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

[Tom Goddard]

This ChimeraX crash is in the Qt window toolkit and we have most often
seen it when an external display is unplugged or plugged in. The crash
report says it crashed in Qt routine displayConfigFinalizedProc(). Did
you plugin or unplug an external display while ChimeraX was running? Of
course that should work but the Qt window toolkit version 6.6 often
crashes on Mac when you do that. It happens especially often on older
Macs with AMD or Intel graphics. We are hoping it is fixed in Qt 6.7 and
you could try the ChimeraX daily build which is currently using Qt 6.7.
We don't have any way to fix the Qt 6.6 problem in ChimeraX 1.8 and I can
only suggest saving a ChimeraX session if you have to plugin or unplug an
external display.

Sorry for the delayed reply. I was on vacation last week.

[jean.millet@…]

Hi, many thanks for providing these explanations regarding external displays issue on Macs.
Best wishes,

Jean Millet