Opened 10 months ago

Closed 4 months ago

#16557 closed defect (duplicate)

Crash on Mac waking from sleep

Reported by: chimerax-bug-report@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Window Toolkit Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description (last modified by Eric Pettersen) 

The following bug report has been submitted:
Platform:        macOS-14.6.1-arm64-arm-64bit
ChimeraX Version: 1.9rc202411210252 (2024-11-21 02:52:12 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Thread 0x000000035704f000 (most recent call first):
  File "/Applications/ChimeraX-1.9-rc2024.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
  File "/Applications/ChimeraX-1.9-rc2024.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9-rc2024.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9-rc2024.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000356043000 (most recent call first):
  File "/Applications/ChimeraX-1.9-rc2024.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
  File "/Applications/ChimeraX-1.9-rc2024.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9-rc2024.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9-rc2024.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000355037000 (most recent call first):
  File "/Applications/ChimeraX-1.9-rc2024.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
  File "/Applications/ChimeraX-1.9-rc2024.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
  File "/Applications/ChimeraX-1.9-rc2024.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
  File "/Applications/ChimeraX-1.9-rc2024.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
  File "/Applications/ChimeraX-1.9-rc2024.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9-rc2024.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9-rc2024.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000035402b000 (most recent call first):
  File "/Applications/ChimeraX-1.9-rc2024.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9-rc2024.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9-rc2024.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9-rc2024.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000035301f000 (most recent call first):
  File "/Applications/ChimeraX-1.9-rc2024.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9-rc2024.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9-rc2024.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9-rc2024.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000352013000 (most recent call first):
  File "/Applications/ChimeraX-1.9-rc2024.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9-rc2024.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9-rc2024.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9-rc2024.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000351007000 (most recent call first):
  File "/Applications/ChimeraX-1.9-rc2024.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9-rc2024.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9-rc2024.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9-rc2024.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00000003474ab000 (most recent call first):
  File "/Applications/ChimeraX-1.9-rc2024.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9-rc2024.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9-rc2024.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9-rc2024.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000034649f000 (most recent call first):
  File "/Applications/ChimeraX-1.9-rc2024.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9-rc2024.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9-rc2024.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9-rc2024.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000345493000 (most recent call first):
  File "/Applications/ChimeraX-1.9-rc2024.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9-rc2024.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9-rc2024.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9-rc2024.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000344487000 (most recent call first):
  File "/Applications/ChimeraX-1.9-rc2024.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9-rc2024.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9-rc2024.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9-rc2024.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000034347b000 (most recent call first):
  File "/Applications/ChimeraX-1.9-rc2024.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9-rc2024.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9-rc2024.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9-rc2024.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000336e63000 (most recent call first):
  File "/Applications/ChimeraX-1.9-rc2024.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9-rc2024.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9-rc2024.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9-rc2024.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000335e57000 (most recent call first):
  File "/Applications/ChimeraX-1.9-rc2024.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9-rc2024.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9-rc2024.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9-rc2024.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000334e4b000 (most recent call first):
  File "/Applications/ChimeraX-1.9-rc2024.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9-rc2024.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9-rc2024.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9-rc2024.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Current thread 0x00000001f77dcf40 (most recent call first):
  File "/Applications/ChimeraX-1.9-rc2024.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
  File "/Applications/ChimeraX-1.9-rc2024.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
  File "/Applications/ChimeraX-1.9-rc2024.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 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, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, 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, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets (total: 55)


{"app_name":"ChimeraX","timestamp":"2025-01-05 16:01:19.00 +0100","app_version":"1.9.0","slice_uuid":"17982d98-65bc-3327-8526-577ec996453c","build_version":"1.9.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 14.6.1 (23G93)","roots_installed":0,"name":"ChimeraX","incident_id":"C3544C54-1F8F-4DB1-829B-B83FCF3A5A5C"}
{
  "uptime" : 66000,
  "procRole" : "Background",
  "version" : 2,
  "userID" : 502,
  "deployVersion" : 210,
  "modelCode" : "Mac15,6",
  "coalitionID" : 5951,
  "osVersion" : {
    "train" : "macOS 14.6.1",
    "build" : "23G93",
    "releaseType" : "User"
  },
  "captureTime" : "2025-01-05 16:01:06.6067 +0100",
  "codeSigningMonitor" : 1,
  "incident" : "C3544C54-1F8F-4DB1-829B-B83FCF3A5A5C",
  "pid" : 15874,
  "translated" : false,
  "cpuType" : "ARM-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2025-01-03 16:23:55.3472 +0100",
  "procStartAbsTime" : 1093280104400,
  "procExitAbsTime" : 1606390502026,
  "procName" : "ChimeraX",
  "procPath" : "\/Applications\/ChimeraX-1.9-rc2024.11.21.app\/Contents\/MacOS\/ChimeraX",
  "bundleInfo" : {"CFBundleShortVersionString":"1.9.0","CFBundleVersion":"1.9.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
  "storeInfo" : {"deviceIdentifierForVendor":"1112644A-6552-556B-B409-B162AF8C8E3B","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "984EEE90-1353-F333-4A00-9E61F488532C",
  "codeSigningID" : "edu.ucsf.cgl.ChimeraX",
  "codeSigningTeamID" : "LWV8X224YF",
  "codeSigningFlags" : 570491649,
  "codeSigningValidationCategory" : 6,
  "codeSigningTrustLevel" : 4294967295,
  "instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRd+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkWzg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
  "wakeTime" : 8772,
  "sleepWakeUUID" : "49E0B5C7-F22A-4EA9-8906-0F06F6A34FFF",
  "sip" : "enabled",
  "vmRegionInfo" : "0x34468d9d2b58 is not in any region.  Bytes after previous region: 56996591905625  Bytes before following region: 48075488023720\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      commpage (reserved)        1000000000-7000000000   [384.0G] ---\/--- SM=NUL  reserved VM address space (unallocated)\n--->  GAP OF 0x5f9000000000 BYTES\n      MALLOC_NANO              600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV  ",
  "exception" : {"codes":"0x0000000000000001, 0x000034468d9d2b58","rawCodes":[1,57477628242776],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x000034468d9d2b58"},
  "termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":15874},
  "vmregioninfo" : "0x34468d9d2b58 is not in any region.  Bytes after previous region: 56996591905625  Bytes before following region: 48075488023720\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      commpage (reserved)        1000000000-7000000000   [384.0G] ---\/--- SM=NUL  reserved VM address space (unallocated)\n--->  GAP OF 0x5f9000000000 BYTES\n      MALLOC_NANO              600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV  ",
  "extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
  "faultingThread" : 0,
  "threads" : [{"threadState":{"x":[{"value":0},{"value":0},{"value":1},{"value":5503220376},{"value":80},{"value":95},{"value":1152921509797066752},{"value":0},{"value":17375688598937194029},{"value":17375688604047180141},{"value":14757395258967641293},{"value":4294967286},{"value":5503220306},{"value":0},{"value":53},{"value":4294967280},{"value":328},{"value":8622302440},{"value":0},{"value":11},{"value":8447184704,"symbolLocation":0,"symbol":"_main_thread"},{"value":259},{"value":8447184928,"symbolLocation":224,"symbol":"_main_thread"},{"value":1},{"value":4326164016,"symbolLocation":0,"symbol":"faulthandler_handlers"},{"value":8452759552,"symbolLocation":0,"symbol":"OBJC_IVAR_$_NSCGSStatusItem._selectedContentFrame"},{"value":8452759552,"symbolLocation":0,"symbol":"OBJC_IVAR_$_NSCGSStatusItem._selectedContentFrame"},{"value":4},{"value":1}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6704127008},"cpsr":{"value":1073745920},"fp":{"value":5503220448},"sp":{"value":5503220416},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6703896048,"matchesCrashFrame":1},"far":{"value":0}},"id":604979,"triggered":true,"name":"CrBrowserMain","queue":"com.apple.main-thread","frames":[{"imageOffset":38384,"symbol":"__pthread_kill","symbolLocation":8,"imageIndex":155},{"imageOffset":27680,"symbol":"pthread_kill","symbolLocation":288,"imageIndex":156},{"imageOffset":262624,"symbol":"raise","symbolLocation":32,"imageIndex":157},{"imageOffset":2417160,"symbol":"faulthandler_fatal_error","symbolLocation":392,"imageIndex":153},{"imageOffset":17796,"symbol":"_sigtramp","symbolLocation":56,"imageIndex":158},{"imageOffset":349344,"imageIndex":85},{"imageOffset":349160,"imageIndex":85},{"imageOffset":380316,"symbol":"_NSViewHierarchyDidChangeBackingProperties","symbolLocation":244,"imageIndex":159},{"imageOffset":11486732,"symbol":"-[NSWindow _postWindowDidChangeBackingPropertiesAndDisplayWindowForPreviousBackingScaleFactor:previousColorSpace:]","symbolLocation":192,"imageIndex":159},{"imageOffset":2095464,"symbol":"__67-[NSWindow _updateSettingsSendingScreenChangeNotificationToScreen:]_block_invoke","symbolLocation":448,"imageIndex":159},{"imageOffset":510204,"symbol":"NSPerformVisuallyAtomicChange","symbolLocation":108,"imageIndex":159},{"imageOffset":2095004,"symbol":"-[NSWindow _updateSettingsSendingScreenChangeNotificationToScreen:]","symbolLocation":96,"imageIndex":159},{"imageOffset":515532,"symbol":"-[NSWindow _setFrameCommon:display:fromServer:]","symbolLocation":1856,"imageIndex":159},{"imageOffset":11458836,"symbol":"-[NSWindow(NSScreenLayout) _setFrame:fromAdjustmentToScreen:anchorIfNeeded:animate:]","symbolLocation":592,"imageIndex":159},{"imageOffset":3274684,"symbol":"-[NSWindow _adjustWindowToScreen]","symbolLocation":1100,"imageIndex":159},{"imageOffset":3405156,"symbol":"-[NSWindow 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===== Log before crash start =====
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.9rc202411210252 (2024-11-21)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Volumes/groups/plaschka/max.graf/Bioinfo/AlphaFold/LENG8_LENG81-100/LENG8_LENG81-100_unrelaxed_rank_1_model_1_seed0.pdb

Chain information for LENG8_LENG81-100_unrelaxed_rank_1_model_1_seed0.pdb #1  
---  
Chain | Description  
B | No description available  
C | No description available  
  
Computing secondary structure  

> open
> /Volumes/groups/plaschka/max.graf/Bioinfo/AlphaFold/LENG8_LENG81-100/LENG8_LENG81-100_unrelaxed_rank_2_model_4_seed0.pdb

Chain information for LENG8_LENG81-100_unrelaxed_rank_2_model_4_seed0.pdb #2  
---  
Chain | Description  
B | No description available  
C | No description available  
  

> open
> /Volumes/groups/plaschka/max.graf/Bioinfo/AlphaFold/LENG8_LENG81-100/LENG8_LENG81-100_unrelaxed_rank_3_model_3_seed0.pdb

Chain information for LENG8_LENG81-100_unrelaxed_rank_3_model_3_seed0.pdb #3  
---  
Chain | Description  
B | No description available  
C | No description available  
  

> open
> /Volumes/groups/plaschka/max.graf/Bioinfo/AlphaFold/LENG8_LENG81-100/LENG8_LENG81-100_unrelaxed_rank_4_model_5_seed0.pdb

Chain information for LENG8_LENG81-100_unrelaxed_rank_4_model_5_seed0.pdb #4  
---  
Chain | Description  
B | No description available  
C | No description available  
  

> open
> /Volumes/groups/plaschka/max.graf/Bioinfo/AlphaFold/LENG8_LENG81-100/LENG8_LENG81-100_unrelaxed_rank_5_model_2_seed0.pdb

Chain information for LENG8_LENG81-100_unrelaxed_rank_5_model_2_seed0.pdb #5  
---  
Chain | Description  
B | No description available  
C | No description available  
  
Computing secondary structure  

> color bychain

> hide #2 models

> hide #3 models

> hide #4 models

> show #2 models

> mmaker #2-5 to #1

Computing secondary structure  
Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker LENG8_LENG81-100_unrelaxed_rank_1_model_1_seed0.pdb, chain B (#1)
with LENG8_LENG81-100_unrelaxed_rank_2_model_4_seed0.pdb, chain B (#2),
sequence alignment score = 4034.1  
RMSD between 117 pruned atom pairs is 0.242 angstroms; (across all 800 pairs:
95.612)  
  
Matchmaker LENG8_LENG81-100_unrelaxed_rank_1_model_1_seed0.pdb, chain B (#1)
with LENG8_LENG81-100_unrelaxed_rank_3_model_3_seed0.pdb, chain B (#3),
sequence alignment score = 4046.7  
RMSD between 236 pruned atom pairs is 0.273 angstroms; (across all 800 pairs:
94.157)  
  
Matchmaker LENG8_LENG81-100_unrelaxed_rank_1_model_1_seed0.pdb, chain B (#1)
with LENG8_LENG81-100_unrelaxed_rank_4_model_5_seed0.pdb, chain B (#4),
sequence alignment score = 4027.5  
RMSD between 7 pruned atom pairs is 1.509 angstroms; (across all 800 pairs:
79.703)  
  
Matchmaker LENG8_LENG81-100_unrelaxed_rank_1_model_1_seed0.pdb, chain B (#1)
with LENG8_LENG81-100_unrelaxed_rank_5_model_2_seed0.pdb, chain B (#5),
sequence alignment score = 4062.3  
RMSD between 245 pruned atom pairs is 0.187 angstroms; (across all 800 pairs:
92.037)  
  

> mmaker #5/B to #1

Computing secondary structure  
Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker LENG8_LENG81-100_unrelaxed_rank_1_model_1_seed0.pdb, chain B (#1)
with LENG8_LENG81-100_unrelaxed_rank_5_model_2_seed0.pdb, chain B (#5),
sequence alignment score = 4062.3  
RMSD between 245 pruned atom pairs is 0.187 angstroms; (across all 800 pairs:
92.037)  
  

> hide #5 models

> hide #2 models

> hide #1 models

> close

> open
> /Volumes/groups/plaschka/shared/alphafold/max.graf/IPscreens/transcription_complexes/2024-08-20_spt5_vs_spliceosome_all/pdb/8_sp-O00267-SPT5H_HUMAN_vs_sp-Q8WUD4-CCD12_HUMAN_unrelaxed_rank_5.pdb

Chain information for
8_sp-O00267-SPT5H_HUMAN_vs_sp-Q8WUD4-CCD12_HUMAN_unrelaxed_rank_5.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Computing secondary structure  

> open
> /Volumes/groups/plaschka/shared/alphafold/max.graf/IPscreens/transcription_complexes/2024-08-20_spt5_vs_spliceosome_all/pdb/8_sp-O00267-SPT5H_HUMAN_vs_sp-Q8WUD4-CCD12_HUMAN_unrelaxed_rank_4.pdb

Chain information for
8_sp-O00267-SPT5H_HUMAN_vs_sp-Q8WUD4-CCD12_HUMAN_unrelaxed_rank_4.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Volumes/groups/plaschka/shared/alphafold/max.graf/IPscreens/transcription_complexes/2024-08-20_spt5_vs_spliceosome_all/pdb/8_sp-O00267-SPT5H_HUMAN_vs_sp-Q8WUD4-CCD12_HUMAN_unrelaxed_rank_3.pdb

Chain information for
8_sp-O00267-SPT5H_HUMAN_vs_sp-Q8WUD4-CCD12_HUMAN_unrelaxed_rank_3.pdb #3  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Volumes/groups/plaschka/shared/alphafold/max.graf/IPscreens/transcription_complexes/2024-08-20_spt5_vs_spliceosome_all/pdb/8_sp-O00267-SPT5H_HUMAN_vs_sp-Q8WUD4-CCD12_HUMAN_unrelaxed_rank_2.pdb

Chain information for
8_sp-O00267-SPT5H_HUMAN_vs_sp-Q8WUD4-CCD12_HUMAN_unrelaxed_rank_2.pdb #4  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Volumes/groups/plaschka/shared/alphafold/max.graf/IPscreens/transcription_complexes/2024-08-20_spt5_vs_spliceosome_all/pdb/8_sp-O00267-SPT5H_HUMAN_vs_sp-Q8WUD4-CCD12_HUMAN_unrelaxed_rank_1.pdb

Chain information for
8_sp-O00267-SPT5H_HUMAN_vs_sp-Q8WUD4-CCD12_HUMAN_unrelaxed_rank_1.pdb #5  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Computing secondary structure  

> color bychain

> hide #1 models

> hide #2 models

> hide #3 models

> hide #4 models

> color byattribute bfactor

49275 atoms, 6265 residues, atom bfactor range 12.8 to 96.4  

> color bychain

> color bfactor #5

9855 atoms, 1253 residues, atom bfactor range 13.6 to 96.4  

> mmaker #1-4 to #5

Computing secondary structure  
Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker
8_sp-O00267-SPT5H_HUMAN_vs_sp-Q8WUD4-CCD12_HUMAN_unrelaxed_rank_1.pdb, chain A
(#5) with
8_sp-O00267-SPT5H_HUMAN_vs_sp-Q8WUD4-CCD12_HUMAN_unrelaxed_rank_5.pdb, chain A
(#1), sequence alignment score = 5377.4  
RMSD between 219 pruned atom pairs is 0.991 angstroms; (across all 1087 pairs:
61.639)  
  
Matchmaker
8_sp-O00267-SPT5H_HUMAN_vs_sp-Q8WUD4-CCD12_HUMAN_unrelaxed_rank_1.pdb, chain A
(#5) with
8_sp-O00267-SPT5H_HUMAN_vs_sp-Q8WUD4-CCD12_HUMAN_unrelaxed_rank_4.pdb, chain A
(#2), sequence alignment score = 5433.2  
RMSD between 249 pruned atom pairs is 0.491 angstroms; (across all 1087 pairs:
60.078)  
  
Matchmaker
8_sp-O00267-SPT5H_HUMAN_vs_sp-Q8WUD4-CCD12_HUMAN_unrelaxed_rank_1.pdb, chain A
(#5) with
8_sp-O00267-SPT5H_HUMAN_vs_sp-Q8WUD4-CCD12_HUMAN_unrelaxed_rank_3.pdb, chain A
(#3), sequence alignment score = 5402  
RMSD between 119 pruned atom pairs is 0.378 angstroms; (across all 1087 pairs:
53.119)  
  
Matchmaker
8_sp-O00267-SPT5H_HUMAN_vs_sp-Q8WUD4-CCD12_HUMAN_unrelaxed_rank_1.pdb, chain A
(#5) with
8_sp-O00267-SPT5H_HUMAN_vs_sp-Q8WUD4-CCD12_HUMAN_unrelaxed_rank_2.pdb, chain A
(#4), sequence alignment score = 5446.4  
RMSD between 96 pruned atom pairs is 0.179 angstroms; (across all 1087 pairs:
49.950)  
  

> mmaker #1-4 to #5/

> matchmaker #1-4 to #5/

Invalid "to" argument: only initial part "#5" of atom specifier valid  

> mmaker #1-4 to #5/A

Computing secondary structure  
Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker
8_sp-O00267-SPT5H_HUMAN_vs_sp-Q8WUD4-CCD12_HUMAN_unrelaxed_rank_1.pdb, chain A
(#5) with
8_sp-O00267-SPT5H_HUMAN_vs_sp-Q8WUD4-CCD12_HUMAN_unrelaxed_rank_5.pdb, chain A
(#1), sequence alignment score = 5377.4  
RMSD between 219 pruned atom pairs is 0.991 angstroms; (across all 1087 pairs:
61.639)  
  
Matchmaker
8_sp-O00267-SPT5H_HUMAN_vs_sp-Q8WUD4-CCD12_HUMAN_unrelaxed_rank_1.pdb, chain A
(#5) with
8_sp-O00267-SPT5H_HUMAN_vs_sp-Q8WUD4-CCD12_HUMAN_unrelaxed_rank_4.pdb, chain A
(#2), sequence alignment score = 5433.2  
RMSD between 249 pruned atom pairs is 0.491 angstroms; (across all 1087 pairs:
60.078)  
  
Matchmaker
8_sp-O00267-SPT5H_HUMAN_vs_sp-Q8WUD4-CCD12_HUMAN_unrelaxed_rank_1.pdb, chain A
(#5) with
8_sp-O00267-SPT5H_HUMAN_vs_sp-Q8WUD4-CCD12_HUMAN_unrelaxed_rank_3.pdb, chain A
(#3), sequence alignment score = 5402  
RMSD between 119 pruned atom pairs is 0.378 angstroms; (across all 1087 pairs:
53.119)  
  
Matchmaker
8_sp-O00267-SPT5H_HUMAN_vs_sp-Q8WUD4-CCD12_HUMAN_unrelaxed_rank_1.pdb, chain A
(#5) with
8_sp-O00267-SPT5H_HUMAN_vs_sp-Q8WUD4-CCD12_HUMAN_unrelaxed_rank_2.pdb, chain A
(#4), sequence alignment score = 5446.4  
RMSD between 96 pruned atom pairs is 0.179 angstroms; (across all 1087 pairs:
49.950)  
  

> show #4 models

> color #4-5 bychain

> show #3 models

> show #2 models

> show #1 models

> hide #3 models

> hide #4 models

> hide #2 models

> select #5/A:1024

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select up

43 atoms, 42 bonds, 6 residues, 1 model selected  

> select up

8510 atoms, 8697 bonds, 1087 residues, 1 model selected  

> select down

43 atoms, 42 bonds, 6 residues, 1 model selected  

> hide #1 models

> mmaker #1-4 to #sel

> matchmaker #1-4 to #sel

Invalid "to" argument: invalid atoms specifier  

> mmaker #1-4 to sel

Computing secondary structure  
Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker
8_sp-O00267-SPT5H_HUMAN_vs_sp-Q8WUD4-CCD12_HUMAN_unrelaxed_rank_1.pdb, chain A
(#5) with
8_sp-O00267-SPT5H_HUMAN_vs_sp-Q8WUD4-CCD12_HUMAN_unrelaxed_rank_5.pdb, chain A
(#1), sequence alignment score = 28.3  
RMSD between 6 pruned atom pairs is 0.067 angstroms; (across all 6 pairs:
0.067)  
  
Matchmaker
8_sp-O00267-SPT5H_HUMAN_vs_sp-Q8WUD4-CCD12_HUMAN_unrelaxed_rank_1.pdb, chain A
(#5) with
8_sp-O00267-SPT5H_HUMAN_vs_sp-Q8WUD4-CCD12_HUMAN_unrelaxed_rank_4.pdb, chain A
(#2), sequence alignment score = 28.3  
RMSD between 6 pruned atom pairs is 0.049 angstroms; (across all 6 pairs:
0.049)  
  
Matchmaker
8_sp-O00267-SPT5H_HUMAN_vs_sp-Q8WUD4-CCD12_HUMAN_unrelaxed_rank_1.pdb, chain A
(#5) with
8_sp-O00267-SPT5H_HUMAN_vs_sp-Q8WUD4-CCD12_HUMAN_unrelaxed_rank_3.pdb, chain A
(#3), sequence alignment score = 28.3  
RMSD between 6 pruned atom pairs is 0.069 angstroms; (across all 6 pairs:
0.069)  
  
Matchmaker
8_sp-O00267-SPT5H_HUMAN_vs_sp-Q8WUD4-CCD12_HUMAN_unrelaxed_rank_1.pdb, chain A
(#5) with
8_sp-O00267-SPT5H_HUMAN_vs_sp-Q8WUD4-CCD12_HUMAN_unrelaxed_rank_2.pdb, chain A
(#4), sequence alignment score = 28.3  
RMSD between 6 pruned atom pairs is 0.040 angstroms; (across all 6 pairs:
0.040)  
  

> show #4 models

> show #3 models

> show #2 models

> show #1 models

> hide #3 models

> hide #2 models

> hide #4 models

> hide #1 models

> show #5/A target s

> show #5/B target a

> color byhetero

> color #5/B byhetero

> open 9FMD

Summary of feedback from opening 9FMD fetched from pdb  
---  
note | Fetching compressed mmCIF 9fmd from http://files.rcsb.org/download/9fmd.cif  
  
9fmd title:  
Integrative model of the human post-catalytic spliceosome (P-complex) [more
info...]  
  
Chain information for 9fmd #6  
---  
Chain | Description | UniProt  
1 | PRKR-interacting protein 1 | PKRI1_HUMAN 1-184  
2 | U2 snRNA |   
3 | Splicing factor ESS-2 homolog | ESS2_HUMAN 1-476  
32 | Protein FAM32A | FA32A_HUMAN 1-112  
5 | U5 snRNA |   
50 | Protein FAM50A | FA50A_HUMAN 1-339  
56 | STING ER exit protein | STEEP_HUMAN 1-222  
6 | U6 snRNA |   
7 | Eukaryotic initiation factor 4A-III | IF4A3_HUMAN 1-411  
8 | RNA-binding protein 8A | RBM8A_HUMAN 1-174  
9 | Protein mago nashi homolog | MGN_HUMAN 3-148  
A | Pre-mRNA-processing-splicing factor 8 | PRP8_HUMAN 1-2335  
B | U5 small nuclear ribonucleoprotein 200 kDa helicase | U520_HUMAN 1-2136  
C | 116 kDa U5 small nuclear ribonucleoprotein component | U5S1_HUMAN 1-972  
D | Pre-mRNA-splicing factor ISY1 homolog | ISY1_HUMAN 1-285  
E | U5 small nuclear ribonucleoprotein 40 kDa protein | SNR40_HUMAN 1-357  
EX | Exon |   
F | Splicing factor Cactin | CATIN_HUMAN 1-758  
H | Pre-mRNA-splicing factor CWC22 homolog | CWC22_HUMAN 1-908  
I | Pre-mRNA-splicing factor SYF1 | SYF1_HUMAN 1-855  
IN | INTRON |   
J | Crooked neck-like protein 1 | CRNL1_HUMAN 1-860  
K | Pre-mRNA-splicing factor SPF27 | SPF27_HUMAN 1-225  
L | Cell division cycle 5-like protein | CDC5L_HUMAN 1-802  
M | Pre-mRNA-splicing factor SYF2 | SYF2_HUMAN 1-243  
N | Protein BUD31 homolog | BUD31_HUMAN 1-144  
NO | Nitric oxide synthase-interacting protein | NOSIP_HUMAN 1-301  
O | Pre-mRNA-splicing factor RBM22 | RBM22_HUMAN 1-420  
P | Spliceosome-associated protein CWC15 homolog | CWC15_HUMAN 1-229  
Q | Intron-binding protein aquarius | AQR_HUMAN 1-1485  
R | SNW domain-containing protein 1 | SNW1_HUMAN 1-536  
S | Peptidyl-prolyl cis-trans isomerase-like 1 | PPIL1_HUMAN 1-166  
SR | Serine/arginine repetitive matrix protein 2 | SRRM2_HUMAN 1-2752  
T | Pleiotropic regulator 1 | PLRG1_HUMAN 1-514  
U | Pre-mRNA-splicing factor SLU7 | SLU7_HUMAN 1-586  
V | ATP-dependent RNA helicase DHX8 | DHX8_HUMAN 1-1220  
W | Pre-mRNA-processing factor 17 | PRP17_HUMAN 1-579  
X | Splicing regulator SDE2 | SDE2_HUMAN 1-451  
Z | Coiled-coil domain-containing protein 12 | CCD12_HUMAN 1-166  
a h | Small nuclear ribonucleoprotein Sm D3 | SMD3_HUMAN 1-126  
b i | Small nuclear ribonucleoprotein-associated proteins B and B' | RSMB_HUMAN 1-240  
c j | Small nuclear ribonucleoprotein Sm D1 | SMD1_HUMAN 1-119  
d k | Small nuclear ribonucleoprotein Sm D2 | SMD2_HUMAN 1-118  
e l | Small nuclear ribonucleoprotein E | RUXE_HUMAN 1-92  
f m | Small nuclear ribonucleoprotein F | RUXF_HUMAN 1-86  
g n | Small nuclear ribonucleoprotein G | RUXG_HUMAN 1-76  
o | U2 small nuclear ribonucleoprotein A' | RU2A_HUMAN 1-255  
p | U2 small nuclear ribonucleoprotein B'' | RU2B_HUMAN 1-225  
q r s t | Pre-mRNA-processing factor 19 | PRP19_HUMAN 1-504  
w | Peptidylprolyl isomerase domain and WD repeat-containing protein 1 | PPWD1_HUMAN 1-646  
x | Splicing factor C9orf78 | TLS1_HUMAN 1-289  
y | Peptidyl-prolyl cis-trans isomerase E | PPIE_HUMAN 1-301  
z | NF-kappa-B-activating protein | NKAP_HUMAN 1-415  
  
Non-standard residues in 9fmd #6  
---  
ATP — adenosine-5'-triphosphate  
GTP — guanosine-5'-triphosphate  
IHP — inositol hexakisphosphate (myo-inositol hexakisphosphate; inositol
1,2,3,4,5,6-hexakisphosphate)  
K — potassium ion  
MG — magnesium ion  
ZN — zinc ion  
  

> close #1-4

> view #6 target c

Expected an integer >= 1 or a keyword  

> view #6

> select #6/Z

265 atoms, 263 bonds, 1 pseudobond, 53 residues, 2 models selected  

> color #6 grey

> color #6 light grey

> hide #6 target acs

> show #6 target c

> color sel green

> select #6/R:41

7 atoms, 7 bonds, 1 residue, 1 model selected  

> mmaker #5/B to sel

Computing secondary structure  
Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 9fmd, chain R (#6) with
8_sp-O00267-SPT5H_HUMAN_vs_sp-Q8WUD4-CCD12_HUMAN_unrelaxed_rank_1.pdb, chain B
(#5), sequence alignment score = 6.1  
Fewer than 3 residues aligned; cannot match 9fmd, chain R with
8_sp-O00267-SPT5H_HUMAN_vs_sp-Q8WUD4-CCD12_HUMAN_unrelaxed_rank_1.pdb, chain B  

> mmaker #5/C to sel

No molecules/chains to match specified  

> view #5

> hide #5 target acs

> show #5 target c

> view all

> mmaker #5/B to #6/Z

Computing secondary structure  
Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 9fmd, chain Z (#6) with
8_sp-O00267-SPT5H_HUMAN_vs_sp-Q8WUD4-CCD12_HUMAN_unrelaxed_rank_1.pdb, chain B
(#5), sequence alignment score = 644.4  
RMSD between 3 pruned atom pairs is 0.653 angstroms; (across all 53 pairs:
13.605)  
  

> sequence chain #6/Z

Alignment identifier is 6/Z  

> select #6/Z:69

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #6/Z:69-75

35 atoms, 34 bonds, 7 residues, 1 model selected  

> hide #!5 models

> select clear

> select #6/Z:115

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #6/Z:115-144

150 atoms, 149 bonds, 30 residues, 1 model selected  

> hide #!6 models

> show #!5 models

> open 8HK1

Summary of feedback from opening 8HK1 fetched from pdb  
---  
notes | Fetching compressed mmCIF 8hk1 from http://files.rcsb.org/download/8hk1.cif  
Fetching CCD 9B0 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/0/9B0/9B0.cif  
  
8hk1 title:  
The cryo-EM structure of human pre-17S U2 snRNP [more info...]  
  
Chain information for 8hk1 #1  
---  
Chain | Description | UniProt  
1 | Splicing factor 3B subunit 1 | SF3B1_HUMAN 1-1304  
2 | Splicing factor 3B subunit 2 | SF3B2_HUMAN 1-895  
3 | Splicing factor 3B subunit 3 | SF3B3_HUMAN 1-1217  
4 | Splicing factor 3B subunit 4 | SF3B4_HUMAN 1-424  
5 | Splicing factor 3B subunit 5 | SF3B5_HUMAN 1-86  
6 | PHD finger-like domain-containing protein 5A | PHF5A_HUMAN 1-110  
A | Splicing factor 3A subunit 1 | SF3A1_HUMAN 1-793  
B | Splicing factor 3A subunit 2 | SF3A2_HUMAN 1-464  
C | Splicing factor 3A subunit 3 | SF3A3_HUMAN 1-501  
D | HIV Tat-specific factor 1 | HTSF1_HUMAN 1-755  
E | ATP-dependent RNA helicase DDX42 | DDX42_HUMAN 1-938  
F | U2 small nuclear ribonucleoprotein A' | RU2A_HUMAN 1-255  
G | U2 small nuclear ribonucleoprotein B'' | RU2B_HUMAN 4-225  
H | U2 snRNA |   
a | Small nuclear ribonucleoprotein Sm D2 | SMD2_HUMAN 1-118  
b | Small nuclear ribonucleoprotein F | RUXF_HUMAN 1-86  
c | Small nuclear ribonucleoprotein E | RUXE_HUMAN 1-92  
d | Small nuclear ribonucleoprotein G | RUXG_HUMAN 1-76  
e | Small nuclear ribonucleoprotein Sm D3 | SMD3_HUMAN 1-126  
f | Small nuclear ribonucleoprotein-associated proteins B and B' | RSMB_HUMAN 1-240  
g | Small nuclear ribonucleoprotein Sm D1 | SMD1_HUMAN 1-119  
  
Non-standard residues in 8hk1 #1  
---  
9B0 —
[(2~{S},3~{S},4~{E},6~{S},7~{R},10~{R})-3,7-dimethyl-2-[(2~{E},4~{E},6~{R})-6-methyl-6-oxidanyl-7-[(2~{R},3~{R})-3-[(2~{R},3~{S})-3-oxidanylpentan-2-yl]oxiran-2-yl]hepta-2,4-dien-2-yl]-7,10-bis(oxidanyl)-12-oxidanylidene-1-oxacyclododec-4-en-6-yl]
4-cycloheptylpiperazine-1-carboxylate  
ZN — zinc ion  
  

> hide #!1 models

> view #1

> hide #!5 models

> view #1

> show #!1 models

> set bgColor white

> view #1 all

Expected an integer >= 1 or a keyword  

> ui tool show "Side View"

> hide #1 target acs

> show #1 target c

> graphics silhouettes true

> view

> color #1 light grey

> select #1/D

930 atoms, 944 bonds, 1 pseudobond, 113 residues, 2 models selected  

> color #1 green

> color #1/D green

> open /Users/max.graf/Downloads/AF-O43719-F1-model_v4.pdb

AF-O43719-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for hiv tat-specific factor 1 (O43719) [more
info...]  
  
Chain information for AF-O43719-F1-model_v4.pdb #2  
---  
Chain | Description | UniProt  
A | hiv tat-specific factor 1 | HTSF1_HUMAN 1-755  
  
Computing secondary structure  

> mmaker #2 to #1/D

Computing secondary structure  
Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 8hk1, chain D (#1) with AF-O43719-F1-model_v4.pdb, chain A (#2),
sequence alignment score = 2907.9  
RMSD between 98 pruned atom pairs is 0.833 angstroms; (across all 113 pairs:
1.613)  
  

> open /Volumes/groups/plaschka/max.graf/color_mapping_chimerax.cxc

> alphafold fetch O43719

Fetching AlphaFold database settings from
https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database3.json  
Fetching compressed AlphaFold O43719 from
https://alphafold.ebi.ac.uk/files/AF-O43719-F1-model_v4.cif  
Chain information for AlphaFold O43719 #3  
---  
Chain | Description | UniProt  
A | HIV Tat-specific factor 1 | HTSF1_HUMAN 1-755  
  
Color AlphaFold O43719 by residue attribute pLDDT_score  

> color :1 #ebff0c

> color :2 #009cff

> color :3 #0060ff

> color :4 #0000ff

> color :5 #003cff

> color :6 #0008ff

> color :7 #0044ff

> color :8 #0048ff

> color :9 #007cff

> color :10 #0074ff

> color :11 #83ff73

> color :12 #ed0400

> color :13 #13fce4

> color :14 #ffb900

> color :15 #ff6f00

> color :16 #ff7300

> color :17 #ff6f00

> color :18 #ff5d00

> color :19 #ff9f00

> color :20 #8aff6d

> color :21 #c1ff36

> color :22 #f8f500

> color :23 white

> color :24 #0064ff

> color :25 #0000ff

> color :26 #0094ff

> color :27 #0044ff

> color :28 #002cff

> color :29 #0054ff

> color :30 #0004ff

> color :31 #001cff

> color :32 #0000ff

> color :33 #0030ff

> color :34 #0000ff

> color :35 #0008ff

> color :36 #0014ff

> color :37 #0050ff

> color :38 #0000ff

> color :39 #0028ff

> color :40 #002cff

> color :41 #0000ff

> color :42 #0040ff

> color :43 #0088ff

> color :44 #0048ff

> color :45 #004cff

> color :46 #0024ff

> color :47 #6dff8a

> color :48 #90ff66

> color :49 #73ff83

> color :50 #ff4300

> color :51 #ff3400

> color :52 #890000

> color :53 #9b0000

> color :54 #00c4ff

> color :55 #ffe600

> color :56 #d60000

> color :57 #ff6f00

> color :58 #b60000

> color :59 #920000

> color :60 #8d0000

> color :61 #840000

> color :62 #ff6f00

> color :63 #e80000

> color :64 #ff6800

> color :65 #ff3000

> color :66 #a40000

> color :67 #8d0000

> color :68 #ff4e00

> color :69 #bb0000

> color :70 #73ff83

> color :71 #a80000

> color :72 #ff3800

> color :73 #ff3f00

> color :74 #ff7e00

> color :75 #c40000

> color :76 #bb0000

> color :77 #ff2500

> color :78 #00acff

> color :79 #0048ff

> color :80 #00e0fb

> color :81 #00d8ff

> color :82 #0080ff

> color :83 #00a4ff

> color :84 #008cff

> color :85 #00bcff

> color :86 #0044ff

> color :87 #0064ff

> color :88 #0024ff

> color :89 #002cff

> color :90 #0054ff

> color :91 #0058ff

> color :92 #0018ff

> color :93 #0000f6

> color :94 #0014ff

> color :95 #0014ff

> color :96 #0008ff

> color :97 #0028ff

> color :98 #0060ff

> color :99 #0058ff

> color :100 #000cff

> color :101 #000cff

> color :102 #0034ff

> color :103 #0044ff

> color :104 #006cff

> color :105 #0004ff

> color :106 #001cff

> color :107 #0060ff

> color :108 #0020ff

> color :109 #0024ff

> color :110 #0074ff

> color :111 #0010ff

> color :112 #006cff

> color :113 #1fffd7

> color :114 white

> color :115 #e1ff16

> color :116 #ffb900

> color :117 #fa0f00

> color :118 #ff2500

> color :119 #ff1300

> color :120 #0cf4eb

> color :121 #e4ff13

> color :122 #0cf4eb

> color :123 #ff2d00

> color :124 #890000

> color :125 #8d0000

> color :126 #49ffad

> color :127 #f60b00

> color :128 #ff4a00

> color :129 #caff2c

> color :130 #87ff70

> color :131 #ff6c00

> color :132 #9f0000

> color :133 #bb0000

> color :134 #f60b00

> color :135 #a80000

> color :136 #920000

> color :137 #a40000

> color :138 #e40000

> color :139 #890000

> color :140 #9b0000

> color :141 #800000

> color :142 #ffb900

> color :143 #920000

> color :144 #ff1600

> color :145 #ff3b00

> color :146 #8aff6d

> color :147 #ff5900

> color :148 #890000

> color :149 #890000

> color :150 #ff5200

> color :151 #9dff5a

> color :152 #ff4a00

> color :153 #960000

> color :154 #ff3f00

> color :155 #c40000

> color :156 #d10000

> color :157 #800000

> color :158 #a80000

> color :159 #c40000

> color :160 #c80000

> color :161 #ff4a00

> color :162 #9f0000

> color :163 #ff3f00

> color :164 #09f0ee

> color :165 #ff3800

> color :166 #ff8600

> color :167 #ff8200

> color :168 #ff2500

> color :169 #9b0000

> color :170 #c40000

> color :171 #8d0000

> color :172 #a40000

> color :173 #890000

> color :174 #da0000

> color :175 #840000

> color :176 white

> color :177 #8aff6d

> color :178 #840000

> color :179 #ff9c00

> color :180 #ff2d00

> color :181 #920000

> color :182 #800000

> color :183 #800000

> color :184 #890000

> color :185 #8d0000

> color :186 #840000

> color :187 #920000

> color :188 #9b0000

> color :189 #9b0000

> color :190 #960000

> color :191 #ff6f00

> color :192 #840000

> color :193 #8d0000

> color :194 #b20000

> color :195 #8aff6d

> color :196 #8d0000

> color :197 #920000

> color :198 #ff8600

> color :199 #ff8d00

> color :200 #ed0400

> color :201 #a80000

> color :202 #890000

> color :203 #ff7a00

> color :204 #ff3400

> color :205 #ff8d00

> color :206 #ff1e00

> color :207 #920000

> color :208 #8d0000

> color :209 #ff4e00

> color :210 #ff9c00

> color :211 #e40000

> color :212 #cd0000

> color :213 #a40000

> color :214 #9b0000

> color :215 #dbff1c

> color :216 #840000

> color :217 #ffb200

> color :218 #800000

> color :219 #ff4e00

> color :220 #bb0000

> color :221 #a80000

> color :222 #840000

> color :223 #ffb200

> color :224 #ad0000

> color :225 #9f0000

> color :226 #ff4a00

> color :227 #ffcc00

> color :228 #cd0000

> color :229 #bb0000

> color :230 #ed0400

> color :231 #da0000

> color :232 #fa0f00

> color :233 #ffb200

> color :234 #ff1600

> color :235 #f60b00

> color :236 #ff2200

> color :237 #fa0f00

> color :238 #ed0400

> color :239 #ff2900

> color :240 #ff9400

> color :241 #87ff70

> color :242 #80ff77

> color :243 #fa0f00

> color :244 #ff9c00

> color :245 #df0000

> color :246 #ffb600

> color :247 #960000

> color :248 #960000

> color :249 #800000

> color :250 #cd0000

> color :251 #8d0000

> color :252 #e40000

> color :253 #ff5d00

> color :254 white

> color :255 #0ff8e7

> color :256 #baff3c

> color :257 #00e4f8

> color :258 #00e4f8

> color :259 #e40000

> color :260 #deff19

> color :261 #ff1600

> color :262 #ff6400

> color :263 #b60000

> color :264 #ff8900

> color :265 #d60000

> color :266 #cd0000

> color :267 #c80000

> color :268 #ff2200

> color :269 #ff3f00

> color :270 #d60000

> color :271 #bb0000

> color :272 #890000

> color :273 #ff4300

> color :274 #bb0000

> color :275 #06ecf1

> color :276 #bf0000

> color :277 #8d0000

> color :278 #ff2500

> color :279 #f1fc06

> color :280 #b60000

> color :281 #a40000

> color :282 #ff7300

> color :283 #ff7a00

> color :284 #c80000

> color :285 #ff4a00

> color :286 #b20000

> color :287 #e80000

> color :288 #ff3800

> color :289 #ff5500

> color :290 #890000

> color :291 #d60000

> color :292 #ffae00

> color :293 #b1ff46

> color :294 #920000

> color :295 #9b0000

> color :296 #8dff6a

> color :297 #df0000

> color :298 #b20000

> color :299 #840000

> color :300 #16ffe1

> color :301 #ff3800

> color :302 #ff4e00

> color :303 #c40000

> color :304 #ff4a00

> color :305 #ff6000

> color :306 #ff2200

> color :307 #920000

> color :308 #840000

> color :309 #ff1a00

> color :310 #9b0000

> color :311 #ff2200

> color :312 #ffab00

> color :313 #800000

> color :314 #c40000

> color :315 #bb0000

> color :316 #ff1e00

> color :317 #c80000

> color :318 #ff9f00

> color :319 #9f0000

> color :320 #ffc400

> color :321 #9dff5a

> color :322 #ffd000

> color :323 #aaff4d

> color :324 #ff3400

> color :325 #cd0000

> color :326 #e80000

> color :327 #0094ff

> color :328 #920000

> color :329 #ff4300

> color :330 white

> color :331 #7aff7d

> color :332 #ff2200

> color :333 #e7ff0f

> color :334 #e80000

> color :335 #9b0000

> color :336 #b20000

> color :337 #8d0000

> color :338 #c40000

> color :339 #da0000

> color :340 #f10800

> color :341 #ffa300

> color :342 #f10800

> color :343 #40ffb7

> color :344 #f10800

> color :345 #3cffba

> color :346 #6aff8d

> color :347 #840000

> color :348 #9b0000

> color :349 #840000

> color :350 #30ffc7

> color :351 #ffb600

> color :352 #b20000

> color :353 #da0000

> color :354 #ff6f00

> color :355 #f60b00

> color :356 #ff5500

> color :357 #890000

> color :358 #ff2900

> color :359 #26ffd1

> color :360 #ffe200

> color :361 #bb0000

> color :362 #ff3000

> color :363 #ff9100

> color :364 #ffae00

> color :365 #960000

> color :366 #ff3b00

> color :367 #1fffd7

> color :368 #c7ff30

> color :369 #890000

> color :370 #ffcc00

> color :371 #00b0ff

> color :372 #d60000

> color :373 #ff2500

> color :374 #00a4ff

> color :375 #0070ff

> color :376 #00ccff

> color :377 #09f0ee

> color :378 #0064ff

> color :379 #0044ff

> color :380 #0034ff

> color :381 #0058ff

> color :382 #0004ff

> color :383 #0000ff

> color :384 #0004ff

> color :385 #0024ff

> color :386 #003cff

> color :387 #0038ff

> color :388 #0020ff

> color :389 #0000fa

> color :390 #0054ff

> color :391 #0044ff

> color :392 #0074ff

> color :393 #001cff

> color :394 #0094ff

> color :395 #00d0ff

> color :396 #00d4ff

> color :397 #00d0ff

> color :398 #0088ff

> color :399 #0024ff

> color :400 #00acff

> color :401 #0064ff

> color :402 #83ff73

> color :403 #00a4ff

> color :404 #00a0ff

> color :405 #0008ff

> color :406 #0024ff

> color :407 #001cff

> color :408 #0010ff

> color :409 #0034ff

> color :410 #0040ff

> color :411 #0074ff

> color :412 #001cff

> color :413 #0010ff

> color :414 #001cff

> color :415 #0068ff

> color :416 #0004ff

> color :417 #0028ff

> color :418 #0008ff

> color :419 #0014ff

> color :420 #0084ff

> color :421 #0034ff

> color :422 #005cff

> color :423 #0098ff

> color :424 #0080ff

> color :425 #0024ff

> color :426 #0034ff

> color :427 #0048ff

> color :428 #00a0ff

> color :429 #0078ff

> color :430 #0074ff

> color :431 #007cff

> color :432 #0088ff

> color :433 #0094ff

> color :434 #0010ff

> color :435 #0070ff

> color :436 #002cff

> color :437 #000cff

> color :438 #000cff

> color :439 #0028ff

> color :440 #000cff

> color :441 #007cff

> color :442 #003cff

> color :443 #0000ff

> color :444 #0014ff

> color :445 #0000ff

> color :446 #0038ff

> color :447 #0014ff

> color :448 #0000ff

> color :449 #0018ff

> color :450 #0054ff

> color :451 #0048ff

> color :452 #0000fa

> color :453 #0000ed

> color :454 #0000ff

> color :455 #0034ff

> color :456 #0034ff

> color :457 #0034ff

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> color :459 #0040ff

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> color :461 #0000ff

> color :462 #0008ff

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> color :464 #0038ff

> color :465 #0040ff

> color :466 #0030ff

> color :467 #0000ff

> color :468 #0054ff

> color :469 #0034ff

> color :470 #0008ff

> color :471 #0018ff

> color :472 #0000ff

> color :473 #003cff

> color :474 #0000ff

> color :475 #0000ff

> color :476 #0000ff

> color :477 #0034ff

> color :478 #0008ff

> color :479 #0000f6

> color :480 #0000ff

> color :481 #0000f6

> color :482 #0004ff

> color :483 #0034ff

> color :484 #001cff

> color :485 #0000e3

> color :486 #002cff

> color :487 #001cff

> color :488 #0000ff

> color :489 #0000ed

> color :490 #0000fa

> color :491 #0000e8

> color :492 #0000fa

> color :493 #0000ff

> color :494 #0000fa

> color :495 #0028ff

> color :496 #0028ff

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> color :498 #0000ed

> color :499 #0000ff

> color :500 #0040ff

> color :501 #0058ff

> color :502 #0034ff

> color :503 #0000ff

> color :504 #0044ff

> color :505 #0044ff

> color :506 #0040ff

> color :507 #0000e3

> color :508 #0000e3

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> color :510 #0000ff

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> color :513 #0050ff

> color :514 #005cff

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> color :516 #0018ff

> color :517 #0000f6

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> color :519 #0050ff

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> color :521 #0004ff

> color :522 #0050ff

> color :523 #0014ff

> color :524 #0010ff

> color :525 #0000df

> color :526 #0000ff

> color :527 #0044ff

> color :528 #0028ff

> color :529 #0008ff

> color :530 #0040ff

> color :531 #0034ff

> color :532 #0040ff

> color :533 #0000ed

> color :534 #0000ff

> color :535 #0000ff

> color :536 #0000ff

> color :537 #006cff

> color :538 #0048ff

> color :539 #0010ff

> color :540 #0054ff

> color :541 #0050ff

> color :542 #0024ff

> color :543 #0020ff

> color :544 #0020ff

> color :545 #0058ff

> color :546 #003cff

> color :547 #0054ff

> color :548 #0014ff

> color :549 #000cff

> color :550 #0060ff

> color :551 #002cff

> color :552 #0000ff

> color :553 #0018ff

> color :554 #0074ff

> color :555 #0068ff

> color :556 #0004ff

> color :557 #0000ff

> color :558 #0050ff

> color :559 #0014ff

> color :560 #0000ff

> color :561 #0014ff

> color :562 #0050ff

> color :563 #0000ff

> color :564 #0030ff

> color :565 #000cff

> color :566 #0058ff

> color :567 #0060ff

> color :568 #0030ff

> color :569 #000cff

> color :570 #0000f6

> color :571 #002cff

> color :572 #0048ff

> color :573 #0014ff

> color :574 #0000df

> color :575 #0010ff

> color :576 #0034ff

> color :577 #0014ff

> color :578 #0000ff

> color :579 #0008ff

> color :580 #003cff

> color :581 #0040ff

> color :582 #0030ff

> color :583 #0000e3

> color :584 #0000e8

> color :585 #0040ff

> color :586 #0030ff

> color :587 #000cff

> color :588 #0000f6

> color :589 #0014ff

> color :590 #0078ff

> color :591 #0054ff

> color :592 #0000f1

> color :593 #0058ff

> color :594 #0060ff

> color :595 #0044ff

> color :596 #002cff

> color :597 #0028ff

> color :598 #0074ff

> color :599 #0014ff

> color :600 #004cff

> color :601 #0068ff

> color :602 #0044ff

> color :603 #0068ff

> color :604 #004cff

> color :605 #002cff

> color :606 #0008ff

> color :607 #0050ff

> color :608 #0070ff

> color :609 #008cff

> color :610 #0030ff

> color :611 #0000ff

> color :612 #0038ff

> color :613 #0060ff

> color :614 #0094ff

> color :615 #002cff

> color :616 #0054ff

> color :617 #0064ff

> color :618 #0028ff

> color :619 #0068ff

> color :620 #0058ff

> color :621 #0024ff

> color :622 #005cff

> color :623 #0028ff

> color :624 #0048ff

> color :625 #0018ff

> color :626 #0070ff

> color :627 #007cff

> color :628 #005cff

> color :629 #0040ff

> color :630 #0048ff

> color :631 #004cff

> color :632 #002cff

> color :633 #0000ff

> color :634 #0054ff

> color :635 #00acff

> color :636 #0088ff

> color :637 #02e8f4

> color :638 #7dff7a

> color :639 #0058ff

> color :640 #0064ff

> color :641 #007cff

> color :642 #0050ff

> color :643 #0020ff

> color :644 #0054ff

> color :645 #0048ff

> color :646 #005cff

> color :647 #001cff

> color :648 #005cff

> color :649 #003cff

> color :650 #0000ff

> color :651 #0024ff

> color :652 #002cff

> color :653 #006cff

> color :654 #0084ff

> color :655 #0008ff

> color :656 #0000ed

> color :657 #0080ff

> color :658 #0020ff

> color :659 #0044ff

> color :660 #003cff

> color :661 #0040ff

> color :662 #0068ff

> color :663 #0020ff

> color :664 #006cff

> color :665 #0064ff

> color :666 #0018ff

> color :667 #0034ff

> color :668 #0030ff

> color :669 #005cff

> color :670 #009cff

> color :671 #00bcff

> color :672 #001cff

> color :673 #00e4f8

> color :674 #00a8ff

> color :675 #006cff

> color :676 #0060ff

> color :677 #004cff

> color :678 #002cff

> color :679 #00a4ff

> color :680 #00a0ff

> color :681 #004cff

> color :682 #0088ff

> color :683 #004cff

> color :684 #0024ff

> color :685 #0024ff

> color :686 #0008ff

> color :687 #0098ff

> color :688 #004cff

> color :689 #0000ff

> color :690 #005cff

> color :691 #0030ff

> color :692 #000cff

> color :693 #0024ff

> color :694 #0064ff

> color :695 #0058ff

> color :696 #0004ff

> color :697 #00c8ff

> color :698 #0058ff

> color :699 #0054ff

> color :700 #0028ff

> color :701 #0030ff

> color :702 #0024ff

> color :703 #0008ff

> color :704 #0090ff

> color :705 #0084ff

> color :706 #0000ff

> color :707 #0084ff

> color :708 #0020ff

> color :709 #0054ff

> color :710 #0044ff

> color :711 #0038ff

> color :712 #0008ff

> color :713 #0008ff

> color :714 #0000ff

> color :715 #0070ff

> color :716 #009cff

> color :717 #0004ff

> color :718 #009cff

> color :719 #0048ff

> color :720 #0078ff

> color :721 #0048ff

> color :722 #004cff

> color :723 #009cff

> color :724 #0024ff

> color :725 #0064ff

> color :726 #0008ff

> color :727 #0000f6

> color :728 #0034ff

> color :729 #0010ff

> color :730 #000cff

> color :731 #0024ff

> color :732 #0000ff

> color :733 #0014ff

> color :734 #00b8ff

> color :735 #00acff

> color :736 #0054ff

> color :737 #0018ff

> color :738 #0004ff

> color :739 #13fce4

> color :740 #007cff

> color :741 #0098ff

> color :742 #5aff9d

> color :743 #5dff9a

> color :744 #baff3c

> color :745 #00b4ff

> color :746 white

> color :747 #30ffc7

> color :748 #00b8ff

> color :749 #00c8ff

> color :750 #00b8ff

> color :751 #00a8ff

> color :752 #0064ff

> color :753 #007cff

> color :754 #007cff

> color :755 #0040ff

executed color_mapping_chimerax.cxc  

> close #2

> mmaker #3 to #1/D

Computing secondary structure  
Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 8hk1, chain D (#1) with AlphaFold O43719, chain A (#3), sequence
alignment score = 2907.9  
RMSD between 98 pruned atom pairs is 0.833 angstroms; (across all 113 pairs:
1.613)  
  

> hide #!1 models

> close #3

> close #1

> close #5-6

> open /Volumes/groups/plaschka/max.graf/color_mapping_chimerax.cxc

> alphafold fetch O43719

Chain information for AlphaFold O43719 #1  
---  
Chain | Description | UniProt  
A | HIV Tat-specific factor 1 | HTSF1_HUMAN 1-755  
  
Color AlphaFold O43719 by residue attribute pLDDT_score  

> color :1 #ebff0c

> color :2 #009cff

> color :3 #0060ff

> color :4 #0000ff

> color :5 #003cff

> color :6 #0008ff

> color :7 #0044ff

> color :8 #0048ff

> color :9 #007cff

> color :10 #0074ff

> color :11 #83ff73

> color :12 #ed0400

> color :13 #13fce4

> color :14 #ffb900

> color :15 #ff6f00

> color :16 #ff7300

> color :17 #ff6f00

> color :18 #ff5d00

> color :19 #ff9f00

> color :20 #8aff6d

> color :21 #c1ff36

> color :22 #f8f500

> color :23 white

> color :24 #0064ff

> color :25 #0000ff

> color :26 #0094ff

> color :27 #0044ff

> color :28 #002cff

> color :29 #0054ff

> color :30 #0004ff

> color :31 #001cff

> color :32 #0000ff

> color :33 #0030ff

> color :34 #0000ff

> color :35 #0008ff

> color :36 #0014ff

> color :37 #0050ff

> color :38 #0000ff

> color :39 #0028ff

> color :40 #002cff

> color :41 #0000ff

> color :42 #0040ff

> color :43 #0088ff

> color :44 #0048ff

> color :45 #004cff

> color :46 #0024ff

> color :47 #6dff8a

> color :48 #90ff66

> color :49 #73ff83

> color :50 #ff4300

> color :51 #ff3400

> color :52 #890000

> color :53 #9b0000

> color :54 #00c4ff

> color :55 #ffe600

> color :56 #d60000

> color :57 #ff6f00

> color :58 #b60000

> color :59 #920000

> color :60 #8d0000

> color :61 #840000

> color :62 #ff6f00

> color :63 #e80000

> color :64 #ff6800

> color :65 #ff3000

> color :66 #a40000

> color :67 #8d0000

> color :68 #ff4e00

> color :69 #bb0000

> color :70 #73ff83

> color :71 #a80000

> color :72 #ff3800

> color :73 #ff3f00

> color :74 #ff7e00

> color :75 #c40000

> color :76 #bb0000

> color :77 #ff2500

> color :78 #00acff

> color :79 #0048ff

> color :80 #00e0fb

> color :81 #00d8ff

> color :82 #0080ff

> color :83 #00a4ff

> color :84 #008cff

> color :85 #00bcff

> color :86 #0044ff

> color :87 #0064ff

> color :88 #0024ff

> color :89 #002cff

> color :90 #0054ff

> color :91 #0058ff

> color :92 #0018ff

> color :93 #0000f6

> color :94 #0014ff

> color :95 #0014ff

> color :96 #0008ff

> color :97 #0028ff

> color :98 #0060ff

> color :99 #0058ff

> color :100 #000cff

> color :101 #000cff

> color :102 #0034ff

> color :103 #0044ff

> color :104 #006cff

> color :105 #0004ff

> color :106 #001cff

> color :107 #0060ff

> color :108 #0020ff

> color :109 #0024ff

> color :110 #0074ff

> color :111 #0010ff

> color :112 #006cff

> color :113 #1fffd7

> color :114 white

> color :115 #e1ff16

> color :116 #ffb900

> color :117 #fa0f00

> color :118 #ff2500

> color :119 #ff1300

> color :120 #0cf4eb

> color :121 #e4ff13

> color :122 #0cf4eb

> color :123 #ff2d00

> color :124 #890000

> color :125 #8d0000

> color :126 #49ffad

> color :127 #f60b00

> color :128 #ff4a00

> color :129 #caff2c

> color :130 #87ff70

> color :131 #ff6c00

> color :132 #9f0000

> color :133 #bb0000

> color :134 #f60b00

> color :135 #a80000

> color :136 #920000

> color :137 #a40000

> color :138 #e40000

> color :139 #890000

> color :140 #9b0000

> color :141 #800000

> color :142 #ffb900

> color :143 #920000

> color :144 #ff1600

> color :145 #ff3b00

> color :146 #8aff6d

> color :147 #ff5900

> color :148 #890000

> color :149 #890000

> color :150 #ff5200

> color :151 #9dff5a

> color :152 #ff4a00

> color :153 #960000

> color :154 #ff3f00

> color :155 #c40000

> color :156 #d10000

> color :157 #800000

> color :158 #a80000

> color :159 #c40000

> color :160 #c80000

> color :161 #ff4a00

> color :162 #9f0000

> color :163 #ff3f00

> color :164 #09f0ee

> color :165 #ff3800

> color :166 #ff8600

> color :167 #ff8200

> color :168 #ff2500

> color :169 #9b0000

> color :170 #c40000

> color :171 #8d0000

> color :172 #a40000

> color :173 #890000

> color :174 #da0000

> color :175 #840000

> color :176 white

> color :177 #8aff6d

> color :178 #840000

> color :179 #ff9c00

> color :180 #ff2d00

> color :181 #920000

> color :182 #800000

> color :183 #800000

> color :184 #890000

> color :185 #8d0000

> color :186 #840000

> color :187 #920000

> color :188 #9b0000

> color :189 #9b0000

> color :190 #960000

> color :191 #ff6f00

> color :192 #840000

> color :193 #8d0000

> color :194 #b20000

> color :195 #8aff6d

> color :196 #8d0000

> color :197 #920000

> color :198 #ff8600

> color :199 #ff8d00

> color :200 #ed0400

> color :201 #a80000

> color :202 #890000

> color :203 #ff7a00

> color :204 #ff3400

> color :205 #ff8d00

> color :206 #ff1e00

> color :207 #920000

> color :208 #8d0000

> color :209 #ff4e00

> color :210 #ff9c00

> color :211 #e40000

> color :212 #cd0000

> color :213 #a40000

> color :214 #9b0000

> color :215 #dbff1c

> color :216 #840000

> color :217 #ffb200

> color :218 #800000

> color :219 #ff4e00

> color :220 #bb0000

> color :221 #a80000

> color :222 #840000

> color :223 #ffb200

> color :224 #ad0000

> color :225 #9f0000

> color :226 #ff4a00

> color :227 #ffcc00

> color :228 #cd0000

> color :229 #bb0000

> color :230 #ed0400

> color :231 #da0000

> color :232 #fa0f00

> color :233 #ffb200

> color :234 #ff1600

> color :235 #f60b00

> color :236 #ff2200

> color :237 #fa0f00

> color :238 #ed0400

> color :239 #ff2900

> color :240 #ff9400

> color :241 #87ff70

> color :242 #80ff77

> color :243 #fa0f00

> color :244 #ff9c00

> color :245 #df0000

> color :246 #ffb600

> color :247 #960000

> color :248 #960000

> color :249 #800000

> color :250 #cd0000

> color :251 #8d0000

> color :252 #e40000

> color :253 #ff5d00

> color :254 white

> color :255 #0ff8e7

> color :256 #baff3c

> color :257 #00e4f8

> color :258 #00e4f8

> color :259 #e40000

> color :260 #deff19

> color :261 #ff1600

> color :262 #ff6400

> color :263 #b60000

> color :264 #ff8900

> color :265 #d60000

> color :266 #cd0000

> color :267 #c80000

> color :268 #ff2200

> color :269 #ff3f00

> color :270 #d60000

> color :271 #bb0000

> color :272 #890000

> color :273 #ff4300

> color :274 #bb0000

> color :275 #06ecf1

> color :276 #bf0000

> color :277 #8d0000

> color :278 #ff2500

> color :279 #f1fc06

> color :280 #b60000

> color :281 #a40000

> color :282 #ff7300

> color :283 #ff7a00

> color :284 #c80000

> color :285 #ff4a00

> color :286 #b20000

> color :287 #e80000

> color :288 #ff3800

> color :289 #ff5500

> color :290 #890000

> color :291 #d60000

> color :292 #ffae00

> color :293 #b1ff46

> color :294 #920000

> color :295 #9b0000

> color :296 #8dff6a

> color :297 #df0000

> color :298 #b20000

> color :299 #840000

> color :300 #16ffe1

> color :301 #ff3800

> color :302 #ff4e00

> color :303 #c40000

> color :304 #ff4a00

> color :305 #ff6000

> color :306 #ff2200

> color :307 #920000

> color :308 #840000

> color :309 #ff1a00

> color :310 #9b0000

> color :311 #ff2200

> color :312 #ffab00

> color :313 #800000

> color :314 #c40000

> color :315 #bb0000

> color :316 #ff1e00

> color :317 #c80000

> color :318 #ff9f00

> color :319 #9f0000

> color :320 #ffc400

> color :321 #9dff5a

> color :322 #ffd000

> color :323 #aaff4d

> color :324 #ff3400

> color :325 #cd0000

> color :326 #e80000

> color :327 #0094ff

> color :328 #920000

> color :329 #ff4300

> color :330 white

> color :331 #7aff7d

> color :332 #ff2200

> color :333 #e7ff0f

> color :334 #e80000

> color :335 #9b0000

> color :336 #b20000

> color :337 #8d0000

> color :338 #c40000

> color :339 #da0000

> color :340 #f10800

> color :341 #ffa300

> color :342 #f10800

> color :343 #40ffb7

> color :344 #f10800

> color :345 #3cffba

> color :346 #6aff8d

> color :347 #840000

> color :348 #9b0000

> color :349 #840000

> color :350 #30ffc7

> color :351 #ffb600

> color :352 #b20000

> color :353 #da0000

> color :354 #ff6f00

> color :355 #f60b00

> color :356 #ff5500

> color :357 #890000

> color :358 #ff2900

> color :359 #26ffd1

> color :360 #ffe200

> color :361 #bb0000

> color :362 #ff3000

> color :363 #ff9100

> color :364 #ffae00

> color :365 #960000

> color :366 #ff3b00

> color :367 #1fffd7

> color :368 #c7ff30

> color :369 #890000

> color :370 #ffcc00

> color :371 #00b0ff

> color :372 #d60000

> color :373 #ff2500

> color :374 #00a4ff

> color :375 #0070ff

> color :376 #00ccff

> color :377 #09f0ee

> color :378 #0064ff

> color :379 #0044ff

> color :380 #0034ff

> color :381 #0058ff

> color :382 #0004ff

> color :383 #0000ff

> color :384 #0004ff

> color :385 #0024ff

> color :386 #003cff

> color :387 #0038ff

> color :388 #0020ff

> color :389 #0000fa

> color :390 #0054ff

> color :391 #0044ff

> color :392 #0074ff

> color :393 #001cff

> color :394 #0094ff

> color :395 #00d0ff

> color :396 #00d4ff

> color :397 #00d0ff

> color :398 #0088ff

> color :399 #0024ff

> color :400 #00acff

> color :401 #0064ff

> color :402 #83ff73

> color :403 #00a4ff

> color :404 #00a0ff

> color :405 #0008ff

> color :406 #0024ff

> color :407 #001cff

> color :408 #0010ff

> color :409 #0034ff

> color :410 #0040ff

> color :411 #0074ff

> color :412 #001cff

> color :413 #0010ff

> color :414 #001cff

> color :415 #0068ff

> color :416 #0004ff

> color :417 #0028ff

> color :418 #0008ff

> color :419 #0014ff

> color :420 #0084ff

> color :421 #0034ff

> color :422 #005cff

> color :423 #0098ff

> color :424 #0080ff

> color :425 #0024ff

> color :426 #0034ff

> color :427 #0048ff

> color :428 #00a0ff

> color :429 #0078ff

> color :430 #0074ff

> color :431 #007cff

> color :432 #0088ff

> color :433 #0094ff

> color :434 #0010ff

> color :435 #0070ff

> color :436 #002cff

> color :437 #000cff

> color :438 #000cff

> color :439 #0028ff

> color :440 #000cff

> color :441 #007cff

> color :442 #003cff

> color :443 #0000ff

> color :444 #0014ff

> color :445 #0000ff

> color :446 #0038ff

> color :447 #0014ff

> color :448 #0000ff

> color :449 #0018ff

> color :450 #0054ff

> color :451 #0048ff

> color :452 #0000fa

> color :453 #0000ed

> color :454 #0000ff

> color :455 #0034ff

> color :456 #0034ff

> color :457 #0034ff

> color :458 #0004ff

> color :459 #0040ff

> color :460 #0034ff

> color :461 #0000ff

> color :462 #0008ff

> color :463 #0000ff

> color :464 #0038ff

> color :465 #0040ff

> color :466 #0030ff

> color :467 #0000ff

> color :468 #0054ff

> color :469 #0034ff

> color :470 #0008ff

> color :471 #0018ff

> color :472 #0000ff

> color :473 #003cff

> color :474 #0000ff

> color :475 #0000ff

> color :476 #0000ff

> color :477 #0034ff

> color :478 #0008ff

> color :479 #0000f6

> color :480 #0000ff

> color :481 #0000f6

> color :482 #0004ff

> color :483 #0034ff

> color :484 #001cff

> color :485 #0000e3

> color :486 #002cff

> color :487 #001cff

> color :488 #0000ff

> color :489 #0000ed

> color :490 #0000fa

> color :491 #0000e8

> color :492 #0000fa

> color :493 #0000ff

> color :494 #0000fa

> color :495 #0028ff

> color :496 #0028ff

> color :497 #0000ff

> color :498 #0000ed

> color :499 #0000ff

> color :500 #0040ff

> color :501 #0058ff

> color :502 #0034ff

> color :503 #0000ff

> color :504 #0044ff

> color :505 #0044ff

> color :506 #0040ff

> color :507 #0000e3

> color :508 #0000e3

> color :509 #004cff

> color :510 #0000ff

> color :511 #0004ff

> color :512 #0000fa

> color :513 #0050ff

> color :514 #005cff

> color :515 #0044ff

> color :516 #0018ff

> color :517 #0000f6

> color :518 #0004ff

> color :519 #0050ff

> color :520 #0034ff

> color :521 #0004ff

> color :522 #0050ff

> color :523 #0014ff

> color :524 #0010ff

> color :525 #0000df

> color :526 #0000ff

> color :527 #0044ff

> color :528 #0028ff

> color :529 #0008ff

> color :530 #0040ff

> color :531 #0034ff

> color :532 #0040ff

> color :533 #0000ed

> color :534 #0000ff

> color :535 #0000ff

> color :536 #0000ff

> color :537 #006cff

> color :538 #0048ff

> color :539 #0010ff

> color :540 #0054ff

> color :541 #0050ff

> color :542 #0024ff

> color :543 #0020ff

> color :544 #0020ff

> color :545 #0058ff

> color :546 #003cff

> color :547 #0054ff

> color :548 #0014ff

> color :549 #000cff

> color :550 #0060ff

> color :551 #002cff

> color :552 #0000ff

> color :553 #0018ff

> color :554 #0074ff

> color :555 #0068ff

> color :556 #0004ff

> color :557 #0000ff

> color :558 #0050ff

> color :559 #0014ff

> color :560 #0000ff

> color :561 #0014ff

> color :562 #0050ff

> color :563 #0000ff

> color :564 #0030ff

> color :565 #000cff

> color :566 #0058ff

> color :567 #0060ff

> color :568 #0030ff

> color :569 #000cff

> color :570 #0000f6

> color :571 #002cff

> color :572 #0048ff

> color :573 #0014ff

> color :574 #0000df

> color :575 #0010ff

> color :576 #0034ff

> color :577 #0014ff

> color :578 #0000ff

> color :579 #0008ff

> color :580 #003cff

> color :581 #0040ff

> color :582 #0030ff

> color :583 #0000e3

> color :584 #0000e8

> color :585 #0040ff

> color :586 #0030ff

> color :587 #000cff

> color :588 #0000f6

> color :589 #0014ff

> color :590 #0078ff

> color :591 #0054ff

> color :592 #0000f1

> color :593 #0058ff

> color :594 #0060ff

> color :595 #0044ff

> color :596 #002cff

> color :597 #0028ff

> color :598 #0074ff

> color :599 #0014ff

> color :600 #004cff

> color :601 #0068ff

> color :602 #0044ff

> color :603 #0068ff

> color :604 #004cff

> color :605 #002cff

> color :606 #0008ff

> color :607 #0050ff

> color :608 #0070ff

> color :609 #008cff

> color :610 #0030ff

> color :611 #0000ff

> color :612 #0038ff

> color :613 #0060ff

> color :614 #0094ff

> color :615 #002cff

> color :616 #0054ff

> color :617 #0064ff

> color :618 #0028ff

> color :619 #0068ff

> color :620 #0058ff

> color :621 #0024ff

> color :622 #005cff

> color :623 #0028ff

> color :624 #0048ff

> color :625 #0018ff

> color :626 #0070ff

> color :627 #007cff

> color :628 #005cff

> color :629 #0040ff

> color :630 #0048ff

> color :631 #004cff

> color :632 #002cff

> color :633 #0000ff

> color :634 #0054ff

> color :635 #00acff

> color :636 #0088ff

> color :637 #02e8f4

> color :638 #7dff7a

> color :639 #0058ff

> color :640 #0064ff

> color :641 #007cff

> color :642 #0050ff

> color :643 #0020ff

> color :644 #0054ff

> color :645 #0048ff

> color :646 #005cff

> color :647 #001cff

> color :648 #005cff

> color :649 #003cff

> color :650 #0000ff

> color :651 #0024ff

> color :652 #002cff

> color :653 #006cff

> color :654 #0084ff

> color :655 #0008ff

> color :656 #0000ed

> color :657 #0080ff

> color :658 #0020ff

> color :659 #0044ff

> color :660 #003cff

> color :661 #0040ff

> color :662 #0068ff

> color :663 #0020ff

> color :664 #006cff

> color :665 #0064ff

> color :666 #0018ff

> color :667 #0034ff

> color :668 #0030ff

> color :669 #005cff

> color :670 #009cff

> color :671 #00bcff

> color :672 #001cff

> color :673 #00e4f8

> color :674 #00a8ff

> color :675 #006cff

> color :676 #0060ff

> color :677 #004cff

> color :678 #002cff

> color :679 #00a4ff

> color :680 #00a0ff

> color :681 #004cff

> color :682 #0088ff

> color :683 #004cff

> color :684 #0024ff

> color :685 #0024ff

> color :686 #0008ff

> color :687 #0098ff

> color :688 #004cff

> color :689 #0000ff

> color :690 #005cff

> color :691 #0030ff

> color :692 #000cff

> color :693 #0024ff

> color :694 #0064ff

> color :695 #0058ff

> color :696 #0004ff

> color :697 #00c8ff

> color :698 #0058ff

> color :699 #0054ff

> color :700 #0028ff

> color :701 #0030ff

> color :702 #0024ff

> color :703 #0008ff

> color :704 #0090ff

> color :705 #0084ff

> color :706 #0000ff

> color :707 #0084ff

> color :708 #0020ff

> color :709 #0054ff

> color :710 #0044ff

> color :711 #0038ff

> color :712 #0008ff

> color :713 #0008ff

> color :714 #0000ff

> color :715 #0070ff

> color :716 #009cff

> color :717 #0004ff

> color :718 #009cff

> color :719 #0048ff

> color :720 #0078ff

> color :721 #0048ff

> color :722 #004cff

> color :723 #009cff

> color :724 #0024ff

> color :725 #0064ff

> color :726 #0008ff

> color :727 #0000f6

> color :728 #0034ff

> color :729 #0010ff

> color :730 #000cff

> color :731 #0024ff

> color :732 #0000ff

> color :733 #0014ff

> color :734 #00b8ff

> color :735 #00acff

> color :736 #0054ff

> color :737 #0018ff

> color :738 #0004ff

> color :739 #13fce4

> color :740 #007cff

> color :741 #0098ff

> color :742 #5aff9d

> color :743 #5dff9a

> color :744 #baff3c

> color :745 #00b4ff

> color :746 white

> color :747 #30ffc7

> color :748 #00b8ff

> color :749 #00c8ff

> color :750 #00b8ff

> color :751 #00a8ff

> color :752 #0064ff

> color :753 #007cff

> color :754 #007cff

> color :755 #0040ff

executed color_mapping_chimerax.cxc  

> open 8HKI

Summary of feedback from opening 8HKI fetched from pdb  
---  
note | Fetching compressed mmCIF 8hki from http://files.rcsb.org/download/8hki.cif  
  
8hki title:  
Human TRiC open state [more info...]  
  
Chain information for 8hki #2  
---  
Chain | Description | UniProt  
A a | T-complex protein 1 subunit alpha | TCPA_HUMAN 1-556  
B b | T-complex protein 1 subunit beta | TCPB_HUMAN 1-535  
D d | T-complex protein 1 subunit delta | TCPD_HUMAN 1-539  
E e | T-complex protein 1 subunit epsilon | TCPE_HUMAN 1-539  
G g | T-complex protein 1 subunit gamma | TCPG_HUMAN 1-545  
H h | T-complex protein 1 subunit eta | TCPH_HUMAN 1-543  
Q q | T-complex protein 1 subunit theta | TCPQ_HUMAN 1-548  
Z z | T-complex protein 1 subunit zeta | TCPZ_HUMAN 1-531  
  
Non-standard residues in 8hki #2  
---  
ADP — adenosine-5'-diphosphate  
  

> mmaker #1 to #2/D

Computing secondary structure  
Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 8hki, chain D (#2) with AlphaFold O43719, chain A (#1), sequence
alignment score = 11.6  
RMSD between 9 pruned atom pairs is 1.364 angstroms; (across all 69 pairs:
36.301)  
  

> hide #2 target acs

> show #2 target c

> close #2

> open 8HK1

8hk1 title:  
The cryo-EM structure of human pre-17S U2 snRNP [more info...]  
  
Chain information for 8hk1 #2  
---  
Chain | Description | UniProt  
1 | Splicing factor 3B subunit 1 | SF3B1_HUMAN 1-1304  
2 | Splicing factor 3B subunit 2 | SF3B2_HUMAN 1-895  
3 | Splicing factor 3B subunit 3 | SF3B3_HUMAN 1-1217  
4 | Splicing factor 3B subunit 4 | SF3B4_HUMAN 1-424  
5 | Splicing factor 3B subunit 5 | SF3B5_HUMAN 1-86  
6 | PHD finger-like domain-containing protein 5A | PHF5A_HUMAN 1-110  
A | Splicing factor 3A subunit 1 | SF3A1_HUMAN 1-793  
B | Splicing factor 3A subunit 2 | SF3A2_HUMAN 1-464  
C | Splicing factor 3A subunit 3 | SF3A3_HUMAN 1-501  
D | HIV Tat-specific factor 1 | HTSF1_HUMAN 1-755  
E | ATP-dependent RNA helicase DDX42 | DDX42_HUMAN 1-938  
F | U2 small nuclear ribonucleoprotein A' | RU2A_HUMAN 1-255  
G | U2 small nuclear ribonucleoprotein B'' | RU2B_HUMAN 4-225  
H | U2 snRNA |   
a | Small nuclear ribonucleoprotein Sm D2 | SMD2_HUMAN 1-118  
b | Small nuclear ribonucleoprotein F | RUXF_HUMAN 1-86  
c | Small nuclear ribonucleoprotein E | RUXE_HUMAN 1-92  
d | Small nuclear ribonucleoprotein G | RUXG_HUMAN 1-76  
e | Small nuclear ribonucleoprotein Sm D3 | SMD3_HUMAN 1-126  
f | Small nuclear ribonucleoprotein-associated proteins B and B' | RSMB_HUMAN 1-240  
g | Small nuclear ribonucleoprotein Sm D1 | SMD1_HUMAN 1-119  
  
Non-standard residues in 8hk1 #2  
---  
9B0 —
[(2~{S},3~{S},4~{E},6~{S},7~{R},10~{R})-3,7-dimethyl-2-[(2~{E},4~{E},6~{R})-6-methyl-6-oxidanyl-7-[(2~{R},3~{R})-3-[(2~{R},3~{S})-3-oxidanylpentan-2-yl]oxiran-2-yl]hepta-2,4-dien-2-yl]-7,10-bis(oxidanyl)-12-oxidanylidene-1-oxacyclododec-4-en-6-yl]
4-cycloheptylpiperazine-1-carboxylate  
ZN — zinc ion  
  

> hide #2 target acs

> show #2 target c

> mmaker #1 to #2/D

Computing secondary structure  
Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 8hk1, chain D (#2) with AlphaFold O43719, chain A (#1), sequence
alignment score = 2907.9  
RMSD between 98 pruned atom pairs is 0.833 angstroms; (across all 113 pairs:
1.613)  
  

> open /Volumes/groups/plaschka/max.graf/LENG8_color_mapping_chimerax.cxc

> alphafold fetch Q96PV6

Fetching compressed AlphaFold Q96PV6 from
https://alphafold.ebi.ac.uk/files/AF-Q96PV6-F1-model_v4.cif  
Chain information for AlphaFold Q96PV6 #3  
---  
Chain | Description | UniProt  
A | Leukocyte receptor cluster member 8 | LENG8_HUMAN 1-800  
  
Color AlphaFold Q96PV6 by residue attribute pLDDT_score  

> color :1 #ff4300

> color :2 #ff7300

> color :3 #a7ff50

> color :4 #5dff9a

> color :5 #16ffe1

> color :6 #c1ff36

> color :7 #6dff8a

> color :8 #0080ff

> color :9 #006cff

> color :10 #0054ff

> color :11 #0014ff

> color :12 #0ff8e7

> color :13 #ff9100

> color :14 #0094ff

> color :15 #0064ff

> color :16 #16ffe1

> color :17 #f1fc06

> color :18 #00a8ff

> color :19 #0078ff

> color :20 #0070ff

> color :21 #0074ff

> color :22 #0094ff

> color :23 #0024ff

> color :24 #004cff

> color :25 #00dcfe

> color :26 #a4ff53

> color :27 #0094ff

> color :28 #00acff

> color :29 #00a8ff

> color :30 #beff39

> color :31 #004cff

> color :32 #33ffc4

> color :33 #16ffe1

> color :34 white

> color :35 #9f0000

> color :36 #b60000

> color :37 #920000

> color :38 #a40000

> color :39 #800000

> color :40 #890000

> color :41 #ad0000

> color :42 #840000

> color :43 #840000

> color :44 #ff1e00

> color :45 #8d0000

> color :46 #890000

> color :47 #e40000

> color :48 #ffab00

> color :49 #c40000

> color :50 #ffc400

> color :51 #ff2900

> color :52 #30ffc7

> color :53 #26ffd1

> color :54 #0ff8e7

> color :55 #00c8ff

> color :56 #00d8ff

> color :57 #0098ff

> color :58 #00b0ff

> color :59 #0078ff

> color :60 #b1ff46

> color :61 #007cff

> color :62 #00c0ff

> color :63 #008cff

> color :64 #005cff

> color :65 #00c4ff

> color :66 #005cff

> color :67 #0090ff

> color :68 #00b4ff

> color :69 #00dcfe

> color :70 #06ecf1

> color :71 #3cffba

> color :72 #b7ff40

> color :73 #09f0ee

> color :74 #46ffb1

> color :75 #13fce4

> color :76 #09f0ee

> color :77 #ebff0c

> color :78 #0ff8e7

> color :79 #1fffd7

> color :80 #06ecf1

> color :81 #00e4f8

> color :82 #6aff8d

> color :83 #56ffa0

> color :84 #8dff6a

> color :85 #a0ff56

> color :86 #fbf100

> color :87 #9aff5d

> color :88 #9dff5a

> color :89 #ff2d00

> color :90 #ff9f00

> color :91 #9aff5d

> color :92 #5dff9a

> color :93 #eeff09

> color :94 #49ffad

> color :95 #50ffa7

> color :96 #00e0fb

> color :97 white

> color :98 #ffc800

> color :99 #87ff70

> color :100 #43ffb4

> color :101 white

> color :102 #1cffdb

> color :103 #97ff60

> color :104 #ffa700

> color :105 #73ff83

> color :106 #63ff94

> color :107 #46ffb1

> color :108 white

> color :109 #40ffb7

> color :110 #56ffa0

> color :111 #2cffca

> color :112 white

> color :113 #00e0fb

> color :114 #00dcfe

> color :115 #0cf4eb

> color :116 #29ffce

> color :117 #b1ff46

> color :118 white

> color :119 #2cffca

> color :120 #00c8ff

> color :121 #00c8ff

> color :122 #00e0fb

> color :123 #1cffdb

> color :124 #0084ff

> color :125 #00c8ff

> color :126 #0088ff

> color :127 #0054ff

> color :128 #0048ff

> color :129 #00c0ff

> color :130 #00b4ff

> color :131 #005cff

> color :132 #007cff

> color :133 #0074ff

> color :134 #0068ff

> color :135 #00b0ff

> color :136 #0094ff

> color :137 #00d4ff

> color :138 white

> color :139 #0058ff

> color :140 #0070ff

> color :141 #007cff

> color :142 #1fffd7

> color :143 #16ffe1

> color :144 #00c4ff

> color :145 #b1ff46

> color :146 #3cffba

> color :147 #00d8ff

> color :148 white

> color :149 #a0ff56

> color :150 #7dff7a

> color :151 #009cff

> color :152 #00b8ff

> color :153 #008cff

> color :154 white

> color :155 #0078ff

> color :156 #0078ff

> color :157 #0030ff

> color :158 #0044ff

> color :159 #0088ff

> color :160 #0080ff

> color :161 #003cff

> color :162 #005cff

> color :163 #0034ff

> color :164 #004cff

> color :165 #0058ff

> color :166 #0038ff

> color :167 #0040ff

> color :168 #0068ff

> color :169 #0034ff

> color :170 #0044ff

> color :171 #0020ff

> color :172 #0000ff

> color :173 #0000ff

> color :174 #0014ff

> color :175 #0044ff

> color :176 #002cff

> color :177 #0010ff

> color :178 #0014ff

> color :179 #001cff

> color :180 #0038ff

> color :181 #0054ff

> color :182 #0088ff

> color :183 #0020ff

> color :184 #0070ff

> color :185 #0038ff

> color :186 #00b0ff

> color :187 #003cff

> color :188 #0054ff

> color :189 #0044ff

> color :190 #0068ff

> color :191 #0038ff

> color :192 #006cff

> color :193 #0044ff

> color :194 #005cff

> color :195 #0064ff

> color :196 #0040ff

> color :197 #0050ff

> color :198 #0014ff

> color :199 #0034ff

> color :200 #0010ff

> color :201 #005cff

> color :202 #003cff

> color :203 #0050ff

> color :204 #0078ff

> color :205 #006cff

> color :206 #001cff

> color :207 #0054ff

> color :208 #0028ff

> color :209 #00a8ff

> color :210 #0020ff

> color :211 #7dff7a

> color :212 #005cff

> color :213 #0080ff

> color :214 #ffb200

> color :215 #00c0ff

> color :216 #ff8900

> color :217 #ff9f00

> color :218 #feed00

> color :219 #30ffc7

> color :220 white

> color :221 #c1ff36

> color :222 #ed0400

> color :223 #1cffdb

> color :224 #ff6c00

> color :225 #ff6000

> color :226 #ff2900

> color :227 #00c0ff

> color :228 #f1fc06

> color :229 #ffc800

> color :230 #ff8200

> color :231 #2cffca

> color :232 #aaff4d

> color :233 #73ff83

> color :234 #deff19

> color :235 #f10800

> color :236 #a80000

> color :237 #e1ff16

> color :238 #ff5200

> color :239 #83ff73

> color :240 #cd0000

> color :241 #e40000

> color :242 #ffb900

> color :243 #ffb200

> color :244 #09f0ee

> color :245 #49ffad

> color :246 #16ffe1

> color :247 #0054ff

> color :248 #00dcfe

> color :249 #0078ff

> color :250 #a0ff56

> color :251 #0048ff

> color :252 #0054ff

> color :253 #0000ff

> color :254 #0014ff

> color :255 #00c0ff

> color :256 #0038ff

> color :257 #004cff

> color :258 #0028ff

> color :259 #0040ff

> color :260 #0038ff

> color :261 #00d8ff

> color :262 #0070ff

> color :263 #0004ff

> color :264 #0050ff

> color :265 #000cff

> color :266 #000cff

> color :267 #0000ff

> color :268 #0ff8e7

> color :269 #00e0fb

> color :270 #0004ff

> color :271 #003cff

> color :272 #002cff

> color :273 #000cff

> color :274 #0020ff

> color :275 #0018ff

> color :276 #000cff

> color :277 #0020ff

> color :278 #0008ff

> color :279 #004cff

> color :280 #005cff

> color :281 #0024ff

> color :282 #0004ff

> color :283 #00b8ff

> color :284 #5dff9a

> color :285 #ff8600

> color :286 #ff3400

> color :287 #80ff77

> color :288 #ff1600

> color :289 #890000

> color :290 #800000

> color :291 #50ffa7

> color :292 #ff9400

> color :293 #960000

> color :294 #b20000

> color :295 #ff9100

> color :296 #960000

> color :297 #920000

> color :298 #ff3400

> color :299 #8d0000

> color :300 #840000

> color :301 #800000

> color :302 #dbff1c

> color :303 #ff7700

> color :304 #840000

> color :305 #ff8d00

> color :306 #ffab00

> color :307 #9f0000

> color :308 #ff6000

> color :309 #ad0000

> color :310 #9f0000

> color :311 #890000

> color :312 #ffae00

> color :313 #bb0000

> color :314 #840000

> color :315 #ff9400

> color :316 #ffe600

> color :317 #800000

> color :318 #9f0000

> color :319 #ff6800

> color :320 #ff9800

> color :321 #8d0000

> color :322 #ff8900

> color :323 #9dff5a

> color :324 #a80000

> color :325 #a80000

> color :326 #e4ff13

> color :327 #a40000

> color :328 #9b0000

> color :329 #ff6000

> color :330 #a80000

> color :331 #fa0f00

> color :332 #ffae00

> color :333 #e80000

> color :334 #bf0000

> color :335 #800000

> color :336 #ffc400

> color :337 #f4f802

> color :338 #890000

> color :339 #ff2500

> color :340 #bf0000

> color :341 #8d0000

> color :342 #ceff29

> color :343 white

> color :344 #0038ff

> color :345 #00a0ff

> color :346 #2cffca

> color :347 #0034ff

> color :348 #003cff

> color :349 #004cff

> color :350 #0ff8e7

> color :351 #23ffd4

> color :352 #8dff6a

> color :353 #ff3400

> color :354 #ff4300

> color :355 #ff9800

> color :356 #ff2500

> color :357 #c80000

> color :358 #ff9400

> color :359 #008cff

> color :360 #0060ff

> color :361 #008cff

> color :362 #0064ff

> color :363 #0030ff

> color :364 #002cff

> color :365 #0030ff

> color :366 #0028ff

> color :367 #00a0ff

> color :368 #0080ff

> color :369 #0038ff

> color :370 #0040ff

> color :371 #0044ff

> color :372 #0038ff

> color :373 #0028ff

> color :374 #0088ff

> color :375 #0080ff

> color :376 #006cff

> color :377 #003cff

> color :378 #0038ff

> color :379 #0010ff

> color :380 #0070ff

> color :381 #0058ff

> color :382 #00acff

> color :383 #00c8ff

> color :384 #0040ff

> color :385 #0038ff

> color :386 #009cff

> color :387 #004cff

> color :388 #0088ff

> color :389 #0078ff

> color :390 #0050ff

> color :391 #007cff

> color :392 #23ffd4

> color :393 #0098ff

> color :394 white

> color :395 #60ff97

> color :396 #0070ff

> color :397 #00d0ff

> color :398 #ffe200

> color :399 #00a0ff

> color :400 #ff3f00

> color :401 #ff2900

> color :402 #ff1600

> color :403 #d1ff26

> color :404 #e40000

> color :405 #fa0f00

> color :406 #f60b00

> color :407 #a80000

> color :408 #beff39

> color :409 #ff2500

> color :410 #dbff1c

> color :411 #00a4ff

> color :412 #c1ff36

> color :413 #deff19

> color :414 #ffde00

> color :415 #ffc800

> color :416 #b7ff40

> color :417 #007cff

> color :418 white

> color :419 #ffd000

> color :420 #beff39

> color :421 #ff6f00

> color :422 #ff8900

> color :423 #ff6f00

> color :424 #9aff5d

> color :425 #ff7a00

> color :426 #80ff77

> color :427 #ffc400

> color :428 #ff9400

> color :429 #007cff

> color :430 #caff2c

> color :431 #6dff8a

> color :432 #ffdb00

> color :433 #ffa300

> color :434 #ff8200

> color :435 #ff7e00

> color :436 #ff9c00

> color :437 #ff9800

> color :438 #00b4ff

> color :439 #eeff09

> color :440 #feed00

> color :441 #dbff1c

> color :442 #ffe200

> color :443 #d7ff1f

> color :444 #d1ff26

> color :445 #00a8ff

> color :446 #c1ff36

> color :447 #7aff7d

> color :448 #0064ff

> color :449 #7aff7d

> color :450 #008cff

> color :451 #0024ff

> color :452 #004cff

> color :453 #0064ff

> color :454 #008cff

> color :455 white

> color :456 #7dff7a

> color :457 #0090ff

> color :458 #0054ff

> color :459 #005cff

> color :460 #0060ff

> color :461 #ff6800

> color :462 #56ffa0

> color :463 #ff9f00

> color :464 #b4ff43

> color :465 #9dff5a

> color :466 #ff5900

> color :467 #ffea00

> color :468 #43ffb4

> color :469 #1cffdb

> color :470 #63ff94

> color :471 #ff5d00

> color :472 #ff4700

> color :473 #ff9400

> color :474 #ff2d00

> color :475 #9aff5d

> color :476 #ff6800

> color :477 #19ffde

> color :478 #06ecf1

> color :479 #ff8d00

> color :480 #ffe200

> color :481 #ff8900

> color :482 #ffea00

> color :483 #004cff

> color :484 #baff3c

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> color :491 #00c0ff

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> color :494 white

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> color :503 #a4ff53

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> color :528 #ff1e00

> color :529 #ffbd00

> color :530 #87ff70

> color :531 #ffa300

> color :532 #00b8ff

> color :533 white

> color :534 #0090ff

> color :535 #0060ff

> color :536 #0034ff

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> color :538 #001cff

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> color :540 #0020ff

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> color :619 #9f0000

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> color :629 #8d0000

> color :630 #f10800

> color :631 #9f0000

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> color :633 #9f0000

> color :634 #ff5200

> color :635 #cd0000

> color :636 #800000

> color :637 #df0000

> color :638 #c80000

> color :639 #800000

> color :640 #9f0000

> color :641 #8d0000

> color :642 #8d0000

> color :643 #800000

> color :644 #b20000

> color :645 #ff1e00

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> color :647 #840000

> color :648 #c80000

> color :649 #ceff29

> color :650 #8d0000

> color :651 #ad0000

> color :652 #00e0fb

> color :653 #ff7700

> color :654 #00b8ff

> color :655 #dbff1c

> color :656 #0064ff

> color :657 #bb0000

> color :658 #d4ff23

> color :659 #63ff94

> color :660 #ff6800

> color :661 #890000

> color :662 #840000

> color :663 #ffb900

> color :664 #e80000

> color :665 #9b0000

> color :666 #960000

> color :667 #ff1e00

> color :668 #ff2500

> color :669 #960000

> color :670 #ff5500

> color :671 #ff4300

> color :672 #bb0000

> color :673 #c80000

> color :674 #d7ff1f

> color :675 #c80000

> color :676 #f1fc06

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> color :681 #e80000

> color :682 #ff1300

> color :683 #ff1a00

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> color :689 #0cf4eb

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> color :692 #007cff

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> color :694 #0078ff

> color :695 #ff7300

> color :696 #bf0000

> color :697 #00e4f8

> color :698 #df0000

> color :699 #e40000

> color :700 #ff1a00

> color :701 #1cffdb

> color :702 #ff3f00

> color :703 #b20000

> color :704 #00d0ff

> color :705 #df0000

> color :706 #bf0000

> color :707 #ff4300

> color :708 #ff9100

> color :709 #ffab00

> color :710 #da0000

> color :711 #ff2500

> color :712 #ff5900

> color :713 #a4ff53

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> color :716 #0080ff

> color :717 #ff2500

> color :718 #ff4300

> color :719 #0038ff

> color :720 #0010ff

> color :721 #ff5200

> color :722 #ad0000

> color :723 #49ffad

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> color :725 #ff8d00

> color :726 #ff9c00

> color :727 #ff6c00

> color :728 #e40000

> color :729 #ff4e00

> color :730 #df0000

> color :731 #ff8200

> color :732 #a40000

> color :733 #e7ff0f

> color :734 #1fffd7

> color :735 #ad0000

> color :736 #a40000

> color :737 #920000

> color :738 #d4ff23

> color :739 #006cff

> color :740 #ed0400

> color :741 #ff3b00

> color :742 #ff5900

> color :743 #fbf100

> color :744 #ff1600

> color :745 #ff3800

> color :746 #c80000

> color :747 #ff5200

> color :748 #cd0000

> color :749 #890000

> color :750 #960000

> color :751 #00d8ff

> color :752 #ff2900

> color :753 #ffdb00

> color :754 #ffc100

> color :755 #0074ff

> color :756 #ffdb00

> color :757 #ff6800

> color :758 #adff49

> color :759 #008cff

> color :760 #ff2500

> color :761 #df0000

> color :762 #ff3800

> color :763 #a40000

> color :764 #16ffe1

> color :765 #5dff9a

> color :766 #06ecf1

> color :767 #0054ff

> color :768 #00d0ff

> color :769 #ff6000

> color :770 #00a4ff

> color :771 #0084ff

> color :772 #b60000

> color :773 #ff4e00

> color :774 #02e8f4

> color :775 #0078ff

> color :776 white

> color :777 #63ff94

> color :778 #ff4700

> color :779 #00a8ff

> color :780 #ffb900

> color :781 #0070ff

> color :782 #b4ff43

> color :783 #0024ff

> color :784 #90ff66

> color :785 #004cff

> color :786 #0040ff

> color :787 #0080ff

> color :788 #ff3000

> color :789 #a80000

> color :790 #9f0000

> color :791 #d10000

> color :792 #00acff

> color :793 #ff1600

> color :794 #56ffa0

> color :795 #1fffd7

> color :796 #0090ff

> color :797 #ffea00

> color :798 #00b0ff

> color :799 #0078ff

> color :800 #ffb900

executed LENG8_color_mapping_chimerax.cxc  

> hide #!2 models

> hide #3 models

> show #3 models

> hide #1 models

> view #3

> select #3/A:513

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #3/A:40

9 atoms, 8 bonds, 1 residue, 1 model selected  


===== Log before crash end =====

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9rc202411210252 (2024-11-21)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Volumes/groups/plaschka/max.graf/LENG8_color_mapping_chimerax.cxc

> alphafold fetch Q96PV6

Chain information for AlphaFold Q96PV6 #1  
---  
Chain | Description | UniProt  
A | Leukocyte receptor cluster member 8 | LENG8_HUMAN 1-800  
  
Color AlphaFold Q96PV6 by residue attribute pLDDT_score  

> color :1 #ff4300

> color :2 #ff7300

> color :3 #a7ff50

> color :4 #5dff9a

> color :5 #16ffe1

> color :6 #c1ff36

> color :7 #6dff8a

> color :8 #0080ff

> color :9 #006cff

> color :10 #0054ff

> color :11 #0014ff

> color :12 #0ff8e7

> color :13 #ff9100

> color :14 #0094ff

> color :15 #0064ff

> color :16 #16ffe1

> color :17 #f1fc06

> color :18 #00a8ff

> color :19 #0078ff

> color :20 #0070ff

> color :21 #0074ff

> color :22 #0094ff

> color :23 #0024ff

> color :24 #004cff

> color :25 #00dcfe

> color :26 #a4ff53

> color :27 #0094ff

> color :28 #00acff

> color :29 #00a8ff

> color :30 #beff39

> color :31 #004cff

> color :32 #33ffc4

> color :33 #16ffe1

> color :34 white

> color :35 #9f0000

> color :36 #b60000

> color :37 #920000

> color :38 #a40000

> color :39 #800000

> color :40 #890000

> color :41 #ad0000

> color :42 #840000

> color :43 #840000

> color :44 #ff1e00

> color :45 #8d0000

> color :46 #890000

> color :47 #e40000

> color :48 #ffab00

> color :49 #c40000

> color :50 #ffc400

> color :51 #ff2900

> color :52 #30ffc7

> color :53 #26ffd1

> color :54 #0ff8e7

> color :55 #00c8ff

> color :56 #00d8ff

> color :57 #0098ff

> color :58 #00b0ff

> color :59 #0078ff

> color :60 #b1ff46

> color :61 #007cff

> color :62 #00c0ff

> color :63 #008cff

> color :64 #005cff

> color :65 #00c4ff

> color :66 #005cff

> color :67 #0090ff

> color :68 #00b4ff

> color :69 #00dcfe

> color :70 #06ecf1

> color :71 #3cffba

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> color :73 #09f0ee

> color :74 #46ffb1

> color :75 #13fce4

> color :76 #09f0ee

> color :77 #ebff0c

> color :78 #0ff8e7

> color :79 #1fffd7

> color :80 #06ecf1

> color :81 #00e4f8

> color :82 #6aff8d

> color :83 #56ffa0

> color :84 #8dff6a

> color :85 #a0ff56

> color :86 #fbf100

> color :87 #9aff5d

> color :88 #9dff5a

> color :89 #ff2d00

> color :90 #ff9f00

> color :91 #9aff5d

> color :92 #5dff9a

> color :93 #eeff09

> color :94 #49ffad

> color :95 #50ffa7

> color :96 #00e0fb

> color :97 white

> color :98 #ffc800

> color :99 #87ff70

> color :100 #43ffb4

> color :101 white

> color :102 #1cffdb

> color :103 #97ff60

> color :104 #ffa700

> color :105 #73ff83

> color :106 #63ff94

> color :107 #46ffb1

> color :108 white

> color :109 #40ffb7

> color :110 #56ffa0

> color :111 #2cffca

> color :112 white

> color :113 #00e0fb

> color :114 #00dcfe

> color :115 #0cf4eb

> color :116 #29ffce

> color :117 #b1ff46

> color :118 white

> color :119 #2cffca

> color :120 #00c8ff

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> color :122 #00e0fb

> color :123 #1cffdb

> color :124 #0084ff

> color :125 #00c8ff

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> color :133 #0074ff

> color :134 #0068ff

> color :135 #00b0ff

> color :136 #0094ff

> color :137 #00d4ff

> color :138 white

> color :139 #0058ff

> color :140 #0070ff

> color :141 #007cff

> color :142 #1fffd7

> color :143 #16ffe1

> color :144 #00c4ff

> color :145 #b1ff46

> color :146 #3cffba

> color :147 #00d8ff

> color :148 white

> color :149 #a0ff56

> color :150 #7dff7a

> color :151 #009cff

> color :152 #00b8ff

> color :153 #008cff

> color :154 white

> color :155 #0078ff

> color :156 #0078ff

> color :157 #0030ff

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> color :167 #0040ff

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> color :209 #00a8ff

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> color :211 #7dff7a

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> color :214 #ffb200

> color :215 #00c0ff

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> color :217 #ff9f00

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> color :219 #30ffc7

> color :220 white

> color :221 #c1ff36

> color :222 #ed0400

> color :223 #1cffdb

> color :224 #ff6c00

> color :225 #ff6000

> color :226 #ff2900

> color :227 #00c0ff

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> color :231 #2cffca

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> color :245 #49ffad

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> color :248 #00dcfe

> color :249 #0078ff

> color :250 #a0ff56

> color :251 #0048ff

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> color :255 #00c0ff

> color :256 #0038ff

> color :257 #004cff

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> color :260 #0038ff

> color :261 #00d8ff

> color :262 #0070ff

> color :263 #0004ff

> color :264 #0050ff

> color :265 #000cff

> color :266 #000cff

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> color :268 #0ff8e7

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> color :271 #003cff

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> color :273 #000cff

> color :274 #0020ff

> color :275 #0018ff

> color :276 #000cff

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> color :278 #0008ff

> color :279 #004cff

> color :280 #005cff

> color :281 #0024ff

> color :282 #0004ff

> color :283 #00b8ff

> color :284 #5dff9a

> color :285 #ff8600

> color :286 #ff3400

> color :287 #80ff77

> color :288 #ff1600

> color :289 #890000

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> color :291 #50ffa7

> color :292 #ff9400

> color :293 #960000

> color :294 #b20000

> color :295 #ff9100

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> color :297 #920000

> color :298 #ff3400

> color :299 #8d0000

> color :300 #840000

> color :301 #800000

> color :302 #dbff1c

> color :303 #ff7700

> color :304 #840000

> color :305 #ff8d00

> color :306 #ffab00

> color :307 #9f0000

> color :308 #ff6000

> color :309 #ad0000

> color :310 #9f0000

> color :311 #890000

> color :312 #ffae00

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> color :314 #840000

> color :315 #ff9400

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> color :317 #800000

> color :318 #9f0000

> color :319 #ff6800

> color :320 #ff9800

> color :321 #8d0000

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> color :323 #9dff5a

> color :324 #a80000

> color :325 #a80000

> color :326 #e4ff13

> color :327 #a40000

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> color :330 #a80000

> color :331 #fa0f00

> color :332 #ffae00

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> color :334 #bf0000

> color :335 #800000

> color :336 #ffc400

> color :337 #f4f802

> color :338 #890000

> color :339 #ff2500

> color :340 #bf0000

> color :341 #8d0000

> color :342 #ceff29

> color :343 white

> color :344 #0038ff

> color :345 #00a0ff

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> color :349 #004cff

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> color :352 #8dff6a

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> color :354 #ff4300

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> color :357 #c80000

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> color :360 #0060ff

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> color :362 #0064ff

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> color :364 #002cff

> color :365 #0030ff

> color :366 #0028ff

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> color :374 #0088ff

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> color :378 #0038ff

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> color :381 #0058ff

> color :382 #00acff

> color :383 #00c8ff

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> color :386 #009cff

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> color :389 #0078ff

> color :390 #0050ff

> color :391 #007cff

> color :392 #23ffd4

> color :393 #0098ff

> color :394 white

> color :395 #60ff97

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> color :400 #ff3f00

> color :401 #ff2900

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> color :403 #d1ff26

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> color :406 #f60b00

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> color :409 #ff2500

> color :410 #dbff1c

> color :411 #00a4ff

> color :412 #c1ff36

> color :413 #deff19

> color :414 #ffde00

> color :415 #ffc800

> color :416 #b7ff40

> color :417 #007cff

> color :418 white

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> color :421 #ff6f00

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> color :425 #ff7a00

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> color :436 #ff9c00

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> color :442 #ffe200

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> color :447 #7aff7d

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> color :450 #008cff

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> color :453 #0064ff

> color :454 #008cff

> color :455 white

> color :456 #7dff7a

> color :457 #0090ff

> color :458 #0054ff

> color :459 #005cff

> color :460 #0060ff

> color :461 #ff6800

> color :462 #56ffa0

> color :463 #ff9f00

> color :464 #b4ff43

> color :465 #9dff5a

> color :466 #ff5900

> color :467 #ffea00

> color :468 #43ffb4

> color :469 #1cffdb

> color :470 #63ff94

> color :471 #ff5d00

> color :472 #ff4700

> color :473 #ff9400

> color :474 #ff2d00

> color :475 #9aff5d

> color :476 #ff6800

> color :477 #19ffde

> color :478 #06ecf1

> color :479 #ff8d00

> color :480 #ffe200

> color :481 #ff8900

> color :482 #ffea00

> color :483 #004cff

> color :484 #baff3c

> color :485 #0038ff

> color :486 #00a4ff

> color :487 #0060ff

> color :488 #007cff

> color :489 #ff6800

> color :490 #c7ff30

> color :491 #00c0ff

> color :492 #ebff0c

> color :493 #ff9800

> color :494 white

> color :495 #0088ff

> color :496 #009cff

> color :497 #004cff

> color :498 #0050ff

> color :499 #36ffc1

> color :500 #0068ff

> color :501 #a0ff56

> color :502 #eeff09

> color :503 #a4ff53

> color :504 #9aff5d

> color :505 #ffd700

> color :506 #ff9c00

> color :507 #02e8f4

> color :508 #e80000

> color :509 #e40000

> color :510 #ffa300

> color :511 #ff8900

> color :512 #840000

> color :513 #c40000

> color :514 #ff5500

> color :515 #800000

> color :516 #800000

> color :517 #e4ff13

> color :518 #00d8ff

> color :519 #a7ff50

> color :520 #0088ff

> color :521 #00b8ff

> color :522 #b4ff43

> color :523 #94ff63

> color :524 #beff39

> color :525 #ff6400

> color :526 #00a0ff

> color :527 #ff5200

> color :528 #ff1e00

> color :529 #ffbd00

> color :530 #87ff70

> color :531 #ffa300

> color :532 #00b8ff

> color :533 white

> color :534 #0090ff

> color :535 #0060ff

> color :536 #0034ff

> color :537 #23ffd4

> color :538 #001cff

> color :539 #0014ff

> color :540 #0020ff

> color :541 #0024ff

> color :542 #00e0fb

> color :543 #0060ff

> color :544 #80ff77

> color :545 #ff4700

> color :546 #006cff

> color :547 #3cffba

> color :548 #90ff66

> color :549 #00dcfe

> color :550 #d10000

> color :551 #43ffb4

> color :552 #800000

> color :553 white

> color :554 #d10000

> color :555 #0040ff

> color :556 #feed00

> color :557 #ff8900

> color :558 #e4ff13

> color :559 #890000

> color :560 #4dffaa

> color :561 #960000

> color :562 #920000

> color :563 #800000

> color :564 #800000

> color :565 #800000

> color :566 #ff5200

> color :567 #ad0000

> color :568 #800000

> color :569 #ff3400

> color :570 #e80000

> color :571 #94ff63

> color :572 #ffe200

> color :573 #a80000

> color :574 #800000

> color :575 #a80000

> color :576 #8aff6d

> color :577 #0030ff

> color :578 #ff1600

> color :579 #840000

> color :580 #9aff5d

> color :581 #adff49

> color :582 #e40000

> color :583 #fa0f00

> color :584 #0008ff

> color :585 #8aff6d

> color :586 #c40000

> color :587 #ff3000

> color :588 #0018ff

> color :589 #a4ff53

> color :590 #a80000

> color :591 #aaff4d

> color :592 #49ffad

> color :593 #80ff77

> color :594 #b7ff40

> color :595 #b60000

> color :596 #920000

> color :597 #4dffaa

> color :598 #e40000

> color :599 #ff3400

> color :600 #8d0000

> color :601 #920000

> color :602 #960000

> color :603 #c80000

> color :604 #800000

> color :605 #b60000

> color :606 #ed0400

> color :607 #800000

> color :608 #840000

> color :609 #800000

> color :610 #9f0000

> color :611 #920000

> color :612 #a40000

> color :613 #9b0000

> color :614 #c40000

> color :615 #ff5200

> color :616 #c80000

> color :617 #b1ff46

> color :618 #36ffc1

> color :619 #9f0000

> color :620 #b20000

> color :621 #e40000

> color :622 #e1ff16

> color :623 #ad0000

> color :624 #890000

> color :625 #840000

> color :626 #ff8d00

> color :627 #800000

> color :628 #bb0000

> color :629 #8d0000

> color :630 #f10800

> color :631 #9f0000

> color :632 #bf0000

> color :633 #9f0000

> color :634 #ff5200

> color :635 #cd0000

> color :636 #800000

> color :637 #df0000

> color :638 #c80000

> color :639 #800000

> color :640 #9f0000

> color :641 #8d0000

> color :642 #8d0000

> color :643 #800000

> color :644 #b20000

> color :645 #ff1e00

> color :646 #9f0000

> color :647 #840000

> color :648 #c80000

> color :649 #ceff29

> color :650 #8d0000

> color :651 #ad0000

> color :652 #00e0fb

> color :653 #ff7700

> color :654 #00b8ff

> color :655 #dbff1c

> color :656 #0064ff

> color :657 #bb0000

> color :658 #d4ff23

> color :659 #63ff94

> color :660 #ff6800

> color :661 #890000

> color :662 #840000

> color :663 #ffb900

> color :664 #e80000

> color :665 #9b0000

> color :666 #960000

> color :667 #ff1e00

> color :668 #ff2500

> color :669 #960000

> color :670 #ff5500

> color :671 #ff4300

> color :672 #bb0000

> color :673 #c80000

> color :674 #d7ff1f

> color :675 #c80000

> color :676 #f1fc06

> color :677 #fa0f00

> color :678 #8d0000

> color :679 #ff3f00

> color :680 #ff1300

> color :681 #e80000

> color :682 #ff1300

> color :683 #ff1a00

> color :684 #ff5900

> color :685 #66ff90

> color :686 #ed0400

> color :687 #8aff6d

> color :688 #0088ff

> color :689 #0cf4eb

> color :690 #a4ff53

> color :691 #ff2900

> color :692 #007cff

> color :693 #ff7300

> color :694 #0078ff

> color :695 #ff7300

> color :696 #bf0000

> color :697 #00e4f8

> color :698 #df0000

> color :699 #e40000

> color :700 #ff1a00

> color :701 #1cffdb

> color :702 #ff3f00

> color :703 #b20000

> color :704 #00d0ff

> color :705 #df0000

> color :706 #bf0000

> color :707 #ff4300

> color :708 #ff9100

> color :709 #ffab00

> color :710 #da0000

> color :711 #ff2500

> color :712 #ff5900

> color :713 #a4ff53

> color :714 #a40000

> color :715 #8d0000

> color :716 #0080ff

> color :717 #ff2500

> color :718 #ff4300

> color :719 #0038ff

> color :720 #0010ff

> color :721 #ff5200

> color :722 #ad0000

> color :723 #49ffad

> color :724 #cd0000

> color :725 #ff8d00

> color :726 #ff9c00

> color :727 #ff6c00

> color :728 #e40000

> color :729 #ff4e00

> color :730 #df0000

> color :731 #ff8200

> color :732 #a40000

> color :733 #e7ff0f

> color :734 #1fffd7

> color :735 #ad0000

> color :736 #a40000

> color :737 #920000

> color :738 #d4ff23

> color :739 #006cff

> color :740 #ed0400

> color :741 #ff3b00

> color :742 #ff5900

> color :743 #fbf100

> color :744 #ff1600

> color :745 #ff3800

> color :746 #c80000

> color :747 #ff5200

> color :748 #cd0000

> color :749 #890000

> color :750 #960000

> color :751 #00d8ff

> color :752 #ff2900

> color :753 #ffdb00

> color :754 #ffc100

> color :755 #0074ff

> color :756 #ffdb00

> color :757 #ff6800

> color :758 #adff49

> color :759 #008cff

> color :760 #ff2500

> color :761 #df0000

> color :762 #ff3800

> color :763 #a40000

> color :764 #16ffe1

> color :765 #5dff9a

> color :766 #06ecf1

> color :767 #0054ff

> color :768 #00d0ff

> color :769 #ff6000

> color :770 #00a4ff

> color :771 #0084ff

> color :772 #b60000

> color :773 #ff4e00

> color :774 #02e8f4

> color :775 #0078ff

> color :776 white

> color :777 #63ff94

> color :778 #ff4700

> color :779 #00a8ff

> color :780 #ffb900

> color :781 #0070ff

> color :782 #b4ff43

> color :783 #0024ff

> color :784 #90ff66

> color :785 #004cff

> color :786 #0040ff

> color :787 #0080ff

> color :788 #ff3000

> color :789 #a80000

> color :790 #9f0000

> color :791 #d10000

> color :792 #00acff

> color :793 #ff1600

> color :794 #56ffa0

> color :795 #1fffd7

> color :796 #0090ff

> color :797 #ffea00

> color :798 #00b0ff

> color :799 #0078ff

> color :800 #ffb900

executed LENG8_color_mapping_chimerax.cxc  

> select /A:291

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:292

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:341

7 atoms, 7 bonds, 1 residue, 1 model selected  

> open
> /Volumes/groups/plaschka/shared/alphafold/max.graf/IPscreens/transcription_complexes/2024-11-26_leng8_100_vs_mRNPcleanedup/pdb/289_LENG8_100_vs_sp-O75448-MED24_HUMAN_unrelaxed_rank_5.pdb

Chain information for
289_LENG8_100_vs_sp-O75448-MED24_HUMAN_unrelaxed_rank_5.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Volumes/groups/plaschka/shared/alphafold/max.graf/IPscreens/transcription_complexes/2024-11-26_leng8_100_vs_mRNPcleanedup/pdb/289_LENG8_100_vs_sp-O75448-MED24_HUMAN_unrelaxed_rank_4.pdb

Chain information for
289_LENG8_100_vs_sp-O75448-MED24_HUMAN_unrelaxed_rank_4.pdb #3  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Volumes/groups/plaschka/shared/alphafold/max.graf/IPscreens/transcription_complexes/2024-11-26_leng8_100_vs_mRNPcleanedup/pdb/289_LENG8_100_vs_sp-O75448-MED24_HUMAN_unrelaxed_rank_3.pdb

Chain information for
289_LENG8_100_vs_sp-O75448-MED24_HUMAN_unrelaxed_rank_3.pdb #4  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Volumes/groups/plaschka/shared/alphafold/max.graf/IPscreens/transcription_complexes/2024-11-26_leng8_100_vs_mRNPcleanedup/pdb/289_LENG8_100_vs_sp-O75448-MED24_HUMAN_unrelaxed_rank_2.pdb

Chain information for
289_LENG8_100_vs_sp-O75448-MED24_HUMAN_unrelaxed_rank_2.pdb #5  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Volumes/groups/plaschka/shared/alphafold/max.graf/IPscreens/transcription_complexes/2024-11-26_leng8_100_vs_mRNPcleanedup/pdb/289_LENG8_100_vs_sp-O75448-MED24_HUMAN_unrelaxed_rank_1.pdb

Chain information for
289_LENG8_100_vs_sp-O75448-MED24_HUMAN_unrelaxed_rank_1.pdb #6  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Computing secondary structure  
[Repeated 4 time(s)]

> hide #1 models

> color #2-6 bychain

> mmaker #2-5 to #6

Computing secondary structure  
[Repeated 4 time(s)]  Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 289_LENG8_100_vs_sp-O75448-MED24_HUMAN_unrelaxed_rank_1.pdb, chain
B (#6) with 289_LENG8_100_vs_sp-O75448-MED24_HUMAN_unrelaxed_rank_5.pdb, chain
B (#2), sequence alignment score = 5103.4  
RMSD between 937 pruned atom pairs is 0.849 angstroms; (across all 989 pairs:
1.552)  
  
Matchmaker 289_LENG8_100_vs_sp-O75448-MED24_HUMAN_unrelaxed_rank_1.pdb, chain
B (#6) with 289_LENG8_100_vs_sp-O75448-MED24_HUMAN_unrelaxed_rank_4.pdb, chain
B (#3), sequence alignment score = 5086  
RMSD between 938 pruned atom pairs is 0.500 angstroms; (across all 989 pairs:
3.934)  
  
Matchmaker 289_LENG8_100_vs_sp-O75448-MED24_HUMAN_unrelaxed_rank_1.pdb, chain
B (#6) with 289_LENG8_100_vs_sp-O75448-MED24_HUMAN_unrelaxed_rank_3.pdb, chain
B (#4), sequence alignment score = 5104.6  
RMSD between 931 pruned atom pairs is 0.783 angstroms; (across all 989 pairs:
2.124)  
  
Matchmaker 289_LENG8_100_vs_sp-O75448-MED24_HUMAN_unrelaxed_rank_1.pdb, chain
B (#6) with 289_LENG8_100_vs_sp-O75448-MED24_HUMAN_unrelaxed_rank_2.pdb, chain
B (#5), sequence alignment score = 5118.4  
RMSD between 903 pruned atom pairs is 0.799 angstroms; (across all 989 pairs:
1.478)  
  

> hide #2 models

> select #4/A:50

6 atoms, 5 bonds, 1 residue, 1 model selected  

> hide #3 models

> hide #4 models

> hide #5 models

> select #6/A:50

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select up

111 atoms, 113 bonds, 14 residues, 1 model selected  

> set bgColor white

> show sel target a

> color sel byhetero

> select up

766 atoms, 785 bonds, 100 residues, 1 model selected  

> select down

111 atoms, 113 bonds, 14 residues, 1 model selected  

> select up

766 atoms, 785 bonds, 100 residues, 1 model selected  

> select ~sel

47893 atoms, 48876 bonds, 6145 residues, 6 models selected  

> select ~sel

766 atoms, 785 bonds, 100 residues, 1 model selected  

> select ~sel

47893 atoms, 48876 bonds, 6145 residues, 6 models selected  

> select ~sel

766 atoms, 785 bonds, 100 residues, 1 model selected  

> select ~sel

47893 atoms, 48876 bonds, 6145 residues, 6 models selected  

> select ~sel

766 atoms, 785 bonds, 100 residues, 1 model selected  

> select ~sel

47893 atoms, 48876 bonds, 6145 residues, 6 models selected  

> select #6/A:50

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select #6/A:36

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #6/A:50

6 atoms, 5 bonds, 1 residue, 1 model selected  

> hide #6 target c

> show #6:36-52 target ac

> color navy

> color #6/B blue

> color #6/A blue

> color #6/A light blue

> color #6/A navy blue

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color #6/A dark blue

> color #6/A sky blue

> color #6/A steel blue

> color #6/A byhetero

> show #6/B target s

> color #6/B light grey

> transparency #6/B 80

> select #6/B:686@CD

1 atom, 1 residue, 1 model selected  

> select clear

> open
> /Volumes/groups/plaschka/shared/alphafold/max.graf/IPscreens/master_thesis/2025-01-05_leng8_100_vs_leng8_ne_int/pdb/114_LENG8_100_vs_sp-Q9NWT1-PK1IP_HUMAN_unrelaxed_rank_5.pdb

Chain information for
114_LENG8_100_vs_sp-Q9NWT1-PK1IP_HUMAN_unrelaxed_rank_5.pdb #7  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Volumes/groups/plaschka/shared/alphafold/max.graf/IPscreens/master_thesis/2025-01-05_leng8_100_vs_leng8_ne_int/pdb/114_LENG8_100_vs_sp-Q9NWT1-PK1IP_HUMAN_unrelaxed_rank_4.pdb

Chain information for
114_LENG8_100_vs_sp-Q9NWT1-PK1IP_HUMAN_unrelaxed_rank_4.pdb #8  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Volumes/groups/plaschka/shared/alphafold/max.graf/IPscreens/master_thesis/2025-01-05_leng8_100_vs_leng8_ne_int/pdb/114_LENG8_100_vs_sp-Q9NWT1-PK1IP_HUMAN_unrelaxed_rank_3.pdb

Chain information for
114_LENG8_100_vs_sp-Q9NWT1-PK1IP_HUMAN_unrelaxed_rank_3.pdb #9  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Volumes/groups/plaschka/shared/alphafold/max.graf/IPscreens/master_thesis/2025-01-05_leng8_100_vs_leng8_ne_int/pdb/114_LENG8_100_vs_sp-Q9NWT1-PK1IP_HUMAN_unrelaxed_rank_2.pdb

Chain information for
114_LENG8_100_vs_sp-Q9NWT1-PK1IP_HUMAN_unrelaxed_rank_2.pdb #10  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Volumes/groups/plaschka/shared/alphafold/max.graf/IPscreens/master_thesis/2025-01-05_leng8_100_vs_leng8_ne_int/pdb/114_LENG8_100_vs_sp-Q9NWT1-PK1IP_HUMAN_unrelaxed_rank_1.pdb

Chain information for
114_LENG8_100_vs_sp-Q9NWT1-PK1IP_HUMAN_unrelaxed_rank_1.pdb #11  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Computing secondary structure  
[Repeated 4 time(s)]

> hide #!6 models

> view #6-11

> color #6-11 bychain

> mmaker #6-10 to #11/B

Computing secondary structure  
[Repeated 5 time(s)]  Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 114_LENG8_100_vs_sp-Q9NWT1-PK1IP_HUMAN_unrelaxed_rank_1.pdb, chain
B (#11) with 289_LENG8_100_vs_sp-O75448-MED24_HUMAN_unrelaxed_rank_1.pdb,
chain A (#6), sequence alignment score = 45  
RMSD between 6 pruned atom pairs is 1.529 angstroms; (across all 57 pairs:
58.441)  
  
Matchmaker 114_LENG8_100_vs_sp-Q9NWT1-PK1IP_HUMAN_unrelaxed_rank_1.pdb, chain
B (#11) with 114_LENG8_100_vs_sp-Q9NWT1-PK1IP_HUMAN_unrelaxed_rank_5.pdb,
chain B (#7), sequence alignment score = 2019.8  
RMSD between 251 pruned atom pairs is 0.130 angstroms; (across all 392 pairs:
45.168)  
  
Matchmaker 114_LENG8_100_vs_sp-Q9NWT1-PK1IP_HUMAN_unrelaxed_rank_1.pdb, chain
B (#11) with 114_LENG8_100_vs_sp-Q9NWT1-PK1IP_HUMAN_unrelaxed_rank_4.pdb,
chain B (#8), sequence alignment score = 2009  
RMSD between 280 pruned atom pairs is 0.108 angstroms; (across all 392 pairs:
32.943)  
  
Matchmaker 114_LENG8_100_vs_sp-Q9NWT1-PK1IP_HUMAN_unrelaxed_rank_1.pdb, chain
B (#11) with 114_LENG8_100_vs_sp-Q9NWT1-PK1IP_HUMAN_unrelaxed_rank_3.pdb,
chain B (#9), sequence alignment score = 2012.6  
RMSD between 229 pruned atom pairs is 0.167 angstroms; (across all 392 pairs:
44.135)  
  
Matchmaker 114_LENG8_100_vs_sp-Q9NWT1-PK1IP_HUMAN_unrelaxed_rank_1.pdb, chain
B (#11) with 114_LENG8_100_vs_sp-Q9NWT1-PK1IP_HUMAN_unrelaxed_rank_2.pdb,
chain B (#10), sequence alignment score = 2019.8  
RMSD between 276 pruned atom pairs is 0.134 angstroms; (across all 392 pairs:
41.262)  
  

> close #8-11

> close #7

> open
> /Volumes/groups/plaschka/shared/alphafold/max.graf/IPscreens/master_thesis/2025-01-05_leng8_100_vs_leng8_ne_int/pdb/75_LENG8_100_vs_sp-P62942-FKB1A_HUMAN_unrelaxed_rank_5.pdb

Chain information for
75_LENG8_100_vs_sp-P62942-FKB1A_HUMAN_unrelaxed_rank_5.pdb #7  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Volumes/groups/plaschka/shared/alphafold/max.graf/IPscreens/master_thesis/2025-01-05_leng8_100_vs_leng8_ne_int/pdb/75_LENG8_100_vs_sp-P62942-FKB1A_HUMAN_unrelaxed_rank_4.pdb

Chain information for
75_LENG8_100_vs_sp-P62942-FKB1A_HUMAN_unrelaxed_rank_4.pdb #8  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Volumes/groups/plaschka/shared/alphafold/max.graf/IPscreens/master_thesis/2025-01-05_leng8_100_vs_leng8_ne_int/pdb/75_LENG8_100_vs_sp-P62942-FKB1A_HUMAN_unrelaxed_rank_3.pdb

Chain information for
75_LENG8_100_vs_sp-P62942-FKB1A_HUMAN_unrelaxed_rank_3.pdb #9  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Volumes/groups/plaschka/shared/alphafold/max.graf/IPscreens/master_thesis/2025-01-05_leng8_100_vs_leng8_ne_int/pdb/75_LENG8_100_vs_sp-P62942-FKB1A_HUMAN_unrelaxed_rank_2.pdb

Chain information for
75_LENG8_100_vs_sp-P62942-FKB1A_HUMAN_unrelaxed_rank_2.pdb #10  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Volumes/groups/plaschka/shared/alphafold/max.graf/IPscreens/master_thesis/2025-01-05_leng8_100_vs_leng8_ne_int/pdb/75_LENG8_100_vs_sp-P62942-FKB1A_HUMAN_unrelaxed_rank_1.pdb

Chain information for
75_LENG8_100_vs_sp-P62942-FKB1A_HUMAN_unrelaxed_rank_1.pdb #11  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Computing secondary structure  
[Repeated 4 time(s)]

> view #6-11

> color #6-11 bychain

> mmaker #6-10 to #11/B

Computing secondary structure  
[Repeated 5 time(s)]  Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 75_LENG8_100_vs_sp-P62942-FKB1A_HUMAN_unrelaxed_rank_1.pdb, chain B
(#11) with 289_LENG8_100_vs_sp-O75448-MED24_HUMAN_unrelaxed_rank_1.pdb, chain
A (#6), sequence alignment score = 5.2  
RMSD between 4 pruned atom pairs is 1.238 angstroms; (across all 65 pairs:
33.861)  
  
Matchmaker 75_LENG8_100_vs_sp-P62942-FKB1A_HUMAN_unrelaxed_rank_1.pdb, chain B
(#11) with 75_LENG8_100_vs_sp-P62942-FKB1A_HUMAN_unrelaxed_rank_5.pdb, chain B
(#7), sequence alignment score = 563.1  
RMSD between 108 pruned atom pairs is 0.138 angstroms; (across all 108 pairs:
0.138)  
  
Matchmaker 75_LENG8_100_vs_sp-P62942-FKB1A_HUMAN_unrelaxed_rank_1.pdb, chain B
(#11) with 75_LENG8_100_vs_sp-P62942-FKB1A_HUMAN_unrelaxed_rank_4.pdb, chain B
(#8), sequence alignment score = 563.1  
RMSD between 108 pruned atom pairs is 0.120 angstroms; (across all 108 pairs:
0.120)  
  
Matchmaker 75_LENG8_100_vs_sp-P62942-FKB1A_HUMAN_unrelaxed_rank_1.pdb, chain B
(#11) with 75_LENG8_100_vs_sp-P62942-FKB1A_HUMAN_unrelaxed_rank_3.pdb, chain B
(#9), sequence alignment score = 551.1  
RMSD between 108 pruned atom pairs is 0.191 angstroms; (across all 108 pairs:
0.191)  
  
Matchmaker 75_LENG8_100_vs_sp-P62942-FKB1A_HUMAN_unrelaxed_rank_1.pdb, chain B
(#11) with 75_LENG8_100_vs_sp-P62942-FKB1A_HUMAN_unrelaxed_rank_2.pdb, chain B
(#10), sequence alignment score = 563.1  
RMSD between 108 pruned atom pairs is 0.112 angstroms; (across all 108 pairs:
0.112)  
  

> close #7-11

> open
> /Volumes/groups/plaschka/shared/alphafold/max.graf/IPscreens/master_thesis/2025-01-05_leng8_100_vs_leng8_ne_int/pdb/95_LENG8_100_vs_sp-Q6PJG2-MDEAS_HUMAN_unrelaxed_rank_5.pdb

Chain information for
95_LENG8_100_vs_sp-Q6PJG2-MDEAS_HUMAN_unrelaxed_rank_5.pdb #7  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Volumes/groups/plaschka/shared/alphafold/max.graf/IPscreens/master_thesis/2025-01-05_leng8_100_vs_leng8_ne_int/pdb/95_LENG8_100_vs_sp-Q6PJG2-MDEAS_HUMAN_unrelaxed_rank_4.pdb

Chain information for
95_LENG8_100_vs_sp-Q6PJG2-MDEAS_HUMAN_unrelaxed_rank_4.pdb #8  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Volumes/groups/plaschka/shared/alphafold/max.graf/IPscreens/master_thesis/2025-01-05_leng8_100_vs_leng8_ne_int/pdb/95_LENG8_100_vs_sp-Q6PJG2-MDEAS_HUMAN_unrelaxed_rank_3.pdb

Chain information for
95_LENG8_100_vs_sp-Q6PJG2-MDEAS_HUMAN_unrelaxed_rank_3.pdb #9  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Volumes/groups/plaschka/shared/alphafold/max.graf/IPscreens/master_thesis/2025-01-05_leng8_100_vs_leng8_ne_int/pdb/95_LENG8_100_vs_sp-Q6PJG2-MDEAS_HUMAN_unrelaxed_rank_2.pdb

Chain information for
95_LENG8_100_vs_sp-Q6PJG2-MDEAS_HUMAN_unrelaxed_rank_2.pdb #10  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Volumes/groups/plaschka/shared/alphafold/max.graf/IPscreens/master_thesis/2025-01-05_leng8_100_vs_leng8_ne_int/pdb/95_LENG8_100_vs_sp-Q6PJG2-MDEAS_HUMAN_unrelaxed_rank_1.pdb

Chain information for
95_LENG8_100_vs_sp-Q6PJG2-MDEAS_HUMAN_unrelaxed_rank_1.pdb #11  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Computing secondary structure  
[Repeated 4 time(s)]

> view #7-11

> color #7-11 bychain

> mmaker #7-10 to #11/B

Computing secondary structure  
[Repeated 4 time(s)]  Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 95_LENG8_100_vs_sp-Q6PJG2-MDEAS_HUMAN_unrelaxed_rank_1.pdb, chain B
(#11) with 95_LENG8_100_vs_sp-Q6PJG2-MDEAS_HUMAN_unrelaxed_rank_5.pdb, chain B
(#7), sequence alignment score = 5110.3  
RMSD between 181 pruned atom pairs is 0.992 angstroms; (across all 1045 pairs:
62.120)  
  
Matchmaker 95_LENG8_100_vs_sp-Q6PJG2-MDEAS_HUMAN_unrelaxed_rank_1.pdb, chain B
(#11) with 95_LENG8_100_vs_sp-Q6PJG2-MDEAS_HUMAN_unrelaxed_rank_4.pdb, chain B
(#8), sequence alignment score = 5098.9  
RMSD between 196 pruned atom pairs is 0.788 angstroms; (across all 1045 pairs:
63.912)  
  
Matchmaker 95_LENG8_100_vs_sp-Q6PJG2-MDEAS_HUMAN_unrelaxed_rank_1.pdb, chain B
(#11) with 95_LENG8_100_vs_sp-Q6PJG2-MDEAS_HUMAN_unrelaxed_rank_3.pdb, chain B
(#9), sequence alignment score = 5091.7  
RMSD between 206 pruned atom pairs is 0.939 angstroms; (across all 1045 pairs:
67.226)  
  
Matchmaker 95_LENG8_100_vs_sp-Q6PJG2-MDEAS_HUMAN_unrelaxed_rank_1.pdb, chain B
(#11) with 95_LENG8_100_vs_sp-Q6PJG2-MDEAS_HUMAN_unrelaxed_rank_2.pdb, chain B
(#10), sequence alignment score = 5097.1  
RMSD between 211 pruned atom pairs is 0.898 angstroms; (across all 1045 pairs:
64.262)  
  

> hide #7 models

> hide #8 models

> hide #9 models

> hide #10 models

> open
> /Volumes/groups/plaschka/shared/alphafold/max.graf/IPscreens/master_thesis/2025-01-05_leng8_100_vs_leng8_ne_int/pdb/291_LENG8_100_vs_sp-Q96E39-RMXL1_HUMAN_unrelaxed_rank_5.pdb

Chain information for
291_LENG8_100_vs_sp-Q96E39-RMXL1_HUMAN_unrelaxed_rank_5.pdb #12  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Volumes/groups/plaschka/shared/alphafold/max.graf/IPscreens/master_thesis/2025-01-05_leng8_100_vs_leng8_ne_int/pdb/291_LENG8_100_vs_sp-Q96E39-RMXL1_HUMAN_unrelaxed_rank_4.pdb

Chain information for
291_LENG8_100_vs_sp-Q96E39-RMXL1_HUMAN_unrelaxed_rank_4.pdb #13  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Volumes/groups/plaschka/shared/alphafold/max.graf/IPscreens/master_thesis/2025-01-05_leng8_100_vs_leng8_ne_int/pdb/291_LENG8_100_vs_sp-Q96E39-RMXL1_HUMAN_unrelaxed_rank_3.pdb

Chain information for
291_LENG8_100_vs_sp-Q96E39-RMXL1_HUMAN_unrelaxed_rank_3.pdb #14  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Volumes/groups/plaschka/shared/alphafold/max.graf/IPscreens/master_thesis/2025-01-05_leng8_100_vs_leng8_ne_int/pdb/291_LENG8_100_vs_sp-Q96E39-RMXL1_HUMAN_unrelaxed_rank_2.pdb

Chain information for
291_LENG8_100_vs_sp-Q96E39-RMXL1_HUMAN_unrelaxed_rank_2.pdb #15  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Volumes/groups/plaschka/shared/alphafold/max.graf/IPscreens/master_thesis/2025-01-05_leng8_100_vs_leng8_ne_int/pdb/291_LENG8_100_vs_sp-Q96E39-RMXL1_HUMAN_unrelaxed_rank_1.pdb

Chain information for
291_LENG8_100_vs_sp-Q96E39-RMXL1_HUMAN_unrelaxed_rank_1.pdb #16  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Computing secondary structure  
[Repeated 4 time(s)]

> close #7-11

> rename #12 id #7

> rename #13 id #8

> rename #14 id #9

> rename #15 id #10

> rename #16 id #11

> mmaker #7-10 to #11/B

Computing secondary structure  
[Repeated 4 time(s)]  Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 291_LENG8_100_vs_sp-Q96E39-RMXL1_HUMAN_unrelaxed_rank_1.pdb, chain
B (#11) with 291_LENG8_100_vs_sp-Q96E39-RMXL1_HUMAN_unrelaxed_rank_5.pdb,
chain B (#7), sequence alignment score = 1960.4  
RMSD between 17 pruned atom pairs is 1.483 angstroms; (across all 390 pairs:
64.327)  
  
Matchmaker 291_LENG8_100_vs_sp-Q96E39-RMXL1_HUMAN_unrelaxed_rank_1.pdb, chain
B (#11) with 291_LENG8_100_vs_sp-Q96E39-RMXL1_HUMAN_unrelaxed_rank_4.pdb,
chain B (#8), sequence alignment score = 1961  
RMSD between 7 pruned atom pairs is 1.518 angstroms; (across all 390 pairs:
48.604)  
  
Matchmaker 291_LENG8_100_vs_sp-Q96E39-RMXL1_HUMAN_unrelaxed_rank_1.pdb, chain
B (#11) with 291_LENG8_100_vs_sp-Q96E39-RMXL1_HUMAN_unrelaxed_rank_3.pdb,
chain B (#9), sequence alignment score = 1958  
RMSD between 19 pruned atom pairs is 1.403 angstroms; (across all 390 pairs:
56.838)  
  
Matchmaker 291_LENG8_100_vs_sp-Q96E39-RMXL1_HUMAN_unrelaxed_rank_1.pdb, chain
B (#11) with 291_LENG8_100_vs_sp-Q96E39-RMXL1_HUMAN_unrelaxed_rank_2.pdb,
chain B (#10), sequence alignment score = 1960.4  
RMSD between 13 pruned atom pairs is 1.251 angstroms; (across all 390 pairs:
54.505)  
  

> view #7-11

> color #7-11 bychain

> mmaker #7-10 to #11/B

Computing secondary structure  
[Repeated 4 time(s)]  Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 291_LENG8_100_vs_sp-Q96E39-RMXL1_HUMAN_unrelaxed_rank_1.pdb, chain
B (#11) with 291_LENG8_100_vs_sp-Q96E39-RMXL1_HUMAN_unrelaxed_rank_5.pdb,
chain B (#7), sequence alignment score = 1960.4  
RMSD between 17 pruned atom pairs is 1.483 angstroms; (across all 390 pairs:
64.327)  
  
Matchmaker 291_LENG8_100_vs_sp-Q96E39-RMXL1_HUMAN_unrelaxed_rank_1.pdb, chain
B (#11) with 291_LENG8_100_vs_sp-Q96E39-RMXL1_HUMAN_unrelaxed_rank_4.pdb,
chain B (#8), sequence alignment score = 1961  
RMSD between 7 pruned atom pairs is 1.518 angstroms; (across all 390 pairs:
48.604)  
  
Matchmaker 291_LENG8_100_vs_sp-Q96E39-RMXL1_HUMAN_unrelaxed_rank_1.pdb, chain
B (#11) with 291_LENG8_100_vs_sp-Q96E39-RMXL1_HUMAN_unrelaxed_rank_3.pdb,
chain B (#9), sequence alignment score = 1958  
RMSD between 19 pruned atom pairs is 1.403 angstroms; (across all 390 pairs:
56.838)  
  
Matchmaker 291_LENG8_100_vs_sp-Q96E39-RMXL1_HUMAN_unrelaxed_rank_1.pdb, chain
B (#11) with 291_LENG8_100_vs_sp-Q96E39-RMXL1_HUMAN_unrelaxed_rank_2.pdb,
chain B (#10), sequence alignment score = 1960.4  
RMSD between 13 pruned atom pairs is 1.251 angstroms; (across all 390 pairs:
54.505)  
  

> mmaker #7-10 to #11

Computing secondary structure  
[Repeated 4 time(s)]  Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 291_LENG8_100_vs_sp-Q96E39-RMXL1_HUMAN_unrelaxed_rank_1.pdb, chain
B (#11) with 291_LENG8_100_vs_sp-Q96E39-RMXL1_HUMAN_unrelaxed_rank_5.pdb,
chain B (#7), sequence alignment score = 1960.4  
RMSD between 17 pruned atom pairs is 1.483 angstroms; (across all 390 pairs:
64.327)  
  
Matchmaker 291_LENG8_100_vs_sp-Q96E39-RMXL1_HUMAN_unrelaxed_rank_1.pdb, chain
B (#11) with 291_LENG8_100_vs_sp-Q96E39-RMXL1_HUMAN_unrelaxed_rank_4.pdb,
chain B (#8), sequence alignment score = 1961  
RMSD between 7 pruned atom pairs is 1.518 angstroms; (across all 390 pairs:
48.604)  
  
Matchmaker 291_LENG8_100_vs_sp-Q96E39-RMXL1_HUMAN_unrelaxed_rank_1.pdb, chain
B (#11) with 291_LENG8_100_vs_sp-Q96E39-RMXL1_HUMAN_unrelaxed_rank_3.pdb,
chain B (#9), sequence alignment score = 1958  
RMSD between 19 pruned atom pairs is 1.403 angstroms; (across all 390 pairs:
56.838)  
  
Matchmaker 291_LENG8_100_vs_sp-Q96E39-RMXL1_HUMAN_unrelaxed_rank_1.pdb, chain
B (#11) with 291_LENG8_100_vs_sp-Q96E39-RMXL1_HUMAN_unrelaxed_rank_2.pdb,
chain B (#10), sequence alignment score = 1960.4  
RMSD between 13 pruned atom pairs is 1.251 angstroms; (across all 390 pairs:
54.505)  
  

> mmaker #7-10 to #11/A

Computing secondary structure  
[Repeated 4 time(s)]  Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 291_LENG8_100_vs_sp-Q96E39-RMXL1_HUMAN_unrelaxed_rank_1.pdb, chain
A (#11) with 291_LENG8_100_vs_sp-Q96E39-RMXL1_HUMAN_unrelaxed_rank_5.pdb,
chain A (#7), sequence alignment score = 490.4  
RMSD between 21 pruned atom pairs is 0.994 angstroms; (across all 100 pairs:
18.359)  
  
Matchmaker 291_LENG8_100_vs_sp-Q96E39-RMXL1_HUMAN_unrelaxed_rank_1.pdb, chain
A (#11) with 291_LENG8_100_vs_sp-Q96E39-RMXL1_HUMAN_unrelaxed_rank_4.pdb,
chain A (#8), sequence alignment score = 471.8  
RMSD between 24 pruned atom pairs is 0.933 angstroms; (across all 100 pairs:
11.795)  
  
Matchmaker 291_LENG8_100_vs_sp-Q96E39-RMXL1_HUMAN_unrelaxed_rank_1.pdb, chain
A (#11) with 291_LENG8_100_vs_sp-Q96E39-RMXL1_HUMAN_unrelaxed_rank_3.pdb,
chain A (#9), sequence alignment score = 469.4  
RMSD between 20 pruned atom pairs is 0.826 angstroms; (across all 100 pairs:
19.390)  
  
Matchmaker 291_LENG8_100_vs_sp-Q96E39-RMXL1_HUMAN_unrelaxed_rank_1.pdb, chain
A (#11) with 291_LENG8_100_vs_sp-Q96E39-RMXL1_HUMAN_unrelaxed_rank_2.pdb,
chain A (#10), sequence alignment score = 461.6  
RMSD between 21 pruned atom pairs is 0.426 angstroms; (across all 100 pairs:
13.749)  
  

> hide #7 models

> hide #8 models

> hide #9 models

> close #9-11

> close #7-8

> open
> /Volumes/groups/plaschka/shared/alphafold/max.graf/IPscreens/master_thesis/2025-01-05_leng8_100_vs_leng8_ne_int/pdb/185_LENG8_100_vs_sp-O00422-SAP18_HUMAN_unrelaxed_rank_5.pdb

Chain information for
185_LENG8_100_vs_sp-O00422-SAP18_HUMAN_unrelaxed_rank_5.pdb #7  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Volumes/groups/plaschka/shared/alphafold/max.graf/IPscreens/master_thesis/2025-01-05_leng8_100_vs_leng8_ne_int/pdb/185_LENG8_100_vs_sp-O00422-SAP18_HUMAN_unrelaxed_rank_4.pdb

Chain information for
185_LENG8_100_vs_sp-O00422-SAP18_HUMAN_unrelaxed_rank_4.pdb #8  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Volumes/groups/plaschka/shared/alphafold/max.graf/IPscreens/master_thesis/2025-01-05_leng8_100_vs_leng8_ne_int/pdb/185_LENG8_100_vs_sp-O00422-SAP18_HUMAN_unrelaxed_rank_3.pdb

Chain information for
185_LENG8_100_vs_sp-O00422-SAP18_HUMAN_unrelaxed_rank_3.pdb #9  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Volumes/groups/plaschka/shared/alphafold/max.graf/IPscreens/master_thesis/2025-01-05_leng8_100_vs_leng8_ne_int/pdb/185_LENG8_100_vs_sp-O00422-SAP18_HUMAN_unrelaxed_rank_2.pdb

Chain information for
185_LENG8_100_vs_sp-O00422-SAP18_HUMAN_unrelaxed_rank_2.pdb #10  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Volumes/groups/plaschka/shared/alphafold/max.graf/IPscreens/master_thesis/2025-01-05_leng8_100_vs_leng8_ne_int/pdb/185_LENG8_100_vs_sp-O00422-SAP18_HUMAN_unrelaxed_rank_1.pdb

Chain information for
185_LENG8_100_vs_sp-O00422-SAP18_HUMAN_unrelaxed_rank_1.pdb #11  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Computing secondary structure  
[Repeated 4 time(s)]

> color #7-11 bychain

> mmaker #7-10 to #11

Computing secondary structure  
[Repeated 4 time(s)]  Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 185_LENG8_100_vs_sp-O00422-SAP18_HUMAN_unrelaxed_rank_1.pdb, chain
B (#11) with 185_LENG8_100_vs_sp-O00422-SAP18_HUMAN_unrelaxed_rank_5.pdb,
chain B (#7), sequence alignment score = 786  
RMSD between 138 pruned atom pairs is 0.362 angstroms; (across all 153 pairs:
1.674)  
  
Matchmaker 185_LENG8_100_vs_sp-O00422-SAP18_HUMAN_unrelaxed_rank_1.pdb, chain
B (#11) with 185_LENG8_100_vs_sp-O00422-SAP18_HUMAN_unrelaxed_rank_4.pdb,
chain B (#8), sequence alignment score = 786  
RMSD between 135 pruned atom pairs is 0.372 angstroms; (across all 153 pairs:
2.107)  
  
Matchmaker 185_LENG8_100_vs_sp-O00422-SAP18_HUMAN_unrelaxed_rank_1.pdb, chain
B (#11) with 185_LENG8_100_vs_sp-O00422-SAP18_HUMAN_unrelaxed_rank_3.pdb,
chain B (#9), sequence alignment score = 786  
RMSD between 137 pruned atom pairs is 0.406 angstroms; (across all 153 pairs:
2.945)  
  
Matchmaker 185_LENG8_100_vs_sp-O00422-SAP18_HUMAN_unrelaxed_rank_1.pdb, chain
B (#11) with 185_LENG8_100_vs_sp-O00422-SAP18_HUMAN_unrelaxed_rank_2.pdb,
chain B (#10), sequence alignment score = 786  
RMSD between 138 pruned atom pairs is 0.380 angstroms; (across all 153 pairs:
1.466)  
  

> close #7-11

> open
> /Volumes/groups/plaschka/shared/alphafold/max.graf/IPscreens/master_thesis/2025-01-05_leng8_100_vs_leng8_ne_int/pdb/78_LENG8_100_vs_sp-Q13901-C1D_HUMAN_unrelaxed_rank_5.pdb

Chain information for 78_LENG8_100_vs_sp-Q13901-C1D_HUMAN_unrelaxed_rank_5.pdb
#7  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Volumes/groups/plaschka/shared/alphafold/max.graf/IPscreens/master_thesis/2025-01-05_leng8_100_vs_leng8_ne_int/pdb/78_LENG8_100_vs_sp-Q13901-C1D_HUMAN_unrelaxed_rank_4.pdb

Chain information for 78_LENG8_100_vs_sp-Q13901-C1D_HUMAN_unrelaxed_rank_4.pdb
#8  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Volumes/groups/plaschka/shared/alphafold/max.graf/IPscreens/master_thesis/2025-01-05_leng8_100_vs_leng8_ne_int/pdb/78_LENG8_100_vs_sp-Q13901-C1D_HUMAN_unrelaxed_rank_3.pdb

Chain information for 78_LENG8_100_vs_sp-Q13901-C1D_HUMAN_unrelaxed_rank_3.pdb
#9  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Volumes/groups/plaschka/shared/alphafold/max.graf/IPscreens/master_thesis/2025-01-05_leng8_100_vs_leng8_ne_int/pdb/78_LENG8_100_vs_sp-Q13901-C1D_HUMAN_unrelaxed_rank_2.pdb

Chain information for 78_LENG8_100_vs_sp-Q13901-C1D_HUMAN_unrelaxed_rank_2.pdb
#10  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Volumes/groups/plaschka/shared/alphafold/max.graf/IPscreens/master_thesis/2025-01-05_leng8_100_vs_leng8_ne_int/pdb/78_LENG8_100_vs_sp-Q13901-C1D_HUMAN_unrelaxed_rank_1.pdb

Chain information for 78_LENG8_100_vs_sp-Q13901-C1D_HUMAN_unrelaxed_rank_1.pdb
#11  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Computing secondary structure  
[Repeated 4 time(s)]

> color #7-11 bychain

> mmaker #7-10 to #11

Computing secondary structure  
[Repeated 4 time(s)]  Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 78_LENG8_100_vs_sp-Q13901-C1D_HUMAN_unrelaxed_rank_1.pdb, chain B
(#11) with 78_LENG8_100_vs_sp-Q13901-C1D_HUMAN_unrelaxed_rank_5.pdb, chain B
(#7), sequence alignment score = 702.7  
RMSD between 92 pruned atom pairs is 0.667 angstroms; (across all 141 pairs:
4.290)  
  
Matchmaker 78_LENG8_100_vs_sp-Q13901-C1D_HUMAN_unrelaxed_rank_1.pdb, chain B
(#11) with 78_LENG8_100_vs_sp-Q13901-C1D_HUMAN_unrelaxed_rank_4.pdb, chain B
(#8), sequence alignment score = 720.1  
RMSD between 93 pruned atom pairs is 0.541 angstroms; (across all 141 pairs:
5.503)  
  
Matchmaker 78_LENG8_100_vs_sp-Q13901-C1D_HUMAN_unrelaxed_rank_1.pdb, chain B
(#11) with 78_LENG8_100_vs_sp-Q13901-C1D_HUMAN_unrelaxed_rank_3.pdb, chain B
(#9), sequence alignment score = 723.1  
RMSD between 95 pruned atom pairs is 0.767 angstroms; (across all 141 pairs:
5.221)  
  
Matchmaker 78_LENG8_100_vs_sp-Q13901-C1D_HUMAN_unrelaxed_rank_1.pdb, chain B
(#11) with 78_LENG8_100_vs_sp-Q13901-C1D_HUMAN_unrelaxed_rank_2.pdb, chain B
(#10), sequence alignment score = 714.7  
RMSD between 95 pruned atom pairs is 0.571 angstroms; (across all 141 pairs:
5.202)  
  




OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M3 Pro
OpenGL vendor: Apple

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: Mac15,6
      Model Number: Z1AV001N8D/A
      Chip: Apple M3 Pro
      Total Number of Cores: 12 (6 performance and 6 efficiency)
      Memory: 36 GB
      System Firmware Version: 10151.140.19
      OS Loader Version: 10151.140.19

Software:

    System Software Overview:

      System Version: macOS 14.6.1 (23G93)
      Kernel Version: Darwin 23.6.0
      Time since boot: 3 days, 9 hours, 18 minutes

Graphics/Displays:

    Apple M3 Pro:

      Chipset Model: Apple M3 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 18
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3024 x 1964 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal


Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 2.4.1
    auditwheel: 6.1.0
    babel: 2.16.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.7.1
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.16.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58.7
    ChimeraX-AtomicLibrary: 14.1.11
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.7
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    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: 2.3
    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: 1.9rc202411210252
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.6
    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: 1.4.1
    ChimeraX-Hbonds: 2.5
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.2.1
    ChimeraX-Label: 1.1.11
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    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: 2.1.6
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.18
    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-MutationScores: 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: 1.14
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.6
    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: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.2
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    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: 3.3.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.14
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.18.1
    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: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.41
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    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: 1.3.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.9
    decorator: 5.1.1
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.55.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.12.1
    html2text: 2024.2.26
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jedi: 0.19.1
    Jinja2: 3.1.4
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.7
    line_profiler: 4.1.3
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.1
    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: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    prompt_toolkit: 3.0.48
    psutil: 6.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.31
    Pygments: 2.18.0
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.0
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.7.1
    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.3
    PyQt6-WebEngineSubwheel-Qt6: 6.7.3
    PyQt6_sip: 13.8.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.2
    qtshim: 1.0
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.10.1
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    tornado: 6.4.2
    traitlets: 5.14.3
    typing_extensions: 4.12.2
    tzdata: 2024.2
    urllib3: 2.2.3
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13

Change History (2)

comment:1 by Eric Pettersen, 10 months ago

Component: Unassigned → Window Toolkit
Description: modified (diff)
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Crash on Mac waking from sleep

comment:2 by Tom Goddard, 4 months ago

Resolution: → duplicate
Status: assigned → closed
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