Opened 2 years ago

Closed 2 years ago

#9723 closed defect (can't reproduce)

Crash in QTabBar::paintEvent

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

Description 

The following bug report has been submitted:
Platform:        macOS-13.5.1-arm64-arm-64bit
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Thread 0x000000030409b000 (most recent call first):
  File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 576 in _handle_results
  File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x000000030308f000 (most recent call first):
  File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 528 in _handle_tasks
  File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x0000000302083000 (most recent call first):
  File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/selectors.py", line 416 in select
  File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/connection.py", line 936 in wait
  File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 499 in _wait_for_updates
  File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 519 in _handle_workers
  File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x0000000301077000 (most recent call first):
  File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x000000030006b000 (most recent call first):
  File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00000002ff05f000 (most recent call first):
  File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00000002fe053000 (most recent call first):
  File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00000002fd047000 (most recent call first):
  File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00000002fc03b000 (most recent call first):
  File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00000002fb02f000 (most recent call first):
  File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00000002fa023000 (most recent call first):
  File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00000002f9017000 (most recent call first):
  File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00000002f800b000 (most recent call first):
  File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00000002f6fff000 (most recent call first):
  File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00000002f5ff3000 (most recent call first):
  File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Current thread 0x00000001ee2aa080 (most recent call first):
  File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 275 in event_loop
  File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 892 in init
  File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1043 in 
  File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
  File "/opt/sbgrid/i386-mac/chimerax/1.6.1/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main


{"app_name":"ChimeraX","timestamp":"2023-09-06 16:52:56.00 -0400","app_version":"1.6.1","slice_uuid":"a5992708-d5b4-36ec-ac0a-e525f6105b56","build_version":"1.6.1.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 13.5.1 (22G90)","roots_installed":0,"name":"ChimeraX","incident_id":"6F5FAE27-D0A6-4CD7-9809-4AEB5272CB67"}
{
  "uptime" : 230000,
  "procRole" : "Background",
  "version" : 2,
  "userID" : 501,
  "deployVersion" : 210,
  "modelCode" : "Mac14,12",
  "coalitionID" : 7380,
  "osVersion" : {
    "train" : "macOS 13.5.1",
    "build" : "22G90",
    "releaseType" : "User"
  },
  "captureTime" : "2023-09-06 16:52:41.6043 -0400",
  "incident" : "6F5FAE27-D0A6-4CD7-9809-4AEB5272CB67",
  "pid" : 10541,
  "translated" : false,
  "cpuType" : "ARM-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2023-08-31 12:52:29.5280 -0400",
  "procStartAbsTime" : 1234867982548,
  "procExitAbsTime" : 5532063896518,
  "procName" : "ChimeraX",
  "procPath" : "\/opt\/sbgrid\/*\/ChimeraX.app\/Contents\/MacOS\/ChimeraX",
  "bundleInfo" : {"CFBundleShortVersionString":"1.6.1","CFBundleVersion":"1.6.1.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
  "storeInfo" : {"deviceIdentifierForVendor":"3623339C-1CED-5156-92E0-88E99AFD32D7","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "2A5BE207-3941-10CB-40FC-B0EE10DCD57E",
  "codeSigningID" : "edu.ucsf.cgl.ChimeraX",
  "codeSigningTeamID" : "LWV8X224YF",
  "codeSigningFlags" : 570491649,
  "codeSigningValidationCategory" : 6,
  "codeSigningTrustLevel" : 0,
  "wakeTime" : 2,
  "sleepWakeUUID" : "FC75B620-DE02-44A0-86C4-849BACB2B5A2",
  "sip" : "enabled",
  "vmRegionInfo" : "0x18 is not in any region.  Bytes before following region: 105553518919656\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      MALLOC_NANO (reserved)   600018000000-600020000000 [128.0M] rw-\/rwx SM=NUL  ...(unallocated)",
  "exception" : {"codes":"0x0000000000000001, 0x0000000000000018","rawCodes":[1,24],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000018"},
  "termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":10541},
  "vmregioninfo" : "0x18 is not in any region.  Bytes before following region: 105553518919656\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      MALLOC_NANO (reserved)   600018000000-600020000000 [128.0M] rw-\/rwx SM=NUL  ...(unallocated)",
  "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" : [{"triggered":true,"id":671798,"threadState":{"x":[{"value":0},{"value":0},{"value":1},{"value":6763658669},{"value":4832132120},{"value":18349196447875198987},{"value":0},{"value":6125823480},{"value":7170717821357955340},{"value":7170717814145169804},{"value":78},{"value":0},{"value":49},{"value":16},{"value":6006243328},{"value":2},{"value":328},{"value":8369533856},{"value":0},{"value":11},{"value":8290738304,"symbolLocation":0,"symbol":"_main_thread"},{"value":259},{"value":8290738528,"symbolLocation":224,"symbol":"_main_thread"},{"value":4480237904},{"value":1},{"value":32769},{"value":32768},{"value":8290744736,"symbolLocation":0,"symbol":"_NSConcreteStackBlock"},{"value":0}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6763478056},"cpsr":{"value":1073745920},"fp":{"value":4832131920},"sp":{"value":4832131888},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6763251556,"matchesCrashFrame":1},"far":{"value":4344318648}},"name":"CrBrowserMain","queue":"com.apple.main-thread","frames":[{"imageOffset":38756,"symbol":"__pthread_kill","symbolLocation":8,"imageIndex":148},{"imageOffset":27688,"symbol":"pthread_kill","symbolLocation":288,"imageIndex":149},{"imageOffset":259180,"symbol":"raise","symbolLocation":32,"imageIndex":150},{"imageOffset":14884,"symbol":"_sigtramp","symbolLocation":56,"imageIndex":151},{"imageOffset":3459388,"symbol":"QMacCGContext::QMacCGContext(QPainter*)","symbolLocation":40,"imageIndex":48},{"imageOffset":43052,"imageIndex":69},{"imageOffset":73708,"imageIndex":69},{"imageOffset":464432,"symbol":"QCommonStyle::drawControl(QStyle::ControlElement, QStyleOption const*, QPainter*, QWidget const*) const","symbolLocation":2132,"imageIndex":47},{"imageOffset":63388,"imageIndex":69},{"imageOffset":710016,"imageIndex":47},{"imageOffset":1933144,"symbol":"QTabBar::paintEvent(QPaintEvent*)","symbolLocation":1584,"imageIndex":47},{"imageOffset":344492,"symbol":"QWidget::event(QEvent*)","symbolLocation":132,"imageIndex":47},{"imageOffset":1931192,"symbol":"QTabBar::event(QEvent*)","symbolLocation":736,"imageIndex":47},{"imageOffset":42768,"symbol":"QApplicationPrivate::notify_helper(QObject*, QEvent*)","symbolLocation":272,"imageIndex":47},{"imageOffset":49644,"symbol":"QApplication::notify(QObject*, QEvent*)","symbolLocation":3396,"imageIndex":47},{"imageOffset":1427128,"symbol":"sipQApplication::notify(QObject*, QEvent*)","symbolLocation":248,"imageIndex":46},{"imageOffset":429724,"symbol":"QCoreApplication::notifyInternal2(QObject*, QEvent*)","symbolLocation":292,"imageIndex":44},{"imageOffset":291900,"symbol":"QWidgetPrivate::drawWidget(QPaintDevice*, QRegion const&, QPoint const&, 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}
===== Log before crash start =====
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> ui tool show AlphaFold

> alphafold search
> KTSAQAINQAVNNLNERAKTLAGGTTNSPAYQATLLALRSVLGLWNSMGYAVICGGYTKSPGENNQKNFHYTDENGNGTTINCGGSTNSNGTHSSNGTNTLKADKNVSLSIEQYEKIHESYQILSKALKQAGLAPLNSKGEKLEAHVTTSKYQQDSQTKTTTSVIDTTNDAQNLLTQAQTIVNTLKDYCPMLIAKSSSGSGGGAATNTPSWQTAGGGKNSCETFGAEFSAASDMINNAQKIVQETQQLSANQPKNITQPHNLNLNTPSSLTALAQKMLKNAQSQAEILKLANQVESDFNKLSSGHLKDYIGKCDMSAISSTNMTMQSQKNNWGNGCAGVEETLTSLKTSAADFNNQTPQINQAQNLANTLIQELGNNPFRNMGMIASSTTNNGSARKKIRLDRKYIVSCKQTEVPLSVPWDPSNQVYLSYNNVSSLKMLVAKDNWVLSSEISQVRLYTLEDDKFLSFHMEMVVHVDAAQAFLLLSDLRQRPEWDKHYRSVELVQQVDEDDAIYHVTSPALGGHTKPQDFVILASRRKPCDNGDPYVIALRSVTLPTHRETPEYRRGETLCSGFCLWREGDQLTKVSYYNQATPGVLNYVTTNVAGLSSEFYTTFKACEQFLLDNRNDLAPSLQTL

Fetching AlphaFold database settings from
https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database3.json  
Webservices job id: U3L0ZIIVHG84TLHD  

> alphafold predict
> KTSAQAINQAVNNLNERAKTLAGGTTNSPAYQATLLALRSVLGLWNSMGYAVICGGYTKSPGENNQKNFHYTDENGNGTTINCGGSTNSNGTHSSNGTNTLKADKNVSLSIEQYEKIHESYQILSKALKQAGLAPLNSKGEKLEAHVTTSKYQQDSQTKTTTSVIDTTNDAQNLLTQAQTIVNTLKDYCPMLIAKSSSGSGGGAATNTPSWQTAGGGKNSCETFGAEFSAASDMINNAQKIVQETQQLSANQPKNITQPHNLNLNTPSSLTALAQKMLKNAQSQAEILKLANQVESDFNKLSSGHLKDYIGKCDMSAISSTNMTMQSQKNNWGNGCAGVEETLTSLKTSAADFNNQTPQINQAQNLANTLIQELGNNPFRNMGMIASSTTNNGSARKKIRLDRKYIVSCKQTEVPLSVPWDPSNQVYLSYNNVSSLKMLVAKDNWVLSSEISQVRLYTLEDDKFLSFHMEMVVHVDAAQAFLLLSDLRQRPEWDKHYRSVELVQQVDEDDAIYHVTSPALGGHTKPQDFVILASRRKPCDNGDPYVIALRSVTLPTHRETPEYRRGETLCSGFCLWREGDQLTKVSYYNQATPGVLNYVTTNVAGLSSEFYTTFKACEQFLLDNRNDLAPSLQTL

Please cite ColabFold: Making protein folding accessible to all. Nature
Methods (2022) if you use these predictions.  
Running AlphaFold prediction  

> alphafold predict
> KTSAQAINQAVNNLNERAKTLAGGTTNSPAYQATLLALRSVLGLWNSMGYAVICGGYTKSPGENNQKNFHYTDENGNGTTINCGGSTNSNGTHSSNGTNTLKADKNVSLSIEQYEKIHESYQILSKALKQAGLAPLNSKGEKLEAHVTTSKYQQDSQTKTTTSVIDTTNDAQNLLTQAQTIVNTLKDYCPMLIAKSSSGSGGGAATNTPSWQTAGGGKNSCETFGAEFSAASDMINNAQKIVQETQQLSANQPKNITQPHNLNLNTPSSLTALAQKMLKNAQSQAEILKLANQVESDFNKLSSGHLKDYIGKCDMSAISSTNMTMQSQKNNWGNGCAGVEETLTSLKTSAADFNNQTPQINQAQNLANTLSARKKIRLDRKYIVSCKQTEVPLSVPWDPSNQVYLSYNNVSSLKMLVAKDNWVLSSEISQVRLYTLEDDKFLSFHMEMVVHVDAAQAFLLLSDLRQRPEWDKHYRSVELVQQVDEDDAIYHVTSPALGGHTKPQDFVILASRRKPCDNGDPYVIALRSVTLPTHRETPEYRRGETLCSGFCLWREGDQLTKVSYYNQATPGVLNYVTTNVAGLSSEFYTTFKACEQFLLDNRNDLAPSLQTL

Running AlphaFold prediction  

> alphafold predict
> KTSAQAINQAVNNLNERAKTLAGGTTNSPAYQATLLALRSVLGLWNSMGYAVICGGYTKSPGENNQKNFHYTDENGNGTTINCGGSTNSNGTHSSNGTNTLKADKNVSLSIEQYEKIHESYQILSKALKQAGLAPLNSKGEKLEAHVTTSKYQQDSQTKTTTSVIDTTNDAQNLLTQAQTIVNTLKDYCPMLIAKSSSGSGGGAATNTPSWQTAGGGKNSCETFGAEFSAASDMINNAQKIVQETQQLSANQPKNITQPHNLNLNTPSSLTALAQKMLKNAQSQAEILKLANQVESDFNKLSSGHLKDYIGKCDMSAISSTNMTMQSQKNNWGNGCAGVEETLTSLKTSAADFNNQTPQINQAQNLANTLSARKKIRLDRKYIVSCKQTEVPLSVPWDPSNQVYLSYNNVSSLKMLVAKDNWVLSSEISQVRLYTLEDDKFLSFHMEMVVHVDAAQAFLLLSDLRQRPEWDKHYRSVELVQQVDEDDAIYHVTSPALGGHTKPQDFVILASRRKPCDNGDPYVIALRSVTLPTHRETPEYRRGETLCSGFCLWREGDQLTKVSYYNQATPGVLNYVTTNVAGLSSEFYTTFKACEQFLLDNRNDLAPSLQTL

Running AlphaFold prediction  
AlphaFold prediction finished  
Results in /Users/eortlund/Downloads/ChimeraX/AlphaFold/prediction_1  

> open
> /Users/eortlund/Downloads/ChimeraX/AlphaFold/prediction_1/best_model.pdb

Chain information for best_model.pdb #1  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/eortlund/Downloads/ChimeraX/AlphaFold/prediction_1/best_model.pdb

Chain information for best_model.pdb #2  
---  
Chain | Description  
A | No description available  
  

> open /Users/eortlund/Downloads/HopQ-LRH1_6AVZ-overlay.cxs

opened ChimeraX session  

> open /Users/eortlund/Downloads/HopQ-LRH1_6AVZ-overlay.cxs

opened ChimeraX session  

> open /Users/eortlund/Downloads/HopQ_LRH1-LBD_best-model.pdb

Chain information for HopQ_LRH1-LBD_best-model.pdb #3  
---  
Chain | Description  
A | No description available  
  

> open /Users/eortlund/Downloads/rcsb_pdb_6VJJ.fasta

Failed opening file /Users/eortlund/Downloads/rcsb_pdb_6VJJ.fasta:  
Sequence '6VJJ_2|Chain B|RAF proto-oncogene serine/threonine-protein
kinase|Homo sapiens (9606)' differs in length from preceding sequences, and it
is therefore impossible to open these sequences as an alignment. If you want
to open the sequences individually, specify 'false' as the value of the
'alignment' keyword in the 'open' command.  

> open /Users/eortlund/Downloads/rcsb_pdb_6VJJ.fasta

Failed opening file /Users/eortlund/Downloads/rcsb_pdb_6VJJ.fasta:  
Sequence '6VJJ_2|Chain B|RAF proto-oncogene serine/threonine-protein
kinase|Homo sapiens (9606)' differs in length from preceding sequences, and it
is therefore impossible to open these sequences as an alignment. If you want
to open the sequences individually, specify 'false' as the value of the
'alignment' keyword in the 'open' command.  

> save /Users/eortlund/Desktop/LRH1_HopQ.cxs

Unsupported scale factor (0.000000) detected on Display0  

QPainter::begin: Paint device returned engine == 0, type: 3  


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

Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open /Users/eortlund/Downloads/RAF_YgjK_6VJJ_overlaid.cxs

Log from Thu Sep 7 09:00:09 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/andrecuevas/Documents/School/Graduate/Dissertation/Projects/megabody/structure_predictions/lrh-1/HopQ-
> LRH1/HopQ_LRH1-LBD_best-model.pdb format pdb

Chain information for HopQ_LRH1-LBD_best-model.pdb #1  
---  
Chain | Description  
A | No description available  
  

> color bfactor palette alphafold

5040 atoms, 652 residues, atom bfactor range 26.3 to 98.9  
Alignment identifier is 1/A  

> select
> /A:14-39,49-69,75-97,144-146,157-177,217-234,266-296,313-348,385-425,429-445,449-451,455-476,480-482,485-511,527-533,535-554,559-570,581-602,609-636,645-651

3079 atoms, 3103 bonds, 388 residues, 1 model selected  

> select /A:266-267

12 atoms, 11 bonds, 2 residues, 1 model selected  

> select /A:266-296

230 atoms, 231 bonds, 31 residues, 1 model selected  

> select /A:313

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

> select /A:313-348

273 atoms, 274 bonds, 36 residues, 1 model selected  

> show sel atoms

> color sel byhetero

> select /A:384-385

11 atoms, 10 bonds, 2 residues, 1 model selected  

> select /A:385-425

317 atoms, 319 bonds, 41 residues, 1 model selected  

> show sel atoms

> color sel byhetero

> select /A:69

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select /A:51

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

> select /A:51-69

141 atoms, 140 bonds, 19 residues, 1 model selected  

> show sel atoms

> color sel byhetero

> select clear

> fetch 6AVZ

Unknown command: fetch 6AVZ  

> open 6AVZ

6avz title:  
Crystal structure of the HopQ-CEACAM3 WT complex [more info...]  
  
Chain information for 6avz #2  
---  
Chain | Description | UniProt  
A | Carcinoembryonic antigen-related cell adhesion molecule 3 | CEAM3_HUMAN
0-107  
B | HopQ | H6A3H4_HELPX 18-442  
E | part of HopQ loop |  
  
Non-standard residues in 6avz #2  
---  
CA — calcium ion  
  

> select #2/A

863 atoms, 859 bonds, 129 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> ui tool show Matchmaker

> matchmaker #2/B to #1/A pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker HopQ_LRH1-LBD_best-model.pdb, chain A (#1) with 6avz, chain B (#2),
sequence alignment score = 2010.6  
RMSD between 305 pruned atom pairs is 0.651 angstroms; (across all 347 pairs:
2.006)  
  

> hide #1 models

> show #1 models

> color #2 #ff7e79ff

> color #2 #ff2600ff

> color #2 #942193ff

> color #2 #941751ff

> color #2 #942193ff

> color #2 #531b93ff

> color #2 #8efa00ff

> select #2/B:405

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

> ui tool show "Show Sequence Viewer"

> sequence chain #2/B

Alignment identifier is 2/B  

> select #2/B:405-406

16 atoms, 15 bonds, 2 residues, 1 model selected  

> select #2/B:405-406

16 atoms, 15 bonds, 2 residues, 1 model selected  

> select #2/B:405-406

16 atoms, 15 bonds, 2 residues, 1 model selected  

> select #2/B:405-419

115 atoms, 115 bonds, 15 residues, 1 model selected  

> show sel atoms

> select #2/B:66

11 atoms, 10 bonds, 1 residue, 1 model selected  

> show sel atoms

> cd
> /Users/andrecuevas/Documents/School/Graduate/Dissertation/Projects/megabody/structure_predictions/lrh-1/HopQ-
> LRH1

Current working directory is:
/Users/andrecuevas/Documents/School/Graduate/Dissertation/Projects/megabody/structure_predictions/lrh-1/HopQ-
LRH1  

> save
> /Users/andrecuevas/Documents/School/Graduate/Dissertation/Projects/megabody/structure_predictions/lrh-1/HopQ-
> LRH1/HopQ-LRH1_6AVZ-overlay.cxs

> select #1/A:422

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

> select #1/A:385

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

> select #1/A:385-422

294 atoms, 296 bonds, 38 residues, 1 model selected  

> select #1/A:422

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

> select #1/A:415-422

66 atoms, 66 bonds, 8 residues, 1 model selected  

> select #1/A:403-404

14 atoms, 14 bonds, 2 residues, 1 model selected  

> select #1/A:404-425

173 atoms, 174 bonds, 22 residues, 1 model selected  

> select #1/A:405

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

> select #1/A:406-425

157 atoms, 157 bonds, 20 residues, 1 model selected  

> select #1/A:405

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

> select #1/A:405-425

166 atoms, 166 bonds, 21 residues, 1 model selected  

> select #1/A:429

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

> select #1/A:430

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

> select #1/A:430-445

128 atoms, 129 bonds, 16 residues, 1 model selected  

> show sel atoms

> color sel byhetero

> select #1/A:455-456

18 atoms, 18 bonds, 2 residues, 1 model selected  

> select #1/A:455-476

175 atoms, 178 bonds, 22 residues, 1 model selected  

> color sel byhetero

> show sel atoms

> color sel byhetero

> close session

> open 6VJJ

Summary of feedback from opening 6VJJ fetched from pdb  
---  
notes | Fetching compressed mmCIF 6vjj from
http://files.rcsb.org/download/6vjj.cif  
Fetching CCD MG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/MG/MG.cif  
Fetching CCD GNP from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/GNP/GNP.cif  
Fetching CCD CL from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/L/CL/CL.cif  
Fetching CCD EDO from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/O/EDO/EDO.cif  
  
6vjj title:  
Crystal Structure of wild-type KRAS4b (GMPPNP-bound) in complex with RAS-
binding domain (RBD) of RAF1/CRAF [more info...]  
  
Chain information for 6vjj #1  
---  
Chain | Description | UniProt  
A | GTPase KRas | RASK_HUMAN 1-169  
B | RAF proto-oncogene serine/threonine-protein kinase | RAF1_HUMAN 52-131  
  
Non-standard residues in 6vjj #1  
---  
CL — chloride ion  
EDO — 1,2-ethanediol (ethylene glycol)  
GNP — phosphoaminophosphonic acid-guanylate ester  
MG — magnesium ion  
MPD — (4S)-2-methyl-2,4-pentanediol  
  

> color bychain

> open 6VJJ

6vjj title:  
Crystal Structure of wild-type KRAS4b (GMPPNP-bound) in complex with RAS-
binding domain (RBD) of RAF1/CRAF [more info...]  
  
Chain information for 6vjj #2  
---  
Chain | Description | UniProt  
A | GTPase KRas | RASK_HUMAN 1-169  
B | RAF proto-oncogene serine/threonine-protein kinase | RAF1_HUMAN 52-131  
  
Non-standard residues in 6vjj #2  
---  
CL — chloride ion  
EDO — 1,2-ethanediol (ethylene glycol)  
GNP — phosphoaminophosphonic acid-guanylate ester  
MG — magnesium ion  
MPD — (4S)-2-methyl-2,4-pentanediol  
  

> select #1/A:81

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

> select up

52 atoms, 53 bonds, 7 residues, 1 model selected  

> select up

1328 atoms, 1349 bonds, 168 residues, 1 model selected  

> color sel byhetero

Alignment identifier is 1/A  

> select add #2

3442 atoms, 3342 bonds, 6 pseudobonds, 566 residues, 3 models selected  

> select add #1

4228 atoms, 3986 bonds, 12 pseudobonds, 796 residues, 4 models selected  

> select subtract #1

2114 atoms, 1993 bonds, 6 pseudobonds, 398 residues, 2 models selected  
Alignment identifier is 2/A  
Alignment identifier is 2/B  

> select #2/B:100

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #2/B:100-106

52 atoms, 52 bonds, 7 residues, 1 model selected  

> select #2/B:100-106

52 atoms, 52 bonds, 7 residues, 1 model selected  

> select #2/B:107-108

13 atoms, 12 bonds, 2 residues, 1 model selected  

> select #2/B:107-108

13 atoms, 12 bonds, 2 residues, 1 model selected  

> select #2/B:100

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #2/B:100-109

74 atoms, 74 bonds, 10 residues, 1 model selected  

> select #2/B:100-110

79 atoms, 79 bonds, 11 residues, 1 model selected  

> show sel atoms

> color sel byhetero

> select clear

> select #2/B:55-57

21 atoms, 20 bonds, 3 residues, 1 model selected  

> select #2/B:55-131

589 atoms, 597 bonds, 77 residues, 1 model selected  

> select #1/B:100

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select clear

> select #1/A:63-64

21 atoms, 21 bonds, 2 residues, 1 model selected  

> select #1/A:63-124

502 atoms, 511 bonds, 62 residues, 1 model selected  

> select #2/B:55

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

> select #2/B:55-58

29 atoms, 28 bonds, 4 residues, 1 model selected  

> select #2/B:100

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #2/B:100-111

90 atoms, 90 bonds, 12 residues, 1 model selected  

> select #2/B:109

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

> select #2/B:109

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

> select #2/B:100

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #2/B:100-101

19 atoms, 18 bonds, 2 residues, 1 model selected  

> ui tool show AlphaFold

Populating font family aliases took 285 ms. Replace uses of missing font
family "Calibri" with one that exists to avoid this cost.  

> alphafold predict
> SKTSNTIRVFLPNKQRTVVNVRNGMSLHDCLMKALKVRGLQPECCAVFRKEETQSGLNNYARVVEKGQYDSLEIPAQVAASWESGRDDAAVFGFIDKEQLDKYVANGGKRSDWTVKFAENRSQDGTLLGYSLLQESVDQASYMYSDNHYLAEMATILGKPEEAKRYRQLAQQLADYINTCMFDPTTQFYYDVRIEDKPLANGCAGKPIVERGKGPEGWSPLFNGAATQANADAVVKVMLDPKEFNTFVPLGTAALTNPAFGADIYWRGRVWVDQFWFGLKGMERYGYRDDALKLADTFFRHAKGLTADGPIQENYNPLTGAQQGAPNFSWSAAHLYMLYNDFFRKQASGGGSGGGGSGGGGSGNADNYKNVINRTGAPQYMKDYDYDDHQRFNPFFDLGAWHGHLLPDGPNTMGGFPGVALLTEEYINFMASNFDRLTVWQDGKKVDFTLEAYSIPGALVQKLTAKDVQVEMTLRFATPRTSLLETKITSNKPLDLVWDGELLEKLEAKEGKPLSDKTIAGEYPDYQRKISATRDGLKVTFGKVRATWDLLTSGESEYQVHKSLPVQTEINGNRFTSKAHINGSTTLYTTYSHLLTAQEVSKEQMQIRDILARPAFYLTASQQRWEEYLKKGLTNPDATPEQTRVAVKAIETLNGNWRSPGGAVKFNTVTPSVTGRWFSGNQTWPWDTWKQAFAMAHFNPDIAKENIRAVFSWQIQPGDSVRPQDVGFVPDLIAWNLSPERGGDGGNWNERNTKPSLAAWSVMEVYNVTQDKTWVAEMYPKLVAYHDWWLRNRDHNGNGVPEYGATRDKAHNTESGEMLFTVKKALDWNTDAASLIGEELQVDFL
> directory /Users/andrecuevas/Downloads/ChimeraX/AlphaFold/RAF_YgjK-RA-
> retained_[N] minimize true templates true

Please cite ColabFold: Making protein folding accessible to all. Nature
Methods (2022) if you use these predictions.  
Running AlphaFold prediction  
AlphaFold prediction finished  
Results in /Users/andrecuevas/Downloads/ChimeraX/AlphaFold/RAF_YgjK-RA-
retained_1  

> open /Users/andrecuevas/Downloads/ChimeraX/AlphaFold/RAF_YgjK-RA-
> retained_1/best_model.pdb

Chain information for best_model.pdb #3  
---  
Chain | Description  
A | No description available  
  

> ui mousemode right zoom

> hide #!1 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!1 models

> ui tool show Matchmaker

> matchmaker #3/A to #1/B pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6vjj, chain B (#1) with best_model.pdb, chain A (#3), sequence
alignment score = 231.5  
RMSD between 46 pruned atom pairs is 0.558 angstroms; (across all 68 pairs:
11.650)  
  

> ui mousemode right translate

> hide #3 models

> show #3 models

> ui mousemode right zoom

> ui mousemode right translate

> hide #!1 models

> ui mousemode right translate

> ui mousemode right zoom

> ui mousemode right translate

> ui mousemode right rotate

> ui mousemode right translate

> show #!1 models

> hide #!1 models

> set bgColor white

> cd
> /Users/andrecuevas/Documents/School/Graduate/Dissertation/Projects/KRAS/structural-
> designs/RAF_YgjK

Current working directory is:
/Users/andrecuevas/Documents/School/Graduate/Dissertation/Projects/KRAS/structural-
designs/RAF_YgjK  

> save RAF-YgjK_01.png transparentBackground true supersample 3

> save RAF-YgjK_02.png transparentBackground true supersample 3

> show #!1 models

> ui mousemode right zoom

> save RAF-YgjK_clashing_01.png transparentBackground true supersample 3

> select add #1

2133 atoms, 2011 bonds, 6 pseudobonds, 400 residues, 3 models selected  

> select add #2

4228 atoms, 3986 bonds, 12 pseudobonds, 796 residues, 4 models selected  

> select add #3

17354 atoms, 17286 bonds, 12 pseudobonds, 1641 residues, 5 models selected  

> hide sel & #3#!1 atoms

> select subtract #1

15240 atoms, 15293 bonds, 6 pseudobonds, 1243 residues, 3 models selected  

> select subtract #2

13126 atoms, 13300 bonds, 845 residues, 1 model selected  

> select subtract #3

Nothing selected  

> hide #!1 models

> show #!1 models

> show #!2 models

> hide #!2 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> select #1/B:131

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

> select add #1/B:130

19 atoms, 18 bonds, 2 residues, 1 model selected  

> select add #1/B:129

27 atoms, 25 bonds, 3 residues, 1 model selected  

> select add #1/B:128

34 atoms, 31 bonds, 4 residues, 1 model selected  

> select add #3/A:840

53 atoms, 49 bonds, 5 residues, 2 models selected  

> select add #3/A:841

70 atoms, 65 bonds, 6 residues, 2 models selected  

> hide sel cartoons

> select #3/A:845

20 atoms, 19 bonds, 1 residue, 1 model selected  

> select add #3/A:844

40 atoms, 39 bonds, 2 residues, 1 model selected  

> select add #3/A:843

52 atoms, 50 bonds, 3 residues, 1 model selected  

> select add #3/A:842

68 atoms, 65 bonds, 4 residues, 1 model selected  

> hide sel cartoons

> save RAF-YgjK_connection_01.png transparentBackground true supersample 3

> select add #3

13126 atoms, 13300 bonds, 845 residues, 1 model selected  

> show sel cartoons

> select add #1

15240 atoms, 15293 bonds, 6 pseudobonds, 1243 residues, 3 models selected  

> show sel cartoons

> save
> /Users/andrecuevas/Documents/School/Graduate/Dissertation/Projects/KRAS/structural-
> designs/RAF_YgjK/RAF_YgjK-RA-retained_1/RAF_YgjK_6VJJ_overlaid.cxs

——— End of log from Thu Sep 7 09:00:09 2023 ———

opened ChimeraX session  
Updating list of available bundles failed: Internal Server Error  




OpenGL version: 4.1 Metal - 83.1
OpenGL renderer: Apple M2 Pro
OpenGL vendor: Apple

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: Mac mini
      Model Identifier: Mac14,12
      Model Number: Z170000G4LL/A
      Chip: Apple M2 Pro
      Total Number of Cores: 12 (8 performance and 4 efficiency)
      Memory: 32 GB
      System Firmware Version: 8422.141.2
      OS Loader Version: 8422.141.2

Software:

    System Software Overview:

      System Version: macOS 13.5.1 (22G90)
      Kernel Version: Darwin 22.6.0
      Time since boot: 8 days, 15 hours, 36 minutes

Graphics/Displays:

    Apple M2 Pro:

      Chipset Model: Apple M2 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 19
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Studio Display:
          Display Type: Retina LCD
          Resolution: 5120 x 2880 Retina
          Display Serial Number: HG2WXFCWDT
          Display Firmware Version: Version 16.4 (Build 20E246)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes


Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9.1
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.10
    ChimeraX-AtomicLibrary: 10.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.8
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6.1
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.1
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.4
    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: 2.0.12
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.3.7
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.1
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.28.4
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.39.3
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.2.22
    imagesize: 1.4.1
    importlib-metadata: 6.6.0
    ipykernel: 6.21.1
    ipython: 8.10.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.6
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.0.2
    jupyter-core: 5.3.0
    jupyterlab-widgets: 3.0.7
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.2
    matplotlib: 3.6.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 2.8.8
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.5.0
    prompt-toolkit: 3.0.38
    psutil: 5.9.4
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.4.2
    PyQt6-Qt6: 6.4.3
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pyzmq: 25.0.2
    qtconsole: 5.4.0
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.28.2
    scipy: 1.9.3
    setuptools: 67.4.0
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4.1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.1
    traitlets: 5.9.0
    typing-extensions: 4.5.0
    tzdata: 2023.3
    urllib3: 1.26.15
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7
    zipp: 3.15.0

Change History (2)

comment:1 by Eric Pettersen, 2 years ago

Cc: Tom Goddard added
Component: Unassigned → Window Toolkit
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Crash in QTabBar::paintEvent

comment:2 by Eric Pettersen, 2 years ago

Resolution: → can't reproduce
Status: accepted → closed

No QPainter::begin message in log for this one.

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