb, chain A (#383),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.915)
> hide sel cartoons
> select #1.17/E
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 #384
---
Chain | Description
B | No description available
> matchmaker #384 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 E (#1.17) with AF3 E2 1-352.pdb, chain B (#384),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #385
---
Chain | Description
B | No description available
> matchmaker #385 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 E (#1.17) with AF3 E2 353-438.pdb, chain B (#385),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.17/F
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 #386
---
Chain | Description
A | No description available
> matchmaker #386 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 F (#1.17) with AF3 CA.pdb, chain A (#386),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #382 dodgerblue
> color #383 dodgerblue
> color #384 #00b305ff
> color #385 #00b305ff
> color #386 #f15839ff
> select #1.18/D
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 #387
---
Chain | Description
A | No description available
> matchmaker #387 to #1.17 & sel
No 'to' model specified
> matchmaker #387 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 D (#1.18) with AF3 E1 1-421.pdb, chain A (#387),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #388
---
Chain | Description
A | No description available
> matchmaker #388 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 D (#1.18) with AF3 E1 422-461.pdb, chain A (#388),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.18/E
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 #389
---
Chain | Description
B | No description available
> matchmaker #389 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 E (#1.18) with AF3 E2 1-352.pdb, chain B (#389),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #390
---
Chain | Description
B | No description available
> matchmaker #390 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 E (#1.18) with AF3 E2 353-438.pdb, chain B (#390),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.18/F
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 #391
---
Chain | Description
A | No description available
> matchmaker #391 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 F (#1.18) with AF3 CA.pdb, chain A (#391),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #387 dodgerblue
> color #388 dodgerblue
> color #389 #00b305ff
> color #390 #00b305ff
> color #391 #f15839ff
> select #1.19/D
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 #392
---
Chain | Description
A | No description available
> matchmaker #391 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 D (#1.19) with AF3 CA.pdb, chain A (#391),
sequence alignment score = 32.6
RMSD between 11 pruned atom pairs is 1.228 angstroms; (across all 110 pairs:
22.710)
> select #1.18/F
1277 atoms, 1305 bonds, 162 residues, 1 model selected
> show sel cartoons
> matchmaker #391 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 F (#1.18) with AF3 CA.pdb, chain A (#391),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> select #1.19/D
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 #393
---
Chain | Description
A | No description available
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> close #393
> matchmaker #392 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 D (#1.19) with AF3 E1 1-421.pdb, chain A (#392),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #393
---
Chain | Description
A | No description available
> matchmaker #393 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 D (#1.19) with AF3 E1 422-461.pdb, chain A (#393),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.19/E
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 #394
---
Chain | Description
B | No description available
> matchmaker #394 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 E (#1.19) with AF3 E2 1-352.pdb, chain B (#394),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #395
---
Chain | Description
B | No description available
> matchmaker #395 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 E (#1.19) with AF3 E2 353-438.pdb, chain B (#395),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.19/F
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 #396
---
Chain | Description
A | No description available
> matchmaker #396 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 F (#1.19) with AF3 CA.pdb, chain A (#396),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #392 dodgerblue
> color #393 dodgerblue
> color #394 #00b305ff
> color #395 #00b305ff
> color #396 #f15839ff
> select #1.20/D
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 #397
---
Chain | Description
A | No description available
> matchmaker #397 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 D (#1.20) with AF3 E1 1-421.pdb, chain A (#397),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #398
---
Chain | Description
A | No description available
> matchmaker #398 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 D (#1.20) with AF3 E1 422-461.pdb, chain A (#398),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.20/E
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 #399
---
Chain | Description
B | No description available
> matchmaker #399 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 E (#1.20) with AF3 E2 1-352.pdb, chain B (#399),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #400
---
Chain | Description
B | No description available
> matchmaker #400 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 E (#1.20) with AF3 E2 353-438.pdb, chain B (#400),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.20/F
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 #401
---
Chain | Description
A | No description available
> matchmaker #401 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 F (#1.20) with AF3 CA.pdb, chain A (#401),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #397 dodgerblue
> color #398 dodgerblue
> color #399 #00b305ff
> color #400 #00b305ff
> color #401 #f15839ff
> save "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" includeMaps true
> select add #347
4419 atoms, 4528 bonds, 583 residues, 2 models selected
> select subtract #347
1277 atoms, 1305 bonds, 162 residues, 1 model selected
> select add #347
4419 atoms, 4528 bonds, 583 residues, 2 models selected
> select subtract #347
1277 atoms, 1305 bonds, 162 residues, 1 model selected
> hide #347-396 models
> select #1.21/D
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 #402
---
Chain | Description
A | No description available
> matchmaker #402 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 D (#1.21) with AF3 E1 1-421.pdb, chain A (#402),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #403
---
Chain | Description
A | No description available
> matchmaker #403 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 D (#1.21) with AF3 E1 422-461.pdb, chain A (#403),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.21/E
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 #404
---
Chain | Description
B | No description available
> matchmaker #404 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 E (#1.21) with AF3 E2 1-352.pdb, chain B (#404),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #405
---
Chain | Description
B | No description available
> matchmaker #405 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 E (#1.21) with AF3 E2 353-438.pdb, chain B (#405),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.21/F
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 #406
---
Chain | Description
A | No description available
> matchmaker #406 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 F (#1.21) with AF3 CA.pdb, chain A (#406),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #402 dodgerblue
> color #403 dodgerblue
> color #404 #00b305ff
> color #405 #00b305ff
> color #406 #f15839ff
> select #1.22/D
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 #407
---
Chain | Description
A | No description available
> matchmaker #407 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 D (#1.22) with AF3 E1 1-421.pdb, chain A (#407),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #408
---
Chain | Description
A | No description available
> matchmaker #408 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 D (#1.22) with AF3 E1 422-461.pdb, chain A (#408),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.22/E
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 #409
---
Chain | Description
B | No description available
> matchmaker #409 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 E (#1.22) with AF3 E2 1-352.pdb, chain B (#409),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #410
---
Chain | Description
B | No description available
> matchmaker #410 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 E (#1.22) with AF3 E2 353-438.pdb, chain B (#410),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
8.673)
> select #1.22/F
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 #411
---
Chain | Description
A | No description available
> matchmaker #411 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 F (#1.22) with AF3 CA.pdb, chain A (#411),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #407 dodgerblue
> color #408 dodgerblue
> color #409 #00b305ff
> color #410 #00b305ff
> color #411 #f15839ff
> select #1.22/E
3304 atoms, 3395 bonds, 423 residues, 1 model selected
> hide sel cartoons
> select #1.23/D
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 #412
---
Chain | Description
A | No description available
> matchmaker #412 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 D (#1.23) with AF3 E1 1-421.pdb, chain A (#412),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #413
---
Chain | Description
A | No description available
> matchmaker #413 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 D (#1.23) with AF3 E1 422-461.pdb, chain A (#413),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.23/F
1277 atoms, 1305 bonds, 162 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> select #1.23/E
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 #414
---
Chain | Description
B | No description available
> matchmaker #414 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 E (#1.23) with AF3 E2 1-352.pdb, chain B (#414),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #415
---
Chain | Description
B | No description available
> matchmaker #415 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 E (#1.23) with AF3 E2 353-438.pdb, chain B (#415),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.23/F
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 #416
---
Chain | Description
A | No description available
> matchmaker #416 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 F (#1.23) with AF3 CA.pdb, chain A (#416),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #412 dodgerblue
> color #413 dodgerblue
> color #414 #00b305ff
> color #415 #00b305ff
> color #416 #f15839ff
> select #1.24/D
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 #417
---
Chain | Description
A | No description available
> matchmaker #417 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 D (#1.24) with AF3 E1 1-421.pdb, chain A (#417),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #418
---
Chain | Description
A | No description available
> matchmaker #418 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 D (#1.24) with AF3 E1 422-461.pdb, chain A (#418),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.24/E
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 #419
---
Chain | Description
B | No description available
> matchmaker #419 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 E (#1.24) with AF3 E2 1-352.pdb, chain B (#419),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #420
---
Chain | Description
B | No description available
> matchmaker #420 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 E (#1.24) with AF3 E2 353-438.pdb, chain B (#420),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.24/F
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 #421
---
Chain | Description
A | No description available
> matchmaker #421 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 F (#1.24) with AF3 CA.pdb, chain A (#421),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #417 dodgerblue
> color #418 dodgerblue
> color #419 #00b305ff
> color #420 #00b305ff
> color #421 #f15839ff
> select #1.25/D
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 #422
---
Chain | Description
A | No description available
> matchmaker #422 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 D (#1.25) with AF3 E1 1-421.pdb, chain A (#422),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #423
---
Chain | Description
A | No description available
> matchmaker #423 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 D (#1.25) with AF3 E1 422-461.pdb, chain A (#423),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.25/E
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 #424
---
Chain | Description
B | No description available
> matchmaker #424 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 E (#1.25) with AF3 E2 1-352.pdb, chain B (#424),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #425
---
Chain | Description
B | No description available
> matchmaker #425 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 E (#1.25) with AF3 E2 353-438.pdb, chain B (#425),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.25/F
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 #426
---
Chain | Description
A | No description available
> matchmaker #426 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 F (#1.25) with AF3 CA.pdb, chain A (#426),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #422 dodgerblue
> color #423 dodgerblue
> color #424 #00b305ff
> color #425 #00b305ff
> color #426 #f15839ff
> select #1.26/D
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 #427
---
Chain | Description
A | No description available
> matchmaker #427 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 D (#1.26) with AF3 E1 1-421.pdb, chain A (#427),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #428
---
Chain | Description
A | No description available
> matchmaker #428 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 D (#1.26) with AF3 E1 422-461.pdb, chain A (#428),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.26/E
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 #429
---
Chain | Description
B | No description available
> matchmaker #429 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 E (#1.26) with AF3 E2 1-352.pdb, chain B (#429),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #430
---
Chain | Description
B | No description available
> matchmaker #430 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 E (#1.26) with AF3 E2 353-438.pdb, chain B (#430),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.26/F
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 #431
---
Chain | Description
A | No description available
> matchmaker #431 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 F (#1.26) with AF3 CA.pdb, chain A (#431),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #427 dodgerblue
> color #428 dodgerblue
> color #429 #00b305ff
> color #430 #00b305ff
> color #431 #f15839ff
> select #1.27/D
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 #432
---
Chain | Description
A | No description available
> matchmaker #432 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 D (#1.27) with AF3 E1 1-421.pdb, chain A (#432),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #433
---
Chain | Description
A | No description available
> matchmaker #433 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 D (#1.27) with AF3 E1 422-461.pdb, chain A (#433),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.27/E
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 #434
---
Chain | Description
B | No description available
> matchmaker #434 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 E (#1.27) with AF3 E2 1-352.pdb, chain B (#434),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #435
---
Chain | Description
B | No description available
> matchmaker #435 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 E (#1.27) with AF3 E2 353-438.pdb, chain B (#435),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.27/F
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 #436
---
Chain | Description
A | No description available
> matchmaker #436 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 F (#1.27) with AF3 CA.pdb, chain A (#436),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #432 dodgerblue
> color #433 dodgerblue
> color #434 #00b305ff
> color #435 #00b305ff
> color #436 #f15839ff
> select #1.28/D
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 #437
---
Chain | Description
A | No description available
> matchmaker #437 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 D (#1.28) with AF3 E1 1-421.pdb, chain A (#437),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #438
---
Chain | Description
A | No description available
> matchmaker #438 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 D (#1.28) with AF3 E1 422-461.pdb, chain A (#438),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.28/E
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 #439
---
Chain | Description
B | No description available
> matchmaker #439 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 E (#1.28) with AF3 E2 1-352.pdb, chain B (#439),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #440
---
Chain | Description
B | No description available
> matchmaker #440 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 E (#1.28) with AF3 E2 353-438.pdb, chain B (#440),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.28/F
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 #441
---
Chain | Description
A | No description available
> matchmaker #441 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 F (#1.28) with AF3 CA.pdb, chain A (#441),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #437 dodgerblue
> color #438 dodgerblue
> color #439 #00b305ff
> color #440 #00b305ff
> color #441 #f15839ff
> select #1.29/D
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 #442
---
Chain | Description
A | No description available
> matchmaker #442 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 D (#1.29) with AF3 E1 1-421.pdb, chain A (#442),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #443
---
Chain | Description
A | No description available
> matchmaker #443 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 D (#1.29) with AF3 E1 422-461.pdb, chain A (#443),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.29/E
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 #444
---
Chain | Description
B | No description available
> matchmaker #444 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 E (#1.29) with AF3 E2 1-352.pdb, chain B (#444),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #445
---
Chain | Description
B | No description available
> matchmaker #445 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 E (#1.29) with AF3 E2 353-438.pdb, chain B (#445),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.29/F
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 #446
---
Chain | Description
A | No description available
> matchmaker #446 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 F (#1.29) with AF3 CA.pdb, chain A (#446),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #442 dodgerblue
> color #443 dodgerblue
> color #444 #00b305ff
> color #445 #00b305ff
> color #446 #f15839ff
> select #1.30/D
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 #447
---
Chain | Description
A | No description available
> matchmaker #447 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 D (#1.30) with AF3 E1 1-421.pdb, chain A (#447),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #448
---
Chain | Description
A | No description available
> matchmaker #448 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 D (#1.30) with AF3 E1 422-461.pdb, chain A (#448),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.30/E
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 #449
---
Chain | Description
B | No description available
> matchmaker #449 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 E (#1.30) with AF3 E2 1-352.pdb, chain B (#449),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #450
---
Chain | Description
B | No description available
> matchmaker #450 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 E (#1.30) with AF3 E2 353-438.pdb, chain B (#450),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.30/F
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 #451
---
Chain | Description
A | No description available
> matchmaker #451 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 F (#1.30) with AF3 CA.pdb, chain A (#451),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #447 dodgerblue
> color #448 dodgerblue
> color #449 #00b305ff
> color #450 #00b305ff
> color #451 #f15839ff
> save "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" includeMaps true
> hide #397-451 models
> select #1.31/D
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 #452
---
Chain | Description
A | No description available
> matchmaker #452 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 D (#1.31) with AF3 E1 1-421.pdb, chain A (#452),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> view sel
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #453
---
Chain | Description
A | No description available
> matchmaker #453 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 D (#1.31) with AF3 E1 422-461.pdb, chain A (#453),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> view
> hide sel cartoons
> select #1.31/E
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 #454
---
Chain | Description
B | No description available
> matchmaker #454 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 E (#1.31) with AF3 E2 1-352.pdb, chain B (#454),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #455
---
Chain | Description
B | No description available
> matchmaker #455 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 E (#1.31) with AF3 E2 353-438.pdb, chain B (#455),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.31/F
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 #456
---
Chain | Description
A | No description available
> matchmaker #456 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 F (#1.31) with AF3 CA.pdb, chain A (#456),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #452 dodgerblue
> color #453 dodgerblue
> color #454 #00b305ff
> color #455 #00b305ff
> color #456 #f15839ff
> select #1.32/D
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 #457
---
Chain | Description
A | No description available
> matchmaker #457 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 D (#1.32) with AF3 E1 1-421.pdb, chain A (#457),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #458
---
Chain | Description
A | No description available
> matchmaker #458 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 D (#1.32) with AF3 E1 422-461.pdb, chain A (#458),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.31/E
3304 atoms, 3395 bonds, 423 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> select #1.32/E
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 #459
---
Chain | Description
B | No description available
> matchmaker #459 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 E (#1.32) with AF3 E2 1-352.pdb, chain B (#459),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #460
---
Chain | Description
B | No description available
> matchmaker #460 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 E (#1.32) with AF3 E2 353-438.pdb, chain B (#460),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.32/F
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 #461
---
Chain | Description
A | No description available
> matchmaker #461 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 F (#1.32) with AF3 CA.pdb, chain A (#461),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #457 dodgerblue
> color #458 dodgerblue
> color #459 #00b305ff
> color #460 #00b305ff
> color #461 #f15839ff
> select #1.33/D
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 #462
---
Chain | Description
A | No description available
> matchmaker #462 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 D (#1.33) with AF3 E1 1-421.pdb, chain A (#462),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #463
---
Chain | Description
A | No description available
> matchmaker #463 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 D (#1.33) with AF3 E1 422-461.pdb, chain A (#463),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.33/E
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 #464
---
Chain | Description
B | No description available
> matchmaker #464 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 E (#1.33) with AF3 E2 1-352.pdb, chain B (#464),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #465
---
Chain | Description
B | No description available
> matchmaker #465 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 E (#1.33) with AF3 E2 353-438.pdb, chain B (#465),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.33/F
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 #466
---
Chain | Description
A | No description available
> matchmaker #466 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 F (#1.33) with AF3 CA.pdb, chain A (#466),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #462 dodgerblue
> color #463 dodgerblue
> color #464 #00b305ff
> color #465 #00b305ff
> color #466 #f15839ff
> select #1.34/D
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 #467
---
Chain | Description
A | No description available
> view
> matchmaker #467 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 D (#1.34) with AF3 E1 1-421.pdb, chain A (#467),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #468
---
Chain | Description
A | No description available
> matchmaker #468 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 D (#1.34) with AF3 E1 422-461.pdb, chain A (#468),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.34/E
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 #469
---
Chain | Description
B | No description available
> matchmaker #469 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 E (#1.34) with AF3 E2 1-352.pdb, chain B (#469),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #470
---
Chain | Description
B | No description available
> matchmaker #470 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 E (#1.34) with AF3 E2 353-438.pdb, chain B (#470),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.34/F
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 #471
---
Chain | Description
A | No description available
> matchmaker #471 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 F (#1.34) with AF3 CA.pdb, chain A (#471),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #467 dodgerblue
> color #468 dodgerblue
> color #469 #00b305ff
> color #470 #00b305ff
> color #471 #f15839ff
> select #1.35/D
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 #472
---
Chain | Description
A | No description available
> matchmaker #472 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 D (#1.35) with AF3 E1 1-421.pdb, chain A (#472),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #473
---
Chain | Description
A | No description available
> matchmaker #473 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 D (#1.35) with AF3 E1 422-461.pdb, chain A (#473),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.35/E
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 #474
---
Chain | Description
B | No description available
> matchmaker #474 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 E (#1.35) with AF3 E2 1-352.pdb, chain B (#474),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #475
---
Chain | Description
B | No description available
> matchmaker #475 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 E (#1.35) with AF3 E2 353-438.pdb, chain B (#475),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.35/F
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 #476
---
Chain | Description
A | No description available
> matchmaker #476 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 F (#1.35) with AF3 CA.pdb, chain A (#476),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #472 dodgerblue
> color #473 dodgerblue
> color #474 #00b305ff
> color #475 #00b305ff
> color #476 #f15839ff
> select #1.36/D
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 #477
---
Chain | Description
A | No description available
> matchmaker #477 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 D (#1.36) with AF3 E1 1-421.pdb, chain A (#477),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #478
---
Chain | Description
A | No description available
> matchmaker #478 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 D (#1.36) with AF3 E1 422-461.pdb, chain A (#478),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.36/E
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 #479
---
Chain | Description
B | No description available
> matchmaker #479 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 E (#1.36) with AF3 E2 1-352.pdb, chain B (#479),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #480
---
Chain | Description
B | No description available
> matchmaker #480 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 E (#1.36) with AF3 E2 353-438.pdb, chain B (#480),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.36/F
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 #481
---
Chain | Description
A | No description available
> matchmaker #481 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 F (#1.36) with AF3 CA.pdb, chain A (#481),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #477 dodgerblue
> color #478 dodgerblue
> color #479 #00b305ff
> color #480 #00b305ff
> color #481 #f15839ff
> select #1.37/D
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 #482
---
Chain | Description
A | No description available
> matchmaker #482 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 D (#1.37) with AF3 E1 1-421.pdb, chain A (#482),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #483
---
Chain | Description
A | No description available
> matchmaker #483 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 D (#1.37) with AF3 E1 422-461.pdb, chain A (#483),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.37/E
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 #484
---
Chain | Description
B | No description available
> matchmaker #484 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 E (#1.37) with AF3 E2 1-352.pdb, chain B (#484),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #485
---
Chain | Description
B | No description available
> matchmaker #485 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 E (#1.37) with AF3 E2 353-438.pdb, chain B (#485),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
[Repeated 1 time(s)]
> select #1.37/F
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 #486
---
Chain | Description
A | No description available
> matchmaker #486 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 F (#1.37) with AF3 CA.pdb, chain A (#486),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
[Repeated 1 time(s)]
> color #482 dodgerblue
> color #483 dodgerblue
> color #484 #00b305ff
> color #485 #00b305ff
> color #486 #f15839ff
> select #1.38/D
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 #487
---
Chain | Description
A | No description available
> matchmaker #487 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 D (#1.38) with AF3 E1 1-421.pdb, chain A (#487),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #488
---
Chain | Description
A | No description available
> matchmaker #488 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 D (#1.38) with AF3 E1 422-461.pdb, chain A (#488),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.38/E
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 #489
---
Chain | Description
B | No description available
> matchmaker #489 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 E (#1.38) with AF3 E2 1-352.pdb, chain B (#489),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #490
---
Chain | Description
B | No description available
> matchmaker #490 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 E (#1.38) with AF3 E2 353-438.pdb, chain B (#490),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.38/F
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 #491
---
Chain | Description
A | No description available
> matchmaker #491 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 F (#1.38) with AF3 CA.pdb, chain A (#491),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
[Repeated 1 time(s)]
> color #487 dodgerblue
> color #488 dodgerblue
> color #489 #00b305ff
> color #490 #00b305ff
> color #491 #f15839ff
> select #1.39/D
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 #492
---
Chain | Description
A | No description available
> matchmaker #492 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 D (#1.39) with AF3 E1 1-421.pdb, chain A (#492),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #493
---
Chain | Description
A | No description available
> matchmaker #493 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 D (#1.39) with AF3 E1 422-461.pdb, chain A (#493),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.39/E
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 #494
---
Chain | Description
B | No description available
> matchmaker #494 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 E (#1.39) with AF3 E2 1-352.pdb, chain B (#494),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #495
---
Chain | Description
B | No description available
> matchmaker #495 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 E (#1.39) with AF3 E2 353-438.pdb, chain B (#495),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.39/F
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 #496
---
Chain | Description
A | No description available
> matchmaker #496 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 F (#1.39) with AF3 CA.pdb, chain A (#496),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #492 dodgerblue
> color #493 dodgerblue
> color #494 #00b305ff
> color #495 #00b305ff
> color #496 #f15839ff
> select #1.40/D
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 #497
---
Chain | Description
A | No description available
> matchmaker #497 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 D (#1.40) with AF3 E1 1-421.pdb, chain A (#497),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #498
---
Chain | Description
A | No description available
> matchmaker #498 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 D (#1.40) with AF3 E1 422-461.pdb, chain A (#498),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.40/E
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 #499
---
Chain | Description
B | No description available
> matchmaker #499 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 E (#1.40) with AF3 E2 1-352.pdb, chain B (#499),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #500
---
Chain | Description
B | No description available
> matchmaker #500 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 E (#1.40) with AF3 E2 353-438.pdb, chain B (#500),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
8.673)
> select #1.40/F
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 #501
---
Chain | Description
A | No description available
> matchmaker #501 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 F (#1.40) with AF3 CA.pdb, chain A (#501),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> select #1.40/E
3304 atoms, 3395 bonds, 423 residues, 1 model selected
> hide sel cartoons
> color #497 dodgerblue
> color #498 dodgerblue
> color #499 #00b305ff
> color #500 #00b305ff
> color #501 #f15839ff
> save "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" includeMaps true
> hide #452-501 models
> select #1.41/D
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 #502
---
Chain | Description
A | No description available
> matchmaker #502 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 D (#1.41) with AF3 E1 1-421.pdb, chain A (#502),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #503
---
Chain | Description
A | No description available
> matchmaker #503 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 D (#1.41) with AF3 E1 422-461.pdb, chain A (#503),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.41/E
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 #504
---
Chain | Description
B | No description available
> matchmaker #504 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 E (#1.41) with AF3 E2 1-352.pdb, chain B (#504),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #505
---
Chain | Description
B | No description available
> matchmaker #505 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 E (#1.41) with AF3 E2 353-438.pdb, chain B (#505),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.41/F
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 #506
---
Chain | Description
A | No description available
> matchmaker #506 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 F (#1.41) with AF3 CA.pdb, chain A (#506),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
[Repeated 1 time(s)]
> color #502 dodgerblue
> color #503 dodgerblue
> color #504 #00b305ff
> color #505 #00b305ff
> color #506 #f15839ff
> select #1.42/D
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 #507
---
Chain | Description
A | No description available
> matchmaker #507 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 D (#1.42) with AF3 E1 1-421.pdb, chain A (#507),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #508
---
Chain | Description
A | No description available
> matchmaker #508 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 D (#1.42) with AF3 E1 422-461.pdb, chain A (#508),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.42/E
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 #509
---
Chain | Description
B | No description available
> matchmaker #509 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 E (#1.42) with AF3 E2 1-352.pdb, chain B (#509),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #510
---
Chain | Description
B | No description available
> matchmaker #510 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 E (#1.42) with AF3 E2 353-438.pdb, chain B (#510),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.42/F
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 #511
---
Chain | Description
A | No description available
> matchmaker #511 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 F (#1.42) with AF3 CA.pdb, chain A (#511),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #507 dodgerblue
> color #508 dodgerblue
> color #509 #00b305ff
> color #510 #00b305ff
> color #511 #f15839ff
> select #1.43/D
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 #512
---
Chain | Description
A | No description available
> matchmaker #512 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 D (#1.43) with AF3 E1 1-421.pdb, chain A (#512),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #513
---
Chain | Description
A | No description available
> matchmaker #513 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 D (#1.43) with AF3 E1 422-461.pdb, chain A (#513),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.43/E
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 #514
---
Chain | Description
B | No description available
> matchmaker #514 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 E (#1.43) with AF3 E2 1-352.pdb, chain B (#514),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #515
---
Chain | Description
B | No description available
> matchmaker #515 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 E (#1.43) with AF3 E2 353-438.pdb, chain B (#515),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.43/F
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 #516
---
Chain | Description
A | No description available
> matchmaker #516 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 F (#1.43) with AF3 CA.pdb, chain A (#516),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #512 dodgerblue
> color #513 dodgerblue
> color #515 #00b305ff
> color #516 #f15839ff
> select #1.44/D
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 #517
---
Chain | Description
A | No description available
> matchmaker #517 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 D (#1.44) with AF3 E1 1-421.pdb, chain A (#517),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #518
---
Chain | Description
A | No description available
> matchmaker #518 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 D (#1.44) with AF3 E1 422-461.pdb, chain A (#518),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.44/E
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 #519
---
Chain | Description
B | No description available
> matchmaker #519 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 E (#1.44) with AF3 E2 1-352.pdb, chain B (#519),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #520
---
Chain | Description
B | No description available
> matchmaker #520 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 E (#1.44) with AF3 E2 353-438.pdb, chain B (#520),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.44/F
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 #521
---
Chain | Description
A | No description available
> matchmaker #521 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 F (#1.44) with AF3 CA.pdb, chain A (#521),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #517 dodgerblue
> color #518 dodgerblue
> color #519 #00b305ff
> color #520 #00b305ff
> color #521 #f15839ff
> select #1.45/D
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 #522
---
Chain | Description
A | No description available
> matchmaker #522 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 D (#1.45) with AF3 E1 1-421.pdb, chain A (#522),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #523
---
Chain | Description
A | No description available
> matchmaker #523 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 D (#1.45) with AF3 E1 422-461.pdb, chain A (#523),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.45/E
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 #524
---
Chain | Description
B | No description available
> matchmaker #524 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 E (#1.45) with AF3 E2 1-352.pdb, chain B (#524),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #525
---
Chain | Description
B | No description available
> matchmaker #525 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 E (#1.45) with AF3 E2 353-438.pdb, chain B (#525),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.45/F
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 #526
---
Chain | Description
A | No description available
> matchmaker #526 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 F (#1.45) with AF3 CA.pdb, chain A (#526),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #522 dodgerblue
> color #523 dodgerblue
> color #524 #00b305ff
> color #525 #00b305ff
> color #526 #f15839ff
> select #1.46/D
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 #527
---
Chain | Description
A | No description available
> matchmaker #527 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 D (#1.46) with AF3 E1 1-421.pdb, chain A (#527),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #528
---
Chain | Description
A | No description available
> matchmaker #528 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 D (#1.46) with AF3 E1 422-461.pdb, chain A (#528),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.46/E
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 #529
---
Chain | Description
B | No description available
> matchmaker #529 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 E (#1.46) with AF3 E2 1-352.pdb, chain B (#529),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #530
---
Chain | Description
B | No description available
> matchmaker #530 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 E (#1.46) with AF3 E2 353-438.pdb, chain B (#530),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.46/F
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 #531
---
Chain | Description
A | No description available
> matchmaker #531 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 F (#1.46) with AF3 CA.pdb, chain A (#531),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #527 dodgerblue
> color #528 dodgerblue
> color #529 #00b305ff
> color #530 #00b305ff
> color #531 #f15839ff
> select #1.47/D
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 #532
---
Chain | Description
A | No description available
> matchmaker #532 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 D (#1.47) with AF3 E1 1-421.pdb, chain A (#532),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #533
---
Chain | Description
A | No description available
> matchmaker #533 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 D (#1.47) with AF3 E1 422-461.pdb, chain A (#533),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.47/E
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 #534
---
Chain | Description
B | No description available
> matchmaker #534 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 E (#1.47) with AF3 E2 1-352.pdb, chain B (#534),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #535
---
Chain | Description
B | No description available
> matchmaker #535 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 E (#1.47) with AF3 E2 353-438.pdb, chain B (#535),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.47/F
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 #536
---
Chain | Description
A | No description available
> matchmaker #536 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 F (#1.47) with AF3 CA.pdb, chain A (#536),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #532 dodgerblue
> color #533 dodgerblue
> color #534 #00b305ff
> color #535 #00b305ff
> color #536 #f15839ff
> select #1.48/D
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 #537
---
Chain | Description
A | No description available
> matchmaker #537 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 D (#1.48) with AF3 E1 1-421.pdb, chain A (#537),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #538
---
Chain | Description
A | No description available
> matchmaker #538 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 D (#1.48) with AF3 E1 422-461.pdb, chain A (#538),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.48/E
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 #539
---
Chain | Description
B | No description available
> matchmaker #539 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 E (#1.48) with AF3 E2 1-352.pdb, chain B (#539),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #540
---
Chain | Description
B | No description available
> matchmaker #540 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 E (#1.48) with AF3 E2 353-438.pdb, chain B (#540),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.48/F
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 #541
---
Chain | Description
A | No description available
> matchmaker #541 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 F (#1.48) with AF3 CA.pdb, chain A (#541),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #537 dodgerblue
> color #538 dodgerblue
> color #539 #00b305ff
> color #540 #00b305ff
> color #541 #f15839ff
> select #1.49/D
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 #542
---
Chain | Description
A | No description available
> matchmaker #542 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 D (#1.49) with AF3 E1 1-421.pdb, chain A (#542),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #543
---
Chain | Description
A | No description available
> matchmaker #543 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 D (#1.49) with AF3 E1 422-461.pdb, chain A (#543),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.49/E
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 #544
---
Chain | Description
B | No description available
> matchmaker #544 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 E (#1.49) with AF3 E2 1-352.pdb, chain B (#544),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #545
---
Chain | Description
B | No description available
> matchmaker #545 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 E (#1.49) with AF3 E2 353-438.pdb, chain B (#545),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.49/F
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 #546
---
Chain | Description
A | No description available
> matchmaker #546 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 F (#1.49) with AF3 CA.pdb, chain A (#546),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #542 dodgerblue
> color #543 dodgerblue
> color #544 #00b305ff
> color #545 #00b305ff
> color #546 #f15839ff
> select #1.50/D
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 #547
---
Chain | Description
A | No description available
> matchmaker #547 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 D (#1.50) with AF3 E1 1-421.pdb, chain A (#547),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #548
---
Chain | Description
A | No description available
> matchmaker #548 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 D (#1.50) with AF3 E1 422-461.pdb, chain A (#548),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.50/E
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 #549
---
Chain | Description
B | No description available
> matchmaker #549 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 E (#1.50) with AF3 E2 1-352.pdb, chain B (#549),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #550
---
Chain | Description
B | No description available
> matchmaker #550 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 E (#1.50) with AF3 E2 353-438.pdb, chain B (#550),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.50/F
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 #551
---
Chain | Description
A | No description available
> matchmaker #551 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 F (#1.50) with AF3 CA.pdb, chain A (#551),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #547 dodgerblue
> color #548 dodgerblue
> color #549 #00b305ff
> color #550 #00b305ff
> color #551 #f15839ff
> save "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" includeMaps true
> hide #502-551 models
> show #547 models
> show #548 models
> select #1.50/D
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
[Repeated 1 time(s)]
> hide #547 models
> hide #548 models
> select #1.51/D
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> show sel cartoons
> view
> open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
Chain information for AF3 E1 1-421.pdb #552
---
Chain | Description
A | No description available
> matchmaker #552 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 D (#1.51) with AF3 E1 1-421.pdb, chain A (#552),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #553
---
Chain | Description
A | No description available
> matchmaker #553 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 D (#1.51) with AF3 E1 422-461.pdb, chain A (#553),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.51/E
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 #554
---
Chain | Description
B | No description available
> matchmaker #554 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 E (#1.51) with AF3 E2 1-352.pdb, chain B (#554),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #555
---
Chain | Description
B | No description available
> matchmaker #555 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 E (#1.51) with AF3 E2 353-438.pdb, chain B (#555),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.51/F
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 #556
---
Chain | Description
A | No description available
> matchmaker #556 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 F (#1.51) with AF3 CA.pdb, chain A (#556),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #552 dodgerblue
> color #553 dodgerblue
> color #554 #00b305ff
> color #555 #00b305ff
> color #556 #f15839ff
> select #1.52/D
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 #557
---
Chain | Description
A | No description available
> matchmaker #557 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 D (#1.52) with AF3 E1 1-421.pdb, chain A (#557),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #558
---
Chain | Description
A | No description available
> matchmaker #558 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 D (#1.52) with AF3 E1 422-461.pdb, chain A (#558),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.52/E
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 #559
---
Chain | Description
B | No description available
> matchmaker #559 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 E (#1.52) with AF3 E2 1-352.pdb, chain B (#559),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #560
---
Chain | Description
B | No description available
> matchmaker #560 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 E (#1.52) with AF3 E2 353-438.pdb, chain B (#560),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.52/F
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 #561
---
Chain | Description
A | No description available
> matchmaker #561 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 F (#1.52) with AF3 CA.pdb, chain A (#561),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #557 dodgerblue
> color #558 dodgerblue
> color #559 #00b305ff
> color #560 #00b305ff
> color #561 #f15839ff
> select #1.53/D
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> select #1.53/D
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 #562
---
Chain | Description
A | No description available
> matchmaker #562 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 D (#1.53) with AF3 E1 1-421.pdb, chain A (#562),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #563
---
Chain | Description
A | No description available
> matchmaker #563 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 D (#1.53) with AF3 E1 422-461.pdb, chain A (#563),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
Chain information for AF3 E2 1-352.pdb #564
---
Chain | Description
B | No description available
> select #1.53/E
3304 atoms, 3395 bonds, 423 residues, 1 model selected
> show sel cartoons
> matchmaker #564 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 E (#1.53) with AF3 E2 1-352.pdb, chain B (#564),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #565
---
Chain | Description
B | No description available
> matchmaker #565 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 E (#1.53) with AF3 E2 353-438.pdb, chain B (#565),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.53/F
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 #566
---
Chain | Description
A | No description available
> matchmaker #566 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 F (#1.53) with AF3 CA.pdb, chain A (#566),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #562 dodgerblue
> color #563 dodgerblue
> color #564 #00b305ff
> color #565 #00b305ff
> color #566 #f15839ff
> select #1.54/D
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 #567
---
Chain | Description
A | No description available
> matchmaker #567 to #1.53 & sel
No 'to' model specified
> matchmaker #567 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 D (#1.54) with AF3 E1 1-421.pdb, chain A (#567),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #568
---
Chain | Description
A | No description available
> matchmaker #568 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 D (#1.54) with AF3 E1 422-461.pdb, chain A (#568),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.54/E
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 #569
---
Chain | Description
B | No description available
> matchmaker #569 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 E (#1.54) with AF3 E2 1-352.pdb, chain B (#569),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #570
---
Chain | Description
B | No description available
> matchmaker #570 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 E (#1.54) with AF3 E2 353-438.pdb, chain B (#570),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.54/F
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 #571
---
Chain | Description
A | No description available
> matchmaker #571 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 F (#1.54) with AF3 CA.pdb, chain A (#571),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #567 dodgerblue
> color #568 dodgerblue
> color #569 #00b305ff
> color #570 #00b305ff
> color #571 #f15839ff
> select #1.55/D
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 #572
---
Chain | Description
A | No description available
> matchmaker #572 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 D (#1.55) with AF3 E1 1-421.pdb, chain A (#572),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #573
---
Chain | Description
A | No description available
> matchmaker #573 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 D (#1.55) with AF3 E1 422-461.pdb, chain A (#573),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.55/E
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 #574
---
Chain | Description
B | No description available
> matchmaker #574 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 E (#1.55) with AF3 E2 1-352.pdb, chain B (#574),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #575
---
Chain | Description
B | No description available
> matchmaker #575 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 E (#1.55) with AF3 E2 353-438.pdb, chain B (#575),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select #1.55/F
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 #576
---
Chain | Description
A | No description available
> matchmaker #576 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 F (#1.55) with AF3 CA.pdb, chain A (#576),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #572 dodgerblue
> color #573 dodgerblue
> color #574 #00b305ff
> color #575 #00b305ff
> color #576 #f15839ff
> select #1.56/D
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 #577
---
Chain | Description
A | No description available
> matchmaker #577 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 D (#1.56) with AF3 E1 1-421.pdb, chain A (#577),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #578
---
Chain | Description
A | No description available
> matchmaker #578 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 D (#1.56) with AF3 E1 422-461.pdb, chain A (#578),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.56/E
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 #579
---
Chain | Description
B | No description available
> matchmaker #579 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 E (#1.56) with AF3 E2 1-352.pdb, chain B (#579),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #580
---
Chain | Description
B | No description available
> matchmaker #580 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 E (#1.56) with AF3 E2 353-438.pdb, chain B (#580),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.56/F
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 #581
---
Chain | Description
A | No description available
> matchmaker #581 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 F (#1.56) with AF3 CA.pdb, chain A (#581),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #577 dodgerblue
> color #578 dodgerblue
> color #579 #00b305ff
> color #580 #00b305ff
> color #581 #f15839ff
> select #1.57/D
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 #582
---
Chain | Description
A | No description available
> matchmaker #582 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 D (#1.57) with AF3 E1 1-421.pdb, chain A (#582),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #583
---
Chain | Description
A | No description available
> matchmaker #583 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 D (#1.57) with AF3 E1 422-461.pdb, chain A (#583),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.57/E
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 #584
---
Chain | Description
B | No description available
> matchmaker #584 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 E (#1.57) with AF3 E2 1-352.pdb, chain B (#584),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #585
---
Chain | Description
B | No description available
> matchmaker #585 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 E (#1.57) with AF3 E2 353-438.pdb, chain B (#585),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.57/F
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 #586
---
Chain | Description
A | No description available
> matchmaker #586 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 F (#1.57) with AF3 CA.pdb, chain A (#586),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #582 dodgerblue
> color #583 dodgerblue
> color #584 #00b305ff
> color #585 #00b305ff
> color #586 #f15839ff
> select #1.58/D
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 #587
---
Chain | Description
A | No description available
> matchmaker #587 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 D (#1.58) with AF3 E1 1-421.pdb, chain A (#587),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #588
---
Chain | Description
A | No description available
> matchmaker #588 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 D (#1.58) with AF3 E1 422-461.pdb, chain A (#588),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel atoms
> hide sel cartoons
> select #1.58/E
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 #589
---
Chain | Description
B | No description available
> matchmaker #589 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 E (#1.58) with AF3 E2 1-352.pdb, chain B (#589),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #590
---
Chain | Description
B | No description available
> matchmaker #590 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 E (#1.58) with AF3 E2 353-438.pdb, chain B (#590),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.58/F
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 #591
---
Chain | Description
A | No description available
> matchmaker #591 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 F (#1.58) with AF3 CA.pdb, chain A (#591),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #587 dodgerblue
> color #588 dodgerblue
> color #589 #00b305ff
> color #590 #00b305ff
> color #591 #f15839ff
> select #1.59/D
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 #592
---
Chain | Description
A | No description available
> matchmaker #592 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 D (#1.59) with AF3 E1 1-421.pdb, chain A (#592),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #593
---
Chain | Description
A | No description available
> matchmaker #593 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 D (#1.59) with AF3 E1 422-461.pdb, chain A (#593),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.59/E
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 #594
---
Chain | Description
B | No description available
> matchmaker #594 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 E (#1.59) with AF3 E2 1-352.pdb, chain B (#594),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #595
---
Chain | Description
B | No description available
> matchmaker #595 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 E (#1.59) with AF3 E2 353-438.pdb, chain B (#595),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.59/F
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 #596
---
Chain | Description
A | No description available
> matchmaker #596 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 F (#1.59) with AF3 CA.pdb, chain A (#596),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel atoms
> hide sel cartoons
> color #592 dodgerblue
> color #593 dodgerblue
> color #594 #00b305ff
> color #595 #00b305ff
> color #596 #f15839ff
> select #1.60/D
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 #597
---
Chain | Description
A | No description available
> matchmaker #597 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 D (#1.60) with AF3 E1 1-421.pdb, chain A (#597),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #598
---
Chain | Description
A | No description available
> matchmaker #598 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 D (#1.60) with AF3 E1 422-461.pdb, chain A (#598),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.60/E
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 #599
---
Chain | Description
B | No description available
> matchmaker #599 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 E (#1.60) with AF3 E2 1-352.pdb, chain B (#599),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #600
---
Chain | Description
B | No description available
> matchmaker #600 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 E (#1.60) with AF3 E2 353-438.pdb, chain B (#600),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.60/F
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 #601
---
Chain | Description
A | No description available
> matchmaker #601 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 F (#1.60) with AF3 CA.pdb, chain A (#601),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #597 dodgerblue
> color #598 dodgerblue
> color #599 #00b305ff
> color #600 #00b305ff
> color #601 #f15839ff
> view sel
No displayed objects specified.
> view
> save "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" includeMaps true
> show #2-601 models
> view
> hide sel cartoons
> save /Users/Jean/Desktop/image1.png supersample 3
> hide #300 models
> show #300 models
> hide #299 models
> show #299 models
> hide #299 models
> show #299 models
> select
2871120 atoms, 2944244 bonds, 373800 residues, 661 models selected
> show sel cartoons
> hide #!1 models
> select subtract #1
962880 atoms, 985560 bonds, 127320 residues, 600 models selected
> select clear
> view
> hide #2-601 cartoons
> show #2-601 atoms
> style #2-601 sphere
Changed 962880 atom styles
> save /Users/Jean/Desktop/image1.png supersample 3
> view
> color #514 #00b305ff
> view
> hide #2-601 atoms
> show #2-601 cartoons
> save /Users/Jean/Desktop/image2.png supersample 3
> hide #2-601 cartoons
> select #1.1/G
3370 atoms, 3467 bonds, 442 residues, 1 model selected
> show #2-601 cartoons
> select clear
> hide #2-601 cartoons
> select clear
> select #1.1/G
3370 atoms, 3467 bonds, 442 residues, 1 model selected
> show #2-601 cartoons
> hide #2-601 models
> select #1.1/G
3370 atoms, 3467 bonds, 442 residues, 1 model selected
> view sel
No displayed objects specified.
> show #!1 models
> select ~sel & ##selected
28434 atoms, 29221 bonds, 3666 residues, 1 model selected
> select ~sel
2842686 atoms, 2915023 bonds, 370134 residues, 661 models selected
> hide sel & #1.1-60 cartoons
> select #1.1/G
3370 atoms, 3467 bonds, 442 residues, 1 model selected
> show sel cartoons
> ui mousemode right select
> select clear
> select #1.1/B:287
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1.1/G
3370 atoms, 3467 bonds, 442 residues, 1 model selected
> hide #1.1 models
> show #1.1 models
> hide #1.1 models
> show #1.1 models
> select add #1.1
31804 atoms, 32688 bonds, 4108 residues, 1 model selected
> select subtract #1.1
Nothing selected
> select #1.1/G
3370 atoms, 3467 bonds, 442 residues, 1 model selected
> select ~sel & ##selected
28434 atoms, 29221 bonds, 3666 residues, 1 model selected
> hide sel cartoons
> open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
Chain information for AF3 E1 1-421.pdb #602
---
Chain | Description
A | No description available
> view sel
No displayed objects specified.
> view
> matchmaker #602 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 (#602),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
3.020)
> select #1.1/G
3370 atoms, 3467 bonds, 442 residues, 1 model selected
> matchmaker #602 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 G (#1.1) with AF3 E1 1-421.pdb, chain A (#602),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #603
---
Chain | Description
A | No description available
> matchmaker #603 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 G (#1.1) with AF3 E1 422-461.pdb, chain A (#603),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.1/H
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 #604
---
Chain | Description
B | No description available
> matchmaker #603 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 H (#1.1) with AF3 E1 422-461.pdb, chain A (#603),
sequence alignment score = 9.2
RMSD between 6 pruned atom pairs is 0.871 angstroms; (across all 11 pairs:
3.614)
> select #1.1/G
3370 atoms, 3467 bonds, 442 residues, 1 model selected
> show sel cartoons
> matchmaker #603 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 G (#1.1) with AF3 E1 422-461.pdb, chain A (#603),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> matchmaker #604 to #1.2 & sel
No 'to' model specified
> matchmaker #604 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 G (#1.1) with AF3 E2 1-352.pdb, chain B (#604),
sequence alignment score = 71.8
RMSD between 4 pruned atom pairs is 1.398 angstroms; (across all 265 pairs:
48.114)
> select #1.1/H
3304 atoms, 3400 bonds, 423 residues, 1 model selected
> matchmaker #604 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 H (#1.1) with AF3 E2 1-352.pdb, chain B (#604),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #605
---
Chain | Description
B | No description available
> matchmaker #605 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 H (#1.1) with AF3 E2 353-438.pdb, chain B (#605),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.150)
> select #1.1/H
3304 atoms, 3400 bonds, 423 residues, 1 model selected
> show sel cartoons
[Repeated 1 time(s)]
> select #1.1/H
3304 atoms, 3400 bonds, 423 residues, 1 model selected
> select #1.1/H
3304 atoms, 3400 bonds, 423 residues, 1 model selected
> show sel cartoons
> show sel atoms
> hide sel cartoons
> hide sel atoms
> select #1.1/G
3370 atoms, 3467 bonds, 442 residues, 1 model selected
> hide sel cartoons
> select #1.1/I
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 #606
---
Chain | Description
A | No description available
> matchmaker #606 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 I (#1.1) with AF3 CA.pdb, chain A (#606), sequence
alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #602 dodgerblue
> color #603 dodgerblue
> color #604 #00b305ff
> color #605 #00b305ff
> color #606 #f15839ff
> save "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" includeMaps true
——— End of log from Tue Jul 16 18:02:55 2024 ———
opened ChimeraX session
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select #1.2/G
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 #607
---
Chain | Description
A | No description available
> matchmaker #607 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 G (#1.2) with AF3 E1 1-421.pdb, chain A (#607),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #608
---
Chain | Description
A | No description available
> matchmaker #608 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 G (#1.2) with AF3 E1 422-461.pdb, chain A (#608),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> select #1.2/H
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 #609
---
Chain | Description
B | No description available
> matchmaker #609 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 H (#1.2) with AF3 E2 1-352.pdb, chain B (#609),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #610
---
Chain | Description
B | No description available
> matchmaker #610 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 H (#1.2) with AF3 E2 353-438.pdb, chain B (#610),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> select #1.2/I
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 #611
---
Chain | Description
A | No description available
> matchmaker #611 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 I (#1.2) with AF3 CA.pdb, chain A (#611), sequence
alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #607 dodgerblue
> color #608 dodgerblue
> color #609 #00b305ff
> color #610 #00b305ff
> color #611 #f15839ff
> select #1.2/G
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> hide sel cartoons
> select #1.3/G
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 #612
---
Chain | Description
A | No description available
> matchmaker #612 to #1.2 & sel
No 'to' model specified
> matchmaker #612 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 G (#1.3) with AF3 E1 1-421.pdb, chain A (#612),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> matchmaker #612 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 G (#1.3) with AF3 E1 1-421.pdb, chain A (#612),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #613
---
Chain | Description
A | No description available
> matchmaker #613 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 G (#1.3) with AF3 E1 422-461.pdb, chain A (#613),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.3/H
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 #614
---
Chain | Description
B | No description available
> matchmaker #614 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 H (#1.3) with AF3 E2 1-352.pdb, chain B (#614),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #615
---
Chain | Description
B | No description available
> matchmaker #615 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 H (#1.3) with AF3 E2 353-438.pdb, chain B (#615),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> select #1.3/I
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 #616
---
Chain | Description
A | No description available
> matchmaker #616 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 I (#1.3) with AF3 CA.pdb, chain A (#616), sequence
alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #612 dodgerblue
> color #613 dodgerblue
> color #614 #00b305ff
> color #615 #00b305ff
> color #616 #f15839ff
> select #1.4/G
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> select #1.3/H
3304 atoms, 3395 bonds, 423 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> select #1.4/G
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 #617
---
Chain | Description
A | No description available
> matchmaker #617 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 G (#1.4) with AF3 E1 1-421.pdb, chain A (#617),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> hide sel cartoons
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #618
---
Chain | Description
A | No description available
> matchmaker #618 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 G (#1.4) with AF3 E1 422-461.pdb, chain A (#618),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.4/H
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 #619
---
Chain | Description
B | No description available
> matchmaker #619 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 H (#1.4) with AF3 E2 1-352.pdb, chain B (#619),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #620
---
Chain | Description
B | No description available
> matchmaker #620 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 H (#1.4) with AF3 E2 353-438.pdb, chain B (#620),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.937 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> select #1.4/I
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 #621
---
Chain | Description
A | No description available
> matchmaker #621 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 I (#1.4) with AF3 CA.pdb, chain A (#621), sequence
alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #617 dodgerblue
> color #618 dodgerblue
> color #619 #00b305ff
> color #620 #00b305ff
> color #621 #f15839ff
> select #1.5/G
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 #622
---
Chain | Description
A | No description available
> matchmaker #622 to #1.4 & sel
No 'to' model specified
> matchmaker #622 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 G (#1.5) with AF3 E1 1-421.pdb, chain A (#622),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #623
---
Chain | Description
A | No description available
> matchmaker #623 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 G (#1.5) with AF3 E1 422-461.pdb, chain A (#623),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.5/H
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 #624
---
Chain | Description
B | No description available
> matchmaker #624 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 H (#1.5) with AF3 E2 1-352.pdb, chain B (#624),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #625
---
Chain | Description
B | No description available
> hide sel cartoons
> show sel cartoons
> matchmaker #625 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 H (#1.5) with AF3 E2 353-438.pdb, chain B (#625),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.150)
> select #1.5/I
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 #626
---
Chain | Description
A | No description available
> matchmaker #626 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 I (#1.5) with AF3 CA.pdb, chain A (#626), sequence
alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #622 dodgerblue
> color #623 dodgerblue
> color #624 #00b305ff
> color #625 #00b305ff
> color #626 #f15839ff
> select #1.5/H
3304 atoms, 3395 bonds, 423 residues, 1 model selected
> hide sel cartoons
> select #1.6/G
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 #627
---
Chain | Description
A | No description available
> matchmaker #627 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 G (#1.6) with AF3 E1 1-421.pdb, chain A (#627),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #628
---
Chain | Description
A | No description available
> matchmaker #628 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 G (#1.6) with AF3 E1 422-461.pdb, chain A (#628),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.6/H
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 #629
---
Chain | Description
B | No description available
> matchmaker #629 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 H (#1.6) with AF3 E2 1-352.pdb, chain B (#629),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #630
---
Chain | Description
B | No description available
> matchmaker #630 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 H (#1.6) with AF3 E2 353-438.pdb, chain B (#630),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> select #1.6/I
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 #631
---
Chain | Description
A | No description available
> matchmaker #631 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 I (#1.6) with AF3 CA.pdb, chain A (#631), sequence
alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #627 dodgerblue
> color #628 dodgerblue
> color #629 #00b305ff
> color #630 #00b305ff
> color #631 #f15839ff
> select #1.7/G
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 #632
---
Chain | Description
A | No description available
> matchmaker #632 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 G (#1.7) with AF3 E1 1-421.pdb, chain A (#632),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #633
---
Chain | Description
A | No description available
> matchmaker #633 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 G (#1.7) with AF3 E1 422-461.pdb, chain A (#633),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.7/H
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 #634
---
Chain | Description
B | No description available
> matchmaker #634 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 H (#1.7) with AF3 E2 1-352.pdb, chain B (#634),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #635
---
Chain | Description
B | No description available
> matchmaker #635 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 H (#1.7) with AF3 E2 353-438.pdb, chain B (#635),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> select #1.7/I
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 #636
---
Chain | Description
A | No description available
> matchmaker #636 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 I (#1.7) with AF3 CA.pdb, chain A (#636), sequence
alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #632 dodgerblue
> color #633 dodgerblue
> color #634 #00b305ff
> color #635 #00b305ff
> color #636 #f15839ff
> select #1.8/G
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 #637
---
Chain | Description
A | No description available
> matchmaker #637 to #1.7 & sel
No 'to' model specified
> matchmaker #637 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 G (#1.8) with AF3 E1 1-421.pdb, chain A (#637),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #638
---
Chain | Description
A | No description available
> matchmaker #638 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 G (#1.8) with AF3 E1 422-461.pdb, chain A (#638),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.8/H
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 #639
---
Chain | Description
B | No description available
> matchmaker #639 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 H (#1.8) with AF3 E2 1-352.pdb, chain B (#639),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #640
---
Chain | Description
B | No description available
> matchmaker #640 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 H (#1.8) with AF3 E2 353-438.pdb, chain B (#640),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> select #1.8/I
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 #641
---
Chain | Description
A | No description available
> matchmaker #641 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 I (#1.8) with AF3 CA.pdb, chain A (#641), sequence
alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #637 dodgerblue
> color #638 dodgerblue
> color #639 #00b305ff
> color #640 #00b305ff
> color #641 #f15839ff
> select #1.9/G
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 #642
---
Chain | Description
A | No description available
> matchmaker #642 to #1.8 & sel
No 'to' model specified
> matchmaker #642 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 G (#1.9) with AF3 E1 1-421.pdb, chain A (#642),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #643
---
Chain | Description
A | No description available
> matchmaker #643 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 G (#1.9) with AF3 E1 422-461.pdb, chain A (#643),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.9/H
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 #644
---
Chain | Description
B | No description available
> matchmaker #644 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 H (#1.9) with AF3 E2 1-352.pdb, chain B (#644),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #645
---
Chain | Description
B | No description available
> matchmaker #645 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 H (#1.9) with AF3 E2 353-438.pdb, chain B (#645),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> select #1.9/I
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 #646
---
Chain | Description
A | No description available
> matchmaker #646 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 I (#1.9) with AF3 CA.pdb, chain A (#646), sequence
alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #642 dodgerblue
> color #643 dodgerblue
> color #644 #00b305ff
> color #645 #00b305ff
> color #646 #f15839ff
> select #1.10/G
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 #647
---
Chain | Description
A | No description available
> matchmaker #647 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 G (#1.10) with AF3 E1 1-421.pdb, chain A (#647),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #648
---
Chain | Description
A | No description available
> matchmaker #648 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 G (#1.10) with AF3 E1 422-461.pdb, chain A (#648),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.996)
> hide sel cartoons
> select #1.10/H
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 #649
---
Chain | Description
B | No description available
> matchmaker #649 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 H (#1.10) with AF3 E2 1-352.pdb, chain B (#649),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #650
---
Chain | Description
B | No description available
> matchmaker #650 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 H (#1.10) with AF3 E2 353-438.pdb, chain B (#650),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.151)
> hide sel cartoons
> select #1.10/I
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 #651
---
Chain | Description
A | No description available
> matchmaker #651 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 I (#1.10) with AF3 CA.pdb, chain A (#651),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #647 dodgerblue
> color #648 dodgerblue
> color #649 #00b305ff
> color #650 #00b305ff
> color #651 #f15839ff
> save "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" includeMaps true
> hide #602 models
> hide #603 models
> hide #604 models
> hide #605 models
> hide #606 models
> hide #607 models
> hide #608 models
> hide #609 models
> hide #610 models
> hide #611 models
> hide #612 models
> hide #613 models
> hide #614 models
> hide #615 models
> hide #616 models
> hide #617 models
> hide #618 models
> hide #619 models
> hide #620 models
> hide #621 models
> hide #622 models
> hide #623 models
> hide #624 models
> hide #625 models
> hide #626 models
> hide #627 models
> hide #628 models
> hide #629 models
> hide #630 models
> hide #631 models
> hide #632 models
> hide #633 models
> hide #634 models
> hide #635 models
> hide #636 models
> hide #637 models
> hide #638 models
> hide #639 models
> hide #640 models
> hide #641 models
> hide #642 models
> hide #643 models
> hide #644 models
> hide #645 models
> hide #646 models
> hide #647 models
> hide #648 models
> hide #649 models
> hide #650 models
> hide #651 models
> select #1.11/G
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 #652
---
Chain | Description
A | No description available
> matchmaker #652 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 G (#1.11) with AF3 E1 1-421.pdb, chain A (#652),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> view
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #653
---
Chain | Description
A | No description available
> matchmaker #653 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 G (#1.11) with AF3 E1 422-461.pdb, chain A (#653),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.11/H
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 #654
---
Chain | Description
B | No description available
> matchmaker #654 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 H (#1.11) with AF3 E2 1-352.pdb, chain B (#654),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #655
---
Chain | Description
B | No description available
> matchmaker #655 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 H (#1.11) with AF3 E2 353-438.pdb, chain B (#655),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.151)
> hide sel cartoons
> select #1.11/I
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 #656
---
Chain | Description
A | No description available
> matchmaker #656 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 I (#1.11) with AF3 CA.pdb, chain A (#656),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #652 dodgerblue
> color #653 dodgerblue
> color #654 #00b305ff
> color #655 #00b305ff
> color #656 #f15839ff
> select #1.12/G
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 #657
---
Chain | Description
A | No description available
> matchmaker #657 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 G (#1.12) with AF3 E1 1-421.pdb, chain A (#657),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #658
---
Chain | Description
A | No description available
> matchmaker #658 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 G (#1.12) with AF3 E1 422-461.pdb, chain A (#658),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.12/H
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 #659
---
Chain | Description
B | No description available
> matchmaker #659 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 H (#1.12) with AF3 E2 1-352.pdb, chain B (#659),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #660
---
Chain | Description
B | No description available
> matchmaker #660 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 H (#1.12) with AF3 E2 353-438.pdb, chain B (#660),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.937 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> select #1.12/I
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 #661
---
Chain | Description
A | No description available
> matchmaker #661 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 I (#1.12) with AF3 CA.pdb, chain A (#661),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #657 dodgerblue
> color #658 dodgerblue
> color #659 #00b305ff
> color #660 #00b305ff
> color #661 #f15839ff
> select #1.13/G
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 #662
---
Chain | Description
A | No description available
> matchmaker #662 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 G (#1.13) with AF3 E1 1-421.pdb, chain A (#662),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #663
---
Chain | Description
A | No description available
> matchmaker #663 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 G (#1.13) with AF3 E1 422-461.pdb, chain A (#663),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.13/I
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 #664
---
Chain | Description
A | No description available
> matchmaker #664 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 I (#1.13) with AF3 CA.pdb, chain A (#664),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> select #1.13/H
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 #665
---
Chain | Description
B | No description available
> matchmaker #665 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 H (#1.13) with AF3 E2 1-352.pdb, chain B (#665),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #666
---
Chain | Description
B | No description available
> matchmaker #666 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 H (#1.13) with AF3 E2 353-438.pdb, chain B (#666),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> close #664
> select #1.13/I
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 #664
---
Chain | Description
A | No description available
> close #666
> close #665
> close #664
> hide sel cartoons
> select #1.13/H
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 #664
---
Chain | Description
B | No description available
> matchmaker #664 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 H (#1.13) with AF3 E2 1-352.pdb, chain B (#664),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #665
---
Chain | Description
B | No description available
> matchmaker #665 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 H (#1.13) with AF3 E2 353-438.pdb, chain B (#665),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> select #1.13/I
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 #666
---
Chain | Description
A | No description available
> matchmaker #666 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 I (#1.13) with AF3 CA.pdb, chain A (#666),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #662 dodgerblue
> color #663 dodgerblue
> color #664 #00b305ff
> color #665 #00b305ff
> color #666 #f15839ff
> select #1.14/G
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 #667
---
Chain | Description
A | No description available
> matchmaker #667 to #1.13 & sel
No 'to' model specified
> matchmaker #667 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 G (#1.14) with AF3 E1 1-421.pdb, chain A (#667),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #668
---
Chain | Description
A | No description available
> matchmaker #668 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 G (#1.14) with AF3 E1 422-461.pdb, chain A (#668),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.13/H
3304 atoms, 3395 bonds, 423 residues, 1 model selected
> show sel cartoons
> select #1.14/H
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 #669
---
Chain | Description
B | No description available
> matchmaker #669 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 H (#1.14) with AF3 E2 1-352.pdb, chain B (#669),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #670
---
Chain | Description
B | No description available
> matchmaker #670 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 H (#1.14) with AF3 E2 353-438.pdb, chain B (#670),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> select #1.14/I
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 #671
---
Chain | Description
A | No description available
> matchmaker #671 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 I (#1.14) with AF3 CA.pdb, chain A (#671),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #667 dodgerblue
> color #668 dodgerblue
> color #669 #00b305ff
> color #670 #00b305ff
> color #671 #f15839ff
> select #1.13/H
3304 atoms, 3395 bonds, 423 residues, 1 model selected
> hide sel cartoons
> select #1.14/G
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> select #1.15/G
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 #672
---
Chain | Description
A | No description available
> matchmaker #672 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 G (#1.15) with AF3 E1 1-421.pdb, chain A (#672),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #673
---
Chain | Description
A | No description available
> matchmaker #673 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 G (#1.15) with AF3 E1 422-461.pdb, chain A (#673),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.15/H
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 #674
---
Chain | Description
B | No description available
> matchmaker #674 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 H (#1.15) with AF3 E2 1-352.pdb, chain B (#674),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #675
---
Chain | Description
B | No description available
> matchmaker #675 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 H (#1.15) with AF3 E2 353-438.pdb, chain B (#675),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> select #1.15/I
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 #676
---
Chain | Description
A | No description available
> matchmaker #676 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 I (#1.15) with AF3 CA.pdb, chain A (#676),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #672 dodgerblue
> color #673 dodgerblue
> color #674 #00b305ff
> color #675 #00b305ff
> color #676 #f15839ff
> select #1.16/G
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 #677
---
Chain | Description
A | No description available
> matchmaker #677 to #1.15 & sel
No 'to' model specified
> matchmaker #677 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 G (#1.16) with AF3 E1 1-421.pdb, chain A (#677),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #678
---
Chain | Description
A | No description available
> matchmaker #678 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 G (#1.16) with AF3 E1 422-461.pdb, chain A (#678),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.16/H
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 #679
---
Chain | Description
B | No description available
> matchmaker #679 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 H (#1.16) with AF3 E2 1-352.pdb, chain B (#679),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #680
---
Chain | Description
B | No description available
> matchmaker #680 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 H (#1.16) with AF3 E2 353-438.pdb, chain B (#680),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.937 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> select #1.16/I
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 #681
---
Chain | Description
A | No description available
> matchmaker #681 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 I (#1.16) with AF3 CA.pdb, chain A (#681),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #677 dodgerblue
> color #678 dodgerblue
> color #679 #00b305ff
> color #680 dodgerblue
> color #680 #00b305ff
> color #681 #f15839ff
> select #1.17/G
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 #682
---
Chain | Description
A | No description available
> matchmaker #682 to #1.16 & sel
No 'to' model specified
> matchmaker #682 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 G (#1.17) with AF3 E1 1-421.pdb, chain A (#682),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #683
---
Chain | Description
A | No description available
> matchmaker #683 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 G (#1.17) with AF3 E1 422-461.pdb, chain A (#683),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.17/H
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 #684
---
Chain | Description
B | No description available
> matchmaker #684 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 H (#1.17) with AF3 E2 1-352.pdb, chain B (#684),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> hide sel cartoons
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #685
---
Chain | Description
B | No description available
> matchmaker #685 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 H (#1.17) with AF3 E2 353-438.pdb, chain B (#685),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.150)
> select #1.17/I
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 #686
---
Chain | Description
A | No description available
> matchmaker #686 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 I (#1.17) with AF3 CA.pdb, chain A (#686),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #682 dodgerblue
> color #683 dodgerblue
> color #684 #00b305ff
> color #685 #00b305ff
> color #686 #f15839ff
> select #1.18/G
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 #687
---
Chain | Description
A | No description available
> matchmaker #687 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 G (#1.18) with AF3 E1 1-421.pdb, chain A (#687),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #688
---
Chain | Description
A | No description available
> matchmaker #688 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 G (#1.18) with AF3 E1 422-461.pdb, chain A (#688),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.18/H
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 #689
---
Chain | Description
B | No description available
> matchmaker #689 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 H (#1.18) with AF3 E2 1-352.pdb, chain B (#689),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #690
---
Chain | Description
B | No description available
> matchmaker #690 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 H (#1.18) with AF3 E2 353-438.pdb, chain B (#690),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> select #1.18/I
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 #691
---
Chain | Description
A | No description available
> matchmaker #691 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 I (#1.18) with AF3 CA.pdb, chain A (#691),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #687 dodgerblue
> color #688 dodgerblue
> color #689 #00b305ff
> color #690 #00b305ff
> color #691 #f15839ff
> select #1.19/G
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 #692
---
Chain | Description
A | No description available
> matchmaker #692 to #1.18 & sel
No 'to' model specified
> matchmaker #692 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 G (#1.19) with AF3 E1 1-421.pdb, chain A (#692),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #693
---
Chain | Description
A | No description available
> matchmaker #693 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 G (#1.19) with AF3 E1 422-461.pdb, chain A (#693),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.19/H
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 #694
---
Chain | Description
B | No description available
> matchmaker #694 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 H (#1.19) with AF3 E2 1-352.pdb, chain B (#694),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #695
---
Chain | Description
B | No description available
> matchmaker #695 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 H (#1.19) with AF3 E2 353-438.pdb, chain B (#695),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> select #1.19/I
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 #696
---
Chain | Description
A | No description available
> matchmaker #696 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 I (#1.19) with AF3 CA.pdb, chain A (#696),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #692 dodgerblue
> color #693 dodgerblue
> color #694 #00b305ff
> color #695 #00b305ff
> color #696 #f15839ff
> select #1.20/G
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 #697
---
Chain | Description
A | No description available
> matchmaker #697 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 G (#1.20) with AF3 E1 1-421.pdb, chain A (#697),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #698
---
Chain | Description
A | No description available
> matchmaker #698 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 G (#1.20) with AF3 E1 422-461.pdb, chain A (#698),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.20/H
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 #699
---
Chain | Description
B | No description available
> matchmaker #699 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 H (#1.20) with AF3 E2 1-352.pdb, chain B (#699),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #700
---
Chain | Description
B | No description available
> matchmaker #700 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 H (#1.20) with AF3 E2 353-438.pdb, chain B (#700),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> select #1.20/I
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 #701
---
Chain | Description
A | No description available
> matchmaker #701 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 I (#1.20) with AF3 CA.pdb, chain A (#701),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #697 dodgerblue
> color #698 dodgerblue
> color #699 #00b305ff
> color #700 #00b305ff
> color #701 #f15839ff
> save "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" includeMaps true
> hide #652 models
> hide #653 models
> hide #654 models
> hide #655 models
> hide #656 models
> hide #657 models
> hide #658 models
> hide #660 models
> hide #661 models
> hide #659 models
> hide #662 models
> hide #663 models
> hide #664 models
> hide #665 models
> hide #666 models
> hide #667 models
> hide #668 models
> hide #669 models
> hide #670 models
> hide #671 models
> hide #672 models
> hide #673 models
> hide #674 models
> hide #675 models
> hide #676 models
> hide #677 models
> hide #678 models
> hide #679 models
> hide #680 models
> hide #681 models
> hide #682 models
> hide #683 models
> hide #684 models
> hide #685 models
> hide #686 models
> hide #687 models
> hide #688 models
> hide #689 models
> hide #690 models
> hide #691 models
> hide #692 models
> hide #693 models
> hide #694 models
> hide #695 models
> hide #696 models
> hide #697 models
> hide #698 models
> hide #699 models
> hide #700 models
> hide #701 models
> select #1.21/G
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> show sel cartoons
> view
> open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
Chain information for AF3 E1 1-421.pdb #702
---
Chain | Description
A | No description available
> matchmaker #702 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 G (#1.21) with AF3 E1 1-421.pdb, chain A (#702),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #703
---
Chain | Description
A | No description available
> matchmaker #703 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 G (#1.21) with AF3 E1 422-461.pdb, chain A (#703),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> select #1.21/H
3304 atoms, 3395 bonds, 423 residues, 1 model selected
> show sel cartoons
[Repeated 1 time(s)]
> open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
Chain information for AF3 E2 1-352.pdb #704
---
Chain | Description
B | No description available
> matchmaker #704 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 H (#1.21) with AF3 E2 1-352.pdb, chain B (#704),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #705
---
Chain | Description
B | No description available
> matchmaker #705 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 H (#1.21) with AF3 E2 353-438.pdb, chain B (#705),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> select #1.21/G
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> hide sel cartoons
> select #1.21/I
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 #706
---
Chain | Description
A | No description available
> matchmaker #706 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 I (#1.21) with AF3 CA.pdb, chain A (#706),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #702 dodgerblue
> color #703 dodgerblue
> color #704 #00b305ff
> color #705 #00b305ff
> color #706 #f15839ff
> select #1.22/G
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 #707
---
Chain | Description
A | No description available
> matchmaker #707 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 G (#1.22) with AF3 E1 1-421.pdb, chain A (#707),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #708
---
Chain | Description
A | No description available
> matchmaker #708 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 G (#1.22) with AF3 E1 422-461.pdb, chain A (#708),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.996)
> hide sel cartoons
> select #1.21/H
3304 atoms, 3395 bonds, 423 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> select #1.22/H
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 #709
---
Chain | Description
B | No description available
> matchmaker #709 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 H (#1.22) with AF3 E2 1-352.pdb, chain B (#709),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #710
---
Chain | Description
B | No description available
> matchmaker #710 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 H (#1.22) with AF3 E2 353-438.pdb, chain B (#710),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.151)
> hide sel cartoons
> select #1.22/I
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 #711
---
Chain | Description
A | No description available
> matchmaker #711 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 I (#1.22) with AF3 CA.pdb, chain A (#711),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #707 dodgerblue
> color #708 dodgerblue
> color #709 #00b305ff
> color #710 #00b305ff
> color #711 #f15839ff
> select #1.23/G
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 #712
---
Chain | Description
A | No description available
> matchmaker #712 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 G (#1.23) with AF3 E1 1-421.pdb, chain A (#712),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #713
---
Chain | Description
A | No description available
> matchmaker #713 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 G (#1.23) with AF3 E1 422-461.pdb, chain A (#713),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.23/H
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 #714
---
Chain | Description
B | No description available
> matchmaker #714 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 H (#1.23) with AF3 E2 1-352.pdb, chain B (#714),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #715
---
Chain | Description
B | No description available
> matchmaker #715 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 H (#1.23) with AF3 E2 353-438.pdb, chain B (#715),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> select #1.23/I
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 #716
---
Chain | Description
A | No description available
> matchmaker #716 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 I (#1.23) with AF3 CA.pdb, chain A (#716),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #712 dodgerblue
> color #713 dodgerblue
> color #714 #00b305ff
> color #715 #00b305ff
> color #716 #f15839ff
> select #1.24/G
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 #717
---
Chain | Description
A | No description available
> matchmaker #717 to #1.23 & sel
No 'to' model specified
> matchmaker #717 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 G (#1.24) with AF3 E1 1-421.pdb, chain A (#717),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #718
---
Chain | Description
A | No description available
> matchmaker #718 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 G (#1.24) with AF3 E1 422-461.pdb, chain A (#718),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.24/H
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 #719
---
Chain | Description
B | No description available
> matchmaker #719 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 H (#1.24) with AF3 E2 1-352.pdb, chain B (#719),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #720
---
Chain | Description
B | No description available
> matchmaker #720 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 H (#1.24) with AF3 E2 353-438.pdb, chain B (#720),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> select #1.24/I
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 #721
---
Chain | Description
A | No description available
> matchmaker #721 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 I (#1.24) with AF3 CA.pdb, chain A (#721),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #717 dodgerblue
> color #718 dodgerblue
> color #719 #00b305ff
> color #720 #00b305ff
> color #721 #f15839ff
> select #1.25/G
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 #722
---
Chain | Description
A | No description available
> matchmaker #722 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 G (#1.25) with AF3 E1 1-421.pdb, chain A (#722),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #723
---
Chain | Description
A | No description available
> matchmaker #723 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 G (#1.25) with AF3 E1 422-461.pdb, chain A (#723),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.25/H
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 #724
---
Chain | Description
B | No description available
> matchmaker #724 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 H (#1.25) with AF3 E2 1-352.pdb, chain B (#724),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #725
---
Chain | Description
B | No description available
> matchmaker #725 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 H (#1.25) with AF3 E2 353-438.pdb, chain B (#725),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> select #1.25/I
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 #726
---
Chain | Description
A | No description available
> matchmaker #726 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 I (#1.25) with AF3 CA.pdb, chain A (#726),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #722 dodgerblue
> color #723 dodgerblue
> color #724 #00b305ff
> color #725 #00b305ff
> color #726 #f15839ff
> select #1.26/G
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 #727
---
Chain | Description
A | No description available
> matchmaker #727 to #1.25 & sel
No 'to' model specified
> matchmaker #727 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 G (#1.26) with AF3 E1 1-421.pdb, chain A (#727),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #728
---
Chain | Description
A | No description available
> matchmaker #728 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 G (#1.26) with AF3 E1 422-461.pdb, chain A (#728),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.26/H
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 #729
---
Chain | Description
B | No description available
> matchmaker #729 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 H (#1.26) with AF3 E2 1-352.pdb, chain B (#729),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #730
---
Chain | Description
B | No description available
> matchmaker #730 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 H (#1.26) with AF3 E2 353-438.pdb, chain B (#730),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> select #1.27/I
1277 atoms, 1305 bonds, 162 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> select #1.26/F
1277 atoms, 1305 bonds, 162 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> select #1.25/H
3304 atoms, 3395 bonds, 423 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> select #1.25/I
1277 atoms, 1305 bonds, 162 residues, 1 model selected
> select #1.26/I
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 #731
---
Chain | Description
A | No description available
> matchmaker #731 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 I (#1.26) with AF3 CA.pdb, chain A (#731),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #727 dodgerblue
> color #728 dodgerblue
> color #729 #00b305ff
> color #730 #00b305ff
> color #731 #f15839ff
> select #1.27/G
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 #732
---
Chain | Description
A | No description available
> matchmaker #732 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 G (#1.27) with AF3 E1 1-421.pdb, chain A (#732),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #733
---
Chain | Description
A | No description available
> matchmaker #733 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 G (#1.27) with AF3 E1 422-461.pdb, chain A (#733),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.27/H
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 #734
---
Chain | Description
B | No description available
> matchmaker #734 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 H (#1.27) with AF3 E2 1-352.pdb, chain B (#734),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #735
---
Chain | Description
B | No description available
> matchmaker #735 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 H (#1.27) with AF3 E2 353-438.pdb, chain B (#735),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.937 angstroms; (across all 84 pairs:
8.151)
> hide sel cartoons
> select #1.27/I
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 #736
---
Chain | Description
A | No description available
> matchmaker #736 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 I (#1.27) with AF3 CA.pdb, chain A (#736),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #732 dodgerblue
> color #733 dodgerblue
> color #734 #00b305ff
> color #735 #00b305ff
> color #736 #f15839ff
> select #1.28/G
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 #737
---
Chain | Description
A | No description available
> matchmaker #737 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 G (#1.28) with AF3 E1 1-421.pdb, chain A (#737),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #738
---
Chain | Description
A | No description available
> matchmaker #738 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 G (#1.28) with AF3 E1 422-461.pdb, chain A (#738),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.28/H
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 #739
---
Chain | Description
B | No description available
> matchmaker #739 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 H (#1.28) with AF3 E2 1-352.pdb, chain B (#739),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #740
---
Chain | Description
B | No description available
> matchmaker #740 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 H (#1.28) with AF3 E2 353-438.pdb, chain B (#740),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> select #1.28/I
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 #741
---
Chain | Description
A | No description available
> matchmaker #741 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 I (#1.28) with AF3 CA.pdb, chain A (#741),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #737 dodgerblue
> color #738 dodgerblue
> color #739 #00b305ff
> color #740 #00b305ff
> color #741 #f15839ff
> select #1.29/G
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 #742
---
Chain | Description
A | No description available
> matchmaker #742 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 G (#1.29) with AF3 E1 1-421.pdb, chain A (#742),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #743
---
Chain | Description
A | No description available
> matchmaker #743 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 G (#1.29) with AF3 E1 422-461.pdb, chain A (#743),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.29/H
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 #744
---
Chain | Description
B | No description available
> matchmaker #744 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 H (#1.29) with AF3 E2 1-352.pdb, chain B (#744),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #745
---
Chain | Description
B | No description available
> matchmaker #745 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 H (#1.29) with AF3 E2 353-438.pdb, chain B (#745),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> select #1.29/I
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 #746
---
Chain | Description
A | No description available
> matchmaker #746 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 I (#1.29) with AF3 CA.pdb, chain A (#746),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #742 dodgerblue
> color #743 dodgerblue
> color #744 #00b305ff
> color #745 #00b305ff
> color #746 #f15839ff
> select #1.30/G
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 #747
---
Chain | Description
A | No description available
> matchmaker #747 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 G (#1.30) with AF3 E1 1-421.pdb, chain A (#747),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #748
---
Chain | Description
A | No description available
> matchmaker #748 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 G (#1.30) with AF3 E1 422-461.pdb, chain A (#748),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.30/H
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 #749
---
Chain | Description
B | No description available
> matchmaker #749 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 H (#1.30) with AF3 E2 1-352.pdb, chain B (#749),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #750
---
Chain | Description
B | No description available
> matchmaker #750 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 H (#1.30) with AF3 E2 353-438.pdb, chain B (#750),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> select #1.30/H
3304 atoms, 3395 bonds, 423 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> select #1.30/I
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 #751
---
Chain | Description
A | No description available
> matchmaker #751 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 I (#1.30) with AF3 CA.pdb, chain A (#751),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #747 dodgerblue
> color #748 dodgerblue
> color #749 #00b305ff
> color #750 #00b305ff
> color #751 #f15839ff
> save "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" includeMaps true
——— End of log from Wed Jul 17 13:58:06 2024 ———
opened ChimeraX session
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> hide #702 models
> hide #703 models
> hide #704 models
> hide #705 models
> hide #706 models
> hide #707 models
> hide #708 models
> hide #709 models
> hide #710 models
> hide #711 models
> hide #712 models
> hide #713 models
> hide #714 models
> hide #715 models
> hide #716 models
> hide #717 models
> hide #718 models
> hide #719 models
> hide #720 models
> hide #721 models
> hide #722 models
> hide #723 models
> hide #724 models
> hide #725 models
> hide #726 models
> hide #727 models
> hide #728 models
> hide #729 models
> hide #730 models
> hide #731 models
> hide #732 models
> hide #733 models
> hide #734 models
> hide #735 models
> hide #736 models
> hide #737 models
> hide #738 models
> hide #739 models
> hide #740 models
> hide #741 models
> hide #742 models
> hide #743 models
> hide #744 models
> hide #745 models
> hide #746 models
> hide #747 models
> hide #748 models
> hide #749 models
> hide #750 models
> hide #751 models
> select #1.31/G
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> show sel cartoons
> view
> open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
Chain information for AF3 E1 1-421.pdb #752
---
Chain | Description
A | No description available
> matchmaker #752 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 A (#1.1) with AF3 E1 1-421.pdb, chain A (#752),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
3.020)
> matchmaker #752 to #1.1 & sel
No 'to' model specified
> matchmaker #752 to #1.1 & sel
No 'to' model specified
> close #752
> hide sel cartoons
> select #1.31/G
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 #752
---
Chain | Description
A | No description available
> matchmaker #752 to #1.1 & sel
No 'to' model specified
> matchmaker #752 & sel to #1.1 & sel
No 'to' model specified
> select #1.1/H
3304 atoms, 3400 bonds, 423 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> select #1.31/G
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> show sel cartoons
> matchmaker #752 to #1.1 & sel
No 'to' model specified
> show #751 models
> show #750 models
> show #749 models
> show #748 models
> show #747 models
> select #1.30/H
3304 atoms, 3395 bonds, 423 residues, 1 model selected
> hide sel cartoons
> show sel cartoons
> hide sel cartoons
> select #1.30/G
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> matchmaker #752 to #1.31 & sel
No 'to' model specified
> select #1.31/G
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> show sel cartoons
> matchmaker #752 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 G (#1.31) with AF3 E1 1-421.pdb, chain A (#752),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> view
> hide sel cartoons
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #753
---
Chain | Description
A | No description available
> matchmaker #753 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 G (#1.31) with AF3 E1 422-461.pdb, chain A (#753),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.31/H
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 #754
---
Chain | Description
B | No description available
> matchmaker #754 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 H (#1.31) with AF3 E2 1-352.pdb, chain B (#754),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #755
---
Chain | Description
B | No description available
> matchmaker #755 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 H (#1.31) with AF3 E2 353-438.pdb, chain B (#755),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> select #1.31/I
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 #756
---
Chain | Description
A | No description available
> matchmaker #756 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 I (#1.31) with AF3 CA.pdb, chain A (#756),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> hide #747 models
> hide #748 models
> hide #749 models
> hide #750 models
> hide #751 models
> color #752 dodgerblue
> color #753 dodgerblue
> color #754 #00b305ff
> color #755 #00b305ff
> color #756 #f15839ff
> select #1.32/G
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> show sel cartoons
[Repeated 1 time(s)]
> view
> open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
Chain information for AF3 E1 1-421.pdb #757
---
Chain | Description
A | No description available
> matchmaker #757 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 G (#1.32) with AF3 E1 1-421.pdb, chain A (#757),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #758
---
Chain | Description
A | No description available
> matchmaker #758 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 G (#1.32) with AF3 E1 422-461.pdb, chain A (#758),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.32/H
3304 atoms, 3395 bonds, 423 residues, 1 model selected
> show sel cartoons
[Repeated 1 time(s)]
> open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
Chain information for AF3 E2 1-352.pdb #759
---
Chain | Description
B | No description available
> matchmaker #759 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 H (#1.32) with AF3 E2 1-352.pdb, chain B (#759),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #760
---
Chain | Description
B | No description available
> matchmaker #760 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 H (#1.32) with AF3 E2 353-438.pdb, chain B (#760),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> select #1.32/I
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 #761
---
Chain | Description
A | No description available
> matchmaker #761 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 I (#1.32) with AF3 CA.pdb, chain A (#761),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #757 dodgerblue
> color #758 dodgerblue
> color #759 #00b305ff
> color #760 #00b305ff
> color #761 #f15839ff
> select #1.33/G
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 #762
---
Chain | Description
A | No description available
> matchmaker #762 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 G (#1.33) with AF3 E1 1-421.pdb, chain A (#762),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #763
---
Chain | Description
A | No description available
> matchmaker #763 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 G (#1.33) with AF3 E1 422-461.pdb, chain A (#763),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> select #1.32/H
3304 atoms, 3395 bonds, 423 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> select #1.33/H
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 #764
---
Chain | Description
B | No description available
> matchmaker #764 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 H (#1.33) with AF3 E2 1-352.pdb, chain B (#764),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #765
---
Chain | Description
B | No description available
> matchmaker #765 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 H (#1.33) with AF3 E2 353-438.pdb, chain B (#765),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.937 angstroms; (across all 84 pairs:
8.151)
> hide sel cartoons
> select #1.33/I
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 #766
---
Chain | Description
A | No description available
> matchmaker #766 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 I (#1.33) with AF3 CA.pdb, chain A (#766),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #762 dodgerblue
> color #763 dodgerblue
> color #764 #00b305ff
> color #765 #00b305ff
> color #766 #f15839ff
> select #1.33/G
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> hide sel cartoons
> select #1.34/G
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 #767
---
Chain | Description
A | No description available
> matchmaker #767 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 G (#1.34) with AF3 E1 1-421.pdb, chain A (#767),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #768
---
Chain | Description
A | No description available
> matchmaker #768 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 G (#1.34) with AF3 E1 422-461.pdb, chain A (#768),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.34/H
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 #769
---
Chain | Description
B | No description available
> matchmaker #769 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 H (#1.34) with AF3 E2 1-352.pdb, chain B (#769),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #770
---
Chain | Description
B | No description available
> matchmaker #770 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 H (#1.34) with AF3 E2 353-438.pdb, chain B (#770),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> select #1.34/I
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 #771
---
Chain | Description
A | No description available
> matchmaker #771 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 I (#1.34) with AF3 CA.pdb, chain A (#771),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #767 dodgerblue
> color #768 dodgerblue
> color #769 #00b305ff
> color #770 #00b305ff
> color #771 #f15839ff
> select #1.35/G
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 #772
---
Chain | Description
A | No description available
> matchmaker #772 to #1.34 & sel
No 'to' model specified
> matchmaker #772 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 G (#1.35) with AF3 E1 1-421.pdb, chain A (#772),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #773
---
Chain | Description
A | No description available
> matchmaker #773 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 G (#1.35) with AF3 E1 422-461.pdb, chain A (#773),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.35/H
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 #774
---
Chain | Description
B | No description available
> matchmaker #774 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 H (#1.35) with AF3 E2 1-352.pdb, chain B (#774),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #775
---
Chain | Description
B | No description available
> matchmaker #775 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 H (#1.35) with AF3 E2 353-438.pdb, chain B (#775),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> select #1.35/I
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 #776
---
Chain | Description
A | No description available
> matchmaker #776 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 I (#1.35) with AF3 CA.pdb, chain A (#776),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #772 dodgerblue
> color #773 dodgerblue
> color #774 #00b305ff
> color #775 #00b305ff
> color #776 #f15839ff
> select #1.36/G
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 #777
---
Chain | Description
A | No description available
> matchmaker #777 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 G (#1.36) with AF3 E1 1-421.pdb, chain A (#777),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #778
---
Chain | Description
A | No description available
> matchmaker #778 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 G (#1.36) with AF3 E1 422-461.pdb, chain A (#778),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.36/H
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 #779
---
Chain | Description
B | No description available
> matchmaker #779 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 H (#1.36) with AF3 E2 1-352.pdb, chain B (#779),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #780
---
Chain | Description
B | No description available
> matchmaker #780 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 H (#1.36) with AF3 E2 353-438.pdb, chain B (#780),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.151)
> hide sel cartoons
> select #1.36/I
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 #781
---
Chain | Description
A | No description available
> matchmaker #781 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 I (#1.36) with AF3 CA.pdb, chain A (#781),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #777 dodgerblue
> color #778 dodgerblue
> color #779 #00b305ff
> color #780 #00b305ff
> color #781 #f15839ff
> select #1.38/G
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 #782
---
Chain | Description
A | No description available
> matchmaker #782 to #1.36 & sel
No 'to' model specified
> matchmaker #782 to #1.37 & sel
No 'to' model specified
> matchmaker #782 to #1.37 & sel
No 'to' model specified
> hide sel cartoons
> select #1.38/G
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> show sel cartoons
> matchmaker #782 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 G (#1.38) with AF3 E1 1-421.pdb, chain A (#782),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #783
---
Chain | Description
A | No description available
> matchmaker #783 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 G (#1.38) with AF3 E1 422-461.pdb, chain A (#783),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.38/H
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 #784
---
Chain | Description
B | No description available
> matchmaker #784 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 H (#1.38) with AF3 E2 1-352.pdb, chain B (#784),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #785
---
Chain | Description
B | No description available
> matchmaker #785 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 H (#1.38) with AF3 E2 353-438.pdb, chain B (#785),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> select #1.38/I
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 #786
---
Chain | Description
A | No description available
> matchmaker #786 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 I (#1.38) with AF3 CA.pdb, chain A (#786),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #782 dodgerblue
> color #783 dodgerblue
> color #784 #00b305ff
> color #785 #00b305ff
> color #786 #f15839ff
> select #1.39/G
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 #787
---
Chain | Description
A | No description available
> matchmaker #787 to #1.38 & sel
No 'to' model specified
> matchmaker #787 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 G (#1.39) with AF3 E1 1-421.pdb, chain A (#787),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #788
---
Chain | Description
A | No description available
> matchmaker #788 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 G (#1.39) with AF3 E1 422-461.pdb, chain A (#788),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.39/H
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 #789
---
Chain | Description
B | No description available
> matchmaker #789 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 H (#1.39) with AF3 E2 1-352.pdb, chain B (#789),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #790
---
Chain | Description
B | No description available
> matchmaker #790 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 H (#1.39) with AF3 E2 353-438.pdb, chain B (#790),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.151)
> hide sel cartoons
> select #1.39/I
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 #791
---
Chain | Description
A | No description available
> matchmaker #791 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 I (#1.39) with AF3 CA.pdb, chain A (#791),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #787 dodgerblue
> color #788 dodgerblue
> color #789 #00b305ff
> color #790 #00b305ff
> color #791 #f15839ff
> select #1.40/G
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 #792
---
Chain | Description
A | No description available
> matchmaker #792 to #1.39 & sel
No 'to' model specified
> matchmaker #792 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 G (#1.40) with AF3 E1 1-421.pdb, chain A (#792),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #793
---
Chain | Description
A | No description available
> matchmaker #793 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 G (#1.40) with AF3 E1 422-461.pdb, chain A (#793),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.40/H
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 #794
---
Chain | Description
B | No description available
> matchmaker #794 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 H (#1.40) with AF3 E2 1-352.pdb, chain B (#794),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #795
---
Chain | Description
B | No description available
> matchmaker #795 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 H (#1.40) with AF3 E2 353-438.pdb, chain B (#795),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> select #1.40/I
1277 atoms, 1305 bonds, 162 residues, 1 model selected
> open "/Users/Jean/Desktop/AF3 CA.pdb"
Chain information for AF3 CA.pdb #796
---
Chain | Description
A | No description available
> matchmaker #796 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 I (#1.40) with AF3 CA.pdb, chain A (#796),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> color #792 dodgerblue
> color #793 dodgerblue
> color #794 #00b305ff
> color #795 #00b305ff
> color #796 #f15839ff
> show #751 models
> show #750 models
> show #749 models
> show #748 models
> show #747 models
> hide #747 models
> hide #748 models
> hide #749 models
> hide #750 models
> hide #751 models
> select #1.37/G
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 #797
---
Chain | Description
A | No description available
> matchmaker #796 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 G (#1.37) with AF3 CA.pdb, chain A (#796),
sequence alignment score = 32.6
RMSD between 10 pruned atom pairs is 1.151 angstroms; (across all 110 pairs:
22.900)
> matchmaker #796 to #1.40 & sel
No 'to' model specified
> select #1.40/I
1277 atoms, 1305 bonds, 162 residues, 1 model selected
> show sel cartoons
> matchmaker #796 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 I (#1.40) with AF3 CA.pdb, chain A (#796),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> select #1.37/G
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> matchmaker #797 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 G (#1.37) with AF3 E1 1-421.pdb, chain A (#797),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #798
---
Chain | Description
A | No description available
> matchmaker #798 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 G (#1.37) with AF3 E1 422-461.pdb, chain A (#798),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.37/H
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 #799
---
Chain | Description
B | No description available
> matchmaker #799 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 H (#1.37) with AF3 E2 1-352.pdb, chain B (#799),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #800
---
Chain | Description
B | No description available
> matchmaker #800 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 H (#1.37) with AF3 E2 353-438.pdb, chain B (#800),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> select #1.37/I
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 #801
---
Chain | Description
A | No description available
> matchmaker #801 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 I (#1.37) with AF3 CA.pdb, chain A (#801),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #797 dodgerblue
> color #798 dodgerblue
> color #799 #00b305ff
> color #800 #00b305ff
> color #801 #f15839ff
> save "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" includeMaps true
> hide #752 models
> hide #753 models
> hide #754 models
> hide #755 models
> hide #756 models
> hide #757 models
> hide #758 models
> hide #759 models
> hide #760 models
> hide #761 models
> hide #762 models
> hide #763 models
> hide #764 models
> hide #765 models
> hide #766 models
> hide #767 models
> hide #768 models
> hide #769 models
> hide #770 models
> hide #771 models
> hide #772 models
> hide #773 models
> hide #774 models
> hide #776 models
> hide #775 models
> hide #777 models
> hide #778 models
> hide #779 models
> hide #780 models
> hide #781 models
> hide #782 models
> hide #783 models
> hide #784 models
> hide #785 models
> hide #786 models
> hide #787 models
> hide #788 models
> hide #789 models
> hide #790 models
> hide #791 models
> hide #792 models
> hide #793 models
> hide #794 models
> hide #795 models
> hide #796 models
> hide #797 models
> hide #798 models
> hide #799 models
> hide #800 models
> hide #801 models
> select #1.38/G
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> select #1.41/G
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> show sel cartoons
> view
> open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
Chain information for AF3 E1 1-421.pdb #802
---
Chain | Description
A | No description available
> matchmaker #802 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 G (#1.41) with AF3 E1 1-421.pdb, chain A (#802),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #803
---
Chain | Description
A | No description available
> matchmaker #803 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 G (#1.41) with AF3 E1 422-461.pdb, chain A (#803),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.41/H
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 #804
---
Chain | Description
B | No description available
> matchmaker #804 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 H (#1.41) with AF3 E2 1-352.pdb, chain B (#804),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #805
---
Chain | Description
B | No description available
> matchmaker #805 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 H (#1.41) with AF3 E2 353-438.pdb, chain B (#805),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> select #1.41/I
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 #806
---
Chain | Description
A | No description available
> matchmaker #806 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 I (#1.41) with AF3 CA.pdb, chain A (#806),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #802 dodgerblue
> color #803 dodgerblue
> color #804 #00b305ff
> color #805 #00b305ff
> color #806 #f15839ff
> select #1.42/G
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 #807
---
Chain | Description
A | No description available
> matchmaker #807 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 G (#1.42) with AF3 E1 1-421.pdb, chain A (#807),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #808
---
Chain | Description
A | No description available
> matchmaker #808 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 G (#1.42) with AF3 E1 422-461.pdb, chain A (#808),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.42/H
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 #809
---
Chain | Description
B | No description available
> matchmaker #809 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 H (#1.42) with AF3 E2 1-352.pdb, chain B (#809),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #810
---
Chain | Description
B | No description available
> matchmaker #810 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 H (#1.42) with AF3 E2 353-438.pdb, chain B (#810),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.151)
> hide sel cartoons
> select #1.42/I
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 #811
---
Chain | Description
A | No description available
> matchmaker #811 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 I (#1.42) with AF3 CA.pdb, chain A (#811),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #807 dodgerblue
> color #808 dodgerblue
> color #809 #00b305ff
> color #810 #00b305ff
> color #811 #f15839ff
> select #1.43/G
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 #812
---
Chain | Description
A | No description available
> matchmaker #812 to #1.42 & sel
No 'to' model specified
> matchmaker #812 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 G (#1.43) with AF3 E1 1-421.pdb, chain A (#812),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #813
---
Chain | Description
A | No description available
> matchmaker #813 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 G (#1.43) with AF3 E1 422-461.pdb, chain A (#813),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.43/H
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 #814
---
Chain | Description
B | No description available
> matchmaker #814 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 H (#1.43) with AF3 E2 1-352.pdb, chain B (#814),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #815
---
Chain | Description
B | No description available
> matchmaker #815 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 H (#1.43) with AF3 E2 353-438.pdb, chain B (#815),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> select #1.43/I
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 #816
---
Chain | Description
A | No description available
> matchmaker #816 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 I (#1.43) with AF3 CA.pdb, chain A (#816),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #812 dodgerblue
> color #813 dodgerblue
> color #814 #00b305ff
> color #815 #00b305ff
> color #816 #f15839ff
> select #1.43/G
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> select #1.44/G
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 #817
---
Chain | Description
A | No description available
> matchmaker #817 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 G (#1.44) with AF3 E1 1-421.pdb, chain A (#817),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #818
---
Chain | Description
A | No description available
> matchmaker #818 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 G (#1.44) with AF3 E1 422-461.pdb, chain A (#818),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.44/H
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 #819
---
Chain | Description
B | No description available
> matchmaker #819 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 H (#1.44) with AF3 E2 1-352.pdb, chain B (#819),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #820
---
Chain | Description
B | No description available
> matchmaker #820 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 H (#1.44) with AF3 E2 353-438.pdb, chain B (#820),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.151)
> show sel cartoons
> hide sel cartoons
> select #1.44/I
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 #821
---
Chain | Description
A | No description available
> matchmaker #821 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 I (#1.44) with AF3 CA.pdb, chain A (#821),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #817 dodgerblue
> color #818 dodgerblue
> color #819 #00b305ff
> color #820 #00b305ff
> color #821 #f15839ff
> select #1.45/G
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 #822
---
Chain | Description
A | No description available
> matchmaker #822 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 G (#1.45) with AF3 E1 1-421.pdb, chain A (#822),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #823
---
Chain | Description
A | No description available
> matchmaker #823 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 G (#1.45) with AF3 E1 422-461.pdb, chain A (#823),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.45/H
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 #824
---
Chain | Description
B | No description available
> matchmaker #824 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 H (#1.45) with AF3 E2 1-352.pdb, chain B (#824),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #825
---
Chain | Description
B | No description available
> matchmaker #825 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 H (#1.45) with AF3 E2 353-438.pdb, chain B (#825),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> select #1.45/I
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 #826
---
Chain | Description
A | No description available
> matchmaker #826 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 I (#1.45) with AF3 CA.pdb, chain A (#826),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #822 dodgerblue
> color #823 dodgerblue
> color #824 #00b305ff
> color #825 #00b305ff
> color #826 #f15839ff
> select #1.46/G
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 #827
---
Chain | Description
A | No description available
> matchmaker #827 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 G (#1.46) with AF3 E1 1-421.pdb, chain A (#827),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #828
---
Chain | Description
A | No description available
> matchmaker #828 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 G (#1.46) with AF3 E1 422-461.pdb, chain A (#828),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.46/H
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 #829
---
Chain | Description
B | No description available
> matchmaker #829 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 H (#1.46) with AF3 E2 1-352.pdb, chain B (#829),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #830
---
Chain | Description
B | No description available
> matchmaker #830 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 H (#1.46) with AF3 E2 353-438.pdb, chain B (#830),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.937 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> select #1.46/I
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 #831
---
Chain | Description
A | No description available
> matchmaker #831 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 I (#1.46) with AF3 CA.pdb, chain A (#831),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #827 dodgerblue
> color #828 dodgerblue
> color #829 #00b305ff
> color #830 #00b305ff
> color #831 #f15839ff
> select #1.47/G
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 #832
---
Chain | Description
A | No description available
> matchmaker #832 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 G (#1.47) with AF3 E1 1-421.pdb, chain A (#832),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #833
---
Chain | Description
A | No description available
> matchmaker #833 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 G (#1.47) with AF3 E1 422-461.pdb, chain A (#833),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.47/H
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 #834
---
Chain | Description
B | No description available
> matchmaker #834 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 H (#1.47) with AF3 E2 1-352.pdb, chain B (#834),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #835
---
Chain | Description
B | No description available
> matchmaker #835 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 H (#1.47) with AF3 E2 353-438.pdb, chain B (#835),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> select #1.47/I
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 #836
---
Chain | Description
A | No description available
> matchmaker #836 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 I (#1.47) with AF3 CA.pdb, chain A (#836),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #832 dodgerblue
> color #833 dodgerblue
> color #834 #00b305ff
> color #835 #00b305ff
> color #836 #f15839ff
> select #1.48/G
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 #837
---
Chain | Description
A | No description available
> matchmaker #837 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 G (#1.48) with AF3 E1 1-421.pdb, chain A (#837),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #838
---
Chain | Description
A | No description available
> matchmaker #838 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 G (#1.48) with AF3 E1 422-461.pdb, chain A (#838),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.48/H
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 #839
---
Chain | Description
B | No description available
> matchmaker #839 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 H (#1.48) with AF3 E2 1-352.pdb, chain B (#839),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #840
---
Chain | Description
B | No description available
> matchmaker #840 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 H (#1.48) with AF3 E2 353-438.pdb, chain B (#840),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> select #1.48/I
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 #841
---
Chain | Description
A | No description available
> matchmaker #841 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 I (#1.48) with AF3 CA.pdb, chain A (#841),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #837 dodgerblue
> color #838 dodgerblue
> color #839 #00b305ff
> color #840 #00b305ff
> color #841 #f15839ff
> select #1.49/G
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 #842
---
Chain | Description
A | No description available
> matchmaker #842 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 G (#1.49) with AF3 E1 1-421.pdb, chain A (#842),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #843
---
Chain | Description
A | No description available
> matchmaker #843 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 G (#1.49) with AF3 E1 422-461.pdb, chain A (#843),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.49/H
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 #844
---
Chain | Description
B | No description available
> matchmaker #844 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 H (#1.49) with AF3 E2 1-352.pdb, chain B (#844),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #845
---
Chain | Description
B | No description available
> matchmaker #845 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 H (#1.49) with AF3 E2 353-438.pdb, chain B (#845),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> select #1.39/I
1277 atoms, 1305 bonds, 162 residues, 1 model selected
> select #1.49/I
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 #846
---
Chain | Description
A | No description available
> matchmaker #846 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 I (#1.49) with AF3 CA.pdb, chain A (#846),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #842 dodgerblue
> color #843 dodgerblue
> color #844 #00b305ff
> color #845 #00b305ff
> color #846 #f15839ff
> select #1.50/G
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 #847
---
Chain | Description
A | No description available
> matchmaker #847 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 G (#1.50) with AF3 E1 1-421.pdb, chain A (#847),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #848
---
Chain | Description
A | No description available
> matchmaker #848 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 G (#1.50) with AF3 E1 422-461.pdb, chain A (#848),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
[Repeated 1 time(s)]
> select #1.50/H
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 #849
---
Chain | Description
B | No description available
> matchmaker #849 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 H (#1.50) with AF3 E2 1-352.pdb, chain B (#849),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #850
---
Chain | Description
B | No description available
> matchmaker #850 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 H (#1.50) with AF3 E2 353-438.pdb, chain B (#850),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.151)
> open "/Users/Jean/Desktop/AF3 CA.pdb"
Chain information for AF3 CA.pdb #851
---
Chain | Description
A | No description available
> hide sel cartoons
> select #1.50/I
1277 atoms, 1305 bonds, 162 residues, 1 model selected
> show sel cartoons
> matchmaker #851 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 I (#1.50) with AF3 CA.pdb, chain A (#851),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #847 dodgerblue
> color #848 dodgerblue
> color #849 #00b305ff
> color #850 #00b305ff
> color #851 #f15839ff
> save "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" includeMaps true
> hide #802 models
> hide #803 models
> hide #804 models
> hide #805 models
> hide #806 models
> hide #807 models
> hide #808 models
> hide #809 models
> hide #810 models
> hide #811 models
> hide #812 models
> hide #813 models
> hide #814 models
> hide #815 models
> hide #816 models
> hide #817 models
> hide #818 models
> hide #819 models
> hide #820 models
> hide #821 models
> hide #822 models
> hide #823 models
> hide #824 models
> hide #825 models
> hide #826 models
> hide #827 models
> hide #828 models
> hide #829 models
> hide #830 models
> hide #831 models
> hide #832 models
> hide #833 models
> hide #834 models
> hide #835 models
> hide #836 models
> hide #837 models
> hide #838 models
> hide #839 models
> hide #840 models
> hide #841 models
> hide #842 models
> hide #844 models
> hide #843 models
> hide #845 models
> hide #846 models
> hide #847 models
> hide #848 models
> hide #849 models
> hide #850 models
> hide #851 models
> select #1.51/G
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> show sel cartoons
[Repeated 1 time(s)]
> view
> open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
Chain information for AF3 E1 1-421.pdb #852
---
Chain | Description
A | No description available
> matchmaker #852 to #1.50 & sel
No 'to' model specified
> matchmaker #852 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 G (#1.51) with AF3 E1 1-421.pdb, chain A (#852),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #853
---
Chain | Description
A | No description available
> matchmaker #853 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 G (#1.51) with AF3 E1 422-461.pdb, chain A (#853),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.996)
> hide sel cartoons
> select #1.51/H
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 #854
---
Chain | Description
B | No description available
> matchmaker #854 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 H (#1.51) with AF3 E2 1-352.pdb, chain B (#854),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #855
---
Chain | Description
B | No description available
> matchmaker #855 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 H (#1.51) with AF3 E2 353-438.pdb, chain B (#855),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.151)
> hide sel cartoons
> select #1.51/I
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 #856
---
Chain | Description
A | No description available
> matchmaker #856 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 I (#1.51) with AF3 CA.pdb, chain A (#856),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #852 dodgerblue
> color #853 dodgerblue
> color #854 #00b305ff
> color #855 #00b305ff
> color #856 #f15839ff
> select #1.52/G
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 #857
---
Chain | Description
A | No description available
> matchmaker #857 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 G (#1.52) with AF3 E1 1-421.pdb, chain A (#857),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #858
---
Chain | Description
A | No description available
> matchmaker #858 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 G (#1.52) with AF3 E1 422-461.pdb, chain A (#858),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.52/H
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 #859
---
Chain | Description
B | No description available
> matchmaker #859 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 H (#1.52) with AF3 E2 1-352.pdb, chain B (#859),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #860
---
Chain | Description
B | No description available
> matchmaker #860 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 H (#1.52) with AF3 E2 353-438.pdb, chain B (#860),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> select #1.52/I
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 #861
---
Chain | Description
A | No description available
> matchmaker #861 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 I (#1.52) with AF3 CA.pdb, chain A (#861),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #857 dodgerblue
> color #858 dodgerblue
> color #859 #00b305ff
> color #860 #00b305ff
> color #861 #f15839ff
> select #1.53/G
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 #862
---
Chain | Description
A | No description available
> matchmaker #862 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 G (#1.53) with AF3 E1 1-421.pdb, chain A (#862),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #863
---
Chain | Description
A | No description available
> matchmaker #863 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 G (#1.53) with AF3 E1 422-461.pdb, chain A (#863),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.53/H
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 #864
---
Chain | Description
B | No description available
> matchmaker #864 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 H (#1.53) with AF3 E2 1-352.pdb, chain B (#864),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #865
---
Chain | Description
B | No description available
> matchmaker #865 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 H (#1.53) with AF3 E2 353-438.pdb, chain B (#865),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> select #1.53/I
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 #866
---
Chain | Description
A | No description available
> matchmaker #866 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 I (#1.53) with AF3 CA.pdb, chain A (#866),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #862 dodgerblue
> color #863 dodgerblue
> color #864 #00b305ff
> color #865 #00b305ff
> color #866 #f15839ff
> select #1.54/G
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 #867
---
Chain | Description
A | No description available
> matchmaker #867 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 G (#1.54) with AF3 E1 1-421.pdb, chain A (#867),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #868
---
Chain | Description
A | No description available
> matchmaker #868 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 G (#1.54) with AF3 E1 422-461.pdb, chain A (#868),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.54/H
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 #869
---
Chain | Description
B | No description available
> matchmaker #869 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 H (#1.54) with AF3 E2 1-352.pdb, chain B (#869),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #870
---
Chain | Description
B | No description available
> matchmaker #870 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 H (#1.54) with AF3 E2 353-438.pdb, chain B (#870),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> select #1.54/I
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 #871
---
Chain | Description
A | No description available
> matchmaker #871 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 I (#1.54) with AF3 CA.pdb, chain A (#871),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #867 dodgerblue
> color #868 dodgerblue
> color #869 #00b305ff
> color #870 #00b305ff
> color #871 #f15839ff
> select #1.55/G
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 #872
---
Chain | Description
A | No description available
> matchmaker #872 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 G (#1.55) with AF3 E1 1-421.pdb, chain A (#872),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #873
---
Chain | Description
A | No description available
> matchmaker #873 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 G (#1.55) with AF3 E1 422-461.pdb, chain A (#873),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
[Repeated 1 time(s)]
> select #1.55/H
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 #874
---
Chain | Description
B | No description available
> matchmaker #874 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 H (#1.55) with AF3 E2 1-352.pdb, chain B (#874),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #875
---
Chain | Description
B | No description available
> matchmaker #875 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 H (#1.55) with AF3 E2 353-438.pdb, chain B (#875),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> select #1.55/I
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 #876
---
Chain | Description
A | No description available
> matchmaker #876 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 I (#1.55) with AF3 CA.pdb, chain A (#876),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #872 dodgerblue
> color #873 dodgerblue
> color #874 #00b305ff
> color #875 #00b305ff
> color #876 #f15839ff
> select #1.56/G
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 #877
---
Chain | Description
A | No description available
> matchmaker #877 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 G (#1.56) with AF3 E1 1-421.pdb, chain A (#877),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #878
---
Chain | Description
A | No description available
> matchmaker #878 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 G (#1.56) with AF3 E1 422-461.pdb, chain A (#878),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
[Repeated 1 time(s)]
> select #1.56/H
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 #879
---
Chain | Description
B | No description available
> matchmaker #879 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 H (#1.56) with AF3 E2 1-352.pdb, chain B (#879),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #880
---
Chain | Description
B | No description available
> matchmaker #880 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 H (#1.56) with AF3 E2 353-438.pdb, chain B (#880),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> select #1.56/I
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 #881
---
Chain | Description
A | No description available
> matchmaker #881 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 I (#1.56) with AF3 CA.pdb, chain A (#881),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #877 dodgerblue
> color #878 dodgerblue
> color #879 #00b305ff
> color #880 #00b305ff
> color #881 #f15839ff
> select #1.57/G
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 #882
---
Chain | Description
A | No description available
> matchmaker #882 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 G (#1.57) with AF3 E1 1-421.pdb, chain A (#882),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #883
---
Chain | Description
A | No description available
> matchmaker #883 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 G (#1.57) with AF3 E1 422-461.pdb, chain A (#883),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.57/H
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 #884
---
Chain | Description
B | No description available
> matchmaker #884 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 H (#1.57) with AF3 E2 1-352.pdb, chain B (#884),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #885
---
Chain | Description
B | No description available
> matchmaker #885 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 H (#1.57) with AF3 E2 353-438.pdb, chain B (#885),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> select #1.57/I
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 #886
---
Chain | Description
A | No description available
> matchmaker #886 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 I (#1.57) with AF3 CA.pdb, chain A (#886),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #882 dodgerblue
> color #883 dodgerblue
> color #884 #00b305ff
> color #885 #00b305ff
> color #886 #f15839ff
> select #1.58/G
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 #887
---
Chain | Description
A | No description available
> matchmaker #887 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 G (#1.58) with AF3 E1 1-421.pdb, chain A (#887),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #888
---
Chain | Description
A | No description available
> matchmaker #888 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 G (#1.58) with AF3 E1 422-461.pdb, chain A (#888),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.58/H
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 #889
---
Chain | Description
B | No description available
> matchmaker #889 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 H (#1.58) with AF3 E2 1-352.pdb, chain B (#889),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #890
---
Chain | Description
B | No description available
> matchmaker #890 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 H (#1.58) with AF3 E2 353-438.pdb, chain B (#890),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> select #1.58/I
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 #891
---
Chain | Description
A | No description available
> matchmaker #891 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 I (#1.58) with AF3 CA.pdb, chain A (#891),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #887 dodgerblue
> color #888 dodgerblue
> color #889 #00b305ff
> color #890 #00b305ff
> color #891 #f15839ff
> select #1.59/G
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 #892
---
Chain | Description
A | No description available
> matchmaker #892 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 G (#1.59) with AF3 E1 1-421.pdb, chain A (#892),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #893
---
Chain | Description
A | No description available
> matchmaker #893 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 G (#1.59) with AF3 E1 422-461.pdb, chain A (#893),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.996)
> hide sel cartoons
> select #1.59/H
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 #894
---
Chain | Description
B | No description available
> matchmaker #894 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 H (#1.59) with AF3 E2 1-352.pdb, chain B (#894),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #895
---
Chain | Description
B | No description available
> matchmaker #895 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 H (#1.59) with AF3 E2 353-438.pdb, chain B (#895),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.151)
> hide sel cartoons
> select #1.59/I
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 #896
---
Chain | Description
A | No description available
> matchmaker #896 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 I (#1.59) with AF3 CA.pdb, chain A (#896),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #892 dodgerblue
> color #893 dodgerblue
> color #894 #00b305ff
> color #895 #00b305ff
> color #896 #f15839ff
> select #1.60/G
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 #897
---
Chain | Description
A | No description available
> matchmaker #897 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 G (#1.60) with AF3 E1 1-421.pdb, chain A (#897),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #898
---
Chain | Description
A | No description available
> matchmaker #898 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 G (#1.60) with AF3 E1 422-461.pdb, chain A (#898),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.60/H
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 #899
---
Chain | Description
B | No description available
> matchmaker #899 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 H (#1.60) with AF3 E2 1-352.pdb, chain B (#899),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #900
---
Chain | Description
B | No description available
> matchmaker #900 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 H (#1.60) with AF3 E2 353-438.pdb, chain B (#900),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> open "/Users/Jean/Desktop/AF3 CA.pdb"
Chain information for AF3 CA.pdb #901
---
Chain | Description
A | No description available
> select #1.60/I
1277 atoms, 1305 bonds, 162 residues, 1 model selected
> show sel cartoons
> matchmaker #901 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 I (#1.60) with AF3 CA.pdb, chain A (#901),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #897 dodgerblue
> color #898 dodgerblue
> color #899 #00b305ff
> color #901 #f15839ff
> color #900 #00b305ff
> save "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" includeMaps true
——— End of log from Wed Jul 17 16:12:00 2024 ———
opened ChimeraX session
> ui tool show Matchmaker
===== Log before crash end =====
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 Wed Jul 17 16:12:00 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 Wed Jul 17 13:58:06 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 Tue Jul 16 18:02:55 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 16:59:09 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
> hide #95 models
> hide #96 models
> hide #97 models
> hide #98 models
> hide #99 models
> hide #100 models
> hide #101 models
> hide #102 models
> hide #103 models
> hide #104 models
> hide #105 models
> hide #106 models
> hide #107 models
> hide #108 models
> hide #109 models
> hide #110 models
> hide #111 models
> hide #112 models
> 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
> hide #138 models
> hide #139 models
> hide #140 models
> hide #141 models
> hide #142 models
> hide #143 models
> hide #144 models
> hide #145 models
> hide #146 models
> hide #147 models
> hide #148 models
> hide #149 models
> hide #150 models
> hide #151 models
> hide #152 models
> hide #153 models
> hide #154 models
> hide #155 models
> hide #156 models
> hide #157 models
> 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
> hide #187 models
> hide #188 models
> hide #189 models
> hide #190 models
> hide #191 models
> hide #192 models
> hide #193 models
> hide #194 models
> hide #195 models
> hide #196 models
> hide #197 models
> hide #198 models
> hide #199 models
> hide #200 models
> hide #201 models
> hide #202 models
> hide #203 models
> hide #204 models
> hide #205 models
> hide #206 models
> hide #207 models
> hide #208 models
> hide #209 models
> hide #210 models
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> hide #212 models
> hide #213 models
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> hide #217 models
> hide #218 models
> hide #219 models
> hide #220 models
> hide #221 models
> hide #222 models
> hide #223 models
> hide #224 models
> hide #225 models
> hide #226 models
> hide #227 models
> hide #228 models
> hide #229 models
> hide #230 models
> hide #231 models
> hide #232 models
> hide #233 models
> hide #234 models
> hide #235 models
> hide #236 models
> hide #237 models
> hide #238 models
> hide #239 models
> hide #240 models
> hide #241 models
> hide #242 models
> hide #243 models
> hide #244 models
> hide #245 models
> hide #246 models
> hide #247 models
> hide #248 models
> hide #249 models
> hide #250 models
> hide #251 models
> hide #252 models
> hide #253 models
> hide #254 models
> hide #255 models
> hide #256 models
> hide #257 models
> hide #258 models
> hide #259 models
> hide #260 models
> hide #261 models
> select #1.53/A
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> select #1.52/A
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> view sel
No displayed objects specified.
> show #!1 models
> select ~sel & ##selected
28434 atoms, 29183 bonds, 3666 residues, 1 model selected
> hide sel cartoons
> select
> #1.1/A#1.2/A#1.3/A#1.4/A#1.5/A#1.6/A#1.7/A#1.8/A#1.9/A#1.10/A#1.11/A#1.12/A#1.13/A#1.14/A#1.15/A#1.16/A#1.17/A#1.18/A#1.19/A#1.20/A#1.21/A#1.22/A#1.23/A#1.24/A#1.25/A#1.26/A#1.27/A#1.28/A#1.29/A#1.30/A#1.31/A#1.32/A#1.33/A#1.34/A#1.35/A#1.36/A#1.37/A#1.38/A#1.39/A#1.40/A#1.41/A#1.42/A#1.43/A#1.44/A#1.45/A#1.46/A#1.47/A#1.48/A#1.49/A#1.50/A#1.51/A#1.52/A#1.53/A#1.54/A#1.55/A#1.56/A#1.57/A#1.58/A#1.59/A#1.60/A#2/A#3/A#6/A#7/A#8/A#11/A#12/A#13/A#16/A#17/A#18/A#21/A#22/A#23/A#26/A#27/A#28/A#31/A#32/A#33/A#36/A#37/A#38/A#41/A#42/A#43/A#46/A#47/A#48/A#51/A#52/A#53/A#56/A#57/A#58/A#61/A#62/A#63/A#66/A#67/A#68/A#71/A#72/A#73/A#76/A#77/A#78/A#81/A#82/A#83/A#86/A#87/A#88/A#91/A#92/A#93/A#96/A#97/A#98/A#101/A#102/A#103/A#106/A#107/A#108/A#111/A#112/A#113/A#116/A#117/A#118/A#121/A#122/A#123/A#126/A#127/A#128/A#131/A#132/A#133/A#136/A#137/A#138/A#141/A#142/A#143/A#146/A#147/A#148/A#151/A#152/A#153/A#156/A#157/A#158/A#161/A#162/A#163/A#166/A#167/A#168/A#171/A#172/A#173/A#176/A#177/A#178/A#181/A#182/A#183/A#186/A#187/A#188/A#191/A#192/A#193/A#196/A#197/A#198/A#201/A#202/A#203/A#206/A#207/A#208/A#211/A#212/A#213/A#216/A#217/A#218/A#221/A#222/A#223/A#226/A#227/A#228/A#231/A#232/A#233/A#236/A#237/A#238/A#241/A#242/A#243/A#246/A#247/A#248/A#251/A#252/A#253/A#256/A#257/A#258/A#261/A
447224 atoms, 458514 bonds, 58916 residues, 216 models selected
> select
2325488 atoms, 2385760 bonds, 301652 residues, 321 models selected
> hide sel & #1.1-60 cartoons
> select #1.53/A
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
Chain information for AF3 E1 1-421.pdb #262
---
Chain | Description
A | No description available
> matchmaker #262 to #1.53 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain A (#1.53) with AF3 E1 1-421.pdb, chain A (#262),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
3.020)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #263
---
Chain | Description
A | No description available
> matchmaker #263 to #1.53 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain A (#1.53) with AF3 E1 422-461.pdb, chain A (#263),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
2.775)
> hide sel cartoons
> select #1.53/B
3304 atoms, 3395 bonds, 423 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
Chain information for AF3 E2 1-352.pdb #264
---
Chain | Description
B | No description available
> matchmaker #264 to #1.53 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain B (#1.53) with AF3 E2 1-352.pdb, chain B (#264),
sequence alignment score = 583.7
RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
5.933)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #265
---
Chain | Description
B | No description available
> matchmaker #265 to #1.53 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain B (#1.53) with AF3 E2 353-438.pdb, chain B (#265),
sequence alignment score = 333.4
RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
8.411)
> hide sel cartoons
> select #1.53/C
1277 atoms, 1305 bonds, 162 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 CA.pdb"
Chain information for AF3 CA.pdb #266
---
Chain | Description
A | No description available
> matchmaker #266 to #1.53 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain C (#1.53) with AF3 CA.pdb, chain A (#266),
sequence alignment score = 328.1
RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
2.714)
> hide sel cartoons
> select #1.54/A
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
Chain information for AF3 E1 1-421.pdb #267
---
Chain | Description
A | No description available
> matchmaker #267 to #1.54 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain A (#1.54) with AF3 E1 1-421.pdb, chain A (#267),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
3.020)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #268
---
Chain | Description
A | No description available
> matchmaker #268 to #1.54 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain A (#1.54) with AF3 E1 422-461.pdb, chain A (#268),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.572 angstroms; (across all 38 pairs:
2.776)
> matchmaker #268 to #1.54 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain A (#1.54) with AF3 E1 422-461.pdb, chain A (#268),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.572 angstroms; (across all 38 pairs:
2.776)
> hide sel cartoons
> select #1.54/B
3304 atoms, 3395 bonds, 423 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
Chain information for AF3 E2 1-352.pdb #269
---
Chain | Description
B | No description available
> matchmaker #269 to #1.54 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain B (#1.54) with AF3 E2 1-352.pdb, chain B (#269),
sequence alignment score = 583.7
RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
5.933)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #270
---
Chain | Description
B | No description available
> matchmaker #270 to #1.54 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain B (#1.54) with AF3 E2 353-438.pdb, chain B (#270),
sequence alignment score = 333.4
RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
8.411)
> hide sel cartoons
> select #1.54/C
1277 atoms, 1305 bonds, 162 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 CA.pdb"
Chain information for AF3 CA.pdb #271
---
Chain | Description
A | No description available
> matchmaker #271 to #1.54 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain C (#1.54) with AF3 CA.pdb, chain A (#271),
sequence alignment score = 328.1
RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
2.714)
> hide sel cartoons
> color #262 dodgerblue
> color #263 dodgerblue
> color #264 #00b305ff
> color #265 #00b305ff
> color #266 #f15839ff
> color #267 dodgerblue
> color #268 dodgerblue
> color #269 #00b305ff
> color #270 #00b305ff
> color #271 #f15839ff
> select #1.55/A
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
Chain information for AF3 E1 1-421.pdb #272
---
Chain | Description
A | No description available
> matchmaker #272 to #1.54 & sel
No 'to' model specified
> matchmaker #272 to #1.55 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain A (#1.55) with AF3 E1 1-421.pdb, chain A (#272),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
3.020)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #273
---
Chain | Description
A | No description available
> matchmaker #273 to #1.55 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain A (#1.55) with AF3 E1 422-461.pdb, chain A (#273),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.572 angstroms; (across all 38 pairs:
2.775)
> hide sel cartoons
> open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
Chain information for AF3 E2 1-352.pdb #274
---
Chain | Description
B | No description available
> select #1.55/B
3304 atoms, 3395 bonds, 423 residues, 1 model selected
> show sel cartoons
> matchmaker #274 to #1.55 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain B (#1.55) with AF3 E2 1-352.pdb, chain B (#274),
sequence alignment score = 583.7
RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
5.933)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #275
---
Chain | Description
B | No description available
> matchmaker #275 to #1.55 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain B (#1.55) with AF3 E2 353-438.pdb, chain B (#275),
sequence alignment score = 322.6
RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
8.411)
> hide sel cartoons
> select #1.55/C
1277 atoms, 1305 bonds, 162 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 CA.pdb"
Chain information for AF3 CA.pdb #276
---
Chain | Description
A | No description available
> matchmaker #276 to #1.55 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain C (#1.55) with AF3 CA.pdb, chain A (#276),
sequence alignment score = 328.1
RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
2.714)
> hide sel cartoons
> color #272 dodgerblue
> color #273 dodgerblue
> color #274 #00b305ff
> color #275 #00b305ff
> color #276 #f15839ff
> select #1.56/A
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
Chain information for AF3 E1 1-421.pdb #277
---
Chain | Description
A | No description available
> matchmaker #277 to #1.55 & sel
No 'to' model specified
> matchmaker #277 to #1.56 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain A (#1.56) with AF3 E1 1-421.pdb, chain A (#277),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
3.020)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #278
---
Chain | Description
A | No description available
> matchmaker #278 to #1.56 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain A (#1.56) with AF3 E1 422-461.pdb, chain A (#278),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.572 angstroms; (across all 38 pairs:
2.775)
> hide sel cartoons
> select #1.56/B
3304 atoms, 3395 bonds, 423 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
Chain information for AF3 E2 1-352.pdb #279
---
Chain | Description
B | No description available
> matchmaker #279 to #1.56 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain B (#1.56) with AF3 E2 1-352.pdb, chain B (#279),
sequence alignment score = 583.7
RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
5.933)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #280
---
Chain | Description
B | No description available
> matchmaker #280 to #1.56 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain B (#1.56) with AF3 E2 353-438.pdb, chain B (#280),
sequence alignment score = 333.4
RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
8.411)
> hide sel cartoons
> select #1.56/C
1277 atoms, 1305 bonds, 162 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 CA.pdb"
Chain information for AF3 CA.pdb #281
---
Chain | Description
A | No description available
> matchmaker #281 to #1.56 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain C (#1.56) with AF3 CA.pdb, chain A (#281),
sequence alignment score = 328.1
RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
2.714)
> hide sel cartoons
> color #277 dodgerblue
> color #278 dodgerblue
> color #279 #00b305ff
> color #280 #00b305ff
> color #281 #f15839ff
> select #1.57/A
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
Chain information for AF3 E1 1-421.pdb #282
---
Chain | Description
A | No description available
> matchmaker #282 to #1.56 & sel
No 'to' model specified
> matchmaker #282 to #1.57 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain A (#1.57) with AF3 E1 1-421.pdb, chain A (#282),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
3.020)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #283
---
Chain | Description
A | No description available
> matchmaker #283 to #1.57 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain A (#1.57) with AF3 E1 422-461.pdb, chain A (#283),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
2.776)
> hide sel cartoons
> select #1.57/B
3304 atoms, 3395 bonds, 423 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
Chain information for AF3 E2 1-352.pdb #284
---
Chain | Description
B | No description available
> matchmaker #284 to #1.57 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain B (#1.57) with AF3 E2 1-352.pdb, chain B (#284),
sequence alignment score = 583.7
RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
5.933)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #285
---
Chain | Description
B | No description available
> matchmaker #285 to #1.57 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain B (#1.57) with AF3 E2 353-438.pdb, chain B (#285),
sequence alignment score = 333.4
RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
8.411)
> hide sel cartoons
[Repeated 1 time(s)]
> select #1.57/C
1277 atoms, 1305 bonds, 162 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 CA.pdb"
Chain information for AF3 CA.pdb #286
---
Chain | Description
A | No description available
> matchmaker #286 to #1.57 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain C (#1.57) with AF3 CA.pdb, chain A (#286),
sequence alignment score = 328.1
RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
2.714)
> hide sel cartoons
> color #282 dodgerblue
> color #283 dodgerblue
> color #284 #00b305ff
> color #285 #00b305ff
> color #286 #f15839ff
> select #1.58/A
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
Chain information for AF3 E1 1-421.pdb #287
---
Chain | Description
A | No description available
> matchmaker #287 to #1.58 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain A (#1.58) with AF3 E1 1-421.pdb, chain A (#287),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
3.020)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #288
---
Chain | Description
A | No description available
> matchmaker #288 to #1.58 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain A (#1.58) with AF3 E1 422-461.pdb, chain A (#288),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
2.775)
> hide sel cartoons
> select #1.58/B
3304 atoms, 3395 bonds, 423 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
Chain information for AF3 E2 1-352.pdb #289
---
Chain | Description
B | No description available
> matchmaker #289 to #1.58 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain B (#1.58) with AF3 E2 1-352.pdb, chain B (#289),
sequence alignment score = 583.7
RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
5.933)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #290
---
Chain | Description
B | No description available
> matchmaker #290 to #1.58 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain B (#1.58) with AF3 E2 353-438.pdb, chain B (#290),
sequence alignment score = 322.6
RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
8.411)
> hide sel cartoons
> select #1.58/C
1277 atoms, 1305 bonds, 162 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 CA.pdb"
Chain information for AF3 CA.pdb #291
---
Chain | Description
A | No description available
> matchmaker #291 to #1.58 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain C (#1.58) with AF3 CA.pdb, chain A (#291),
sequence alignment score = 328.1
RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
2.714)
> hide sel cartoons
> color #287 dodgerblue
> color #288 dodgerblue
> color #289 #00b305ff
> color #290 #00b305ff
> color #291 #f15839ff
> select #1.59/A
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
Chain information for AF3 E1 1-421.pdb #292
---
Chain | Description
A | No description available
> matchmaker #291 to #1.59 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain A (#1.59) with AF3 CA.pdb, chain A (#291),
sequence alignment score = 32.6
RMSD between 11 pruned atom pairs is 1.204 angstroms; (across all 110 pairs:
22.675)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #293
---
Chain | Description
A | No description available
> matchmaker #291 to #1.58 & sel
No 'to' model specified
> select #1.58/C
1277 atoms, 1305 bonds, 162 residues, 1 model selected
> show sel cartoons
> matchmaker #291 to #1.58 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain C (#1.58) with AF3 CA.pdb, chain A (#291),
sequence alignment score = 328.1
RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
2.714)
> hide sel cartoons
> select #1.59/A
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> matchmaker #292 to #1.59 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain A (#1.59) with AF3 E1 1-421.pdb, chain A (#292),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
3.020)
> matchmaker #293 to #1.59 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain A (#1.59) with AF3 E1 422-461.pdb, chain A (#293),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
2.776)
> select #1.39/B
3304 atoms, 3395 bonds, 423 residues, 1 model selected
> select #1.59/A
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> hide sel cartoons
> select #1.59/B
3304 atoms, 3395 bonds, 423 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
Chain information for AF3 E2 1-352.pdb #294
---
Chain | Description
B | No description available
> matchmaker #294 to #1.59 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain B (#1.59) with AF3 E2 1-352.pdb, chain B (#294),
sequence alignment score = 583.7
RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
5.933)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #295
---
Chain | Description
B | No description available
> matchmaker #295 to #1.59 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain B (#1.59) with AF3 E2 353-438.pdb, chain B (#295),
sequence alignment score = 322.6
RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
8.411)
> hide sel cartoons
> select #1.59/C
1277 atoms, 1305 bonds, 162 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 CA.pdb"
Chain information for AF3 CA.pdb #296
---
Chain | Description
A | No description available
> matchmaker #296 to #1.59 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain C (#1.59) with AF3 CA.pdb, chain A (#296),
sequence alignment score = 328.1
RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
2.714)
> hide sel cartoons
> color #292 dodgerblue
> color #293 dodgerblue
> color #294 #00b305ff
> color #295 #00b305ff
> color #296 #f15839ff
> select #1.60/A
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
Chain information for AF3 E1 1-421.pdb #297
---
Chain | Description
A | No description available
> matchmaker #297 to #1.60 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain A (#1.60) with AF3 E1 1-421.pdb, chain A (#297),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
3.020)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #298
---
Chain | Description
A | No description available
> matchmaker #298 to #1.60 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain A (#1.60) with AF3 E1 422-461.pdb, chain A (#298),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
2.776)
> hide sel cartoons
> select #1.60/B
3304 atoms, 3395 bonds, 423 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
Chain information for AF3 E2 1-352.pdb #299
---
Chain | Description
B | No description available
> matchmaker #299 to #1.60 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain B (#1.60) with AF3 E2 1-352.pdb, chain B (#299),
sequence alignment score = 583.7
RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
5.933)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #300
---
Chain | Description
B | No description available
> matchmaker #300 to #1.60 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain B (#1.60) with AF3 E2 353-438.pdb, chain B (#300),
sequence alignment score = 333.4
RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
8.411)
> hide sel cartoons
> select #1.60/C
1277 atoms, 1305 bonds, 162 residues, 1 model selected
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 CA.pdb"
Chain information for AF3 CA.pdb #301
---
Chain | Description
A | No description available
> matchmaker #301 to #1.60 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3j0c.pdb1, chain C (#1.60) with AF3 CA.pdb, chain A (#301),
sequence alignment score = 328.1
RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
2.714)
> hide sel cartoons
> color #297 dodgerblue
> color #298 dodgerblue
> color #299 #00b305ff
> color #300 #00b305ff
> color #301 #f15839ff
> save "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" includeMaps true
——— End of log from Mon Jul 15 16:48:15 2024 ———
opened ChimeraX session
> show #2 models
> show #3 models
> show #4 models
> show #5 models
> show #6 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
[Repeated 1 time(s)]
> hide #2-6,262-301#1.2-60 target m
> show #1.2 target m
> hide #1.1 target m
> hide #!1 models
> show #2 models
> show #3 models
> show #4 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> show #5 models
> show #6 models
> show #7 models
> show #8 models
> show #9 models
> show #10 models
> show #11 models
> show #12 models
> show #13 models
> show #14 models
> show #15 models
> show #16 models
> show #17 models
> show #18 models
> show #19 models
> show #20 models
> show #21 models
> show #22 models
> show #23 models
> show #24 models
> show #25 models
> show #26 models
> show #27 models
> show #28 models
> show #29 models
> show #30 models
> show #31 models
> show #32 models
> show #33 models
> show #34 models
> show #35 models
> show #36 models
> show #37 models
> show #38 models
> show #39 models
> show #40 models
> show #41 models
> show #42 models
> show #43 models
> show #44 models
> show #45 models
> show #46 models
> show #47 models
> show #48 models
> show #49 models
> show #50 models
> show #51 models
> show #52 models
> show #53 models
> show #54 models
> show #55 models
> show #56 models
> show #57 models
> show #58 models
> show #59 models
> show #60 models
> show #61 models
> show #62 models
> show #63 models
> show #64 models
> show #65 models
> show #66 models
> show #67 models
> show #68 models
> show #69 models
> show #70 models
> show #71 models
> show #72 models
> show #73 models
> show #74 models
> show #75 models
> show #76 models
> show #77 models
> show #78 models
> show #79 models
> show #80 models
> show #81 models
> show #82 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> show #82-301 models
> hide #2-301 models
> show #2-301 models
> save "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" includeMaps true
——— End of log from Mon Jul 15 16:59:09 2024 ———
opened ChimeraX session
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select #1.1/D
3370 atoms, 3467 bonds, 442 residues, 1 model selected
> show #2-301 cartoons
> view sel
No displayed objects specified.
> select add #1
1908240 atoms, 1958684 bonds, 246480 residues, 61 models selected
> hide #1.2 models
> show #1.1 models
> hide #1.1 models
> show #1.1 models
> show sel & #1.1 cartoons
> hide #1.1 models
> hide #!1 models
> show #1.1 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select subtract #1
Nothing selected
> hide #!1 models
> hide #1.1 models
> show #1.1 models
> show #1.2 models
> show #1.3 models
> show #1.4 models
> select
2389680 atoms, 2451464 bonds, 310140 residues, 361 models selected
> show sel & #2-301#1.1-4 cartoons
> hide #!1 models
> show #!1 models
> show #1.5 models
> show #1.6 models
> show #1.7 models
> hide #1.7 models
> show #1.7 models
> show #1.8 models
> ui tool show "Selection Inspector"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
[Repeated 1 time(s)]
> setattr sel struct display true
Assigning display attribute to 360 items
> select #1.1/A
3370 atoms, 3467 bonds, 442 residues, 1 model selected
> select ~sel & ##selected
28434 atoms, 29221 bonds, 3666 residues, 1 model selected
> hide sel cartoons
> select
2389680 atoms, 2451464 bonds, 310140 residues, 361 models selected
> hide sel cartoons
> select #1.1/A
3370 atoms, 3467 bonds, 442 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> select #1.1/D
3370 atoms, 3467 bonds, 442 residues, 1 model selected
> show sel cartoons
> 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 #302
---
Chain | Description
A | No description available
> matchmaker #301 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 D (#1.1) with AF3 CA.pdb, chain A (#301), sequence
alignment score = 32.6
RMSD between 11 pruned atom pairs is 1.228 angstroms; (across all 110 pairs:
22.710)
> select #1.60/C
1277 atoms, 1305 bonds, 162 residues, 1 model selected
> show sel cartoons
> hide #301 models
> show #301 models
> select add #301
2536 atoms, 2591 bonds, 324 residues, 2 models selected
> hide #301 models
> show #301 models
> color #301 #f15839ff
> show sel cartoons
> select subtract #301
1277 atoms, 1305 bonds, 162 residues, 1 model selected
> 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
> hide #301 models
> select #1.1/D
3370 atoms, 3467 bonds, 442 residues, 1 model selected
> matchmaker #302 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 D (#1.1) with AF3 E1 1-421.pdb, chain A (#302),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #303
---
Chain | Description
A | No description available
> matchmaker #303 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 D (#1.1) with AF3 E1 422-461.pdb, chain A (#303),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> select #1.1/E
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 #304
---
Chain | Description
B | No description available
> matchmaker #304 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 E (#1.1) with AF3 E2 1-352.pdb, chain B (#304),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #305
---
Chain | Description
B | No description available
> matchmaker #305 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 E (#1.1) with AF3 E2 353-438.pdb, chain B (#305),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
8.673)
> select #1.1/F
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 #306
---
Chain | Description
A | No description available
> matchmaker #306 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 F (#1.1) with AF3 CA.pdb, chain A (#306), sequence
alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> select #1.1/F
1277 atoms, 1305 bonds, 162 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> select #1.1/E
3304 atoms, 3400 bonds, 423 residues, 1 model selected
> hide sel cartoons
> select #1.1/D
3370 atoms, 3467 bonds, 442 residues, 1 model selected
> hide sel cartoons
> color #302 dodgerblue
> color #303 dodgerblue
> color #304 #00b305ff
> color #305 #00b305ff
> color #306 #f15839ff
> select #1.2/D
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 #307
---
Chain | Description
A | No description available
> matchmaker #307 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 D (#1.2) with AF3 E1 1-421.pdb, chain A (#307),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #308
---
Chain | Description
A | No description available
> matchmaker #308 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 D (#1.2) with AF3 E1 422-461.pdb, chain A (#308),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
[Repeated 1 time(s)]
> select #1.2/E
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 #309
---
Chain | Description
B | No description available
> matchmaker #309 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 E (#1.2) with AF3 E2 1-352.pdb, chain B (#309),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #310
---
Chain | Description
B | No description available
> matchmaker #310 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 E (#1.2) with AF3 E2 353-438.pdb, chain B (#310),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.2/F
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 #311
---
Chain | Description
A | No description available
> matchmaker #311 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 F (#1.2) with AF3 CA.pdb, chain A (#311), sequence
alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #307 dodgerblue
> color #308 dodgerblue
> color #309 #00b305ff
> color #310 #00b305ff
> color #311 #f15839ff
> select #1.3/D
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 #312
---
Chain | Description
A | No description available
> matchmaker #312 to #1.2 & sel
No 'to' model specified
> matchmaker #312 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 D (#1.3) with AF3 E1 1-421.pdb, chain A (#312),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #313
---
Chain | Description
A | No description available
> matchmaker #313 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 D (#1.3) with AF3 E1 422-461.pdb, chain A (#313),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.3/B
3304 atoms, 3395 bonds, 423 residues, 1 model selected
> select #1.3/E
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 #314
---
Chain | Description
B | No description available
> matchmaker #314 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 E (#1.3) with AF3 E2 1-352.pdb, chain B (#314),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #315
---
Chain | Description
B | No description available
> matchmaker #315 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 E (#1.3) with AF3 E2 353-438.pdb, chain B (#315),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.3/F
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 #316
---
Chain | Description
A | No description available
> matchmaker #316 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 F (#1.3) with AF3 CA.pdb, chain A (#316), sequence
alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #312 dodgerblue
> color #313 dodgerblue
> color #314 #00b305ff
> color #315 #00b305ff
> color #316 #f15839ff
> select #1.4/D
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 #317
---
Chain | Description
A | No description available
> matchmaker #317 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 D (#1.4) with AF3 E1 1-421.pdb, chain A (#317),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #318
---
Chain | Description
A | No description available
> matchmaker #318 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 D (#1.4) with AF3 E1 422-461.pdb, chain A (#318),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.4/E
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 #319
---
Chain | Description
B | No description available
> matchmaker #319 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 E (#1.4) with AF3 E2 1-352.pdb, chain B (#319),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #320
---
Chain | Description
B | No description available
> matchmaker #320 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 E (#1.4) with AF3 E2 353-438.pdb, chain B (#320),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.4/F
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 #321
---
Chain | Description
A | No description available
> matchmaker #321 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 F (#1.4) with AF3 CA.pdb, chain A (#321), sequence
alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #317 dodgerblue
> color #318 dodgerblue
> color #319 #00b305ff
> color #320 #00b305ff
> color #321 #f15839ff
> select #1.5/D
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 #322
---
Chain | Description
A | No description available
> matchmaker #322 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 D (#1.5) with AF3 E1 1-421.pdb, chain A (#322),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #323
---
Chain | Description
A | No description available
> matchmaker #323 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 D (#1.5) with AF3 E1 422-461.pdb, chain A (#323),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.915)
> hide sel cartoons
> select #1.5/E
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 #324
---
Chain | Description
B | No description available
> matchmaker #324 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 E (#1.5) with AF3 E2 1-352.pdb, chain B (#324),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #325
---
Chain | Description
B | No description available
> matchmaker #325 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 E (#1.5) with AF3 E2 353-438.pdb, chain B (#325),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.5/F
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 #326
---
Chain | Description
A | No description available
> matchmaker #326 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 F (#1.5) with AF3 CA.pdb, chain A (#326), sequence
alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #322 dodgerblue
> color #323 dodgerblue
> color #324 #00b305ff
> color #325 #00b305ff
> color #326 #f15839ff
> select #1.6/D
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 #327
---
Chain | Description
A | No description available
> matchmaker #327 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 D (#1.6) with AF3 E1 1-421.pdb, chain A (#327),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #328
---
Chain | Description
A | No description available
> matchmaker #328 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 D (#1.6) with AF3 E1 422-461.pdb, chain A (#328),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.6/E
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 #329
---
Chain | Description
B | No description available
> matchmaker #329 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 E (#1.6) with AF3 E2 1-352.pdb, chain B (#329),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #330
---
Chain | Description
B | No description available
> matchmaker #330 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 E (#1.6) with AF3 E2 353-438.pdb, chain B (#330),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.6/F
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 #331
---
Chain | Description
A | No description available
> matchmaker #331 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 F (#1.6) with AF3 CA.pdb, chain A (#331), sequence
alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #327 dodgerblue
> color #328 dodgerblue
> color #329 #00b305ff
> color #330 #00b305ff
> color #331 #f15839ff
> select #1.7/D
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 #332
---
Chain | Description
A | No description available
> matchmaker #332 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 D (#1.7) with AF3 E1 1-421.pdb, chain A (#332),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #333
---
Chain | Description
A | No description available
> matchmaker #333 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 D (#1.7) with AF3 E1 422-461.pdb, chain A (#333),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.7/E
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 #334
---
Chain | Description
B | No description available
> matchmaker #334 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 E (#1.7) with AF3 E2 1-352.pdb, chain B (#334),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #335
---
Chain | Description
B | No description available
> matchmaker #335 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 E (#1.7) with AF3 E2 353-438.pdb, chain B (#335),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.7/F
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 #336
---
Chain | Description
A | No description available
> matchmaker #336 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 F (#1.7) with AF3 CA.pdb, chain A (#336), sequence
alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #332 dodgerblue
> color #333 dodgerblue
> color #334 #00b305ff
> color #335 #00b305ff
> color #336 #f15839ff
> select #1.8/D
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 #337
---
Chain | Description
A | No description available
> matchmaker #337 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 D (#1.8) with AF3 E1 1-421.pdb, chain A (#337),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #338
---
Chain | Description
A | No description available
> matchmaker #338 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 D (#1.8) with AF3 E1 422-461.pdb, chain A (#338),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.8/E
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 #339
---
Chain | Description
B | No description available
> matchmaker #339 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 E (#1.8) with AF3 E2 1-352.pdb, chain B (#339),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #340
---
Chain | Description
B | No description available
> matchmaker #340 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 E (#1.8) with AF3 E2 353-438.pdb, chain B (#340),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.8/F
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 #341
---
Chain | Description
A | No description available
> matchmaker #341 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 F (#1.8) with AF3 CA.pdb, chain A (#341), sequence
alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #337 dodgerblue
> color #338 dodgerblue
> color #339 #00b305ff
> color #340 #00b305ff
> color #341 #f15839ff
> select #1.9/D
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 #342
---
Chain | Description
A | No description available
> matchmaker #342 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 D (#1.9) with AF3 E1 1-421.pdb, chain A (#342),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #343
---
Chain | Description
A | No description available
> matchmaker #343 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 D (#1.9) with AF3 E1 422-461.pdb, chain A (#343),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.9/E
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 #344
---
Chain | Description
B | No description available
> matchmaker #344 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 E (#1.9) with AF3 E2 1-352.pdb, chain B (#344),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #345
---
Chain | Description
B | No description available
> matchmaker #345 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 E (#1.9) with AF3 E2 353-438.pdb, chain B (#345),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.9/F
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 #346
---
Chain | Description
A | No description available
> matchmaker #346 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 F (#1.9) with AF3 CA.pdb, chain A (#346), sequence
alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #342 dodgerblue
> color #343 dodgerblue
> color #344 #00b305ff
> color #345 #00b305ff
> color #346 #f15839ff
> save "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" includeMaps true
> hide #302-346 models
> select #1.10/D
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 #347
---
Chain | Description
A | No description available
> matchmaker #347 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 D (#1.10) with AF3 E1 1-421.pdb, chain A (#347),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #348
---
Chain | Description
A | No description available
> matchmaker #348 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 D (#1.10) with AF3 E1 422-461.pdb, chain A (#348),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.10/E
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 #349
---
Chain | Description
B | No description available
> matchmaker #349 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 E (#1.10) with AF3 E2 1-352.pdb, chain B (#349),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #350
---
Chain | Description
B | No description available
> matchmaker #350 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 E (#1.10) with AF3 E2 353-438.pdb, chain B (#350),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.10/F
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 #351
---
Chain | Description
A | No description available
> matchmaker #351 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 F (#1.10) with AF3 CA.pdb, chain A (#351),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #347 dodgerblue
> color #348 dodgerblue
> color #349 #00b305ff
> color #350 #00b305ff
> color #351 #f15839ff
> save "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" includeMaps true
> select #1.11/D
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 #352
---
Chain | Description
A | No description available
> matchmaker #352 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 D (#1.11) with AF3 E1 1-421.pdb, chain A (#352),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> view sel
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #353
---
Chain | Description
A | No description available
> matchmaker #353 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 D (#1.11) with AF3 E1 422-461.pdb, chain A (#353),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.11/E
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 #354
---
Chain | Description
B | No description available
> matchmaker #354 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 E (#1.11) with AF3 E2 1-352.pdb, chain B (#354),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #355
---
Chain | Description
B | No description available
> matchmaker #355 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 E (#1.11) with AF3 E2 353-438.pdb, chain B (#355),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.11/F
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 #356
---
Chain | Description
A | No description available
> matchmaker #356 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 F (#1.11) with AF3 CA.pdb, chain A (#356),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #352 dodgerblue
> color #353 dodgerblue
> color #354 #00b305ff
> color #355 #00b305ff
> color #356 #f15839ff
> select #1.12/D
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 #357
---
Chain | Description
A | No description available
> matchmaker #357 to #1.11 & sel
No 'to' model specified
> matchmaker #357 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 D (#1.12) with AF3 E1 1-421.pdb, chain A (#357),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #358
---
Chain | Description
A | No description available
> matchmaker #358 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 D (#1.12) with AF3 E1 422-461.pdb, chain A (#358),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.12/E
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 #359
---
Chain | Description
B | No description available
> matchmaker #359 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 E (#1.12) with AF3 E2 1-352.pdb, chain B (#359),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #360
---
Chain | Description
B | No description available
> matchmaker #360 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 E (#1.12) with AF3 E2 353-438.pdb, chain B (#360),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.12/F
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 #361
---
Chain | Description
A | No description available
> matchmaker #361 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 F (#1.12) with AF3 CA.pdb, chain A (#361),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #357 dodgerblue
> color #358 dodgerblue
> color #359 #00b305ff
> color #360 #00b305ff
> color #361 #f15839ff
> select #1.13/D
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> show sel cartoons
> lighting soft
> lighting full
> lighting simple
> lighting soft
[Repeated 1 time(s)]
> view
> open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
Chain information for AF3 E1 1-421.pdb #362
---
Chain | Description
A | No description available
> matchmaker #362 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 D (#1.13) with AF3 E1 1-421.pdb, chain A (#362),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #363
---
Chain | Description
A | No description available
> matchmaker #363 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 D (#1.13) with AF3 E1 422-461.pdb, chain A (#363),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> lighting simple
> select #1.13/E
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 #364
---
Chain | Description
B | No description available
> matchmaker #364 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 E (#1.13) with AF3 E2 1-352.pdb, chain B (#364),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #365
---
Chain | Description
B | No description available
> matchmaker #365 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 E (#1.13) with AF3 E2 353-438.pdb, chain B (#365),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.13/F
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 #366
---
Chain | Description
A | No description available
> matchmaker #366 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 F (#1.13) with AF3 CA.pdb, chain A (#366),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #362 dodgerblue
> color #363 dodgerblue
> color #364 #00b305ff
> color #365 #00b305ff
> color #366 #f15839ff
> select #1.14/D
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 #367
---
Chain | Description
A | No description available
> matchmaker #367 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 D (#1.14) with AF3 E1 1-421.pdb, chain A (#367),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #368
---
Chain | Description
A | No description available
> matchmaker #368 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 D (#1.14) with AF3 E1 422-461.pdb, chain A (#368),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.14/E
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 #369
---
Chain | Description
B | No description available
> matchmaker #369 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 E (#1.14) with AF3 E2 1-352.pdb, chain B (#369),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #370
---
Chain | Description
B | No description available
> matchmaker #370 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 E (#1.14) with AF3 E2 353-438.pdb, chain B (#370),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.14/F
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 #371
---
Chain | Description
A | No description available
> matchmaker #371 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 F (#1.14) with AF3 CA.pdb, chain A (#371),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #367 dodgerblue
> color #368 dodgerblue
> color #369 #00b305ff
> color #370 #00b305ff
> color #371 #f15839ff
> select #1.16/D
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 #372
---
Chain | Description
A | No description available
> hide sel cartoons
> select #1.15/D
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> show sel cartoons
> matchmaker #372 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 D (#1.15) with AF3 E1 1-421.pdb, chain A (#372),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #373
---
Chain | Description
A | No description available
> matchmaker #373 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 D (#1.15) with AF3 E1 422-461.pdb, chain A (#373),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.15/E
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 #374
---
Chain | Description
B | No description available
> matchmaker #374 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 E (#1.15) with AF3 E2 1-352.pdb, chain B (#374),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #375
---
Chain | Description
B | No description available
> matchmaker #375 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 E (#1.15) with AF3 E2 353-438.pdb, chain B (#375),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.15/F
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 #376
---
Chain | Description
A | No description available
> matchmaker #376 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 F (#1.15) with AF3 CA.pdb, chain A (#376),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #372 dodgerblue
> color #373 dodgerblue
> color #374 #00b305ff
> color #375 #00b305ff
> color #376 #f15839ff
> select #1.16/D
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 #377
---
Chain | Description
A | No description available
> matchmaker #377 to #1.15 & sel
No 'to' model specified
> matchmaker #377 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 D (#1.16) with AF3 E1 1-421.pdb, chain A (#377),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #378
---
Chain | Description
A | No description available
> matchmaker #378 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 D (#1.16) with AF3 E1 422-461.pdb, chain A (#378),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.16/E
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 #379
---
Chain | Description
B | No description available
> matchmaker #379 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 E (#1.16) with AF3 E2 1-352.pdb, chain B (#379),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #380
---
Chain | Description
B | No description available
> matchmaker #380 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 E (#1.16) with AF3 E2 353-438.pdb, chain B (#380),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.16/F
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 #381
---
Chain | Description
A | No description available
> matchmaker #381 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 F (#1.16) with AF3 CA.pdb, chain A (#381),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #377 dodgerblue
> color #378 dodgerblue
> color #379 #00b305ff
> color #380 #00b305ff
> color #381 #f15839ff
> select #1.17/D
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 #382
---
Chain | Description
A | No description available
> matchmaker #382 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 D (#1.17) with AF3 E1 1-421.pdb, chain A (#382),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #383
---
Chain | Description
A | No description available
> matchmaker #383 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 D (#1.17) with AF3 E1 422-461.pdb, chain A (#383),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.915)
> hide sel cartoons
> select #1.17/E
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 #384
---
Chain | Description
B | No description available
> matchmaker #384 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 E (#1.17) with AF3 E2 1-352.pdb, chain B (#384),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #385
---
Chain | Description
B | No description available
> matchmaker #385 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 E (#1.17) with AF3 E2 353-438.pdb, chain B (#385),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.17/F
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 #386
---
Chain | Description
A | No description available
> matchmaker #386 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 F (#1.17) with AF3 CA.pdb, chain A (#386),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #382 dodgerblue
> color #383 dodgerblue
> color #384 #00b305ff
> color #385 #00b305ff
> color #386 #f15839ff
> select #1.18/D
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 #387
---
Chain | Description
A | No description available
> matchmaker #387 to #1.17 & sel
No 'to' model specified
> matchmaker #387 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 D (#1.18) with AF3 E1 1-421.pdb, chain A (#387),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #388
---
Chain | Description
A | No description available
> matchmaker #388 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 D (#1.18) with AF3 E1 422-461.pdb, chain A (#388),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.18/E
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 #389
---
Chain | Description
B | No description available
> matchmaker #389 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 E (#1.18) with AF3 E2 1-352.pdb, chain B (#389),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #390
---
Chain | Description
B | No description available
> matchmaker #390 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 E (#1.18) with AF3 E2 353-438.pdb, chain B (#390),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.18/F
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 #391
---
Chain | Description
A | No description available
> matchmaker #391 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 F (#1.18) with AF3 CA.pdb, chain A (#391),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #387 dodgerblue
> color #388 dodgerblue
> color #389 #00b305ff
> color #390 #00b305ff
> color #391 #f15839ff
> select #1.19/D
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 #392
---
Chain | Description
A | No description available
> matchmaker #391 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 D (#1.19) with AF3 CA.pdb, chain A (#391),
sequence alignment score = 32.6
RMSD between 11 pruned atom pairs is 1.228 angstroms; (across all 110 pairs:
22.710)
> select #1.18/F
1277 atoms, 1305 bonds, 162 residues, 1 model selected
> show sel cartoons
> matchmaker #391 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 F (#1.18) with AF3 CA.pdb, chain A (#391),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> select #1.19/D
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 #393
---
Chain | Description
A | No description available
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> close #393
> matchmaker #392 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 D (#1.19) with AF3 E1 1-421.pdb, chain A (#392),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #393
---
Chain | Description
A | No description available
> matchmaker #393 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 D (#1.19) with AF3 E1 422-461.pdb, chain A (#393),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.19/E
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 #394
---
Chain | Description
B | No description available
> matchmaker #394 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 E (#1.19) with AF3 E2 1-352.pdb, chain B (#394),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #395
---
Chain | Description
B | No description available
> matchmaker #395 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 E (#1.19) with AF3 E2 353-438.pdb, chain B (#395),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.19/F
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 #396
---
Chain | Description
A | No description available
> matchmaker #396 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 F (#1.19) with AF3 CA.pdb, chain A (#396),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #392 dodgerblue
> color #393 dodgerblue
> color #394 #00b305ff
> color #395 #00b305ff
> color #396 #f15839ff
> select #1.20/D
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 #397
---
Chain | Description
A | No description available
> matchmaker #397 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 D (#1.20) with AF3 E1 1-421.pdb, chain A (#397),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #398
---
Chain | Description
A | No description available
> matchmaker #398 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 D (#1.20) with AF3 E1 422-461.pdb, chain A (#398),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.20/E
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 #399
---
Chain | Description
B | No description available
> matchmaker #399 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 E (#1.20) with AF3 E2 1-352.pdb, chain B (#399),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #400
---
Chain | Description
B | No description available
> matchmaker #400 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 E (#1.20) with AF3 E2 353-438.pdb, chain B (#400),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.20/F
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 #401
---
Chain | Description
A | No description available
> matchmaker #401 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 F (#1.20) with AF3 CA.pdb, chain A (#401),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #397 dodgerblue
> color #398 dodgerblue
> color #399 #00b305ff
> color #400 #00b305ff
> color #401 #f15839ff
> save "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" includeMaps true
> select add #347
4419 atoms, 4528 bonds, 583 residues, 2 models selected
> select subtract #347
1277 atoms, 1305 bonds, 162 residues, 1 model selected
> select add #347
4419 atoms, 4528 bonds, 583 residues, 2 models selected
> select subtract #347
1277 atoms, 1305 bonds, 162 residues, 1 model selected
> hide #347-396 models
> select #1.21/D
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 #402
---
Chain | Description
A | No description available
> matchmaker #402 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 D (#1.21) with AF3 E1 1-421.pdb, chain A (#402),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #403
---
Chain | Description
A | No description available
> matchmaker #403 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 D (#1.21) with AF3 E1 422-461.pdb, chain A (#403),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.21/E
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 #404
---
Chain | Description
B | No description available
> matchmaker #404 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 E (#1.21) with AF3 E2 1-352.pdb, chain B (#404),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #405
---
Chain | Description
B | No description available
> matchmaker #405 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 E (#1.21) with AF3 E2 353-438.pdb, chain B (#405),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.21/F
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 #406
---
Chain | Description
A | No description available
> matchmaker #406 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 F (#1.21) with AF3 CA.pdb, chain A (#406),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #402 dodgerblue
> color #403 dodgerblue
> color #404 #00b305ff
> color #405 #00b305ff
> color #406 #f15839ff
> select #1.22/D
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 #407
---
Chain | Description
A | No description available
> matchmaker #407 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 D (#1.22) with AF3 E1 1-421.pdb, chain A (#407),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #408
---
Chain | Description
A | No description available
> matchmaker #408 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 D (#1.22) with AF3 E1 422-461.pdb, chain A (#408),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.22/E
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 #409
---
Chain | Description
B | No description available
> matchmaker #409 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 E (#1.22) with AF3 E2 1-352.pdb, chain B (#409),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #410
---
Chain | Description
B | No description available
> matchmaker #410 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 E (#1.22) with AF3 E2 353-438.pdb, chain B (#410),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
8.673)
> select #1.22/F
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 #411
---
Chain | Description
A | No description available
> matchmaker #411 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 F (#1.22) with AF3 CA.pdb, chain A (#411),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #407 dodgerblue
> color #408 dodgerblue
> color #409 #00b305ff
> color #410 #00b305ff
> color #411 #f15839ff
> select #1.22/E
3304 atoms, 3395 bonds, 423 residues, 1 model selected
> hide sel cartoons
> select #1.23/D
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 #412
---
Chain | Description
A | No description available
> matchmaker #412 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 D (#1.23) with AF3 E1 1-421.pdb, chain A (#412),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #413
---
Chain | Description
A | No description available
> matchmaker #413 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 D (#1.23) with AF3 E1 422-461.pdb, chain A (#413),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.23/F
1277 atoms, 1305 bonds, 162 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> select #1.23/E
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 #414
---
Chain | Description
B | No description available
> matchmaker #414 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 E (#1.23) with AF3 E2 1-352.pdb, chain B (#414),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #415
---
Chain | Description
B | No description available
> matchmaker #415 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 E (#1.23) with AF3 E2 353-438.pdb, chain B (#415),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.23/F
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 #416
---
Chain | Description
A | No description available
> matchmaker #416 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 F (#1.23) with AF3 CA.pdb, chain A (#416),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #412 dodgerblue
> color #413 dodgerblue
> color #414 #00b305ff
> color #415 #00b305ff
> color #416 #f15839ff
> select #1.24/D
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 #417
---
Chain | Description
A | No description available
> matchmaker #417 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 D (#1.24) with AF3 E1 1-421.pdb, chain A (#417),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #418
---
Chain | Description
A | No description available
> matchmaker #418 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 D (#1.24) with AF3 E1 422-461.pdb, chain A (#418),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.24/E
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 #419
---
Chain | Description
B | No description available
> matchmaker #419 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 E (#1.24) with AF3 E2 1-352.pdb, chain B (#419),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #420
---
Chain | Description
B | No description available
> matchmaker #420 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 E (#1.24) with AF3 E2 353-438.pdb, chain B (#420),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.24/F
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 #421
---
Chain | Description
A | No description available
> matchmaker #421 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 F (#1.24) with AF3 CA.pdb, chain A (#421),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #417 dodgerblue
> color #418 dodgerblue
> color #419 #00b305ff
> color #420 #00b305ff
> color #421 #f15839ff
> select #1.25/D
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 #422
---
Chain | Description
A | No description available
> matchmaker #422 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 D (#1.25) with AF3 E1 1-421.pdb, chain A (#422),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #423
---
Chain | Description
A | No description available
> matchmaker #423 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 D (#1.25) with AF3 E1 422-461.pdb, chain A (#423),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.25/E
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 #424
---
Chain | Description
B | No description available
> matchmaker #424 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 E (#1.25) with AF3 E2 1-352.pdb, chain B (#424),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #425
---
Chain | Description
B | No description available
> matchmaker #425 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 E (#1.25) with AF3 E2 353-438.pdb, chain B (#425),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.25/F
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 #426
---
Chain | Description
A | No description available
> matchmaker #426 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 F (#1.25) with AF3 CA.pdb, chain A (#426),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #422 dodgerblue
> color #423 dodgerblue
> color #424 #00b305ff
> color #425 #00b305ff
> color #426 #f15839ff
> select #1.26/D
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 #427
---
Chain | Description
A | No description available
> matchmaker #427 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 D (#1.26) with AF3 E1 1-421.pdb, chain A (#427),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #428
---
Chain | Description
A | No description available
> matchmaker #428 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 D (#1.26) with AF3 E1 422-461.pdb, chain A (#428),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.26/E
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 #429
---
Chain | Description
B | No description available
> matchmaker #429 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 E (#1.26) with AF3 E2 1-352.pdb, chain B (#429),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #430
---
Chain | Description
B | No description available
> matchmaker #430 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 E (#1.26) with AF3 E2 353-438.pdb, chain B (#430),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.26/F
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 #431
---
Chain | Description
A | No description available
> matchmaker #431 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 F (#1.26) with AF3 CA.pdb, chain A (#431),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #427 dodgerblue
> color #428 dodgerblue
> color #429 #00b305ff
> color #430 #00b305ff
> color #431 #f15839ff
> select #1.27/D
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 #432
---
Chain | Description
A | No description available
> matchmaker #432 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 D (#1.27) with AF3 E1 1-421.pdb, chain A (#432),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #433
---
Chain | Description
A | No description available
> matchmaker #433 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 D (#1.27) with AF3 E1 422-461.pdb, chain A (#433),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.27/E
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 #434
---
Chain | Description
B | No description available
> matchmaker #434 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 E (#1.27) with AF3 E2 1-352.pdb, chain B (#434),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #435
---
Chain | Description
B | No description available
> matchmaker #435 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 E (#1.27) with AF3 E2 353-438.pdb, chain B (#435),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.27/F
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 #436
---
Chain | Description
A | No description available
> matchmaker #436 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 F (#1.27) with AF3 CA.pdb, chain A (#436),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #432 dodgerblue
> color #433 dodgerblue
> color #434 #00b305ff
> color #435 #00b305ff
> color #436 #f15839ff
> select #1.28/D
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 #437
---
Chain | Description
A | No description available
> matchmaker #437 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 D (#1.28) with AF3 E1 1-421.pdb, chain A (#437),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #438
---
Chain | Description
A | No description available
> matchmaker #438 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 D (#1.28) with AF3 E1 422-461.pdb, chain A (#438),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.28/E
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 #439
---
Chain | Description
B | No description available
> matchmaker #439 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 E (#1.28) with AF3 E2 1-352.pdb, chain B (#439),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #440
---
Chain | Description
B | No description available
> matchmaker #440 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 E (#1.28) with AF3 E2 353-438.pdb, chain B (#440),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.28/F
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 #441
---
Chain | Description
A | No description available
> matchmaker #441 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 F (#1.28) with AF3 CA.pdb, chain A (#441),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #437 dodgerblue
> color #438 dodgerblue
> color #439 #00b305ff
> color #440 #00b305ff
> color #441 #f15839ff
> select #1.29/D
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 #442
---
Chain | Description
A | No description available
> matchmaker #442 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 D (#1.29) with AF3 E1 1-421.pdb, chain A (#442),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #443
---
Chain | Description
A | No description available
> matchmaker #443 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 D (#1.29) with AF3 E1 422-461.pdb, chain A (#443),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.29/E
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 #444
---
Chain | Description
B | No description available
> matchmaker #444 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 E (#1.29) with AF3 E2 1-352.pdb, chain B (#444),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #445
---
Chain | Description
B | No description available
> matchmaker #445 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 E (#1.29) with AF3 E2 353-438.pdb, chain B (#445),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.29/F
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 #446
---
Chain | Description
A | No description available
> matchmaker #446 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 F (#1.29) with AF3 CA.pdb, chain A (#446),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #442 dodgerblue
> color #443 dodgerblue
> color #444 #00b305ff
> color #445 #00b305ff
> color #446 #f15839ff
> select #1.30/D
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 #447
---
Chain | Description
A | No description available
> matchmaker #447 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 D (#1.30) with AF3 E1 1-421.pdb, chain A (#447),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #448
---
Chain | Description
A | No description available
> matchmaker #448 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 D (#1.30) with AF3 E1 422-461.pdb, chain A (#448),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.30/E
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 #449
---
Chain | Description
B | No description available
> matchmaker #449 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 E (#1.30) with AF3 E2 1-352.pdb, chain B (#449),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #450
---
Chain | Description
B | No description available
> matchmaker #450 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 E (#1.30) with AF3 E2 353-438.pdb, chain B (#450),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.30/F
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 #451
---
Chain | Description
A | No description available
> matchmaker #451 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 F (#1.30) with AF3 CA.pdb, chain A (#451),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #447 dodgerblue
> color #448 dodgerblue
> color #449 #00b305ff
> color #450 #00b305ff
> color #451 #f15839ff
> save "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" includeMaps true
> hide #397-451 models
> select #1.31/D
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 #452
---
Chain | Description
A | No description available
> matchmaker #452 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 D (#1.31) with AF3 E1 1-421.pdb, chain A (#452),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> view sel
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #453
---
Chain | Description
A | No description available
> matchmaker #453 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 D (#1.31) with AF3 E1 422-461.pdb, chain A (#453),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> view
> hide sel cartoons
> select #1.31/E
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 #454
---
Chain | Description
B | No description available
> matchmaker #454 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 E (#1.31) with AF3 E2 1-352.pdb, chain B (#454),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #455
---
Chain | Description
B | No description available
> matchmaker #455 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 E (#1.31) with AF3 E2 353-438.pdb, chain B (#455),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.31/F
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 #456
---
Chain | Description
A | No description available
> matchmaker #456 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 F (#1.31) with AF3 CA.pdb, chain A (#456),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #452 dodgerblue
> color #453 dodgerblue
> color #454 #00b305ff
> color #455 #00b305ff
> color #456 #f15839ff
> select #1.32/D
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 #457
---
Chain | Description
A | No description available
> matchmaker #457 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 D (#1.32) with AF3 E1 1-421.pdb, chain A (#457),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #458
---
Chain | Description
A | No description available
> matchmaker #458 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 D (#1.32) with AF3 E1 422-461.pdb, chain A (#458),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.31/E
3304 atoms, 3395 bonds, 423 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> select #1.32/E
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 #459
---
Chain | Description
B | No description available
> matchmaker #459 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 E (#1.32) with AF3 E2 1-352.pdb, chain B (#459),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #460
---
Chain | Description
B | No description available
> matchmaker #460 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 E (#1.32) with AF3 E2 353-438.pdb, chain B (#460),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.32/F
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 #461
---
Chain | Description
A | No description available
> matchmaker #461 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 F (#1.32) with AF3 CA.pdb, chain A (#461),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #457 dodgerblue
> color #458 dodgerblue
> color #459 #00b305ff
> color #460 #00b305ff
> color #461 #f15839ff
> select #1.33/D
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 #462
---
Chain | Description
A | No description available
> matchmaker #462 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 D (#1.33) with AF3 E1 1-421.pdb, chain A (#462),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #463
---
Chain | Description
A | No description available
> matchmaker #463 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 D (#1.33) with AF3 E1 422-461.pdb, chain A (#463),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.33/E
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 #464
---
Chain | Description
B | No description available
> matchmaker #464 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 E (#1.33) with AF3 E2 1-352.pdb, chain B (#464),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #465
---
Chain | Description
B | No description available
> matchmaker #465 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 E (#1.33) with AF3 E2 353-438.pdb, chain B (#465),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.33/F
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 #466
---
Chain | Description
A | No description available
> matchmaker #466 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 F (#1.33) with AF3 CA.pdb, chain A (#466),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #462 dodgerblue
> color #463 dodgerblue
> color #464 #00b305ff
> color #465 #00b305ff
> color #466 #f15839ff
> select #1.34/D
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 #467
---
Chain | Description
A | No description available
> view
> matchmaker #467 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 D (#1.34) with AF3 E1 1-421.pdb, chain A (#467),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #468
---
Chain | Description
A | No description available
> matchmaker #468 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 D (#1.34) with AF3 E1 422-461.pdb, chain A (#468),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.34/E
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 #469
---
Chain | Description
B | No description available
> matchmaker #469 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 E (#1.34) with AF3 E2 1-352.pdb, chain B (#469),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #470
---
Chain | Description
B | No description available
> matchmaker #470 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 E (#1.34) with AF3 E2 353-438.pdb, chain B (#470),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.34/F
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 #471
---
Chain | Description
A | No description available
> matchmaker #471 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 F (#1.34) with AF3 CA.pdb, chain A (#471),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #467 dodgerblue
> color #468 dodgerblue
> color #469 #00b305ff
> color #470 #00b305ff
> color #471 #f15839ff
> select #1.35/D
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 #472
---
Chain | Description
A | No description available
> matchmaker #472 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 D (#1.35) with AF3 E1 1-421.pdb, chain A (#472),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #473
---
Chain | Description
A | No description available
> matchmaker #473 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 D (#1.35) with AF3 E1 422-461.pdb, chain A (#473),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.35/E
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 #474
---
Chain | Description
B | No description available
> matchmaker #474 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 E (#1.35) with AF3 E2 1-352.pdb, chain B (#474),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #475
---
Chain | Description
B | No description available
> matchmaker #475 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 E (#1.35) with AF3 E2 353-438.pdb, chain B (#475),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.35/F
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 #476
---
Chain | Description
A | No description available
> matchmaker #476 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 F (#1.35) with AF3 CA.pdb, chain A (#476),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #472 dodgerblue
> color #473 dodgerblue
> color #474 #00b305ff
> color #475 #00b305ff
> color #476 #f15839ff
> select #1.36/D
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 #477
---
Chain | Description
A | No description available
> matchmaker #477 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 D (#1.36) with AF3 E1 1-421.pdb, chain A (#477),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #478
---
Chain | Description
A | No description available
> matchmaker #478 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 D (#1.36) with AF3 E1 422-461.pdb, chain A (#478),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.36/E
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 #479
---
Chain | Description
B | No description available
> matchmaker #479 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 E (#1.36) with AF3 E2 1-352.pdb, chain B (#479),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #480
---
Chain | Description
B | No description available
> matchmaker #480 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 E (#1.36) with AF3 E2 353-438.pdb, chain B (#480),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.36/F
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 #481
---
Chain | Description
A | No description available
> matchmaker #481 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 F (#1.36) with AF3 CA.pdb, chain A (#481),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #477 dodgerblue
> color #478 dodgerblue
> color #479 #00b305ff
> color #480 #00b305ff
> color #481 #f15839ff
> select #1.37/D
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 #482
---
Chain | Description
A | No description available
> matchmaker #482 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 D (#1.37) with AF3 E1 1-421.pdb, chain A (#482),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #483
---
Chain | Description
A | No description available
> matchmaker #483 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 D (#1.37) with AF3 E1 422-461.pdb, chain A (#483),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.37/E
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 #484
---
Chain | Description
B | No description available
> matchmaker #484 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 E (#1.37) with AF3 E2 1-352.pdb, chain B (#484),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #485
---
Chain | Description
B | No description available
> matchmaker #485 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 E (#1.37) with AF3 E2 353-438.pdb, chain B (#485),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
[Repeated 1 time(s)]
> select #1.37/F
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 #486
---
Chain | Description
A | No description available
> matchmaker #486 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 F (#1.37) with AF3 CA.pdb, chain A (#486),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
[Repeated 1 time(s)]
> color #482 dodgerblue
> color #483 dodgerblue
> color #484 #00b305ff
> color #485 #00b305ff
> color #486 #f15839ff
> select #1.38/D
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 #487
---
Chain | Description
A | No description available
> matchmaker #487 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 D (#1.38) with AF3 E1 1-421.pdb, chain A (#487),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #488
---
Chain | Description
A | No description available
> matchmaker #488 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 D (#1.38) with AF3 E1 422-461.pdb, chain A (#488),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.38/E
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 #489
---
Chain | Description
B | No description available
> matchmaker #489 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 E (#1.38) with AF3 E2 1-352.pdb, chain B (#489),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #490
---
Chain | Description
B | No description available
> matchmaker #490 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 E (#1.38) with AF3 E2 353-438.pdb, chain B (#490),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.38/F
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 #491
---
Chain | Description
A | No description available
> matchmaker #491 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 F (#1.38) with AF3 CA.pdb, chain A (#491),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
[Repeated 1 time(s)]
> color #487 dodgerblue
> color #488 dodgerblue
> color #489 #00b305ff
> color #490 #00b305ff
> color #491 #f15839ff
> select #1.39/D
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 #492
---
Chain | Description
A | No description available
> matchmaker #492 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 D (#1.39) with AF3 E1 1-421.pdb, chain A (#492),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #493
---
Chain | Description
A | No description available
> matchmaker #493 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 D (#1.39) with AF3 E1 422-461.pdb, chain A (#493),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.39/E
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 #494
---
Chain | Description
B | No description available
> matchmaker #494 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 E (#1.39) with AF3 E2 1-352.pdb, chain B (#494),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #495
---
Chain | Description
B | No description available
> matchmaker #495 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 E (#1.39) with AF3 E2 353-438.pdb, chain B (#495),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.39/F
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 #496
---
Chain | Description
A | No description available
> matchmaker #496 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 F (#1.39) with AF3 CA.pdb, chain A (#496),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #492 dodgerblue
> color #493 dodgerblue
> color #494 #00b305ff
> color #495 #00b305ff
> color #496 #f15839ff
> select #1.40/D
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 #497
---
Chain | Description
A | No description available
> matchmaker #497 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 D (#1.40) with AF3 E1 1-421.pdb, chain A (#497),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #498
---
Chain | Description
A | No description available
> matchmaker #498 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 D (#1.40) with AF3 E1 422-461.pdb, chain A (#498),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.40/E
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 #499
---
Chain | Description
B | No description available
> matchmaker #499 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 E (#1.40) with AF3 E2 1-352.pdb, chain B (#499),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #500
---
Chain | Description
B | No description available
> matchmaker #500 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 E (#1.40) with AF3 E2 353-438.pdb, chain B (#500),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
8.673)
> select #1.40/F
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 #501
---
Chain | Description
A | No description available
> matchmaker #501 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 F (#1.40) with AF3 CA.pdb, chain A (#501),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> select #1.40/E
3304 atoms, 3395 bonds, 423 residues, 1 model selected
> hide sel cartoons
> color #497 dodgerblue
> color #498 dodgerblue
> color #499 #00b305ff
> color #500 #00b305ff
> color #501 #f15839ff
> save "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" includeMaps true
> hide #452-501 models
> select #1.41/D
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 #502
---
Chain | Description
A | No description available
> matchmaker #502 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 D (#1.41) with AF3 E1 1-421.pdb, chain A (#502),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #503
---
Chain | Description
A | No description available
> matchmaker #503 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 D (#1.41) with AF3 E1 422-461.pdb, chain A (#503),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.41/E
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 #504
---
Chain | Description
B | No description available
> matchmaker #504 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 E (#1.41) with AF3 E2 1-352.pdb, chain B (#504),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #505
---
Chain | Description
B | No description available
> matchmaker #505 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 E (#1.41) with AF3 E2 353-438.pdb, chain B (#505),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.41/F
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 #506
---
Chain | Description
A | No description available
> matchmaker #506 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 F (#1.41) with AF3 CA.pdb, chain A (#506),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
[Repeated 1 time(s)]
> color #502 dodgerblue
> color #503 dodgerblue
> color #504 #00b305ff
> color #505 #00b305ff
> color #506 #f15839ff
> select #1.42/D
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 #507
---
Chain | Description
A | No description available
> matchmaker #507 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 D (#1.42) with AF3 E1 1-421.pdb, chain A (#507),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #508
---
Chain | Description
A | No description available
> matchmaker #508 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 D (#1.42) with AF3 E1 422-461.pdb, chain A (#508),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.42/E
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 #509
---
Chain | Description
B | No description available
> matchmaker #509 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 E (#1.42) with AF3 E2 1-352.pdb, chain B (#509),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #510
---
Chain | Description
B | No description available
> matchmaker #510 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 E (#1.42) with AF3 E2 353-438.pdb, chain B (#510),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.42/F
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 #511
---
Chain | Description
A | No description available
> matchmaker #511 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 F (#1.42) with AF3 CA.pdb, chain A (#511),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #507 dodgerblue
> color #508 dodgerblue
> color #509 #00b305ff
> color #510 #00b305ff
> color #511 #f15839ff
> select #1.43/D
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 #512
---
Chain | Description
A | No description available
> matchmaker #512 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 D (#1.43) with AF3 E1 1-421.pdb, chain A (#512),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #513
---
Chain | Description
A | No description available
> matchmaker #513 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 D (#1.43) with AF3 E1 422-461.pdb, chain A (#513),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.43/E
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 #514
---
Chain | Description
B | No description available
> matchmaker #514 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 E (#1.43) with AF3 E2 1-352.pdb, chain B (#514),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #515
---
Chain | Description
B | No description available
> matchmaker #515 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 E (#1.43) with AF3 E2 353-438.pdb, chain B (#515),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.43/F
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 #516
---
Chain | Description
A | No description available
> matchmaker #516 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 F (#1.43) with AF3 CA.pdb, chain A (#516),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #512 dodgerblue
> color #513 dodgerblue
> color #515 #00b305ff
> color #516 #f15839ff
> select #1.44/D
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 #517
---
Chain | Description
A | No description available
> matchmaker #517 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 D (#1.44) with AF3 E1 1-421.pdb, chain A (#517),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #518
---
Chain | Description
A | No description available
> matchmaker #518 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 D (#1.44) with AF3 E1 422-461.pdb, chain A (#518),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.44/E
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 #519
---
Chain | Description
B | No description available
> matchmaker #519 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 E (#1.44) with AF3 E2 1-352.pdb, chain B (#519),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #520
---
Chain | Description
B | No description available
> matchmaker #520 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 E (#1.44) with AF3 E2 353-438.pdb, chain B (#520),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.44/F
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 #521
---
Chain | Description
A | No description available
> matchmaker #521 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 F (#1.44) with AF3 CA.pdb, chain A (#521),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #517 dodgerblue
> color #518 dodgerblue
> color #519 #00b305ff
> color #520 #00b305ff
> color #521 #f15839ff
> select #1.45/D
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 #522
---
Chain | Description
A | No description available
> matchmaker #522 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 D (#1.45) with AF3 E1 1-421.pdb, chain A (#522),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #523
---
Chain | Description
A | No description available
> matchmaker #523 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 D (#1.45) with AF3 E1 422-461.pdb, chain A (#523),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.45/E
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 #524
---
Chain | Description
B | No description available
> matchmaker #524 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 E (#1.45) with AF3 E2 1-352.pdb, chain B (#524),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #525
---
Chain | Description
B | No description available
> matchmaker #525 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 E (#1.45) with AF3 E2 353-438.pdb, chain B (#525),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.45/F
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 #526
---
Chain | Description
A | No description available
> matchmaker #526 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 F (#1.45) with AF3 CA.pdb, chain A (#526),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #522 dodgerblue
> color #523 dodgerblue
> color #524 #00b305ff
> color #525 #00b305ff
> color #526 #f15839ff
> select #1.46/D
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 #527
---
Chain | Description
A | No description available
> matchmaker #527 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 D (#1.46) with AF3 E1 1-421.pdb, chain A (#527),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #528
---
Chain | Description
A | No description available
> matchmaker #528 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 D (#1.46) with AF3 E1 422-461.pdb, chain A (#528),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.46/E
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 #529
---
Chain | Description
B | No description available
> matchmaker #529 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 E (#1.46) with AF3 E2 1-352.pdb, chain B (#529),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #530
---
Chain | Description
B | No description available
> matchmaker #530 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 E (#1.46) with AF3 E2 353-438.pdb, chain B (#530),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.46/F
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 #531
---
Chain | Description
A | No description available
> matchmaker #531 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 F (#1.46) with AF3 CA.pdb, chain A (#531),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #527 dodgerblue
> color #528 dodgerblue
> color #529 #00b305ff
> color #530 #00b305ff
> color #531 #f15839ff
> select #1.47/D
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 #532
---
Chain | Description
A | No description available
> matchmaker #532 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 D (#1.47) with AF3 E1 1-421.pdb, chain A (#532),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #533
---
Chain | Description
A | No description available
> matchmaker #533 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 D (#1.47) with AF3 E1 422-461.pdb, chain A (#533),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.47/E
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 #534
---
Chain | Description
B | No description available
> matchmaker #534 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 E (#1.47) with AF3 E2 1-352.pdb, chain B (#534),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #535
---
Chain | Description
B | No description available
> matchmaker #535 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 E (#1.47) with AF3 E2 353-438.pdb, chain B (#535),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.47/F
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 #536
---
Chain | Description
A | No description available
> matchmaker #536 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 F (#1.47) with AF3 CA.pdb, chain A (#536),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #532 dodgerblue
> color #533 dodgerblue
> color #534 #00b305ff
> color #535 #00b305ff
> color #536 #f15839ff
> select #1.48/D
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 #537
---
Chain | Description
A | No description available
> matchmaker #537 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 D (#1.48) with AF3 E1 1-421.pdb, chain A (#537),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #538
---
Chain | Description
A | No description available
> matchmaker #538 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 D (#1.48) with AF3 E1 422-461.pdb, chain A (#538),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.48/E
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 #539
---
Chain | Description
B | No description available
> matchmaker #539 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 E (#1.48) with AF3 E2 1-352.pdb, chain B (#539),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #540
---
Chain | Description
B | No description available
> matchmaker #540 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 E (#1.48) with AF3 E2 353-438.pdb, chain B (#540),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.48/F
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 #541
---
Chain | Description
A | No description available
> matchmaker #541 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 F (#1.48) with AF3 CA.pdb, chain A (#541),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #537 dodgerblue
> color #538 dodgerblue
> color #539 #00b305ff
> color #540 #00b305ff
> color #541 #f15839ff
> select #1.49/D
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 #542
---
Chain | Description
A | No description available
> matchmaker #542 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 D (#1.49) with AF3 E1 1-421.pdb, chain A (#542),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #543
---
Chain | Description
A | No description available
> matchmaker #543 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 D (#1.49) with AF3 E1 422-461.pdb, chain A (#543),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.49/E
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 #544
---
Chain | Description
B | No description available
> matchmaker #544 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 E (#1.49) with AF3 E2 1-352.pdb, chain B (#544),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #545
---
Chain | Description
B | No description available
> matchmaker #545 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 E (#1.49) with AF3 E2 353-438.pdb, chain B (#545),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.49/F
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 #546
---
Chain | Description
A | No description available
> matchmaker #546 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 F (#1.49) with AF3 CA.pdb, chain A (#546),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #542 dodgerblue
> color #543 dodgerblue
> color #544 #00b305ff
> color #545 #00b305ff
> color #546 #f15839ff
> select #1.50/D
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 #547
---
Chain | Description
A | No description available
> matchmaker #547 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 D (#1.50) with AF3 E1 1-421.pdb, chain A (#547),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #548
---
Chain | Description
A | No description available
> matchmaker #548 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 D (#1.50) with AF3 E1 422-461.pdb, chain A (#548),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.50/E
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 #549
---
Chain | Description
B | No description available
> matchmaker #549 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 E (#1.50) with AF3 E2 1-352.pdb, chain B (#549),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #550
---
Chain | Description
B | No description available
> matchmaker #550 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 E (#1.50) with AF3 E2 353-438.pdb, chain B (#550),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.50/F
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 #551
---
Chain | Description
A | No description available
> matchmaker #551 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 F (#1.50) with AF3 CA.pdb, chain A (#551),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #547 dodgerblue
> color #548 dodgerblue
> color #549 #00b305ff
> color #550 #00b305ff
> color #551 #f15839ff
> save "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" includeMaps true
> hide #502-551 models
> show #547 models
> show #548 models
> select #1.50/D
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
[Repeated 1 time(s)]
> hide #547 models
> hide #548 models
> select #1.51/D
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> show sel cartoons
> view
> open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
Chain information for AF3 E1 1-421.pdb #552
---
Chain | Description
A | No description available
> matchmaker #552 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 D (#1.51) with AF3 E1 1-421.pdb, chain A (#552),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #553
---
Chain | Description
A | No description available
> matchmaker #553 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 D (#1.51) with AF3 E1 422-461.pdb, chain A (#553),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.51/E
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 #554
---
Chain | Description
B | No description available
> matchmaker #554 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 E (#1.51) with AF3 E2 1-352.pdb, chain B (#554),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #555
---
Chain | Description
B | No description available
> matchmaker #555 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 E (#1.51) with AF3 E2 353-438.pdb, chain B (#555),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.51/F
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 #556
---
Chain | Description
A | No description available
> matchmaker #556 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 F (#1.51) with AF3 CA.pdb, chain A (#556),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #552 dodgerblue
> color #553 dodgerblue
> color #554 #00b305ff
> color #555 #00b305ff
> color #556 #f15839ff
> select #1.52/D
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 #557
---
Chain | Description
A | No description available
> matchmaker #557 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 D (#1.52) with AF3 E1 1-421.pdb, chain A (#557),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #558
---
Chain | Description
A | No description available
> matchmaker #558 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 D (#1.52) with AF3 E1 422-461.pdb, chain A (#558),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.52/E
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 #559
---
Chain | Description
B | No description available
> matchmaker #559 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 E (#1.52) with AF3 E2 1-352.pdb, chain B (#559),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #560
---
Chain | Description
B | No description available
> matchmaker #560 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 E (#1.52) with AF3 E2 353-438.pdb, chain B (#560),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.52/F
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 #561
---
Chain | Description
A | No description available
> matchmaker #561 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 F (#1.52) with AF3 CA.pdb, chain A (#561),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #557 dodgerblue
> color #558 dodgerblue
> color #559 #00b305ff
> color #560 #00b305ff
> color #561 #f15839ff
> select #1.53/D
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> select #1.53/D
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 #562
---
Chain | Description
A | No description available
> matchmaker #562 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 D (#1.53) with AF3 E1 1-421.pdb, chain A (#562),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #563
---
Chain | Description
A | No description available
> matchmaker #563 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 D (#1.53) with AF3 E1 422-461.pdb, chain A (#563),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
Chain information for AF3 E2 1-352.pdb #564
---
Chain | Description
B | No description available
> select #1.53/E
3304 atoms, 3395 bonds, 423 residues, 1 model selected
> show sel cartoons
> matchmaker #564 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 E (#1.53) with AF3 E2 1-352.pdb, chain B (#564),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #565
---
Chain | Description
B | No description available
> matchmaker #565 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 E (#1.53) with AF3 E2 353-438.pdb, chain B (#565),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.53/F
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 #566
---
Chain | Description
A | No description available
> matchmaker #566 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 F (#1.53) with AF3 CA.pdb, chain A (#566),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #562 dodgerblue
> color #563 dodgerblue
> color #564 #00b305ff
> color #565 #00b305ff
> color #566 #f15839ff
> select #1.54/D
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 #567
---
Chain | Description
A | No description available
> matchmaker #567 to #1.53 & sel
No 'to' model specified
> matchmaker #567 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 D (#1.54) with AF3 E1 1-421.pdb, chain A (#567),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #568
---
Chain | Description
A | No description available
> matchmaker #568 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 D (#1.54) with AF3 E1 422-461.pdb, chain A (#568),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.54/E
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 #569
---
Chain | Description
B | No description available
> matchmaker #569 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 E (#1.54) with AF3 E2 1-352.pdb, chain B (#569),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #570
---
Chain | Description
B | No description available
> matchmaker #570 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 E (#1.54) with AF3 E2 353-438.pdb, chain B (#570),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.54/F
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 #571
---
Chain | Description
A | No description available
> matchmaker #571 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 F (#1.54) with AF3 CA.pdb, chain A (#571),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #567 dodgerblue
> color #568 dodgerblue
> color #569 #00b305ff
> color #570 #00b305ff
> color #571 #f15839ff
> select #1.55/D
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 #572
---
Chain | Description
A | No description available
> matchmaker #572 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 D (#1.55) with AF3 E1 1-421.pdb, chain A (#572),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #573
---
Chain | Description
A | No description available
> matchmaker #573 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 D (#1.55) with AF3 E1 422-461.pdb, chain A (#573),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.55/E
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 #574
---
Chain | Description
B | No description available
> matchmaker #574 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 E (#1.55) with AF3 E2 1-352.pdb, chain B (#574),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #575
---
Chain | Description
B | No description available
> matchmaker #575 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 E (#1.55) with AF3 E2 353-438.pdb, chain B (#575),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select #1.55/F
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 #576
---
Chain | Description
A | No description available
> matchmaker #576 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 F (#1.55) with AF3 CA.pdb, chain A (#576),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #572 dodgerblue
> color #573 dodgerblue
> color #574 #00b305ff
> color #575 #00b305ff
> color #576 #f15839ff
> select #1.56/D
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 #577
---
Chain | Description
A | No description available
> matchmaker #577 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 D (#1.56) with AF3 E1 1-421.pdb, chain A (#577),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #578
---
Chain | Description
A | No description available
> matchmaker #578 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 D (#1.56) with AF3 E1 422-461.pdb, chain A (#578),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.56/E
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 #579
---
Chain | Description
B | No description available
> matchmaker #579 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 E (#1.56) with AF3 E2 1-352.pdb, chain B (#579),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #580
---
Chain | Description
B | No description available
> matchmaker #580 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 E (#1.56) with AF3 E2 353-438.pdb, chain B (#580),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.56/F
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 #581
---
Chain | Description
A | No description available
> matchmaker #581 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 F (#1.56) with AF3 CA.pdb, chain A (#581),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #577 dodgerblue
> color #578 dodgerblue
> color #579 #00b305ff
> color #580 #00b305ff
> color #581 #f15839ff
> select #1.57/D
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 #582
---
Chain | Description
A | No description available
> matchmaker #582 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 D (#1.57) with AF3 E1 1-421.pdb, chain A (#582),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #583
---
Chain | Description
A | No description available
> matchmaker #583 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 D (#1.57) with AF3 E1 422-461.pdb, chain A (#583),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.57/E
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 #584
---
Chain | Description
B | No description available
> matchmaker #584 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 E (#1.57) with AF3 E2 1-352.pdb, chain B (#584),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #585
---
Chain | Description
B | No description available
> matchmaker #585 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 E (#1.57) with AF3 E2 353-438.pdb, chain B (#585),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.57/F
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 #586
---
Chain | Description
A | No description available
> matchmaker #586 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 F (#1.57) with AF3 CA.pdb, chain A (#586),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #582 dodgerblue
> color #583 dodgerblue
> color #584 #00b305ff
> color #585 #00b305ff
> color #586 #f15839ff
> select #1.58/D
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 #587
---
Chain | Description
A | No description available
> matchmaker #587 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 D (#1.58) with AF3 E1 1-421.pdb, chain A (#587),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #588
---
Chain | Description
A | No description available
> matchmaker #588 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 D (#1.58) with AF3 E1 422-461.pdb, chain A (#588),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel atoms
> hide sel cartoons
> select #1.58/E
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 #589
---
Chain | Description
B | No description available
> matchmaker #589 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 E (#1.58) with AF3 E2 1-352.pdb, chain B (#589),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #590
---
Chain | Description
B | No description available
> matchmaker #590 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 E (#1.58) with AF3 E2 353-438.pdb, chain B (#590),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.58/F
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 #591
---
Chain | Description
A | No description available
> matchmaker #591 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 F (#1.58) with AF3 CA.pdb, chain A (#591),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #587 dodgerblue
> color #588 dodgerblue
> color #589 #00b305ff
> color #590 #00b305ff
> color #591 #f15839ff
> select #1.59/D
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 #592
---
Chain | Description
A | No description available
> matchmaker #592 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 D (#1.59) with AF3 E1 1-421.pdb, chain A (#592),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #593
---
Chain | Description
A | No description available
> matchmaker #593 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 D (#1.59) with AF3 E1 422-461.pdb, chain A (#593),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.59/E
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 #594
---
Chain | Description
B | No description available
> matchmaker #594 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 E (#1.59) with AF3 E2 1-352.pdb, chain B (#594),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #595
---
Chain | Description
B | No description available
> matchmaker #595 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 E (#1.59) with AF3 E2 353-438.pdb, chain B (#595),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.59/F
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 #596
---
Chain | Description
A | No description available
> matchmaker #596 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 F (#1.59) with AF3 CA.pdb, chain A (#596),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel atoms
> hide sel cartoons
> color #592 dodgerblue
> color #593 dodgerblue
> color #594 #00b305ff
> color #595 #00b305ff
> color #596 #f15839ff
> select #1.60/D
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 #597
---
Chain | Description
A | No description available
> matchmaker #597 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 D (#1.60) with AF3 E1 1-421.pdb, chain A (#597),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
3.032)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #598
---
Chain | Description
A | No description available
> matchmaker #598 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 D (#1.60) with AF3 E1 422-461.pdb, chain A (#598),
sequence alignment score = 626.9
RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
2.916)
> hide sel cartoons
> select #1.60/E
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 #599
---
Chain | Description
B | No description available
> matchmaker #599 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 E (#1.60) with AF3 E2 1-352.pdb, chain B (#599),
sequence alignment score = 594.5
RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
6.147)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #600
---
Chain | Description
B | No description available
> matchmaker #600 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 E (#1.60) with AF3 E2 353-438.pdb, chain B (#600),
sequence alignment score = 340.2
RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
8.673)
> hide sel cartoons
> select #1.60/F
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 #601
---
Chain | Description
A | No description available
> matchmaker #601 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 F (#1.60) with AF3 CA.pdb, chain A (#601),
sequence alignment score = 335.3
RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.550)
> hide sel cartoons
> color #597 dodgerblue
> color #598 dodgerblue
> color #599 #00b305ff
> color #600 #00b305ff
> color #601 #f15839ff
> view sel
No displayed objects specified.
> view
> save "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" includeMaps true
> show #2-601 models
> view
> hide sel cartoons
> save /Users/Jean/Desktop/image1.png supersample 3
> hide #300 models
> show #300 models
> hide #299 models
> show #299 models
> hide #299 models
> show #299 models
> select
2871120 atoms, 2944244 bonds, 373800 residues, 661 models selected
> show sel cartoons
> hide #!1 models
> select subtract #1
962880 atoms, 985560 bonds, 127320 residues, 600 models selected
> select clear
> view
> hide #2-601 cartoons
> show #2-601 atoms
> style #2-601 sphere
Changed 962880 atom styles
> save /Users/Jean/Desktop/image1.png supersample 3
> view
> color #514 #00b305ff
> view
> hide #2-601 atoms
> show #2-601 cartoons
> save /Users/Jean/Desktop/image2.png supersample 3
> hide #2-601 cartoons
> select #1.1/G
3370 atoms, 3467 bonds, 442 residues, 1 model selected
> show #2-601 cartoons
> select clear
> hide #2-601 cartoons
> select clear
> select #1.1/G
3370 atoms, 3467 bonds, 442 residues, 1 model selected
> show #2-601 cartoons
> hide #2-601 models
> select #1.1/G
3370 atoms, 3467 bonds, 442 residues, 1 model selected
> view sel
No displayed objects specified.
> show #!1 models
> select ~sel & ##selected
28434 atoms, 29221 bonds, 3666 residues, 1 model selected
> select ~sel
2842686 atoms, 2915023 bonds, 370134 residues, 661 models selected
> hide sel & #1.1-60 cartoons
> select #1.1/G
3370 atoms, 3467 bonds, 442 residues, 1 model selected
> show sel cartoons
> ui mousemode right select
> select clear
> select #1.1/B:287
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1.1/G
3370 atoms, 3467 bonds, 442 residues, 1 model selected
> hide #1.1 models
> show #1.1 models
> hide #1.1 models
> show #1.1 models
> select add #1.1
31804 atoms, 32688 bonds, 4108 residues, 1 model selected
> select subtract #1.1
Nothing selected
> select #1.1/G
3370 atoms, 3467 bonds, 442 residues, 1 model selected
> select ~sel & ##selected
28434 atoms, 29221 bonds, 3666 residues, 1 model selected
> hide sel cartoons
> open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
Chain information for AF3 E1 1-421.pdb #602
---
Chain | Description
A | No description available
> view sel
No displayed objects specified.
> view
> matchmaker #602 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 (#602),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
3.020)
> select #1.1/G
3370 atoms, 3467 bonds, 442 residues, 1 model selected
> matchmaker #602 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 G (#1.1) with AF3 E1 1-421.pdb, chain A (#602),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #603
---
Chain | Description
A | No description available
> matchmaker #603 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 G (#1.1) with AF3 E1 422-461.pdb, chain A (#603),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.1/H
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 #604
---
Chain | Description
B | No description available
> matchmaker #603 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 H (#1.1) with AF3 E1 422-461.pdb, chain A (#603),
sequence alignment score = 9.2
RMSD between 6 pruned atom pairs is 0.871 angstroms; (across all 11 pairs:
3.614)
> select #1.1/G
3370 atoms, 3467 bonds, 442 residues, 1 model selected
> show sel cartoons
> matchmaker #603 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 G (#1.1) with AF3 E1 422-461.pdb, chain A (#603),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> matchmaker #604 to #1.2 & sel
No 'to' model specified
> matchmaker #604 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 G (#1.1) with AF3 E2 1-352.pdb, chain B (#604),
sequence alignment score = 71.8
RMSD between 4 pruned atom pairs is 1.398 angstroms; (across all 265 pairs:
48.114)
> select #1.1/H
3304 atoms, 3400 bonds, 423 residues, 1 model selected
> matchmaker #604 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 H (#1.1) with AF3 E2 1-352.pdb, chain B (#604),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #605
---
Chain | Description
B | No description available
> matchmaker #605 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 H (#1.1) with AF3 E2 353-438.pdb, chain B (#605),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.150)
> select #1.1/H
3304 atoms, 3400 bonds, 423 residues, 1 model selected
> show sel cartoons
[Repeated 1 time(s)]
> select #1.1/H
3304 atoms, 3400 bonds, 423 residues, 1 model selected
> select #1.1/H
3304 atoms, 3400 bonds, 423 residues, 1 model selected
> show sel cartoons
> show sel atoms
> hide sel cartoons
> hide sel atoms
> select #1.1/G
3370 atoms, 3467 bonds, 442 residues, 1 model selected
> hide sel cartoons
> select #1.1/I
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 #606
---
Chain | Description
A | No description available
> matchmaker #606 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 I (#1.1) with AF3 CA.pdb, chain A (#606), sequence
alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #602 dodgerblue
> color #603 dodgerblue
> color #604 #00b305ff
> color #605 #00b305ff
> color #606 #f15839ff
> save "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" includeMaps true
——— End of log from Tue Jul 16 18:02:55 2024 ———
opened ChimeraX session
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select #1.2/G
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 #607
---
Chain | Description
A | No description available
> matchmaker #607 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 G (#1.2) with AF3 E1 1-421.pdb, chain A (#607),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #608
---
Chain | Description
A | No description available
> matchmaker #608 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 G (#1.2) with AF3 E1 422-461.pdb, chain A (#608),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> select #1.2/H
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 #609
---
Chain | Description
B | No description available
> matchmaker #609 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 H (#1.2) with AF3 E2 1-352.pdb, chain B (#609),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #610
---
Chain | Description
B | No description available
> matchmaker #610 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 H (#1.2) with AF3 E2 353-438.pdb, chain B (#610),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> select #1.2/I
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 #611
---
Chain | Description
A | No description available
> matchmaker #611 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 I (#1.2) with AF3 CA.pdb, chain A (#611), sequence
alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #607 dodgerblue
> color #608 dodgerblue
> color #609 #00b305ff
> color #610 #00b305ff
> color #611 #f15839ff
> select #1.2/G
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> hide sel cartoons
> select #1.3/G
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 #612
---
Chain | Description
A | No description available
> matchmaker #612 to #1.2 & sel
No 'to' model specified
> matchmaker #612 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 G (#1.3) with AF3 E1 1-421.pdb, chain A (#612),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> matchmaker #612 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 G (#1.3) with AF3 E1 1-421.pdb, chain A (#612),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #613
---
Chain | Description
A | No description available
> matchmaker #613 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 G (#1.3) with AF3 E1 422-461.pdb, chain A (#613),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.3/H
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 #614
---
Chain | Description
B | No description available
> matchmaker #614 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 H (#1.3) with AF3 E2 1-352.pdb, chain B (#614),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #615
---
Chain | Description
B | No description available
> matchmaker #615 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 H (#1.3) with AF3 E2 353-438.pdb, chain B (#615),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> select #1.3/I
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 #616
---
Chain | Description
A | No description available
> matchmaker #616 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 I (#1.3) with AF3 CA.pdb, chain A (#616), sequence
alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #612 dodgerblue
> color #613 dodgerblue
> color #614 #00b305ff
> color #615 #00b305ff
> color #616 #f15839ff
> select #1.4/G
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> select #1.3/H
3304 atoms, 3395 bonds, 423 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> select #1.4/G
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 #617
---
Chain | Description
A | No description available
> matchmaker #617 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 G (#1.4) with AF3 E1 1-421.pdb, chain A (#617),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> hide sel cartoons
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #618
---
Chain | Description
A | No description available
> matchmaker #618 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 G (#1.4) with AF3 E1 422-461.pdb, chain A (#618),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.4/H
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 #619
---
Chain | Description
B | No description available
> matchmaker #619 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 H (#1.4) with AF3 E2 1-352.pdb, chain B (#619),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #620
---
Chain | Description
B | No description available
> matchmaker #620 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 H (#1.4) with AF3 E2 353-438.pdb, chain B (#620),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.937 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> select #1.4/I
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 #621
---
Chain | Description
A | No description available
> matchmaker #621 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 I (#1.4) with AF3 CA.pdb, chain A (#621), sequence
alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #617 dodgerblue
> color #618 dodgerblue
> color #619 #00b305ff
> color #620 #00b305ff
> color #621 #f15839ff
> select #1.5/G
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 #622
---
Chain | Description
A | No description available
> matchmaker #622 to #1.4 & sel
No 'to' model specified
> matchmaker #622 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 G (#1.5) with AF3 E1 1-421.pdb, chain A (#622),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #623
---
Chain | Description
A | No description available
> matchmaker #623 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 G (#1.5) with AF3 E1 422-461.pdb, chain A (#623),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.5/H
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 #624
---
Chain | Description
B | No description available
> matchmaker #624 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 H (#1.5) with AF3 E2 1-352.pdb, chain B (#624),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #625
---
Chain | Description
B | No description available
> hide sel cartoons
> show sel cartoons
> matchmaker #625 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 H (#1.5) with AF3 E2 353-438.pdb, chain B (#625),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.150)
> select #1.5/I
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 #626
---
Chain | Description
A | No description available
> matchmaker #626 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 I (#1.5) with AF3 CA.pdb, chain A (#626), sequence
alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #622 dodgerblue
> color #623 dodgerblue
> color #624 #00b305ff
> color #625 #00b305ff
> color #626 #f15839ff
> select #1.5/H
3304 atoms, 3395 bonds, 423 residues, 1 model selected
> hide sel cartoons
> select #1.6/G
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 #627
---
Chain | Description
A | No description available
> matchmaker #627 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 G (#1.6) with AF3 E1 1-421.pdb, chain A (#627),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #628
---
Chain | Description
A | No description available
> matchmaker #628 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 G (#1.6) with AF3 E1 422-461.pdb, chain A (#628),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.6/H
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 #629
---
Chain | Description
B | No description available
> matchmaker #629 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 H (#1.6) with AF3 E2 1-352.pdb, chain B (#629),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #630
---
Chain | Description
B | No description available
> matchmaker #630 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 H (#1.6) with AF3 E2 353-438.pdb, chain B (#630),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> select #1.6/I
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 #631
---
Chain | Description
A | No description available
> matchmaker #631 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 I (#1.6) with AF3 CA.pdb, chain A (#631), sequence
alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #627 dodgerblue
> color #628 dodgerblue
> color #629 #00b305ff
> color #630 #00b305ff
> color #631 #f15839ff
> select #1.7/G
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 #632
---
Chain | Description
A | No description available
> matchmaker #632 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 G (#1.7) with AF3 E1 1-421.pdb, chain A (#632),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #633
---
Chain | Description
A | No description available
> matchmaker #633 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 G (#1.7) with AF3 E1 422-461.pdb, chain A (#633),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.7/H
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 #634
---
Chain | Description
B | No description available
> matchmaker #634 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 H (#1.7) with AF3 E2 1-352.pdb, chain B (#634),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #635
---
Chain | Description
B | No description available
> matchmaker #635 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 H (#1.7) with AF3 E2 353-438.pdb, chain B (#635),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> select #1.7/I
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 #636
---
Chain | Description
A | No description available
> matchmaker #636 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 I (#1.7) with AF3 CA.pdb, chain A (#636), sequence
alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #632 dodgerblue
> color #633 dodgerblue
> color #634 #00b305ff
> color #635 #00b305ff
> color #636 #f15839ff
> select #1.8/G
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 #637
---
Chain | Description
A | No description available
> matchmaker #637 to #1.7 & sel
No 'to' model specified
> matchmaker #637 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 G (#1.8) with AF3 E1 1-421.pdb, chain A (#637),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #638
---
Chain | Description
A | No description available
> matchmaker #638 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 G (#1.8) with AF3 E1 422-461.pdb, chain A (#638),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.8/H
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 #639
---
Chain | Description
B | No description available
> matchmaker #639 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 H (#1.8) with AF3 E2 1-352.pdb, chain B (#639),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #640
---
Chain | Description
B | No description available
> matchmaker #640 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 H (#1.8) with AF3 E2 353-438.pdb, chain B (#640),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> select #1.8/I
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 #641
---
Chain | Description
A | No description available
> matchmaker #641 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 I (#1.8) with AF3 CA.pdb, chain A (#641), sequence
alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #637 dodgerblue
> color #638 dodgerblue
> color #639 #00b305ff
> color #640 #00b305ff
> color #641 #f15839ff
> select #1.9/G
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 #642
---
Chain | Description
A | No description available
> matchmaker #642 to #1.8 & sel
No 'to' model specified
> matchmaker #642 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 G (#1.9) with AF3 E1 1-421.pdb, chain A (#642),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #643
---
Chain | Description
A | No description available
> matchmaker #643 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 G (#1.9) with AF3 E1 422-461.pdb, chain A (#643),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.9/H
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 #644
---
Chain | Description
B | No description available
> matchmaker #644 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 H (#1.9) with AF3 E2 1-352.pdb, chain B (#644),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #645
---
Chain | Description
B | No description available
> matchmaker #645 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 H (#1.9) with AF3 E2 353-438.pdb, chain B (#645),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> select #1.9/I
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 #646
---
Chain | Description
A | No description available
> matchmaker #646 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 I (#1.9) with AF3 CA.pdb, chain A (#646), sequence
alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #642 dodgerblue
> color #643 dodgerblue
> color #644 #00b305ff
> color #645 #00b305ff
> color #646 #f15839ff
> select #1.10/G
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 #647
---
Chain | Description
A | No description available
> matchmaker #647 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 G (#1.10) with AF3 E1 1-421.pdb, chain A (#647),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #648
---
Chain | Description
A | No description available
> matchmaker #648 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 G (#1.10) with AF3 E1 422-461.pdb, chain A (#648),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.996)
> hide sel cartoons
> select #1.10/H
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 #649
---
Chain | Description
B | No description available
> matchmaker #649 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 H (#1.10) with AF3 E2 1-352.pdb, chain B (#649),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #650
---
Chain | Description
B | No description available
> matchmaker #650 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 H (#1.10) with AF3 E2 353-438.pdb, chain B (#650),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.151)
> hide sel cartoons
> select #1.10/I
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 #651
---
Chain | Description
A | No description available
> matchmaker #651 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 I (#1.10) with AF3 CA.pdb, chain A (#651),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #647 dodgerblue
> color #648 dodgerblue
> color #649 #00b305ff
> color #650 #00b305ff
> color #651 #f15839ff
> save "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" includeMaps true
> hide #602 models
> hide #603 models
> hide #604 models
> hide #605 models
> hide #606 models
> hide #607 models
> hide #608 models
> hide #609 models
> hide #610 models
> hide #611 models
> hide #612 models
> hide #613 models
> hide #614 models
> hide #615 models
> hide #616 models
> hide #617 models
> hide #618 models
> hide #619 models
> hide #620 models
> hide #621 models
> hide #622 models
> hide #623 models
> hide #624 models
> hide #625 models
> hide #626 models
> hide #627 models
> hide #628 models
> hide #629 models
> hide #630 models
> hide #631 models
> hide #632 models
> hide #633 models
> hide #634 models
> hide #635 models
> hide #636 models
> hide #637 models
> hide #638 models
> hide #639 models
> hide #640 models
> hide #641 models
> hide #642 models
> hide #643 models
> hide #644 models
> hide #645 models
> hide #646 models
> hide #647 models
> hide #648 models
> hide #649 models
> hide #650 models
> hide #651 models
> select #1.11/G
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 #652
---
Chain | Description
A | No description available
> matchmaker #652 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 G (#1.11) with AF3 E1 1-421.pdb, chain A (#652),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> view
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #653
---
Chain | Description
A | No description available
> matchmaker #653 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 G (#1.11) with AF3 E1 422-461.pdb, chain A (#653),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.11/H
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 #654
---
Chain | Description
B | No description available
> matchmaker #654 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 H (#1.11) with AF3 E2 1-352.pdb, chain B (#654),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #655
---
Chain | Description
B | No description available
> matchmaker #655 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 H (#1.11) with AF3 E2 353-438.pdb, chain B (#655),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.151)
> hide sel cartoons
> select #1.11/I
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 #656
---
Chain | Description
A | No description available
> matchmaker #656 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 I (#1.11) with AF3 CA.pdb, chain A (#656),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #652 dodgerblue
> color #653 dodgerblue
> color #654 #00b305ff
> color #655 #00b305ff
> color #656 #f15839ff
> select #1.12/G
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 #657
---
Chain | Description
A | No description available
> matchmaker #657 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 G (#1.12) with AF3 E1 1-421.pdb, chain A (#657),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #658
---
Chain | Description
A | No description available
> matchmaker #658 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 G (#1.12) with AF3 E1 422-461.pdb, chain A (#658),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.12/H
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 #659
---
Chain | Description
B | No description available
> matchmaker #659 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 H (#1.12) with AF3 E2 1-352.pdb, chain B (#659),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #660
---
Chain | Description
B | No description available
> matchmaker #660 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 H (#1.12) with AF3 E2 353-438.pdb, chain B (#660),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.937 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> select #1.12/I
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 #661
---
Chain | Description
A | No description available
> matchmaker #661 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 I (#1.12) with AF3 CA.pdb, chain A (#661),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #657 dodgerblue
> color #658 dodgerblue
> color #659 #00b305ff
> color #660 #00b305ff
> color #661 #f15839ff
> select #1.13/G
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 #662
---
Chain | Description
A | No description available
> matchmaker #662 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 G (#1.13) with AF3 E1 1-421.pdb, chain A (#662),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #663
---
Chain | Description
A | No description available
> matchmaker #663 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 G (#1.13) with AF3 E1 422-461.pdb, chain A (#663),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.13/I
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 #664
---
Chain | Description
A | No description available
> matchmaker #664 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 I (#1.13) with AF3 CA.pdb, chain A (#664),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> select #1.13/H
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 #665
---
Chain | Description
B | No description available
> matchmaker #665 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 H (#1.13) with AF3 E2 1-352.pdb, chain B (#665),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #666
---
Chain | Description
B | No description available
> matchmaker #666 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 H (#1.13) with AF3 E2 353-438.pdb, chain B (#666),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> close #664
> select #1.13/I
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 #664
---
Chain | Description
A | No description available
> close #666
> close #665
> close #664
> hide sel cartoons
> select #1.13/H
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 #664
---
Chain | Description
B | No description available
> matchmaker #664 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 H (#1.13) with AF3 E2 1-352.pdb, chain B (#664),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #665
---
Chain | Description
B | No description available
> matchmaker #665 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 H (#1.13) with AF3 E2 353-438.pdb, chain B (#665),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> select #1.13/I
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 #666
---
Chain | Description
A | No description available
> matchmaker #666 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 I (#1.13) with AF3 CA.pdb, chain A (#666),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #662 dodgerblue
> color #663 dodgerblue
> color #664 #00b305ff
> color #665 #00b305ff
> color #666 #f15839ff
> select #1.14/G
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 #667
---
Chain | Description
A | No description available
> matchmaker #667 to #1.13 & sel
No 'to' model specified
> matchmaker #667 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 G (#1.14) with AF3 E1 1-421.pdb, chain A (#667),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #668
---
Chain | Description
A | No description available
> matchmaker #668 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 G (#1.14) with AF3 E1 422-461.pdb, chain A (#668),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.13/H
3304 atoms, 3395 bonds, 423 residues, 1 model selected
> show sel cartoons
> select #1.14/H
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 #669
---
Chain | Description
B | No description available
> matchmaker #669 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 H (#1.14) with AF3 E2 1-352.pdb, chain B (#669),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #670
---
Chain | Description
B | No description available
> matchmaker #670 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 H (#1.14) with AF3 E2 353-438.pdb, chain B (#670),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> select #1.14/I
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 #671
---
Chain | Description
A | No description available
> matchmaker #671 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 I (#1.14) with AF3 CA.pdb, chain A (#671),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #667 dodgerblue
> color #668 dodgerblue
> color #669 #00b305ff
> color #670 #00b305ff
> color #671 #f15839ff
> select #1.13/H
3304 atoms, 3395 bonds, 423 residues, 1 model selected
> hide sel cartoons
> select #1.14/G
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> select #1.15/G
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 #672
---
Chain | Description
A | No description available
> matchmaker #672 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 G (#1.15) with AF3 E1 1-421.pdb, chain A (#672),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #673
---
Chain | Description
A | No description available
> matchmaker #673 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 G (#1.15) with AF3 E1 422-461.pdb, chain A (#673),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.15/H
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 #674
---
Chain | Description
B | No description available
> matchmaker #674 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 H (#1.15) with AF3 E2 1-352.pdb, chain B (#674),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #675
---
Chain | Description
B | No description available
> matchmaker #675 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 H (#1.15) with AF3 E2 353-438.pdb, chain B (#675),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> select #1.15/I
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 #676
---
Chain | Description
A | No description available
> matchmaker #676 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 I (#1.15) with AF3 CA.pdb, chain A (#676),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #672 dodgerblue
> color #673 dodgerblue
> color #674 #00b305ff
> color #675 #00b305ff
> color #676 #f15839ff
> select #1.16/G
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 #677
---
Chain | Description
A | No description available
> matchmaker #677 to #1.15 & sel
No 'to' model specified
> matchmaker #677 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 G (#1.16) with AF3 E1 1-421.pdb, chain A (#677),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #678
---
Chain | Description
A | No description available
> matchmaker #678 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 G (#1.16) with AF3 E1 422-461.pdb, chain A (#678),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.16/H
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 #679
---
Chain | Description
B | No description available
> matchmaker #679 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 H (#1.16) with AF3 E2 1-352.pdb, chain B (#679),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #680
---
Chain | Description
B | No description available
> matchmaker #680 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 H (#1.16) with AF3 E2 353-438.pdb, chain B (#680),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.937 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> select #1.16/I
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 #681
---
Chain | Description
A | No description available
> matchmaker #681 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 I (#1.16) with AF3 CA.pdb, chain A (#681),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #677 dodgerblue
> color #678 dodgerblue
> color #679 #00b305ff
> color #680 dodgerblue
> color #680 #00b305ff
> color #681 #f15839ff
> select #1.17/G
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 #682
---
Chain | Description
A | No description available
> matchmaker #682 to #1.16 & sel
No 'to' model specified
> matchmaker #682 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 G (#1.17) with AF3 E1 1-421.pdb, chain A (#682),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #683
---
Chain | Description
A | No description available
> matchmaker #683 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 G (#1.17) with AF3 E1 422-461.pdb, chain A (#683),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.17/H
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 #684
---
Chain | Description
B | No description available
> matchmaker #684 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 H (#1.17) with AF3 E2 1-352.pdb, chain B (#684),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> hide sel cartoons
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #685
---
Chain | Description
B | No description available
> matchmaker #685 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 H (#1.17) with AF3 E2 353-438.pdb, chain B (#685),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.150)
> select #1.17/I
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 #686
---
Chain | Description
A | No description available
> matchmaker #686 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 I (#1.17) with AF3 CA.pdb, chain A (#686),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #682 dodgerblue
> color #683 dodgerblue
> color #684 #00b305ff
> color #685 #00b305ff
> color #686 #f15839ff
> select #1.18/G
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 #687
---
Chain | Description
A | No description available
> matchmaker #687 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 G (#1.18) with AF3 E1 1-421.pdb, chain A (#687),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #688
---
Chain | Description
A | No description available
> matchmaker #688 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 G (#1.18) with AF3 E1 422-461.pdb, chain A (#688),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.18/H
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 #689
---
Chain | Description
B | No description available
> matchmaker #689 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 H (#1.18) with AF3 E2 1-352.pdb, chain B (#689),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #690
---
Chain | Description
B | No description available
> matchmaker #690 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 H (#1.18) with AF3 E2 353-438.pdb, chain B (#690),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> select #1.18/I
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 #691
---
Chain | Description
A | No description available
> matchmaker #691 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 I (#1.18) with AF3 CA.pdb, chain A (#691),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #687 dodgerblue
> color #688 dodgerblue
> color #689 #00b305ff
> color #690 #00b305ff
> color #691 #f15839ff
> select #1.19/G
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 #692
---
Chain | Description
A | No description available
> matchmaker #692 to #1.18 & sel
No 'to' model specified
> matchmaker #692 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 G (#1.19) with AF3 E1 1-421.pdb, chain A (#692),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #693
---
Chain | Description
A | No description available
> matchmaker #693 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 G (#1.19) with AF3 E1 422-461.pdb, chain A (#693),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.19/H
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 #694
---
Chain | Description
B | No description available
> matchmaker #694 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 H (#1.19) with AF3 E2 1-352.pdb, chain B (#694),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #695
---
Chain | Description
B | No description available
> matchmaker #695 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 H (#1.19) with AF3 E2 353-438.pdb, chain B (#695),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> select #1.19/I
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 #696
---
Chain | Description
A | No description available
> matchmaker #696 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 I (#1.19) with AF3 CA.pdb, chain A (#696),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #692 dodgerblue
> color #693 dodgerblue
> color #694 #00b305ff
> color #695 #00b305ff
> color #696 #f15839ff
> select #1.20/G
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 #697
---
Chain | Description
A | No description available
> matchmaker #697 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 G (#1.20) with AF3 E1 1-421.pdb, chain A (#697),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #698
---
Chain | Description
A | No description available
> matchmaker #698 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 G (#1.20) with AF3 E1 422-461.pdb, chain A (#698),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.20/H
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 #699
---
Chain | Description
B | No description available
> matchmaker #699 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 H (#1.20) with AF3 E2 1-352.pdb, chain B (#699),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #700
---
Chain | Description
B | No description available
> matchmaker #700 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 H (#1.20) with AF3 E2 353-438.pdb, chain B (#700),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> select #1.20/I
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 #701
---
Chain | Description
A | No description available
> matchmaker #701 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 I (#1.20) with AF3 CA.pdb, chain A (#701),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #697 dodgerblue
> color #698 dodgerblue
> color #699 #00b305ff
> color #700 #00b305ff
> color #701 #f15839ff
> save "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" includeMaps true
> hide #652 models
> hide #653 models
> hide #654 models
> hide #655 models
> hide #656 models
> hide #657 models
> hide #658 models
> hide #660 models
> hide #661 models
> hide #659 models
> hide #662 models
> hide #663 models
> hide #664 models
> hide #665 models
> hide #666 models
> hide #667 models
> hide #668 models
> hide #669 models
> hide #670 models
> hide #671 models
> hide #672 models
> hide #673 models
> hide #674 models
> hide #675 models
> hide #676 models
> hide #677 models
> hide #678 models
> hide #679 models
> hide #680 models
> hide #681 models
> hide #682 models
> hide #683 models
> hide #684 models
> hide #685 models
> hide #686 models
> hide #687 models
> hide #688 models
> hide #689 models
> hide #690 models
> hide #691 models
> hide #692 models
> hide #693 models
> hide #694 models
> hide #695 models
> hide #696 models
> hide #697 models
> hide #698 models
> hide #699 models
> hide #700 models
> hide #701 models
> select #1.21/G
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> show sel cartoons
> view
> open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
Chain information for AF3 E1 1-421.pdb #702
---
Chain | Description
A | No description available
> matchmaker #702 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 G (#1.21) with AF3 E1 1-421.pdb, chain A (#702),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #703
---
Chain | Description
A | No description available
> matchmaker #703 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 G (#1.21) with AF3 E1 422-461.pdb, chain A (#703),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> select #1.21/H
3304 atoms, 3395 bonds, 423 residues, 1 model selected
> show sel cartoons
[Repeated 1 time(s)]
> open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
Chain information for AF3 E2 1-352.pdb #704
---
Chain | Description
B | No description available
> matchmaker #704 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 H (#1.21) with AF3 E2 1-352.pdb, chain B (#704),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #705
---
Chain | Description
B | No description available
> matchmaker #705 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 H (#1.21) with AF3 E2 353-438.pdb, chain B (#705),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> select #1.21/G
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> hide sel cartoons
> select #1.21/I
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 #706
---
Chain | Description
A | No description available
> matchmaker #706 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 I (#1.21) with AF3 CA.pdb, chain A (#706),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #702 dodgerblue
> color #703 dodgerblue
> color #704 #00b305ff
> color #705 #00b305ff
> color #706 #f15839ff
> select #1.22/G
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 #707
---
Chain | Description
A | No description available
> matchmaker #707 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 G (#1.22) with AF3 E1 1-421.pdb, chain A (#707),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #708
---
Chain | Description
A | No description available
> matchmaker #708 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 G (#1.22) with AF3 E1 422-461.pdb, chain A (#708),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.996)
> hide sel cartoons
> select #1.21/H
3304 atoms, 3395 bonds, 423 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> select #1.22/H
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 #709
---
Chain | Description
B | No description available
> matchmaker #709 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 H (#1.22) with AF3 E2 1-352.pdb, chain B (#709),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #710
---
Chain | Description
B | No description available
> matchmaker #710 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 H (#1.22) with AF3 E2 353-438.pdb, chain B (#710),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.151)
> hide sel cartoons
> select #1.22/I
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 #711
---
Chain | Description
A | No description available
> matchmaker #711 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 I (#1.22) with AF3 CA.pdb, chain A (#711),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #707 dodgerblue
> color #708 dodgerblue
> color #709 #00b305ff
> color #710 #00b305ff
> color #711 #f15839ff
> select #1.23/G
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 #712
---
Chain | Description
A | No description available
> matchmaker #712 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 G (#1.23) with AF3 E1 1-421.pdb, chain A (#712),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #713
---
Chain | Description
A | No description available
> matchmaker #713 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 G (#1.23) with AF3 E1 422-461.pdb, chain A (#713),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.23/H
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 #714
---
Chain | Description
B | No description available
> matchmaker #714 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 H (#1.23) with AF3 E2 1-352.pdb, chain B (#714),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #715
---
Chain | Description
B | No description available
> matchmaker #715 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 H (#1.23) with AF3 E2 353-438.pdb, chain B (#715),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> select #1.23/I
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 #716
---
Chain | Description
A | No description available
> matchmaker #716 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 I (#1.23) with AF3 CA.pdb, chain A (#716),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #712 dodgerblue
> color #713 dodgerblue
> color #714 #00b305ff
> color #715 #00b305ff
> color #716 #f15839ff
> select #1.24/G
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 #717
---
Chain | Description
A | No description available
> matchmaker #717 to #1.23 & sel
No 'to' model specified
> matchmaker #717 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 G (#1.24) with AF3 E1 1-421.pdb, chain A (#717),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #718
---
Chain | Description
A | No description available
> matchmaker #718 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 G (#1.24) with AF3 E1 422-461.pdb, chain A (#718),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.24/H
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 #719
---
Chain | Description
B | No description available
> matchmaker #719 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 H (#1.24) with AF3 E2 1-352.pdb, chain B (#719),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #720
---
Chain | Description
B | No description available
> matchmaker #720 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 H (#1.24) with AF3 E2 353-438.pdb, chain B (#720),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> select #1.24/I
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 #721
---
Chain | Description
A | No description available
> matchmaker #721 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 I (#1.24) with AF3 CA.pdb, chain A (#721),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #717 dodgerblue
> color #718 dodgerblue
> color #719 #00b305ff
> color #720 #00b305ff
> color #721 #f15839ff
> select #1.25/G
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 #722
---
Chain | Description
A | No description available
> matchmaker #722 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 G (#1.25) with AF3 E1 1-421.pdb, chain A (#722),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #723
---
Chain | Description
A | No description available
> matchmaker #723 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 G (#1.25) with AF3 E1 422-461.pdb, chain A (#723),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.25/H
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 #724
---
Chain | Description
B | No description available
> matchmaker #724 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 H (#1.25) with AF3 E2 1-352.pdb, chain B (#724),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #725
---
Chain | Description
B | No description available
> matchmaker #725 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 H (#1.25) with AF3 E2 353-438.pdb, chain B (#725),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> select #1.25/I
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 #726
---
Chain | Description
A | No description available
> matchmaker #726 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 I (#1.25) with AF3 CA.pdb, chain A (#726),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #722 dodgerblue
> color #723 dodgerblue
> color #724 #00b305ff
> color #725 #00b305ff
> color #726 #f15839ff
> select #1.26/G
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 #727
---
Chain | Description
A | No description available
> matchmaker #727 to #1.25 & sel
No 'to' model specified
> matchmaker #727 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 G (#1.26) with AF3 E1 1-421.pdb, chain A (#727),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #728
---
Chain | Description
A | No description available
> matchmaker #728 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 G (#1.26) with AF3 E1 422-461.pdb, chain A (#728),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.26/H
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 #729
---
Chain | Description
B | No description available
> matchmaker #729 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 H (#1.26) with AF3 E2 1-352.pdb, chain B (#729),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #730
---
Chain | Description
B | No description available
> matchmaker #730 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 H (#1.26) with AF3 E2 353-438.pdb, chain B (#730),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> select #1.27/I
1277 atoms, 1305 bonds, 162 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> select #1.26/F
1277 atoms, 1305 bonds, 162 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> select #1.25/H
3304 atoms, 3395 bonds, 423 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> select #1.25/I
1277 atoms, 1305 bonds, 162 residues, 1 model selected
> select #1.26/I
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 #731
---
Chain | Description
A | No description available
> matchmaker #731 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 I (#1.26) with AF3 CA.pdb, chain A (#731),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #727 dodgerblue
> color #728 dodgerblue
> color #729 #00b305ff
> color #730 #00b305ff
> color #731 #f15839ff
> select #1.27/G
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 #732
---
Chain | Description
A | No description available
> matchmaker #732 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 G (#1.27) with AF3 E1 1-421.pdb, chain A (#732),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #733
---
Chain | Description
A | No description available
> matchmaker #733 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 G (#1.27) with AF3 E1 422-461.pdb, chain A (#733),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.27/H
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 #734
---
Chain | Description
B | No description available
> matchmaker #734 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 H (#1.27) with AF3 E2 1-352.pdb, chain B (#734),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #735
---
Chain | Description
B | No description available
> matchmaker #735 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 H (#1.27) with AF3 E2 353-438.pdb, chain B (#735),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.937 angstroms; (across all 84 pairs:
8.151)
> hide sel cartoons
> select #1.27/I
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 #736
---
Chain | Description
A | No description available
> matchmaker #736 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 I (#1.27) with AF3 CA.pdb, chain A (#736),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #732 dodgerblue
> color #733 dodgerblue
> color #734 #00b305ff
> color #735 #00b305ff
> color #736 #f15839ff
> select #1.28/G
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 #737
---
Chain | Description
A | No description available
> matchmaker #737 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 G (#1.28) with AF3 E1 1-421.pdb, chain A (#737),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #738
---
Chain | Description
A | No description available
> matchmaker #738 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 G (#1.28) with AF3 E1 422-461.pdb, chain A (#738),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.28/H
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 #739
---
Chain | Description
B | No description available
> matchmaker #739 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 H (#1.28) with AF3 E2 1-352.pdb, chain B (#739),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #740
---
Chain | Description
B | No description available
> matchmaker #740 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 H (#1.28) with AF3 E2 353-438.pdb, chain B (#740),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> select #1.28/I
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 #741
---
Chain | Description
A | No description available
> matchmaker #741 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 I (#1.28) with AF3 CA.pdb, chain A (#741),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #737 dodgerblue
> color #738 dodgerblue
> color #739 #00b305ff
> color #740 #00b305ff
> color #741 #f15839ff
> select #1.29/G
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 #742
---
Chain | Description
A | No description available
> matchmaker #742 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 G (#1.29) with AF3 E1 1-421.pdb, chain A (#742),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #743
---
Chain | Description
A | No description available
> matchmaker #743 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 G (#1.29) with AF3 E1 422-461.pdb, chain A (#743),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.29/H
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 #744
---
Chain | Description
B | No description available
> matchmaker #744 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 H (#1.29) with AF3 E2 1-352.pdb, chain B (#744),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #745
---
Chain | Description
B | No description available
> matchmaker #745 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 H (#1.29) with AF3 E2 353-438.pdb, chain B (#745),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> select #1.29/I
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 #746
---
Chain | Description
A | No description available
> matchmaker #746 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 I (#1.29) with AF3 CA.pdb, chain A (#746),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #742 dodgerblue
> color #743 dodgerblue
> color #744 #00b305ff
> color #745 #00b305ff
> color #746 #f15839ff
> select #1.30/G
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 #747
---
Chain | Description
A | No description available
> matchmaker #747 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 G (#1.30) with AF3 E1 1-421.pdb, chain A (#747),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #748
---
Chain | Description
A | No description available
> matchmaker #748 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 G (#1.30) with AF3 E1 422-461.pdb, chain A (#748),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.30/H
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 #749
---
Chain | Description
B | No description available
> matchmaker #749 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 H (#1.30) with AF3 E2 1-352.pdb, chain B (#749),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #750
---
Chain | Description
B | No description available
> matchmaker #750 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 H (#1.30) with AF3 E2 353-438.pdb, chain B (#750),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> select #1.30/H
3304 atoms, 3395 bonds, 423 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> select #1.30/I
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 #751
---
Chain | Description
A | No description available
> matchmaker #751 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 I (#1.30) with AF3 CA.pdb, chain A (#751),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #747 dodgerblue
> color #748 dodgerblue
> color #749 #00b305ff
> color #750 #00b305ff
> color #751 #f15839ff
> save "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" includeMaps true
——— End of log from Wed Jul 17 13:58:06 2024 ———
opened ChimeraX session
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> hide #702 models
> hide #703 models
> hide #704 models
> hide #705 models
> hide #706 models
> hide #707 models
> hide #708 models
> hide #709 models
> hide #710 models
> hide #711 models
> hide #712 models
> hide #713 models
> hide #714 models
> hide #715 models
> hide #716 models
> hide #717 models
> hide #718 models
> hide #719 models
> hide #720 models
> hide #721 models
> hide #722 models
> hide #723 models
> hide #724 models
> hide #725 models
> hide #726 models
> hide #727 models
> hide #728 models
> hide #729 models
> hide #730 models
> hide #731 models
> hide #732 models
> hide #733 models
> hide #734 models
> hide #735 models
> hide #736 models
> hide #737 models
> hide #738 models
> hide #739 models
> hide #740 models
> hide #741 models
> hide #742 models
> hide #743 models
> hide #744 models
> hide #745 models
> hide #746 models
> hide #747 models
> hide #748 models
> hide #749 models
> hide #750 models
> hide #751 models
> select #1.31/G
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> show sel cartoons
> view
> open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
Chain information for AF3 E1 1-421.pdb #752
---
Chain | Description
A | No description available
> matchmaker #752 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 A (#1.1) with AF3 E1 1-421.pdb, chain A (#752),
sequence alignment score = 1060.7
RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
3.020)
> matchmaker #752 to #1.1 & sel
No 'to' model specified
> matchmaker #752 to #1.1 & sel
No 'to' model specified
> close #752
> hide sel cartoons
> select #1.31/G
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 #752
---
Chain | Description
A | No description available
> matchmaker #752 to #1.1 & sel
No 'to' model specified
> matchmaker #752 & sel to #1.1 & sel
No 'to' model specified
> select #1.1/H
3304 atoms, 3400 bonds, 423 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> select #1.31/G
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> show sel cartoons
> matchmaker #752 to #1.1 & sel
No 'to' model specified
> show #751 models
> show #750 models
> show #749 models
> show #748 models
> show #747 models
> select #1.30/H
3304 atoms, 3395 bonds, 423 residues, 1 model selected
> hide sel cartoons
> show sel cartoons
> hide sel cartoons
> select #1.30/G
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> matchmaker #752 to #1.31 & sel
No 'to' model specified
> select #1.31/G
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> show sel cartoons
> matchmaker #752 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 G (#1.31) with AF3 E1 1-421.pdb, chain A (#752),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> view
> hide sel cartoons
> show sel cartoons
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #753
---
Chain | Description
A | No description available
> matchmaker #753 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 G (#1.31) with AF3 E1 422-461.pdb, chain A (#753),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.31/H
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 #754
---
Chain | Description
B | No description available
> matchmaker #754 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 H (#1.31) with AF3 E2 1-352.pdb, chain B (#754),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #755
---
Chain | Description
B | No description available
> matchmaker #755 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 H (#1.31) with AF3 E2 353-438.pdb, chain B (#755),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> select #1.31/I
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 #756
---
Chain | Description
A | No description available
> matchmaker #756 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 I (#1.31) with AF3 CA.pdb, chain A (#756),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> hide #747 models
> hide #748 models
> hide #749 models
> hide #750 models
> hide #751 models
> color #752 dodgerblue
> color #753 dodgerblue
> color #754 #00b305ff
> color #755 #00b305ff
> color #756 #f15839ff
> select #1.32/G
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> show sel cartoons
[Repeated 1 time(s)]
> view
> open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
Chain information for AF3 E1 1-421.pdb #757
---
Chain | Description
A | No description available
> matchmaker #757 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 G (#1.32) with AF3 E1 1-421.pdb, chain A (#757),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #758
---
Chain | Description
A | No description available
> matchmaker #758 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 G (#1.32) with AF3 E1 422-461.pdb, chain A (#758),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.32/H
3304 atoms, 3395 bonds, 423 residues, 1 model selected
> show sel cartoons
[Repeated 1 time(s)]
> open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
Chain information for AF3 E2 1-352.pdb #759
---
Chain | Description
B | No description available
> matchmaker #759 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 H (#1.32) with AF3 E2 1-352.pdb, chain B (#759),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #760
---
Chain | Description
B | No description available
> matchmaker #760 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 H (#1.32) with AF3 E2 353-438.pdb, chain B (#760),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> select #1.32/I
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 #761
---
Chain | Description
A | No description available
> matchmaker #761 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 I (#1.32) with AF3 CA.pdb, chain A (#761),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #757 dodgerblue
> color #758 dodgerblue
> color #759 #00b305ff
> color #760 #00b305ff
> color #761 #f15839ff
> select #1.33/G
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 #762
---
Chain | Description
A | No description available
> matchmaker #762 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 G (#1.33) with AF3 E1 1-421.pdb, chain A (#762),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #763
---
Chain | Description
A | No description available
> matchmaker #763 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 G (#1.33) with AF3 E1 422-461.pdb, chain A (#763),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> select #1.32/H
3304 atoms, 3395 bonds, 423 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> select #1.33/H
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 #764
---
Chain | Description
B | No description available
> matchmaker #764 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 H (#1.33) with AF3 E2 1-352.pdb, chain B (#764),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #765
---
Chain | Description
B | No description available
> matchmaker #765 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 H (#1.33) with AF3 E2 353-438.pdb, chain B (#765),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.937 angstroms; (across all 84 pairs:
8.151)
> hide sel cartoons
> select #1.33/I
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 #766
---
Chain | Description
A | No description available
> matchmaker #766 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 I (#1.33) with AF3 CA.pdb, chain A (#766),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #762 dodgerblue
> color #763 dodgerblue
> color #764 #00b305ff
> color #765 #00b305ff
> color #766 #f15839ff
> select #1.33/G
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> hide sel cartoons
> select #1.34/G
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 #767
---
Chain | Description
A | No description available
> matchmaker #767 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 G (#1.34) with AF3 E1 1-421.pdb, chain A (#767),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #768
---
Chain | Description
A | No description available
> matchmaker #768 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 G (#1.34) with AF3 E1 422-461.pdb, chain A (#768),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.34/H
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 #769
---
Chain | Description
B | No description available
> matchmaker #769 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 H (#1.34) with AF3 E2 1-352.pdb, chain B (#769),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #770
---
Chain | Description
B | No description available
> matchmaker #770 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 H (#1.34) with AF3 E2 353-438.pdb, chain B (#770),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> select #1.34/I
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 #771
---
Chain | Description
A | No description available
> matchmaker #771 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 I (#1.34) with AF3 CA.pdb, chain A (#771),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #767 dodgerblue
> color #768 dodgerblue
> color #769 #00b305ff
> color #770 #00b305ff
> color #771 #f15839ff
> select #1.35/G
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 #772
---
Chain | Description
A | No description available
> matchmaker #772 to #1.34 & sel
No 'to' model specified
> matchmaker #772 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 G (#1.35) with AF3 E1 1-421.pdb, chain A (#772),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #773
---
Chain | Description
A | No description available
> matchmaker #773 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 G (#1.35) with AF3 E1 422-461.pdb, chain A (#773),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.35/H
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 #774
---
Chain | Description
B | No description available
> matchmaker #774 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 H (#1.35) with AF3 E2 1-352.pdb, chain B (#774),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #775
---
Chain | Description
B | No description available
> matchmaker #775 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 H (#1.35) with AF3 E2 353-438.pdb, chain B (#775),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> select #1.35/I
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 #776
---
Chain | Description
A | No description available
> matchmaker #776 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 I (#1.35) with AF3 CA.pdb, chain A (#776),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #772 dodgerblue
> color #773 dodgerblue
> color #774 #00b305ff
> color #775 #00b305ff
> color #776 #f15839ff
> select #1.36/G
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 #777
---
Chain | Description
A | No description available
> matchmaker #777 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 G (#1.36) with AF3 E1 1-421.pdb, chain A (#777),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #778
---
Chain | Description
A | No description available
> matchmaker #778 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 G (#1.36) with AF3 E1 422-461.pdb, chain A (#778),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.36/H
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 #779
---
Chain | Description
B | No description available
> matchmaker #779 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 H (#1.36) with AF3 E2 1-352.pdb, chain B (#779),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #780
---
Chain | Description
B | No description available
> matchmaker #780 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 H (#1.36) with AF3 E2 353-438.pdb, chain B (#780),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.151)
> hide sel cartoons
> select #1.36/I
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 #781
---
Chain | Description
A | No description available
> matchmaker #781 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 I (#1.36) with AF3 CA.pdb, chain A (#781),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #777 dodgerblue
> color #778 dodgerblue
> color #779 #00b305ff
> color #780 #00b305ff
> color #781 #f15839ff
> select #1.38/G
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 #782
---
Chain | Description
A | No description available
> matchmaker #782 to #1.36 & sel
No 'to' model specified
> matchmaker #782 to #1.37 & sel
No 'to' model specified
> matchmaker #782 to #1.37 & sel
No 'to' model specified
> hide sel cartoons
> select #1.38/G
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> show sel cartoons
> matchmaker #782 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 G (#1.38) with AF3 E1 1-421.pdb, chain A (#782),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #783
---
Chain | Description
A | No description available
> matchmaker #783 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 G (#1.38) with AF3 E1 422-461.pdb, chain A (#783),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.38/H
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 #784
---
Chain | Description
B | No description available
> matchmaker #784 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 H (#1.38) with AF3 E2 1-352.pdb, chain B (#784),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #785
---
Chain | Description
B | No description available
> matchmaker #785 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 H (#1.38) with AF3 E2 353-438.pdb, chain B (#785),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> select #1.38/I
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 #786
---
Chain | Description
A | No description available
> matchmaker #786 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 I (#1.38) with AF3 CA.pdb, chain A (#786),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #782 dodgerblue
> color #783 dodgerblue
> color #784 #00b305ff
> color #785 #00b305ff
> color #786 #f15839ff
> select #1.39/G
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 #787
---
Chain | Description
A | No description available
> matchmaker #787 to #1.38 & sel
No 'to' model specified
> matchmaker #787 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 G (#1.39) with AF3 E1 1-421.pdb, chain A (#787),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #788
---
Chain | Description
A | No description available
> matchmaker #788 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 G (#1.39) with AF3 E1 422-461.pdb, chain A (#788),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.39/H
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 #789
---
Chain | Description
B | No description available
> matchmaker #789 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 H (#1.39) with AF3 E2 1-352.pdb, chain B (#789),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #790
---
Chain | Description
B | No description available
> matchmaker #790 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 H (#1.39) with AF3 E2 353-438.pdb, chain B (#790),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.151)
> hide sel cartoons
> select #1.39/I
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 #791
---
Chain | Description
A | No description available
> matchmaker #791 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 I (#1.39) with AF3 CA.pdb, chain A (#791),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #787 dodgerblue
> color #788 dodgerblue
> color #789 #00b305ff
> color #790 #00b305ff
> color #791 #f15839ff
> select #1.40/G
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 #792
---
Chain | Description
A | No description available
> matchmaker #792 to #1.39 & sel
No 'to' model specified
> matchmaker #792 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 G (#1.40) with AF3 E1 1-421.pdb, chain A (#792),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #793
---
Chain | Description
A | No description available
> matchmaker #793 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 G (#1.40) with AF3 E1 422-461.pdb, chain A (#793),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.40/H
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 #794
---
Chain | Description
B | No description available
> matchmaker #794 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 H (#1.40) with AF3 E2 1-352.pdb, chain B (#794),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #795
---
Chain | Description
B | No description available
> matchmaker #795 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 H (#1.40) with AF3 E2 353-438.pdb, chain B (#795),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> select #1.40/I
1277 atoms, 1305 bonds, 162 residues, 1 model selected
> open "/Users/Jean/Desktop/AF3 CA.pdb"
Chain information for AF3 CA.pdb #796
---
Chain | Description
A | No description available
> matchmaker #796 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 I (#1.40) with AF3 CA.pdb, chain A (#796),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> color #792 dodgerblue
> color #793 dodgerblue
> color #794 #00b305ff
> color #795 #00b305ff
> color #796 #f15839ff
> show #751 models
> show #750 models
> show #749 models
> show #748 models
> show #747 models
> hide #747 models
> hide #748 models
> hide #749 models
> hide #750 models
> hide #751 models
> select #1.37/G
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 #797
---
Chain | Description
A | No description available
> matchmaker #796 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 G (#1.37) with AF3 CA.pdb, chain A (#796),
sequence alignment score = 32.6
RMSD between 10 pruned atom pairs is 1.151 angstroms; (across all 110 pairs:
22.900)
> matchmaker #796 to #1.40 & sel
No 'to' model specified
> select #1.40/I
1277 atoms, 1305 bonds, 162 residues, 1 model selected
> show sel cartoons
> matchmaker #796 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 I (#1.40) with AF3 CA.pdb, chain A (#796),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> select #1.37/G
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> matchmaker #797 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 G (#1.37) with AF3 E1 1-421.pdb, chain A (#797),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #798
---
Chain | Description
A | No description available
> matchmaker #798 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 G (#1.37) with AF3 E1 422-461.pdb, chain A (#798),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.37/H
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 #799
---
Chain | Description
B | No description available
> matchmaker #799 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 H (#1.37) with AF3 E2 1-352.pdb, chain B (#799),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #800
---
Chain | Description
B | No description available
> matchmaker #800 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 H (#1.37) with AF3 E2 353-438.pdb, chain B (#800),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> select #1.37/I
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 #801
---
Chain | Description
A | No description available
> matchmaker #801 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 I (#1.37) with AF3 CA.pdb, chain A (#801),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #797 dodgerblue
> color #798 dodgerblue
> color #799 #00b305ff
> color #800 #00b305ff
> color #801 #f15839ff
> save "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" includeMaps true
> hide #752 models
> hide #753 models
> hide #754 models
> hide #755 models
> hide #756 models
> hide #757 models
> hide #758 models
> hide #759 models
> hide #760 models
> hide #761 models
> hide #762 models
> hide #763 models
> hide #764 models
> hide #765 models
> hide #766 models
> hide #767 models
> hide #768 models
> hide #769 models
> hide #770 models
> hide #771 models
> hide #772 models
> hide #773 models
> hide #774 models
> hide #776 models
> hide #775 models
> hide #777 models
> hide #778 models
> hide #779 models
> hide #780 models
> hide #781 models
> hide #782 models
> hide #783 models
> hide #784 models
> hide #785 models
> hide #786 models
> hide #787 models
> hide #788 models
> hide #789 models
> hide #790 models
> hide #791 models
> hide #792 models
> hide #793 models
> hide #794 models
> hide #795 models
> hide #796 models
> hide #797 models
> hide #798 models
> hide #799 models
> hide #800 models
> hide #801 models
> select #1.38/G
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> select #1.41/G
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> show sel cartoons
> view
> open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
Chain information for AF3 E1 1-421.pdb #802
---
Chain | Description
A | No description available
> matchmaker #802 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 G (#1.41) with AF3 E1 1-421.pdb, chain A (#802),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #803
---
Chain | Description
A | No description available
> matchmaker #803 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 G (#1.41) with AF3 E1 422-461.pdb, chain A (#803),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.41/H
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 #804
---
Chain | Description
B | No description available
> matchmaker #804 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 H (#1.41) with AF3 E2 1-352.pdb, chain B (#804),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #805
---
Chain | Description
B | No description available
> matchmaker #805 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 H (#1.41) with AF3 E2 353-438.pdb, chain B (#805),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> select #1.41/I
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 #806
---
Chain | Description
A | No description available
> matchmaker #806 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 I (#1.41) with AF3 CA.pdb, chain A (#806),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #802 dodgerblue
> color #803 dodgerblue
> color #804 #00b305ff
> color #805 #00b305ff
> color #806 #f15839ff
> select #1.42/G
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 #807
---
Chain | Description
A | No description available
> matchmaker #807 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 G (#1.42) with AF3 E1 1-421.pdb, chain A (#807),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #808
---
Chain | Description
A | No description available
> matchmaker #808 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 G (#1.42) with AF3 E1 422-461.pdb, chain A (#808),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.42/H
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 #809
---
Chain | Description
B | No description available
> matchmaker #809 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 H (#1.42) with AF3 E2 1-352.pdb, chain B (#809),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #810
---
Chain | Description
B | No description available
> matchmaker #810 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 H (#1.42) with AF3 E2 353-438.pdb, chain B (#810),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.151)
> hide sel cartoons
> select #1.42/I
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 #811
---
Chain | Description
A | No description available
> matchmaker #811 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 I (#1.42) with AF3 CA.pdb, chain A (#811),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #807 dodgerblue
> color #808 dodgerblue
> color #809 #00b305ff
> color #810 #00b305ff
> color #811 #f15839ff
> select #1.43/G
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 #812
---
Chain | Description
A | No description available
> matchmaker #812 to #1.42 & sel
No 'to' model specified
> matchmaker #812 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 G (#1.43) with AF3 E1 1-421.pdb, chain A (#812),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #813
---
Chain | Description
A | No description available
> matchmaker #813 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 G (#1.43) with AF3 E1 422-461.pdb, chain A (#813),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.43/H
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 #814
---
Chain | Description
B | No description available
> matchmaker #814 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 H (#1.43) with AF3 E2 1-352.pdb, chain B (#814),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #815
---
Chain | Description
B | No description available
> matchmaker #815 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 H (#1.43) with AF3 E2 353-438.pdb, chain B (#815),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> select #1.43/I
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 #816
---
Chain | Description
A | No description available
> matchmaker #816 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 I (#1.43) with AF3 CA.pdb, chain A (#816),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #812 dodgerblue
> color #813 dodgerblue
> color #814 #00b305ff
> color #815 #00b305ff
> color #816 #f15839ff
> select #1.43/G
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> select #1.44/G
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 #817
---
Chain | Description
A | No description available
> matchmaker #817 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 G (#1.44) with AF3 E1 1-421.pdb, chain A (#817),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #818
---
Chain | Description
A | No description available
> matchmaker #818 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 G (#1.44) with AF3 E1 422-461.pdb, chain A (#818),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.44/H
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 #819
---
Chain | Description
B | No description available
> matchmaker #819 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 H (#1.44) with AF3 E2 1-352.pdb, chain B (#819),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #820
---
Chain | Description
B | No description available
> matchmaker #820 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 H (#1.44) with AF3 E2 353-438.pdb, chain B (#820),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.151)
> show sel cartoons
> hide sel cartoons
> select #1.44/I
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 #821
---
Chain | Description
A | No description available
> matchmaker #821 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 I (#1.44) with AF3 CA.pdb, chain A (#821),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #817 dodgerblue
> color #818 dodgerblue
> color #819 #00b305ff
> color #820 #00b305ff
> color #821 #f15839ff
> select #1.45/G
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 #822
---
Chain | Description
A | No description available
> matchmaker #822 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 G (#1.45) with AF3 E1 1-421.pdb, chain A (#822),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #823
---
Chain | Description
A | No description available
> matchmaker #823 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 G (#1.45) with AF3 E1 422-461.pdb, chain A (#823),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.45/H
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 #824
---
Chain | Description
B | No description available
> matchmaker #824 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 H (#1.45) with AF3 E2 1-352.pdb, chain B (#824),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #825
---
Chain | Description
B | No description available
> matchmaker #825 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 H (#1.45) with AF3 E2 353-438.pdb, chain B (#825),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> select #1.45/I
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 #826
---
Chain | Description
A | No description available
> matchmaker #826 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 I (#1.45) with AF3 CA.pdb, chain A (#826),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #822 dodgerblue
> color #823 dodgerblue
> color #824 #00b305ff
> color #825 #00b305ff
> color #826 #f15839ff
> select #1.46/G
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 #827
---
Chain | Description
A | No description available
> matchmaker #827 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 G (#1.46) with AF3 E1 1-421.pdb, chain A (#827),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #828
---
Chain | Description
A | No description available
> matchmaker #828 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 G (#1.46) with AF3 E1 422-461.pdb, chain A (#828),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.46/H
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 #829
---
Chain | Description
B | No description available
> matchmaker #829 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 H (#1.46) with AF3 E2 1-352.pdb, chain B (#829),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #830
---
Chain | Description
B | No description available
> matchmaker #830 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 H (#1.46) with AF3 E2 353-438.pdb, chain B (#830),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.937 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> select #1.46/I
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 #831
---
Chain | Description
A | No description available
> matchmaker #831 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 I (#1.46) with AF3 CA.pdb, chain A (#831),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #827 dodgerblue
> color #828 dodgerblue
> color #829 #00b305ff
> color #830 #00b305ff
> color #831 #f15839ff
> select #1.47/G
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 #832
---
Chain | Description
A | No description available
> matchmaker #832 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 G (#1.47) with AF3 E1 1-421.pdb, chain A (#832),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #833
---
Chain | Description
A | No description available
> matchmaker #833 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 G (#1.47) with AF3 E1 422-461.pdb, chain A (#833),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.47/H
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 #834
---
Chain | Description
B | No description available
> matchmaker #834 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 H (#1.47) with AF3 E2 1-352.pdb, chain B (#834),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #835
---
Chain | Description
B | No description available
> matchmaker #835 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 H (#1.47) with AF3 E2 353-438.pdb, chain B (#835),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> select #1.47/I
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 #836
---
Chain | Description
A | No description available
> matchmaker #836 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 I (#1.47) with AF3 CA.pdb, chain A (#836),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #832 dodgerblue
> color #833 dodgerblue
> color #834 #00b305ff
> color #835 #00b305ff
> color #836 #f15839ff
> select #1.48/G
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 #837
---
Chain | Description
A | No description available
> matchmaker #837 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 G (#1.48) with AF3 E1 1-421.pdb, chain A (#837),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #838
---
Chain | Description
A | No description available
> matchmaker #838 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 G (#1.48) with AF3 E1 422-461.pdb, chain A (#838),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.48/H
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 #839
---
Chain | Description
B | No description available
> matchmaker #839 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 H (#1.48) with AF3 E2 1-352.pdb, chain B (#839),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #840
---
Chain | Description
B | No description available
> matchmaker #840 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 H (#1.48) with AF3 E2 353-438.pdb, chain B (#840),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> select #1.48/I
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 #841
---
Chain | Description
A | No description available
> matchmaker #841 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 I (#1.48) with AF3 CA.pdb, chain A (#841),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #837 dodgerblue
> color #838 dodgerblue
> color #839 #00b305ff
> color #840 #00b305ff
> color #841 #f15839ff
> select #1.49/G
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 #842
---
Chain | Description
A | No description available
> matchmaker #842 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 G (#1.49) with AF3 E1 1-421.pdb, chain A (#842),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #843
---
Chain | Description
A | No description available
> matchmaker #843 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 G (#1.49) with AF3 E1 422-461.pdb, chain A (#843),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.49/H
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 #844
---
Chain | Description
B | No description available
> matchmaker #844 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 H (#1.49) with AF3 E2 1-352.pdb, chain B (#844),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #845
---
Chain | Description
B | No description available
> matchmaker #845 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 H (#1.49) with AF3 E2 353-438.pdb, chain B (#845),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> select #1.39/I
1277 atoms, 1305 bonds, 162 residues, 1 model selected
> select #1.49/I
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 #846
---
Chain | Description
A | No description available
> matchmaker #846 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 I (#1.49) with AF3 CA.pdb, chain A (#846),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #842 dodgerblue
> color #843 dodgerblue
> color #844 #00b305ff
> color #845 #00b305ff
> color #846 #f15839ff
> select #1.50/G
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 #847
---
Chain | Description
A | No description available
> matchmaker #847 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 G (#1.50) with AF3 E1 1-421.pdb, chain A (#847),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #848
---
Chain | Description
A | No description available
> matchmaker #848 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 G (#1.50) with AF3 E1 422-461.pdb, chain A (#848),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
[Repeated 1 time(s)]
> select #1.50/H
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 #849
---
Chain | Description
B | No description available
> matchmaker #849 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 H (#1.50) with AF3 E2 1-352.pdb, chain B (#849),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #850
---
Chain | Description
B | No description available
> matchmaker #850 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 H (#1.50) with AF3 E2 353-438.pdb, chain B (#850),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.151)
> open "/Users/Jean/Desktop/AF3 CA.pdb"
Chain information for AF3 CA.pdb #851
---
Chain | Description
A | No description available
> hide sel cartoons
> select #1.50/I
1277 atoms, 1305 bonds, 162 residues, 1 model selected
> show sel cartoons
> matchmaker #851 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 I (#1.50) with AF3 CA.pdb, chain A (#851),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #847 dodgerblue
> color #848 dodgerblue
> color #849 #00b305ff
> color #850 #00b305ff
> color #851 #f15839ff
> save "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" includeMaps true
> hide #802 models
> hide #803 models
> hide #804 models
> hide #805 models
> hide #806 models
> hide #807 models
> hide #808 models
> hide #809 models
> hide #810 models
> hide #811 models
> hide #812 models
> hide #813 models
> hide #814 models
> hide #815 models
> hide #816 models
> hide #817 models
> hide #818 models
> hide #819 models
> hide #820 models
> hide #821 models
> hide #822 models
> hide #823 models
> hide #824 models
> hide #825 models
> hide #826 models
> hide #827 models
> hide #828 models
> hide #829 models
> hide #830 models
> hide #831 models
> hide #832 models
> hide #833 models
> hide #834 models
> hide #835 models
> hide #836 models
> hide #837 models
> hide #838 models
> hide #839 models
> hide #840 models
> hide #841 models
> hide #842 models
> hide #844 models
> hide #843 models
> hide #845 models
> hide #846 models
> hide #847 models
> hide #848 models
> hide #849 models
> hide #850 models
> hide #851 models
> select #1.51/G
3370 atoms, 3461 bonds, 442 residues, 1 model selected
> show sel cartoons
[Repeated 1 time(s)]
> view
> open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
Chain information for AF3 E1 1-421.pdb #852
---
Chain | Description
A | No description available
> matchmaker #852 to #1.50 & sel
No 'to' model specified
> matchmaker #852 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 G (#1.51) with AF3 E1 1-421.pdb, chain A (#852),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #853
---
Chain | Description
A | No description available
> matchmaker #853 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 G (#1.51) with AF3 E1 422-461.pdb, chain A (#853),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.996)
> hide sel cartoons
> select #1.51/H
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 #854
---
Chain | Description
B | No description available
> matchmaker #854 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 H (#1.51) with AF3 E2 1-352.pdb, chain B (#854),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #855
---
Chain | Description
B | No description available
> matchmaker #855 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 H (#1.51) with AF3 E2 353-438.pdb, chain B (#855),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.151)
> hide sel cartoons
> select #1.51/I
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 #856
---
Chain | Description
A | No description available
> matchmaker #856 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 I (#1.51) with AF3 CA.pdb, chain A (#856),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #852 dodgerblue
> color #853 dodgerblue
> color #854 #00b305ff
> color #855 #00b305ff
> color #856 #f15839ff
> select #1.52/G
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 #857
---
Chain | Description
A | No description available
> matchmaker #857 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 G (#1.52) with AF3 E1 1-421.pdb, chain A (#857),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #858
---
Chain | Description
A | No description available
> matchmaker #858 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 G (#1.52) with AF3 E1 422-461.pdb, chain A (#858),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.52/H
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 #859
---
Chain | Description
B | No description available
> matchmaker #859 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 H (#1.52) with AF3 E2 1-352.pdb, chain B (#859),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #860
---
Chain | Description
B | No description available
> matchmaker #860 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 H (#1.52) with AF3 E2 353-438.pdb, chain B (#860),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> select #1.52/I
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 #861
---
Chain | Description
A | No description available
> matchmaker #861 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 I (#1.52) with AF3 CA.pdb, chain A (#861),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #857 dodgerblue
> color #858 dodgerblue
> color #859 #00b305ff
> color #860 #00b305ff
> color #861 #f15839ff
> select #1.53/G
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 #862
---
Chain | Description
A | No description available
> matchmaker #862 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 G (#1.53) with AF3 E1 1-421.pdb, chain A (#862),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #863
---
Chain | Description
A | No description available
> matchmaker #863 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 G (#1.53) with AF3 E1 422-461.pdb, chain A (#863),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.53/H
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 #864
---
Chain | Description
B | No description available
> matchmaker #864 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 H (#1.53) with AF3 E2 1-352.pdb, chain B (#864),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #865
---
Chain | Description
B | No description available
> matchmaker #865 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 H (#1.53) with AF3 E2 353-438.pdb, chain B (#865),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> select #1.53/I
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 #866
---
Chain | Description
A | No description available
> matchmaker #866 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 I (#1.53) with AF3 CA.pdb, chain A (#866),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #862 dodgerblue
> color #863 dodgerblue
> color #864 #00b305ff
> color #865 #00b305ff
> color #866 #f15839ff
> select #1.54/G
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 #867
---
Chain | Description
A | No description available
> matchmaker #867 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 G (#1.54) with AF3 E1 1-421.pdb, chain A (#867),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #868
---
Chain | Description
A | No description available
> matchmaker #868 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 G (#1.54) with AF3 E1 422-461.pdb, chain A (#868),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.54/H
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 #869
---
Chain | Description
B | No description available
> matchmaker #869 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 H (#1.54) with AF3 E2 1-352.pdb, chain B (#869),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #870
---
Chain | Description
B | No description available
> matchmaker #870 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 H (#1.54) with AF3 E2 353-438.pdb, chain B (#870),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> select #1.54/I
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 #871
---
Chain | Description
A | No description available
> matchmaker #871 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 I (#1.54) with AF3 CA.pdb, chain A (#871),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #867 dodgerblue
> color #868 dodgerblue
> color #869 #00b305ff
> color #870 #00b305ff
> color #871 #f15839ff
> select #1.55/G
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 #872
---
Chain | Description
A | No description available
> matchmaker #872 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 G (#1.55) with AF3 E1 1-421.pdb, chain A (#872),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #873
---
Chain | Description
A | No description available
> matchmaker #873 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 G (#1.55) with AF3 E1 422-461.pdb, chain A (#873),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
[Repeated 1 time(s)]
> select #1.55/H
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 #874
---
Chain | Description
B | No description available
> matchmaker #874 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 H (#1.55) with AF3 E2 1-352.pdb, chain B (#874),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #875
---
Chain | Description
B | No description available
> matchmaker #875 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 H (#1.55) with AF3 E2 353-438.pdb, chain B (#875),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> select #1.55/I
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 #876
---
Chain | Description
A | No description available
> matchmaker #876 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 I (#1.55) with AF3 CA.pdb, chain A (#876),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #872 dodgerblue
> color #873 dodgerblue
> color #874 #00b305ff
> color #875 #00b305ff
> color #876 #f15839ff
> select #1.56/G
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 #877
---
Chain | Description
A | No description available
> matchmaker #877 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 G (#1.56) with AF3 E1 1-421.pdb, chain A (#877),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #878
---
Chain | Description
A | No description available
> matchmaker #878 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 G (#1.56) with AF3 E1 422-461.pdb, chain A (#878),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
[Repeated 1 time(s)]
> select #1.56/H
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 #879
---
Chain | Description
B | No description available
> matchmaker #879 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 H (#1.56) with AF3 E2 1-352.pdb, chain B (#879),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #880
---
Chain | Description
B | No description available
> matchmaker #880 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 H (#1.56) with AF3 E2 353-438.pdb, chain B (#880),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> select #1.56/I
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 #881
---
Chain | Description
A | No description available
> matchmaker #881 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 I (#1.56) with AF3 CA.pdb, chain A (#881),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #877 dodgerblue
> color #878 dodgerblue
> color #879 #00b305ff
> color #880 #00b305ff
> color #881 #f15839ff
> select #1.57/G
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 #882
---
Chain | Description
A | No description available
> matchmaker #882 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 G (#1.57) with AF3 E1 1-421.pdb, chain A (#882),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #883
---
Chain | Description
A | No description available
> matchmaker #883 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 G (#1.57) with AF3 E1 422-461.pdb, chain A (#883),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.57/H
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 #884
---
Chain | Description
B | No description available
> matchmaker #884 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 H (#1.57) with AF3 E2 1-352.pdb, chain B (#884),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #885
---
Chain | Description
B | No description available
> matchmaker #885 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 H (#1.57) with AF3 E2 353-438.pdb, chain B (#885),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> select #1.57/I
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 #886
---
Chain | Description
A | No description available
> matchmaker #886 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 I (#1.57) with AF3 CA.pdb, chain A (#886),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #882 dodgerblue
> color #883 dodgerblue
> color #884 #00b305ff
> color #885 #00b305ff
> color #886 #f15839ff
> select #1.58/G
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 #887
---
Chain | Description
A | No description available
> matchmaker #887 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 G (#1.58) with AF3 E1 1-421.pdb, chain A (#887),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #888
---
Chain | Description
A | No description available
> matchmaker #888 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 G (#1.58) with AF3 E1 422-461.pdb, chain A (#888),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.58/H
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 #889
---
Chain | Description
B | No description available
> matchmaker #889 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 H (#1.58) with AF3 E2 1-352.pdb, chain B (#889),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #890
---
Chain | Description
B | No description available
> matchmaker #890 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 H (#1.58) with AF3 E2 353-438.pdb, chain B (#890),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> select #1.58/I
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 #891
---
Chain | Description
A | No description available
> matchmaker #891 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 I (#1.58) with AF3 CA.pdb, chain A (#891),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #887 dodgerblue
> color #888 dodgerblue
> color #889 #00b305ff
> color #890 #00b305ff
> color #891 #f15839ff
> select #1.59/G
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 #892
---
Chain | Description
A | No description available
> matchmaker #892 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 G (#1.59) with AF3 E1 1-421.pdb, chain A (#892),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #893
---
Chain | Description
A | No description available
> matchmaker #893 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 G (#1.59) with AF3 E1 422-461.pdb, chain A (#893),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.996)
> hide sel cartoons
> select #1.59/H
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 #894
---
Chain | Description
B | No description available
> matchmaker #894 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 H (#1.59) with AF3 E2 1-352.pdb, chain B (#894),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #895
---
Chain | Description
B | No description available
> matchmaker #895 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 H (#1.59) with AF3 E2 353-438.pdb, chain B (#895),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.151)
> hide sel cartoons
> select #1.59/I
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 #896
---
Chain | Description
A | No description available
> matchmaker #896 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 I (#1.59) with AF3 CA.pdb, chain A (#896),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #892 dodgerblue
> color #893 dodgerblue
> color #894 #00b305ff
> color #895 #00b305ff
> color #896 #f15839ff
> select #1.60/G
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 #897
---
Chain | Description
A | No description available
> matchmaker #897 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 G (#1.60) with AF3 E1 1-421.pdb, chain A (#897),
sequence alignment score = 1060.7
RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
2.985)
> open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
Chain information for AF3 E1 422-461.pdb #898
---
Chain | Description
A | No description available
> matchmaker #898 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 G (#1.60) with AF3 E1 422-461.pdb, chain A (#898),
sequence alignment score = 626.9
RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
2.997)
> hide sel cartoons
> select #1.60/H
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 #899
---
Chain | Description
B | No description available
> matchmaker #899 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 H (#1.60) with AF3 E2 1-352.pdb, chain B (#899),
sequence alignment score = 590.9
RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
6.107)
> open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
Chain information for AF3 E2 353-438.pdb #900
---
Chain | Description
B | No description available
> matchmaker #900 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 H (#1.60) with AF3 E2 353-438.pdb, chain B (#900),
sequence alignment score = 329.4
RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
8.150)
> hide sel cartoons
> open "/Users/Jean/Desktop/AF3 CA.pdb"
Chain information for AF3 CA.pdb #901
---
Chain | Description
A | No description available
> select #1.60/I
1277 atoms, 1305 bonds, 162 residues, 1 model selected
> show sel cartoons
> matchmaker #901 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 I (#1.60) with AF3 CA.pdb, chain A (#901),
sequence alignment score = 306.5
RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
2.689)
> hide sel cartoons
> color #897 dodgerblue
> color #898 dodgerblue
> color #899 #00b305ff
> color #901 #f15839ff
> color #900 #00b305ff
> save "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" includeMaps true
——— End of log from Wed Jul 17 16:12:00 2024 ———
opened ChimeraX session
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: 1 hour, 32 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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