Crash changing Mac display configuration

[jean.millet@…]

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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{
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  "procRole" : "Foreground",
  "version" : 2,
  "userID" : 502,
  "deployVersion" : 210,
  "modelCode" : "MacBookPro15,1",
  "coalitionID" : 1165,
  "osVersion" : {
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    "build" : "23F79",
    "releaseType" : "User"
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  "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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(pooled)","threadState":{"r13":{"value":5501853107712},"rax":{"value":260},"rflags":{"value":583},"cpu":{"value":0},"r14":{"value":123145506729984},"rsi":{"value":5501853107712},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":1280},"r10":{"value":0},"r9":{"value":160},"r15":{"value":1280},"rbx":{"value":22},"trap":{"value":133},"err":{"value":33554737},"r11":{"value":582},"rip":{"value":140703373414266},"rbp":{"value":123145506729536},"rsp":{"value":123145506729384},"r12":{"value":999999000},"rcx":{"value":123145506729384},"flavor":"x86_THREAD_STATE","rdi":{"value":105553169063232}},"frames":[{"imageOffset":16250,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":154},{"imageOffset":26355,"symbol":"_pthread_cond_wait","symbolLocation":1211,"imageIndex":155},{"imageOffset":2231844,"imageIndex":109},{"imageOffset":2231525,"symbol":"QWaitCondition::wait(QMutex*, QDeadlineTimer)","symbolLocation":85,"imageIndex":109},{"imageOffset":2209261,"imageIndex":109},{"imageOffset":2191737,"imageIndex":109},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":155},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":155}]},{"id":267460,"name":"ThreadPoolForegroundWorker","threadState":{"r13":{"value":17179869442},"rax":{"value":268451845},"rflags":{"value":514},"cpu":{"value":0},"r14":{"value":32},"rsi":{"value":17179869442},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":0},"r10":{"value":260700219899904},"r9":{"value":260700219899904},"r15":{"value":260700219899904},"rbx":{"value":123145515130160},"trap":{"value":133},"err":{"value":16777263},"r11":{"value":514},"rip":{"value":140703373403086},"rbp":{"value":123145515129488},"rsp":{"value":123145515129384},"r12":{"value":33000},"rcx":{"value":123145515129384},"flavor":"x86_THREAD_STATE","rdi":{"value":123145515130160}},"frames":[{"imageOffset":5070,"symbol":"mach_msg2_trap","symbolLocation":10,"imageIndex":154},{"imageOffset":64648,"symbol":"mach_msg2_internal","symbolLocation":84,"imageIndex":154},{"imageOffset":34064,"symbol":"mach_msg_overwrite","symbolLocation":653,"imageIndex":154},{"imageOffset":5821,"symbol":"mach_msg","symbolLocation":19,"imageIndex":154},{"imageOffset":75634614,"imageIndex":92},{"imageOffset":75039302,"imageIndex":92},{"imageOffset":75293834,"imageIndex":92},{"imageOffset":75297738,"imageIndex":92},{"imageOffset":75295997,"imageIndex":92},{"imageOffset":75295727,"imageIndex":92},{"imageOffset":75466040,"imageIndex":92},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":155},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":155}]},{"id":267462,"name":"ThreadPoolForegroundWorker","threadState":{"r13":{"value":17179869442},"rax":{"value":268451845},"rflags":{"value":514},"cpu":{"value":0},"r14":{"value":32},"rsi":{"value":17179869442},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":0},"r10":{"value":449970838700032},"r9":{"value":449970838700032},"r15":{"value":449970838700032},"rbx":{"value":123145523531056},"trap":{"value":133},"err":{"value":16777263},"r11":{"value":514},"rip":{"value":140703373403086},"rbp":{"value":123145523530384},"rsp":{"value":123145523530280},"r12":{"value":33000},"rcx":{"value":123145523530280},"flavor":"x86_THREAD_STATE","rdi":{"value":123145523531056}},"frames":[{"imageOffset":5070,"symbol":"mach_msg2_trap","symbolLocation":10,"imageIndex":154},{"imageOffset":64648,"symbol":"mach_msg2_internal","symbolLocation":84,"imageIndex":154},{"imageOffset":34064,"symbol":"mach_msg_overwrite","symbolLocation":653,"imageIndex":154},{"imageOffset":5821,"symbol":"mach_msg","symbolLocation":19,"imageIndex":154},{"imageOffset":75634614,"imageIndex":92},{"imageOffset":75039302,"imageIndex":92},{"imageOffset":75293834,"imageIndex":92},{"imageOffset":75296343,"imageIndex":92},{"imageOffset":75295997,"imageIndex":92},{"imageOffset":75295727,"imageIndex":92},{"imageOffset":75466040,"imageIndex":92},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":155},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":155}]},{"id":267472,"name":"ThreadPoolBackgroundWorker","threadState":{"r13":{"value":17179869442},"rax":{"value":268451845},"rflags":{"value":514},"cpu":{"value":0},"r14":{"value":32},"rsi":{"value":17179869442},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":0},"r10":{"value":436604900474880},"r9":{"value":436604900474880},"r15":{"value":436604900474880},"rbx":{"value":123145624341808},"trap":{"value":133},"err":{"value":16777263},"r11":{"value":514},"rip":{"value":140703373403086},"rbp":{"value":123145624341136},"rsp":{"value":123145624341032},"r12":{"value":33000},"rcx":{"value":123145624341032},"flavor":"x86_THREAD_STATE","rdi":{"value":123145624341808}},"frames":[{"imageOffset":5070,"symbol":"mach_msg2_trap","symbolLocation":10,"imageIndex":154},{"imageOffset":64648,"symbol":"mach_msg2_internal","symbolLocation":84,"imageIndex":154},{"imageOffset":34064,"symbol":"mach_msg_overwrite","symbolLocation":653,"imageIndex":154},{"imageOffset":5821,"symbol":"mach_msg","symbolLocation":19,"imageIndex":154},{"imageOffset":75634614,"imageIndex":92},{"imageOffset":75039302,"imageIndex":92},{"imageOffset":75293834,"imageIndex":92},{"imageOffset":75296343,"imageIndex":92},{"imageOffset":75295853,"imageIndex":92},{"imageOffset":75295764,"imageIndex":92},{"imageOffset":75466040,"imageIndex":92},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":155},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":155}]}],
  "usedImages" : [
[deleted to fit within ticket size limits],
  "sharedCache" : {
  "base" : 140703369224192,
  "size" : 25769803776,
  "uuid" : "b48cfc6b-b7ed-3343-97fb-f5187dc04df8"
},
  "vmSummary" : "ReadOnly portion of Libraries: Total=1.2G resident=0K(0%) swapped_out_or_unallocated=1.2G(100%)\nWritable regions: Total=53.2G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=53.2G(100%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nAccelerate framework               128K        1 \nActivity Tracing                   256K        1 \nCG image                           224K       16 \nColorSync                          252K       31 \nCoreAnimation                      628K       54 \nCoreGraphics                        16K        3 \nCoreUI image data                 4212K       30 \nFoundation                          40K        2 \nIOKit                             23.3M        3 \nKernel Alloc Once                    8K        1 \nMALLOC                            52.6G      230 \nMALLOC guard page                   48K       12 \nMach message                        16K        3 \nOpenGL GLSL                        384K        4 \nSTACK GUARD                        180K       45 \nStack                            180.9M       46 \nStack Guard                       56.0M        1 \nVM_ALLOCATE                      354.0M      394 \nVM_ALLOCATE (reserved)            64.0M        1         reserved VM address space (unallocated)\n__CTF                               824        1 \n__DATA                            45.6M      799 \n__DATA_CONST                      65.5M      463 \n__DATA_DIRTY                      1842K      230 \n__FONT_DATA                        2352        1 \n__GLSLBUILTINS                    5174K        1 \n__INFO_FILTER                         8        1 \n__LINKEDIT                       212.2M      156 \n__OBJC_RO                         71.8M        1 \n__OBJC_RW                         2200K        2 \n__TEXT                             1.0G      804 \ndyld private memory                552K        9 \nmapped file                      229.1M       70 \nshared memory                     3012K       32 \n===========                     =======  ======= \nTOTAL                             54.9G     3448 \nTOTAL, minus reserved VM space    54.9G     3448 \n",
  "legacyInfo" : {
  "threadTriggered" : {
    "name" : "CrBrowserMain",
    "queue" : "com.apple.main-thread"
  }
},
  "logWritingSignature" : "8071ce58fceff1ea152430ccb08a9c3180a353b9",
  "trialInfo" : {
  "rollouts" : [
    {
      "rolloutId" : "648c94d4ebdf9e3e398fa708",
      "factorPackIds" : {
        "SIRI_UNDERSTANDING_NL_OVERRIDES" : "65a8104b6712a43e7922cab8"
      },
      "deploymentId" : 240000171
    },
    {
      "rolloutId" : "639124e81d92412bfb4880b3",
      "factorPackIds" : {

      },
      "deploymentId" : 240000012
    }
  ],
  "experiments" : [
    {
      "treatmentId" : "c47ab4cc-c9c3-4b5d-a87c-e2433ce02597",
      "experimentId" : "6639bc6ba73d460582162323",
      "deploymentId" : 400000006
    }
  ]
}
}
===== 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)  
  

[deleted to fit within ticket size limits]
> 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