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Opened 10 months ago
Closed 3 months ago
#16557 closed defect (duplicate)
Crash on Mac waking from sleep
| Reported by: | 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 )
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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fault"},"pc":{"value":6704106784},"far":{"value":0}}},{"id":948729,"frames":[{"imageOffset":7456,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":156}],"threadState":{"x":[{"value":6172291072},{"value":166499},{"value":6171754496},{"value":0},{"value":409602},{"value":18446744073709551615},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0}],"flavor":"ARM_THREAD_STATE64","lr":{"value":0},"cpsr":{"value":4096},"fp":{"value":0},"sp":{"value":6172291072},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6704106784},"far":{"value":0}}}],
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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
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> color :14 #ffb900
> color :15 #ff6f00
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> color :17 #ff6f00
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> color :20 #8aff6d
> color :21 #c1ff36
> color :22 #f8f500
> color :23 white
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> color :25 #0000ff
> color :26 #0094ff
> color :27 #0044ff
> color :28 #002cff
> color :29 #0054ff
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> color :31 #001cff
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> color :33 #0030ff
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> color :44 #0048ff
> color :45 #004cff
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> color :80 #00e0fb
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> color :104 #006cff
> color :105 #0004ff
> color :106 #001cff
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> color :117 #fa0f00
> color :118 #ff2500
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> color :134 #f60b00
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> color :142 #ffb900
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> color :145 #ff3b00
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> color :302 #ff4e00
> color :303 #c40000
> color :304 #ff4a00
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> 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
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> color :321 #9dff5a
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> color :325 #cd0000
> color :326 #e80000
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> color :328 #920000
> color :329 #ff4300
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> color :331 #7aff7d
> color :332 #ff2200
> color :333 #e7ff0f
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> color :335 #9b0000
> color :336 #b20000
> color :337 #8d0000
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> color :361 #bb0000
> color :362 #ff3000
> color :363 #ff9100
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> color :373 #ff2500
> color :374 #00a4ff
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> color :392 #0074ff
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> color :417 #0028ff
> color :418 #0008ff
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> color :420 #0084ff
> color :421 #0034ff
> color :422 #005cff
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> color :425 #0024ff
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> color :428 #00a0ff
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> color :435 #0070ff
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> color :450 #0054ff
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> 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
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> 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
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> color :558 #0050ff
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> color :561 #0014ff
> color :562 #0050ff
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> color :564 #0030ff
> color :565 #000cff
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> 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
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> color :586 #0030ff
> color :587 #000cff
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> 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
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> color :605 #002cff
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> color :609 #008cff
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> color :611 #0000ff
> color :612 #0038ff
> color :613 #0060ff
> color :614 #0094ff
> color :615 #002cff
> color :616 #0054ff
> color :617 #0064ff
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> 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
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> 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
> 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
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> 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
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> 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
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> 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
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> color :9 #006cff
> color :10 #0054ff
> color :11 #0014ff
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> color :13 #ff9100
> color :14 #0094ff
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> color :29 #00a8ff
> color :30 #beff39
> color :31 #004cff
> color :32 #33ffc4
> color :33 #16ffe1
> color :34 white
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> color :36 #b60000
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> color :38 #a40000
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> color :40 #890000
> color :41 #ad0000
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> 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 , 10 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash on Mac waking from sleep |
comment:2 by , 3 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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