Opened 21 months ago

Last modified 21 months ago

#14606 feedback defect

Qt fatal error: Failed to initialize graphics backend for OpenGL

Reported by: ea2941@… 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-13.0.1-arm64-arm-64bit
ChimeraX Version: 1.8.dev202402080317 (2024-02-08 03:17:03 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Qt fatal error: Failed to initialize graphics backend for OpenGL.
Fatal Python error: Aborted

Current thread 0x00000001e420e500 (most recent call first):
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 864 in rapid_access_shown
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 199 in build
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 722 in init
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1069 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.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, chimerax.surface._surface, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.core._mac_util (total: 45)


{"app_name":"ChimeraX","timestamp":"2024-02-16 21:14:50.00 -0500","app_version":"1.8.0","slice_uuid":"17982d98-65bc-3327-8526-577ec996453c","build_version":"1.8.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":1,"is_first_party":0,"bug_type":"309","os_version":"macOS 13.0.1 (22A400)","roots_installed":0,"name":"ChimeraX","incident_id":"8F231145-E25E-4F4B-88A3-27DF3A2AE5B1"}
{
  "uptime" : 50000,
  "procRole" : "Foreground",
  "version" : 2,
  "userID" : 501,
  "deployVersion" : 210,
  "modelCode" : "MacBookAir10,1",
  "coalitionID" : 1536,
  "osVersion" : {
    "train" : "macOS 13.0.1",
    "build" : "22A400",
    "releaseType" : "User"
  },
  "captureTime" : "2024-02-16 21:14:50.0694 -0500",
  "incident" : "8F231145-E25E-4F4B-88A3-27DF3A2AE5B1",
  "pid" : 17759,
  "translated" : false,
  "cpuType" : "ARM-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2024-02-16 21:14:47.4092 -0500",
  "procStartAbsTime" : 1206344835993,
  "procExitAbsTime" : 1206408387042,
  "procName" : "ChimeraX",
  "procPath" : "\/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
  "bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
  "storeInfo" : {"deviceIdentifierForVendor":"4FC8EC12-17F3-5733-BD8A-CD2A3751BE5F","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "4DCC9E87-056F-F26B-C4CF-08DC042B5D41",
  "wakeTime" : 3198,
  "sleepWakeUUID" : "12E307B7-78F3-4324-BA86-9C48591FF602",
  "sip" : "disabled",
  "exception" : {"codes":"0x0000000000000000, 0x0000000000000000","rawCodes":[0,0],"type":"EXC_CRASH","signal":"SIGABRT"},
  "ktriageinfo" : "VM - pmap_enter retried due to resource shortage\nVM - pmap_enter retried due to resource shortage\nVM - pmap_enter retried due to resource shortage\nVM - pmap_enter retried due to resource shortage\nVM - pmap_enter retried due to resource shortage\n",
  "asi" : {"libsystem_c.dylib":["abort() called"]},
  "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":2344969,"threadState":{"x":[{"value":0},{"value":0},{"value":1},{"value":4967070360},{"value":99},{"value":103},{"value":10},{"value":0},{"value":4248487224613607016},{"value":4248487224007586664},{"value":14757395258967641293},{"value":4294967286},{"value":4967070290},{"value":0},{"value":52},{"value":4294967280},{"value":328},{"value":8204437928},{"value":0},{"value":6},{"value":8122328320,"symbolLocation":0,"symbol":"_main_thread"},{"value":259},{"value":8122328544,"symbolLocation":224,"symbol":"_main_thread"},{"value":1},{"value":4359292464,"symbolLocation":0,"symbol":"faulthandler_handlers"},{"value":49},{"value":0},{"value":105553173790720},{"value":4960569920}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6588505324},"cpsr":{"value":1073745920},"fp":{"value":4967070432},"sp":{"value":4967070400},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6588281380,"matchesCrashFrame":1},"far":{"value":5357536344}},"name":"CrBrowserMain","queue":"com.apple.main-thread","frames":[{"imageOffset":37412,"symbol":"__pthread_kill","symbolLocation":8,"imageIndex":0},{"imageOffset":27884,"symbol":"pthread_kill","symbolLocation":288,"imageIndex":1},{"imageOffset":268880,"symbol":"raise","symbolLocation":32,"imageIndex":2},{"imageOffset":2417160,"symbol":"faulthandler_fatal_error","symbolLocation":392,"imageIndex":3},{"imageOffset":17060,"symbol":"_sigtramp","symbolLocation":56,"imageIndex":4},{"imageOffset":27884,"symbol":"pthread_kill","symbolLocation":288,"imageIndex":1},{"imageOffset":496328,"symbol":"abort","symbolLocation":180,"imageIndex":2},{"imageOffset":28996,"symbol":"qAbort()","symbolLocation":12,"imageIndex":5},{"imageOffset":44796,"imageIndex":5},{"imageOffset":2985276,"symbol":"QMessageLogger::fatal(char const*, ...) const","symbolLocation":120,"imageIndex":5},{"imageOffset":70868,"imageIndex":6},{"imageOffset":48732,"imageIndex":6},{"imageOffset":49324,"imageIndex":6},{"imageOffset":51836,"symbol":"QQuickWidget::resizeEvent(QResizeEvent*)","symbolLocation":484,"imageIndex":6},{"imageOffset":64836,"imageIndex":7},{"imageOffset":358692,"symbol":"QWidget::event(QEvent*)","symbolLocation":984,"imageIndex":8},{"imageOffset":56700,"symbol":"QQuickWidget::event(QEvent*)","symbolLocation":720,"imageIndex":6},{"imageOffset":65796,"imageIndex":7},{"imageOffset":56464,"symbol":"QApplicationPrivate::notify_helper(QObject*, QEvent*)","symbolLocation":272,"imageIndex":8},{"imageOffset":63548,"symbol":"QApplication::notify(QObject*, QEvent*)","symbolLocation":3396,"imageIndex":8},{"imageOffset":1428996,"symbol":"sipQApplication::notify(QObject*, QEvent*)","symbolLocation":248,"imageIndex":9},{"imageOffset":417088,"symbol":"QCoreApplication::notifyInternal2(QObject*, QEvent*)","symbolLocation":208,"imageIndex":5},{"imageOffset":331520,"symbol":"QWidgetPrivate::sendPendingMoveAndResizeEvents(bool, bool)","symbolLocation":248,"imageIndex":8},{"imageOffset":353532,"symbol":"QWidgetPrivate::show_helper()","symbolLocation":52,"imageIndex":8},{"imageOffset":354460,"symbol":"QWidgetPrivate::showChildren(bool)","symbolLocation":296,"imageIndex":8},{"imageOffset":353564,"symbol":"QWidgetPrivate::show_helper()","symbolLocation":84,"imageIndex":8},{"imageOffset":357000,"symbol":"QWidgetPrivate::setVisible(bool)","symbolLocation":864,"imageIndex":8},{"imageOffset":39248,"symbol":"sipQWebEngineView::setVisible(bool)","symbolLocation":140,"imageIndex":10},{"imageOffset":354288,"symbol":"QWidgetPrivate::showChildren(bool)","symbolLocation":124,"imageIndex":8},{"imageOffset":353564,"symbol":"QWidgetPrivate::show_helper()","symbolLocation":84,"imageIndex":8},{"imageOffset":357000,"symbol":"QWidgetPrivate::setVisible(bool)","symbolLocation":864,"imageIndex":8},{"imageOffset":1524628,"symbol":"sipQWidget::setVisible(bool)","symbolLocation":140,"imageIndex":9},{"imageOffset":261796,"symbol":"QStackedLayout::setCurrentIndex(int)","symbolLocation":384,"imageIndex":8},{"imageOffset":1829300,"symbol":"meth_QStackedWidget_setCurrentWidget(_object*, _object*)","symbolLocation":104,"imageIndex":9},{"imageOffset":1004504,"symbol":"cfunction_call","symbolLocation":96,"imageIndex":3},{"imageOffset":594156,"symbol":"_PyObject_MakeTpCall","symbolLocation":128,"imageIndex":3},{"imageOffset":1789244,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":54984,"imageIndex":3},{"imageOffset":1811404,"symbol":"_PyEval_Vector","symbolLocation":156,"imageIndex":3},{"imageOffset":661780,"symbol":"property_descr_set","symbolLocation":124,"imageIndex":3},{"imageOffset":1039020,"symbol":"_PyObject_GenericSetAttrWithDict","symbolLocation":296,"imageIndex":3},{"imageOffset":1034116,"symbol":"PyObject_SetAttr","symbolLocation":96,"imageIndex":3},{"imageOffset":1754304,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":20044,"imageIndex":3},{"imageOffset":1729512,"symbol":"PyEval_EvalCode","symbolLocation":276,"imageIndex":3},{"imageOffset":1707120,"symbol":"builtin_exec","symbolLocation":428,"imageIndex":3},{"imageOffset":1007044,"symbol":"cfunction_vectorcall_FASTCALL_KEYWORDS","symbolLocation":80,"imageIndex":3},{"imageOffset":1788292,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":54032,"imageIndex":3},{"imageOffset":1811404,"symbol":"_PyEval_Vector","symbolLocation":156,"imageIndex":3},{"imageOffset":2389028,"symbol":"pymain_run_module","symbolLocation":256,"imageIndex":3},{"imageOffset":2387652,"symbol":"Py_RunMain","symbolLocation":1784,"imageIndex":3},{"imageOffset":2392180,"symbol":"pymain_main","symbolLocation":52,"imageIndex":3},{"imageOffset":2392116,"symbol":"Py_Main","symbolLocation":36,"imageIndex":3},{"imageOffset":15700,"symbol":"main","symbolLocation":128,"imageIndex":11},{"imageOffset":24144,"symbol":"start","symbolLocation":2544,"imageIndex":12}]},{"id":2345001,"frames":[{"imageOffset":17892,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":0},{"imageOffset":30264,"symbol":"_pthread_cond_wait","symbolLocation":1232,"imageIndex":1},{"imageOffset":1502040,"symbol":"blas_thread_server","symbolLocation":360,"imageIndex":13},{"imageOffset":28780,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":7724,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":2345002,"frames":[{"imageOffset":17892,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":0},{"imageOffset":30264,"symbol":"_pthread_cond_wait","symbolLocation":1232,"imageIndex":1},{"imageOffset":1502040,"symbol":"blas_thread_server","symbolLocation":360,"imageIndex":13},{"imageOffset":28780,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":7724,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":2345003,"frames":[{"imageOffset":17892,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":0},{"imageOffset":30264,"symbol":"_pthread_cond_wait","symbolLocation":1232,"imageIndex":1},{"imageOffset":1502040,"symbol":"blas_thread_server","symbolLocation":360,"imageIndex":13},{"imageOffset":28780,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":7724,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":2345004,"frames":[{"imageOffset":17892,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":0},{"imageOffset":30264,"symbol":"_pthread_cond_wait","symbolLocation":1232,"imageIndex":1},{"imageOffset":1502040,"symbol":"blas_thread_server","symbolLocation":360,"imageIndex":13},{"imageOffset":28780,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":7724,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":2345005,"frames":[{"imageOffset":17892,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":0},{"imageOffset":30264,"symbol":"_pthread_cond_wait","symbolLocation":1232,"imageIndex":1},{"imageOffset":1502040,"symbol":"blas_thread_server","symbolLocation":360,"imageIndex":13},{"imageOffset":28780,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":7724,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":2345006,"frames":[{"imageOffset":17892,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":0},{"imageOffset":30264,"symbol":"_pthread_cond_wait","symbolLocation":1232,"imageIndex":1},{"imageOffset":1502040,"symbol":"blas_thread_server","symbolLocation":360,"imageIndex":13},{"imageOffset":28780,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":7724,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":2345007,"frames":[{"imageOffset":17892,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":0},{"imageOffset":30264,"symbol":"_pthread_cond_wait","symbolLocation":1232,"imageIndex":1},{"imageOffset":1502040,"symbol":"blas_thread_server","symbolLocation":360,"imageIndex":13},{"imageOffset":28780,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":7724,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":2345016,"frames":[{"imageOffset":7704,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":1}]},{"id":2345017,"frames":[{"imageOffset":7704,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":1}]},{"id":2345018,"frames":[{"imageOffset":7704,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":1}]},{"id":2345073,"name":"com.apple.coremedia.rootQueue.47","frames":[{"imageOffset":3460,"symbol":"semaphore_timedwait_trap","symbolLocation":8,"imageIndex":0},{"imageOffset":19228,"symbol":"_dispatch_sema4_timedwait","symbolLocation":64,"imageIndex":14},{"imageOffset":20764,"symbol":"_dispatch_semaphore_wait_slow","symbolLocation":76,"imageIndex":14},{"imageOffset":89448,"symbol":"_dispatch_worker_thread","symbolLocation":324,"imageIndex":14},{"imageOffset":28780,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":7724,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":2345082,"name":"com.apple.coremedia.rootQueue.47","frames":[{"imageOffset":3460,"symbol":"semaphore_timedwait_trap","symbolLocation":8,"imageIndex":0},{"imageOffset":19228,"symbol":"_dispatch_sema4_timedwait","symbolLocation":64,"imageIndex":14},{"imageOffset":20764,"symbol":"_dispatch_semaphore_wait_slow","symbolLocation":76,"imageIndex":14},{"imageOffset":89448,"symbol":"_dispatch_worker_thread","symbolLocation":324,"imageIndex":14},{"imageOffset":28780,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":7724,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":2345086,"name":"ThreadPoolServiceThread","frames":[{"imageOffset":51208,"symbol":"kevent64","symbolLocation":8,"imageIndex":0},{"imageOffset":56727496,"imageIndex":15},{"imageOffset":56727288,"imageIndex":15},{"imageOffset":56233836,"imageIndex":15},{"imageOffset":55985340,"imageIndex":15},{"imageOffset":56364424,"imageIndex":15},{"imageOffset":56271272,"imageIndex":15},{"imageOffset":56364816,"imageIndex":15},{"imageOffset":56519652,"imageIndex":15},{"imageOffset":28780,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":7724,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":2345087,"name":"ThreadPoolForegroundWorker","frames":[{"imageOffset":3568,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":0},{"imageOffset":75992,"symbol":"mach_msg2_internal","symbolLocation":80,"imageIndex":0},{"imageOffset":38456,"symbol":"mach_msg_overwrite","symbolLocation":540,"imageIndex":0},{"imageOffset":4460,"symbol":"mach_msg","symbolLocation":24,"imageIndex":0},{"imageOffset":56546788,"imageIndex":15},{"imageOffset":56317548,"imageIndex":15},{"imageOffset":56320244,"imageIndex":15},{"imageOffset":56319264,"imageIndex":15},{"imageOffset":56519652,"imageIndex":15},{"imageOffset":28780,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":7724,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":2345088,"name":"ThreadPoolBackgroundWorker","frames":[{"imageOffset":3568,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":0},{"imageOffset":75992,"symbol":"mach_msg2_internal","symbolLocation":80,"imageIndex":0},{"imageOffset":38456,"symbol":"mach_msg_overwrite","symbolLocation":540,"imageIndex":0},{"imageOffset":4460,"symbol":"mach_msg","symbolLocation":24,"imageIndex":0},{"imageOffset":56546788,"imageIndex":15},{"imageOffset":56317548,"imageIndex":15},{"imageOffset":56319620,"imageIndex":15},{"imageOffset":56319132,"imageIndex":15},{"imageOffset":56519652,"imageIndex":15},{"imageOffset":28780,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":7724,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":2345089,"name":"Chrome_IOThread","frames":[{"imageOffset":51208,"symbol":"kevent64","symbolLocation":8,"imageIndex":0},{"imageOffset":56727496,"imageIndex":15},{"imageOffset":56727288,"imageIndex":15},{"imageOffset":56233836,"imageIndex":15},{"imageOffset":55985340,"imageIndex":15},{"imageOffset":56364424,"imageIndex":15},{"imageOffset":40590340,"imageIndex":15},{"imageOffset":56364816,"imageIndex":15},{"imageOffset":56519652,"imageIndex":15},{"imageOffset":28780,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":7724,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":2345090,"name":"NetworkConfigWatcher","frames":[{"imageOffset":3568,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":0},{"imageOffset":75992,"symbol":"mach_msg2_internal","symbolLocation":80,"imageIndex":0},{"imageOffset":38456,"symbol":"mach_msg_overwrite","symbolLocation":540,"imageIndex":0},{"imageOffset":4460,"symbol":"mach_msg","symbolLocation":24,"imageIndex":0},{"imageOffset":56546788,"imageIndex":15},{"imageOffset":55801148,"imageIndex":15},{"imageOffset":56233836,"imageIndex":15},{"imageOffset":55985340,"imageIndex":15},{"imageOffset":56364424,"imageIndex":15},{"imageOffset":56364816,"imageIndex":15},{"imageOffset":56519652,"imageIndex":15},{"imageOffset":28780,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":7724,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":2345091,"name":"ThreadPoolForegroundWorker","frames":[{"imageOffset":3568,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":0},{"imageOffset":75992,"symbol":"mach_msg2_internal","symbolLocation":80,"imageIndex":0},{"imageOffset":38456,"symbol":"mach_msg_overwrite","symbolLocation":540,"imageIndex":0},{"imageOffset":4460,"symbol":"mach_msg","symbolLocation":24,"imageIndex":0},{"imageOffset":56546788,"imageIndex":15},{"imageOffset":56317548,"imageIndex":15},{"imageOffset":56320244,"imageIndex":15},{"imageOffset":56319264,"imageIndex":15},{"imageOffset":56519652,"imageIndex":15},{"imageOffset":28780,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":7724,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":2345092,"name":"ThreadPoolForegroundWorker","frames":[{"imageOffset":3568,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":0},{"imageOffset":75992,"symbol":"mach_msg2_internal","symbolLocation":80,"imageIndex":0},{"imageOffset":38456,"symbol":"mach_msg_overwrite","symbolLocation":540,"imageIndex":0},{"imageOffset":4460,"symbol":"mach_msg","symbolLocation":24,"imageIndex":0},{"imageOffset":56546788,"imageIndex":15},{"imageOffset":56317548,"imageIndex":15},{"imageOffset":56320244,"imageIndex":15},{"imageOffset":56319264,"imageIndex":15},{"imageOffset":56519652,"imageIndex":15},{"imageOffset":28780,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":7724,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":2345093,"name":"ThreadPoolForegroundWorker","frames":[{"imageOffset":3568,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":0},{"imageOffset":75992,"symbol":"mach_msg2_internal","symbolLocation":80,"imageIndex":0},{"imageOffset":38456,"symbol":"mach_msg_overwrite","symbolLocation":540,"imageIndex":0},{"imageOffset":4460,"symbol":"mach_msg","symbolLocation":24,"imageIndex":0},{"imageOffset":56546788,"imageIndex":15},{"imageOffset":56317548,"imageIndex":15},{"imageOffset":56319620,"imageIndex":15},{"imageOffset":56319264,"imageIndex":15},{"imageOffset":56519652,"imageIndex":15},{"imageOffset":28780,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":7724,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":2345094,"name":"CompositorTileWorker1","frames":[{"imageOffset":17892,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":0},{"imageOffset":30264,"symbol":"_pthread_cond_wait","symbolLocation":1232,"imageIndex":1},{"imageOffset":56516680,"imageIndex":15},{"imageOffset":85569508,"imageIndex":15},{"imageOffset":56519652,"imageIndex":15},{"imageOffset":28780,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":7724,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":2345095,"name":"Chrome_InProcGpuThread","frames":[{"imageOffset":3568,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":0},{"imageOffset":75992,"symbol":"mach_msg2_internal","symbolLocation":80,"imageIndex":0},{"imageOffset":38456,"symbol":"mach_msg_overwrite","symbolLocation":540,"imageIndex":0},{"imageOffset":4460,"symbol":"mach_msg","symbolLocation":24,"imageIndex":0},{"imageOffset":56546788,"imageIndex":15},{"imageOffset":55801148,"imageIndex":15},{"imageOffset":56233836,"imageIndex":15},{"imageOffset":55985340,"imageIndex":15},{"imageOffset":56364424,"imageIndex":15},{"imageOffset":56364816,"imageIndex":15},{"imageOffset":56519652,"imageIndex":15},{"imageOffset":28780,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":7724,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":2345096,"name":"Chrome_ChildIOThread","frames":[{"imageOffset":51208,"symbol":"kevent64","symbolLocation":8,"imageIndex":0},{"imageOffset":56727496,"imageIndex":15},{"imageOffset":56727288,"imageIndex":15},{"imageOffset":56233836,"imageIndex":15},{"imageOffset":55985340,"imageIndex":15},{"imageOffset":56364424,"imageIndex":15},{"imageOffset":56364816,"imageIndex":15},{"imageOffset":56519652,"imageIndex":15},{"imageOffset":28780,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":7724,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":2345097,"name":"VizCompositorThread","frames":[{"imageOffset":3568,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":0},{"imageOffset":75992,"symbol":"mach_msg2_internal","symbolLocation":80,"imageIndex":0},{"imageOffset":38456,"symbol":"mach_msg_overwrite","symbolLocation":540,"imageIndex":0},{"imageOffset":4460,"symbol":"mach_msg","symbolLocation":24,"imageIndex":0},{"imageOffset":56546788,"imageIndex":15},{"imageOffset":56546224,"imageIndex":15},{"imageOffset":55801248,"imageIndex":15},{"imageOffset":56233836,"imageIndex":15},{"imageOffset":55985340,"imageIndex":15},{"imageOffset":56364424,"imageIndex":15},{"imageOffset":56364816,"imageIndex":15},{"imageOffset":56519652,"imageIndex":15},{"imageOffset":28780,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":7724,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":2345098,"name":"NetworkConfigWatcher","frames":[{"imageOffset":3568,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":0},{"imageOffset":75992,"symbol":"mach_msg2_internal","symbolLocation":80,"imageIndex":0},{"imageOffset":38456,"symbol":"mach_msg_overwrite","symbolLocation":540,"imageIndex":0},{"imageOffset":4460,"symbol":"mach_msg","symbolLocation":24,"imageIndex":0},{"imageOffset":56546788,"imageIndex":15},{"imageOffset":55801148,"imageIndex":15},{"imageOffset":56233836,"imageIndex":15},{"imageOffset":55985340,"imageIndex":15},{"imageOffset":56364424,"imageIndex":15},{"imageOffset":56364816,"imageIndex":15},{"imageOffset":56519652,"imageIndex":15},{"imageOffset":28780,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":7724,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":2345103,"name":"NetworkService","frames":[{"imageOffset":51208,"symbol":"kevent64","symbolLocation":8,"imageIndex":0},{"imageOffset":56727496,"imageIndex":15},{"imageOffset":56727288,"imageIndex":15},{"imageOffset":56233836,"imageIndex":15},{"imageOffset":55985340,"imageIndex":15},{"imageOffset":56364424,"imageIndex":15},{"imageOffset":56364816,"imageIndex":15},{"imageOffset":56519652,"imageIndex":15},{"imageOffset":28780,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":7724,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":2345104,"name":"NetworkConfigWatcher","frames":[{"imageOffset":3568,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":0},{"imageOffset":75992,"symbol":"mach_msg2_internal","symbolLocation":80,"imageIndex":0},{"imageOffset":38456,"symbol":"mach_msg_overwrite","symbolLocation":540,"imageIndex":0},{"imageOffset":4460,"symbol":"mach_msg","symbolLocation":24,"imageIndex":0},{"imageOffset":56546788,"imageIndex":15},{"imageOffset":55801148,"imageIndex":15},{"imageOffset":56233836,"imageIndex":15},{"imageOffset":55985340,"imageIndex":15},{"imageOffset":56364424,"imageIndex":15},{"imageOffset":56364816,"imageIndex":15},{"imageOffset":56519652,"imageIndex":15},{"imageOffset":28780,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":7724,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":2345105,"name":"ThreadPoolSingleThreadForegroundBlocking0","frames":[{"imageOffset":3568,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":0},{"imageOffset":75992,"symbol":"mach_msg2_internal","symbolLocation":80,"imageIndex":0},{"imageOffset":38456,"symbol":"mach_msg_overwrite","symbolLocation":540,"imageIndex":0},{"imageOffset":4460,"symbol":"mach_msg","symbolLocation":24,"imageIndex":0},{"imageOffset":56546788,"imageIndex":15},{"imageOffset":56317548,"imageIndex":15},{"imageOffset":56320244,"imageIndex":15},{"imageOffset":56319352,"imageIndex":15},{"imageOffset":56519652,"imageIndex":15},{"imageOffset":28780,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":7724,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":2345111,"frames":[{"imageOffset":7704,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":1}]},{"id":2345121,"name":"Thread (pooled)","frames":[{"imageOffset":17892,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":0},{"imageOffset":30264,"symbol":"_pthread_cond_wait","symbolLocation":1232,"imageIndex":1},{"imageOffset":1898236,"imageIndex":5},{"imageOffset":1897396,"imageIndex":5},{"imageOffset":1897204,"symbol":"QWaitCondition::wait(QMutex*, QDeadlineTimer)","symbolLocation":108,"imageIndex":5},{"imageOffset":1874940,"imageIndex":5},{"imageOffset":1858444,"imageIndex":5},{"imageOffset":28780,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":7724,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":2345122,"name":"Thread (pooled)","frames":[{"imageOffset":17892,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":0},{"imageOffset":30264,"symbol":"_pthread_cond_wait","symbolLocation":1232,"imageIndex":1},{"imageOffset":1898236,"imageIndex":5},{"imageOffset":1897396,"imageIndex":5},{"imageOffset":1897204,"symbol":"QWaitCondition::wait(QMutex*, QDeadlineTimer)","symbolLocation":108,"imageIndex":5},{"imageOffset":1874940,"imageIndex":5},{"imageOffset":1858444,"imageIndex":5},{"imageOffset":28780,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":7724,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":2345123,"name":"Thread (pooled)","frames":[{"imageOffset":17892,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":0},{"imageOffset":30264,"symbol":"_pthread_cond_wait","symbolLocation":1232,"imageIndex":1},{"imageOffset":1898236,"imageIndex":5},{"imageOffset":1897396,"imageIndex":5},{"imageOffset":1897204,"symbol":"QWaitCondition::wait(QMutex*, QDeadlineTimer)","symbolLocation":108,"imageIndex":5},{"imageOffset":1874940,"imageIndex":5},{"imageOffset":1858444,"imageIndex":5},{"imageOffset":28780,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":7724,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":2345124,"name":"Thread (pooled)","frames":[{"imageOffset":17892,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":0},{"imageOffset":30264,"symbol":"_pthread_cond_wait","symbolLocation":1232,"imageIndex":1},{"imageOffset":1898236,"imageIndex":5},{"imageOffset":1897396,"imageIndex":5},{"imageOffset":1897204,"symbol":"QWaitCondition::wait(QMutex*, QDeadlineTimer)","symbolLocation":108,"imageIndex":5},{"imageOffset":1874940,"imageIndex":5},{"imageOffset":1858444,"imageIndex":5},{"imageOffset":28780,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":7724,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]}],
  "usedImages" : [
  {
    "source" : "P",
    "arch" : "arm64e",
    "base" : 6588243968,
    "size" : 233468,
    "uuid" : "6d6644d3-3db3-34c4-b1e3-c675ec5360f0",
    "path" : "\/usr\/lib\/system\/libsystem_kernel.dylib",
    "name" : "libsystem_kernel.dylib"
  },
  {
    "source" : "P",
    "arch" : "arm64e",
    "base" : 6588477440,
    "size" : 53244,
    "uuid" : "886caca0-5762-3640-8db2-3fa3b911c062",
    "path" : "\/usr\/lib\/system\/libsystem_pthread.dylib",
    "name" : "libsystem_pthread.dylib"
  },
  {
    "source" : "P",
    "arch" : "arm64e",
    "base" : 6587195392,
    "size" : 528372,
    "uuid" : "a3869999-0792-3e09-b3fb-5e87ae4639be",
    "path" : "\/usr\/lib\/system\/libsystem_c.dylib",
    "name" : "libsystem_c.dylib"
  },
  {
    "source" : "P",
    "arch" : "arm64",
    "base" : 4355014656,
    "CFBundleShortVersionString" : "3.11.4, (c) 2001-2023 Python Software Foundation.",
    "CFBundleIdentifier" : "org.python.python",
    "size" : 3948544,
    "uuid" : "88bffd37-99d8-36ab-9b95-9f54b30bd667",
    "path" : "\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/Python",
    "name" : "Python",
    "CFBundleVersion" : "3.11.4"
  },
  {
    "source" : "P",
    "arch" : "arm64e",
    "base" : 6588678144,
    "size" : 32764,
    "uuid" : "78189670-2f47-332c-9a59-a210157aa97b",
    "path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
    "name" : "libsystem_platform.dylib"
  },
  {
    "source" : "P",
    "arch" : "arm64",
    "base" : 4406411264,
    "size" : 4587520,
    "uuid" : "7b11213a-bd62-384b-9835-2bf9bacff4a0",
    "path" : "\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtCore.framework\/Versions\/A\/QtCore",
    "name" : "QtCore"
  },
  {
    "source" : "P",
    "arch" : "arm64",
    "base" : 4413652992,
    "size" : 81920,
    "uuid" : "3fded43f-082d-3be2-86c3-2ed4b9cf5452",
    "path" : "\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtQuickWidgets.framework\/Versions\/A\/QtQuickWidgets",
    "name" : "QtQuickWidgets"
  },
  {
    "source" : "P",
    "arch" : "arm64",
    "base" : 4401545216,
    "size" : 81920,
    "uuid" : "5ca059a1-2fcb-3812-b126-6ced10520321",
    "path" : "\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtWebEngineWidgets.framework\/Versions\/A\/QtWebEngineWidgets",
    "name" : "QtWebEngineWidgets"
  },
  {
    "source" : "P",
    "arch" : "arm64",
    "base" : 4676419584,
    "size" : 4521984,
    "uuid" : "1cb5b95a-41b5-3897-a39d-1305dac761eb",
    "path" : "\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtWidgets.framework\/Versions\/A\/QtWidgets",
    "name" : "QtWidgets"
  },
  {
    "source" : "P",
    "arch" : "arm64",
    "base" : 4417748992,
    "size" : 3047424,
    "uuid" : "b2d23268-944f-3492-8cfd-24699ae18bab",
    "path" : "\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/QtWidgets.abi3.so",
    "name" : "QtWidgets.abi3.so"
  },
  {
    "source" : "P",
    "arch" : "arm64",
    "base" : 4413489152,
    "size" : 65536,
    "uuid" : "774dae53-02a0-3570-92a6-2acc517c646f",
    "path" : "\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/QtWebEngineWidgets.abi3.so",
    "name" : "QtWebEngineWidgets.abi3.so"
  },
  {
    "source" : "P",
    "arch" : "arm64",
    "base" : 4340170752,
    "CFBundleShortVersionString" : "1.8.0",
    "CFBundleIdentifier" : "edu.ucsf.cgl.ChimeraX",
    "size" : 16384,
    "uuid" : "17982d98-65bc-3327-8526-577ec996453c",
    "path" : "\/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
    "name" : "ChimeraX",
    "CFBundleVersion" : "1.8.0.0"
  },
  {
    "source" : "P",
    "arch" : "arm64e",
    "base" : 6585163776,
    "size" : 566464,
    "uuid" : "de46dd52-4994-3fd8-b4b4-e352a1a19354",
    "path" : "\/usr\/lib\/dyld",
    "name" : "dyld"
  },
  {
    "source" : "P",
    "arch" : "arm64",
    "base" : 4374462464,
    "size" : 21299200,
    "uuid" : "9854a721-2573-3169-81ec-19ea40ce8077",
    "path" : "\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/numpy\/.dylibs\/libopenblas64_.0.dylib",
    "name" : "libopenblas64_.0.dylib"
  },
  {
    "source" : "P",
    "arch" : "arm64e",
    "base" : 6586888192,
    "size" : 294912,
    "uuid" : "40c9c98c-00d6-3e8e-9ad3-2ed6cf0d0cfe",
    "path" : "\/usr\/lib\/system\/libdispatch.dylib",
    "name" : "libdispatch.dylib"
  },
  {
    "source" : "P",
    "arch" : "arm64",
    "base" : 5771362304,
    "size" : 144654336,
    "uuid" : "21c8f378-4426-330a-89d1-26ab67c6fa56",
    "path" : "\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtWebEngineCore.framework\/Versions\/A\/QtWebEngineCore",
    "name" : "QtWebEngineCore"
  }
],
  "sharedCache" : {
  "base" : 6584516608,
  "size" : 3403612160,
  "uuid" : "2d053604-1cb6-3821-a8df-360eb2eb519b"
},
  "vmSummary" : "ReadOnly portion of Libraries: Total=1.5G resident=0K(0%) swapped_out_or_unallocated=1.5G(100%)\nWritable regions: Total=1.8G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=1.8G(100%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nActivity Tracing                   256K        1 \nColorSync                          544K       24 \nCoreGraphics                        16K        1 \nFoundation                          16K        1 \nKernel Alloc Once                   32K        1 \nMALLOC                           298.8M       59 \nMALLOC guard page                  192K       10 \nMALLOC_MEDIUM (reserved)         720.0M        6         reserved VM address space (unallocated)\nMALLOC_NANO (reserved)           384.0M        1         reserved VM address space (unallocated)\nMach message                        32K        2 \nSTACK GUARD                        528K       33 \nStack                            145.3M       34 \nStack Guard                       56.0M        1 \nVM_ALLOCATE                      154.2M       67 \nVM_ALLOCATE (reserved)           160.0M        3         reserved VM address space (unallocated)\n__AUTH                            1815K      342 \n__AUTH_CONST                      24.3M      565 \n__CTF                               756        1 \n__DATA                            20.5M      693 \n__DATA_CONST                      36.5M      702 \n__DATA_DIRTY                      1973K      224 \n__FONT_DATA                        2352        1 \n__GLSLBUILTINS                    5174K        1 \n__LINKEDIT                       789.9M      137 \n__OBJC_CONST                      4560K      307 \n__OBJC_RO                         65.1M        1 \n__OBJC_RW                         1981K        1 \n__TEXT                           796.2M      724 \ndyld private memory                448K        3 \nmapped file                      205.5M       35 \nshared memory                      880K       16 \n===========                     =======  ======= \nTOTAL                              3.8G     3997 \nTOTAL, minus reserved VM space     2.5G     3997 \n",
  "legacyInfo" : {
  "threadTriggered" : {
    "name" : "CrBrowserMain",
    "queue" : "com.apple.main-thread"
  }
},
  "trialInfo" : {
  "rollouts" : [
    {
      "rolloutId" : "60356660bbe37970735c5624",
      "factorPackIds" : {

      },
      "deploymentId" : 240000027
    },
    {
      "rolloutId" : "62b4513af75dc926494899c6",
      "factorPackIds" : {
        "COREOS_ICD" : "62fbe3cfa9a700130f60b3ea"
      },
      "deploymentId" : 240000019
    }
  ],
  "experiments" : [

  ]
}
}


Log:
UCSF ChimeraX version: 1.8.dev202402080317 (2024-02-08)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "/Users/emmanuelafriyie/Documents/Cryo-EM/Cryo-EM Maps/WW4-HECT_nb
> complexes/WW4-HECT_nb.C11 Complex/3.1A Map/Color maps/Recoloring of
> domains/Selected color_further coloring of NLobe and CLobe/Map for
> paper/orange_corniflowerblue_Forestgreen_salmon_2.cxs"

Opened cryosparc_P36_J2540_006_volume_map_sharp.mrc as #2, grid size
256,256,256, pixel 1.03, shown at level 0.087, step 1, values float32  
Opened cryosparc_P36_J2540_006_volume_map_sharp.mrc as #4, grid size
256,256,256, pixel 1.03, shown at level 0.0961, step 1, values float32  
Log from Sat Feb 3 20:20:01 2024UCSF ChimeraX version: 1.7rc202312120032
(2023-12-12)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Users/emmanuelafriyie/Documents/Cryo-EM/Cryo-EM Maps/WW4-HECT_nb
> complexes/WW4-HECT_nb.C11 Complex/3.1A Map/Color maps/Recoloring of
> domains/Selected color_further coloring of NLobe and
> CLobe/orange_corniflowerblue_Forestgreen_salmon.cxs"

Opened cryosparc_P36_J2540_006_volume_map_sharp.mrc as #2, grid size
256,256,256, pixel 1.03, shown at level 0.087, step 1, values float32  
Opened cryosparc_P36_J2540_006_volume_map_sharp.mrc as #4, grid size
256,256,256, pixel 1.03, shown at level 0.0961, step 1, values float32  
Log from Sat Feb 3 20:12:39 2024UCSF ChimeraX version: 1.7rc202312120032
(2023-12-12)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Users/emmanuelafriyie/Documents/Cryo-EM/Cryo-EM Maps/WW4-HECT_nb
> complexes/WW4-HECT_nb.C11 Complex/3.1A Map/Color maps/Recoloring of
> domains/orange_corniflower_medium purple.cxs"

Opened cryosparc_P36_J2540_006_volume_map_sharp.mrc as #2, grid size
256,256,256, pixel 1.03, shown at level 0.087, step 1, values float32  
Opened cryosparc_P36_J2540_006_volume_map_sharp.mrc as #4, grid size
256,256,256, pixel 1.03, shown at level 0.0961, step 1, values float32  
Log from Tue Jan 30 09:08:53 2024UCSF ChimeraX version: 1.7rc202312120032
(2023-12-12)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Users/emmanuelafriyie/Documents/Cryo-EM/Cryo-EM Maps/WW4-HECT_nb
> complexes/WW4-HECT_nb.C11 Complex/3.1A Map/Color maps/Recoloring of
> domains/lightseagreen_corniflower_medium purple.cxs"

Opened cryosparc_P36_J2540_006_volume_map_sharp.mrc as #2, grid size
256,256,256, pixel 1.03, shown at level 0.087, step 1, values float32  
Opened cryosparc_P36_J2540_006_volume_map_sharp.mrc as #4, grid size
256,256,256, pixel 1.03, shown at level 0.0961, step 1, values float32  
Log from Tue Jan 30 08:55:37 2024UCSF ChimeraX version: 1.7rc202312120032
(2023-12-12)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Users/emmanuelafriyie/Documents/Cryo-EM/Cryo-EM Maps/WW4-HECT_nb
> complexes/WW4-HECT_nb.C11 Complex/3.1A Map/Color maps/Recoloring of
> domains/lightseagreen_peru_seagreen.cxs"

Opened cryosparc_P36_J2540_006_volume_map_sharp.mrc as #2, grid size
256,256,256, pixel 1.03, shown at level 0.087, step 1, values float32  
Opened cryosparc_P36_J2540_006_volume_map_sharp.mrc as #4, grid size
256,256,256, pixel 1.03, shown at level 0.0961, step 1, values float32  
Log from Mon Jan 29 22:44:44 2024UCSF ChimeraX version: 1.7rc202312120032
(2023-12-12)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Users/emmanuelafriyie/Documents/Cryo-EM/Cryo-EM Maps/WW4-HECT_nb
> complexes/WW4-HECT_nb.C11 Complex/3.1A Map/Color maps/Recoloring of
> domains/nb.C11_3.1_publication.cxs"

Opened cryosparc_P36_J2540_006_volume_map_sharp.mrc as #2, grid size
256,256,256, pixel 1.03, shown at level 0.087, step 1, values float32  
Opened cryosparc_P36_J2540_006_volume_map_sharp.mrc as #4, grid size
256,256,256, pixel 1.03, shown at level 0.0961, step 1, values float32  
Log from Mon Jan 29 22:27:59 2024UCSF ChimeraX version: 1.7rc202312120032
(2023-12-12)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Users/emmanuelafriyie/Documents/Cryo-EM/Cryo-EM Maps/WW4-HECT_nb
> complexes/WW4-HECT_nb.C11 Complex/3.1A Map/Color maps/Cyan_colored.cxs"

Opened cryosparc_P36_J2540_006_volume_map_sharp.mrc as #2, grid size
256,256,256, pixel 1.03, shown at level 0.087, step 1, values float32  
Opened cryosparc_P36_J2540_006_volume_map_sharp.mrc as #4, grid size
256,256,256, pixel 1.03, shown at level 0.0961, step 1, values float32  
Log from Mon Jan 15 14:08:09 2024UCSF ChimeraX version: 1.7rc202312120032
(2023-12-12)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Users/emmanuelafriyie/Documents/Cryo-EM/Cryo-EM Maps/WW4-HECT_nb
> complexes/WW4-HECT_nb.C11 Complex/3.1A Map/Color maps/3.1A map_colored
> domains_soft_surface_updated_WW4_1.cxs"

Opened cryosparc_P36_J2540_006_volume_map_sharp.mrc as #2, grid size
256,256,256, pixel 1.03, shown at level 0.087, step 1, values float32  
Opened cryosparc_P36_J2540_006_volume_map_sharp.mrc as #4, grid size
256,256,256, pixel 1.03, shown at level 0.0961, step 1, values float32  
Log from Sat Jan 13 20:04:54 2024

> alias hid hide $1 models

> alias sho show $1 models

> camera ortho

UCSF ChimeraX version: 1.7rc202312120032 (2023-12-12)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/emmanuelafriyie/Documents/Cryo-EM/Cryo-EM Maps/WW4-HECT_nb
> complexes/WW4-HECT_nb.C11 Complex/3.1A Map/combine_C11_3.1A-coot-0_INC4.pdb"

Chain information for combine_C11_3.1A-coot-0_INC4.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open "/Users/emmanuelafriyie/Documents/Cryo-EM/Cryo-EM Maps/WW4-HECT_nb
> complexes/WW4-HECT_nb.C11 Complex/3.1A
> Map/cryosparc_P36_J2540_006_volume_map_sharp.mrc"

Opened cryosparc_P36_J2540_006_volume_map_sharp.mrc as #2, grid size
256,256,256, pixel 1.03, shown at level 0.0253, step 1, values float32  

> volume #2 level 0.1345

> ui tool show "Hide Dust"

> surface dust #2 size 6.16

> show surfaces

[Repeated 1 time(s)]

> hide surfaces

> open "/Users/emmanuelafriyie/Documents/Cryo-EM/Cryo-EM Maps/WW4-HECT_nb
> complexes/WW4-HECT_nb.C11 Complex/3.1A
> Map/combine_C11_3.1A-coot-0_adjusted.pdb"

Chain information for combine_C11_3.1A-coot-0_adjusted.pdb #3  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> ui tool show "Model Panel"

> hide #!1 models

> volume #2 level 0.08698

> volume #2 level 0.07509

> ui tool show "Hide Dust"

> surface dust #2 size 1.03

[Repeated 1 time(s)]

> ui tool show "Hide Dust"

> surface dust #2 size 1.03

[Repeated 1 time(s)]

> volume #2 level 0.08698

> ui tool show "Hide Dust"

> surface dust #2 size 1.03

> surface dust #2 size 1.13

> surface dust #2 size 1.03

> surface dust #2 size 6.73

[Repeated 1 time(s)]

> open "/Users/emmanuelafriyie/Documents/Cryo-EM/Cryo-EM Maps/WW4-HECT_nb
> complexes/WW4-HECT_nb.C11 Complex/3.1A
> Map/cryosparc_P36_J2540_006_volume_map_sharp.mrc"

Opened cryosparc_P36_J2540_006_volume_map_sharp.mrc as #4, grid size
256,256,256, pixel 1.03, shown at level 0.0253, step 1, values float32  

> volume #4 level 0.08167

> hide #!3 models

> hide #!2 models

> show #!3 models

> show #!1 models

> ui tool show "Hide Dust"

> surface dust #4 size 6.16

Color zone shortcut requires 1 displayed atomic model and 1 map, got 2 atomic
models, 1 maps.  

[Repeated 1 time(s)]

> hide #!3 models

> hide #!1 models

> show #!1 models

> show #!3 models

> hide #!1 models

> hide #!3 models

> show #!1 models

> hide #!4 models

> show #!1 surfaces

> transparency #1 70

> select #1/A

950 atoms, 972 bonds, 122 residues, 1 model selected  

> color (#!1 & sel) red

> undo

> show #!4 models

> hide #!1 models

> select add #1

4433 atoms, 4552 bonds, 539 residues, 2 models selected  

> select subtract #1

2 models selected  

> select #3/A

950 atoms, 972 bonds, 122 residues, 1 model selected  

> select add #3

4433 atoms, 4552 bonds, 539 residues, 1 model selected  

> select subtract #3

Nothing selected  

> select #3/B

3483 atoms, 3580 bonds, 417 residues, 1 model selected  

> ui tool show "Color Zone"

> show #!3 models

> select add #3

4433 atoms, 4552 bonds, 539 residues, 1 model selected  

> select subtract #3

Nothing selected  

> color zone #4 near #3 distance 6.16

> hide #!3 models

> hide #!4 models

> show #!4 models

> select #4

2 models selected  

> select #4

2 models selected  

> select #4

2 models selected  

> select #4

2 models selected  

> select #4

2 models selected  

> select #4

2 models selected  

> select #4

2 models selected  

> select #4

2 models selected  

> select subtract #4

Nothing selected  

> select #4

2 models selected  

> select subtract #4

Nothing selected  

> show #!3 models

> select #4

2 models selected  

> select #4

2 models selected  

No atoms selected for color zoning  

> hide #!3 models

> select clear

> hide #!4 models

> show #!3 models

> select #3/A

950 atoms, 972 bonds, 122 residues, 1 model selected  

> color sel orange red

> select clear

> select #3:514-542

253 atoms, 261 bonds, 29 residues, 1 model selected  

> color sel lime

> select #3:468-504

313 atoms, 324 bonds, 37 residues, 1 model selected  

> color sel lime

> select #3/A

950 atoms, 972 bonds, 122 residues, 1 model selected  

> select clear

> select #3:543-end

2917 atoms, 2994 bonds, 351 residues, 1 model selected  

> color sel cyan

> color sel magenta

> select clear

> show #!4 models

> color zone #4 near #3 distance 6.16

> hide #!3 models

> show #!3 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> save "/Users/emmanuelafriyie/Documents/Cryo-EM/Cryo-EM Maps/WW4-HECT_nb
> complexes/WW4-HECT_nb.C11 Complex/3.1A Map/New Folder/3.1A map.cxs"

[Errno 20] Not a directory: '/Users/emmanuelafriyie/Documents/Cryo-EM/Cryo-EM
Maps/WW4-HECT_nb complexes/WW4-HECT_nb.C11 Complex/3.1A Map/New Folder'  

> save "/Users/emmanuelafriyie/Documents/Cryo-EM/Cryo-EM Maps/WW4-HECT_nb
> complexes/WW4-HECT_nb.C11 Complex/3.1A Map/Color maps/3.1A map_colored
> domains.cxs"

> hide #!4 models

> show #!4 models

> lighting soft

> volume #4 level 0.09607

> save "/Users/emmanuelafriyie/Documents/Cryo-EM/Cryo-EM Maps/WW4-HECT_nb
> complexes/WW4-HECT_nb.C11 Complex/3.1A Map/Color maps/3.1A map_colored
> domains_soft_surface.cxs"

> undo

> show #!4 models

> lighting simple

> lighting soft

> hide #!4 models

> select #3:514-533

181 atoms, 187 bonds, 20 residues, 1 model selected  

> color sel lime

> select #3:534-end

2989 atoms, 3068 bonds, 360 residues, 1 model selected  

> color sel magenta

> select add #3

4433 atoms, 4552 bonds, 539 residues, 1 model selected  

> select subtract #3

Nothing selected  

> show #!4 models

> color zone #4 near #3 distance 6.16

> save "/Users/emmanuelafriyie/Documents/Cryo-EM/Cryo-EM Maps/WW4-HECT_nb
> complexes/WW4-HECT_nb.C11 Complex/3.1A Map/Color maps/3.1A map_colored
> domains_soft_surface_updated_WW4.cxs"

> lighting soft

[Repeated 1 time(s)]

> preset "overall look" "publication 1 (silhouettes)"

Using preset: Overall Look / Publication 1 (Silhouettes)  

> set bgColor #ffffff00

Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t
    lighting depthCue f

  

> select add #4

2 models selected  

> select subtract #4

Nothing selected  

> undo

[Repeated 3 time(s)]

> hide #!4 models

> show #!4 models

> hide #!2 models

> hide #!4 models

> show #!4 models

> color zone #4 near #3 distance 6.16

> combine #3

> rename #5 Coot_combine_C11_3.1A_adjusted

> rename #5 Coot_combine_C11_3.1A_adjusted.pdb

> hide #!3 models

> hide #!4 models

> save "/Users/emmanuelafriyie/Documents/Cryo-EM/Cryo-EM Maps/WW4-HECT_nb
> complexes/WW4-HECT_nb.C11 Complex/3.1A Map/Color maps/3.1A map_colored
> domains_soft_surface_updated_WW4_1.cxs"

——— End of log from Sat Jan 13 20:04:54 2024 ———

opened ChimeraX session  

> ui tool show "Model Panel"

> show #!4 models

> hide #!5 models

> show #!5 models

> hide #!4 models

> select :514-42

Nothing selected  

> select :514-442

Nothing selected  

> select :514-542

759 atoms, 783 bonds, 87 residues, 3 models selected  

> select :468-504

939 atoms, 972 bonds, 111 residues, 3 models selected  

> select :468-504, 514-522

1161 atoms, 1203 bonds, 138 residues, 3 models selected  

> select :468-504, 514-519

1068 atoms, 1107 bonds, 129 residues, 3 models selected  

> select :468-504, 514-522

1161 atoms, 1203 bonds, 138 residues, 3 models selected  

> select :521-end

9348 atoms, 9597 bonds, 1119 residues, 3 models selected  

> color (#!5 & sel) magenta

> select :468-504, 514-523

1188 atoms, 1230 bonds, 141 residues, 3 models selected  

> color (#!5 & sel) lime

[Repeated 1 time(s)]

> combine #5

> rename #6 "Cyan_ Coot_combine_C11_3.1A_adjusted.pdb"

> select #6/A

950 atoms, 972 bonds, 122 residues, 1 model selected  

> color sel cyan

> color sel light sea green

> undo

> select clear

> show #!4 models

> hide #!4 models

> ui tool show "Color Zone"

> show #!2 models

> hide #!2 models

> show #!2 models

> color zone #2 near #6 distance 6.16

> hide #!5 models

> hide #!6 models

> show #!1 models

> hide #!1 models

> show #!6 models

> hide #!2 models

> select :468-504, 514-526

1704 atoms, 1764 bonds, 200 residues, 4 models selected  

> select :468-504, 514-525

1656 atoms, 1712 bonds, 196 residues, 4 models selected  

> select :468-504, 514-526

1704 atoms, 1764 bonds, 200 residues, 4 models selected  

> color (#!6 & sel) lime

> color zone #2 near #6 distance 6.16

> show #!2 models

> select add #6

5711 atoms, 5875 bonds, 689 residues, 5 models selected  

> hide #!6 models

> select subtract #6

1278 atoms, 1323 bonds, 150 residues, 4 models selected  

> hide #!2 models

> show #!6 models

> show #!1 models

> hide #!1 models

> show #!2 models

> color zone #2 near #6 distance 5.9

> color zone #2 near #6 distance 4.07

> color zone #2 near #6 distance 3.99

> color zone #2 near #6 distance 6.15

> hide #!6 models

> color zone #2 near #6 distance 6.25

> color zone #2 near #6 distance 6.35

> color zone #2 near #6 distance 6.45

> color zone #2 near #6 distance 6.55

> color zone #2 near #6 distance 6.65

> color zone #2 near #6 distance 6.75

> color zone #2 near #6 distance 6.85

> color zone #2 near #6 distance 6.95

> color zone #2 near #6 distance 7.05

> color zone #2 near #6 distance 7.15

> color zone #2 near #6 distance 7.25

> color zone #2 near #6 distance 7.35

> color zone #2 near #6 distance 7.45

> color zone #2 near #6 distance 7.55

> color zone #2 near #6 distance 7.65

> color zone #2 near #6 distance 7.75

> color zone #2 near #6 distance 7.85

> color zone #2 near #6 distance 7.95

> color zone #2 near #6 distance 8.05

> color zone #2 near #6 distance 8

> color zone #2 near #6 distance 6

> color zone #2 near #6 distance 61

> color zone #2 near #6 distance 61.5

> color zone #2 near #6 distance 61

> color zone #2 near #6 distance 6

> color zone #2 near #6 distance 6.1

> color zone #2 near #6 distance 6.15

[Repeated 1 time(s)]

> save "/Users/emmanuelafriyie/Documents/Cryo-EM/Cryo-EM Maps/WW4-HECT_nb
> complexes/WW4-HECT_nb.C11 Complex/3.1A Map/Color maps/Cyan_colored.cxs"

——— End of log from Mon Jan 15 14:08:09 2024 ———

opened ChimeraX session  

> ui tool show "Model Panel"

> select add #5

5285 atoms, 5434 bonds, 639 residues, 3 models selected  

> select add #3

9292 atoms, 9545 bonds, 1128 residues, 3 models selected  

> show #!4 models

> hide #!2 models

> show #!2 models

> hide #!4 models

> select subtract #5

4859 atoms, 4993 bonds, 589 residues, 2 models selected  

> select subtract #3

426 atoms, 441 bonds, 50 residues, 1 model selected  

> show #!6 models

> show #!5 models

> hide #!5 models

> hide #!2 models

> select :468-504, 514-526

1704 atoms, 1764 bonds, 200 residues, 4 models selected  

> select add #3

5711 atoms, 5875 bonds, 689 residues, 5 models selected  

> select add #5

9718 atoms, 9986 bonds, 1178 residues, 5 models selected  

> select subtract #3

5285 atoms, 5434 bonds, 639 residues, 4 models selected  

> select subtract #5

852 atoms, 882 bonds, 100 residues, 3 models selected  

> ui tool show "Color Actions"

> color sel hot pink

> undo

> color sel steel blue

[Repeated 1 time(s)]

> ui tool show "Color Actions"

[Repeated 2 time(s)]

> color sel green

> color sel lime green

> select clear

> select #6/a:1-end

950 atoms, 972 bonds, 122 residues, 1 model selected  

> select #6/a

950 atoms, 972 bonds, 122 residues, 1 model selected  

> color sel deep sky blue

> select clear

> lighting simple

> select #6/b

3483 atoms, 3580 bonds, 417 residues, 1 model selected  

> select #6/b: 527-end

3057 atoms, 3138 bonds, 367 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel rosy brown

> select clear

> select #6/b: 527-end

3057 atoms, 3138 bonds, 367 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel burly wood

> select clear

> ui tool show "Color Actions"

> color tan

> undo

> select #6/b: 527-end

3057 atoms, 3138 bonds, 367 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel tan

> color sel burly wood

> color sel wheat

> undo

> select clear

> ui tool show "Color Actions"

> select #6/b: 527-end

3057 atoms, 3138 bonds, 367 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel peru

> select clear

> dssp #6

> lighting soft

> lighting simple

> select #6/a

950 atoms, 972 bonds, 122 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel turquoise

> select clear

> undo

> select clear

> ui tool show "Color Zone"

> color zone #2 near #6 distance 1.03

[Repeated 1 time(s)]

> show #!2 models

> hide #!6 models

> hide #!2 models

> show #!2 models

> show #!1 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> hide #!1 models

> show #!2 models

> hide #!2 models

> show #!6 models

> color single #2

> show #!2 models

> color zone #2 near #6 distance 1.03

> combine #2

No structures specified  

> hide #!6 models

> hide #!2 models

> show #!2 models

> show #!1 models

> hide #!1 models

> hide #!2 models

> show #!2 models

> show #!5 models

> hide #!2 models

> hide #!5 models

> show #!6 models

> combine #6

> hide #!6 models

> ui tool show "Color Actions"

> select #7/a

950 atoms, 972 bonds, 122 residues, 1 model selected  

> color sel turquoise

[Repeated 1 time(s)]

> undo

> select clear

> color zone #2 near #7 distance 1.03

> show #!2 models

> hide #!7 models

> color zone #2 near #7 distance 3.11

> color zone #2 near #7 distance 7.19

> color zone #2 near #7 distance 6.85

> color zone #2 near #7 distance 10.37

> color zone #2 near #7 distance 12.76

> show #!6 models

> hide #!2 models

> hide #!6 models

> show #!7 models

> show #!2 models

> color zone #2 near #7 distance 12.51

> color zone #2 near #7 distance 5.79

> color zone #2 near #7 distance 5.51

> color zone #2 near #7 distance 7.71

> color zone #2 near #7 distance 7.41

> color zone #2 near #7 distance 10.69

> save "/Users/emmanuelafriyie/Documents/Cryo-EM/Cryo-EM Maps/WW4-HECT_nb
> complexes/WW4-HECT_nb.C11 Complex/3.1A Map/Color maps/Recoloring of
> domains/nb.C11_3.1_publication.cxs"

——— End of log from Mon Jan 29 22:27:59 2024 ———

opened ChimeraX session  

> select #2

2 models selected  

> select #2

2 models selected  

> select #2

2 models selected  

> ui tool show "Color Zone"

> color zone #2 near #7 distance 1.03

No atoms selected for color zoning  

> undo

> color single #2

> undo

> select clear

> ui tool show "Model Panel"

> hide #!7 models

> ui tool show "Color Actions"

> select #7/a

950 atoms, 972 bonds, 122 residues, 1 model selected  

> select #7/a

950 atoms, 972 bonds, 122 residues, 1 model selected  

> show #!7 models

> select add #7

4433 atoms, 4552 bonds, 539 residues, 1 model selected  

> select subtract #7

Nothing selected  

> hide #!2 models

> select #7/a

950 atoms, 972 bonds, 122 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel light sea green

> select clear

> ui tool show "Color Zone"

No atoms selected for color zoning  

> color zone #2 near #7 distance 1.04

> show #!2 models

> color zone #2 near #7 distance 1.03

> color zone #2 near #7 distance 4.61

> color zone #2 near #7 distance 4.57

> color zone #2 near #7 distance 11.45

> save "/Users/emmanuelafriyie/Documents/Cryo-EM/Cryo-EM Maps/WW4-HECT_nb
> complexes/WW4-HECT_nb.C11 Complex/3.1A Map/Color maps/Recoloring of
> domains/lightseagreen_peru_forestgreen.cxs"

> hide #!7 models

> select :468-504, 514-526:

Expected an objects specifier or a keyword  

> select #7:468-504, 514-526

426 atoms, 441 bonds, 50 residues, 1 model selected  

> show #!7 models

> show #!3 models

> hide #!2 models

> hide #!3 models

> ui tool show "Color Actions"

> color sel chartreuse

> color sel sea green

> select clear

> show #!2 models

> color zone #2 near #7 distance 11.45

> save "/Users/emmanuelafriyie/Documents/Cryo-EM/Cryo-EM Maps/WW4-HECT_nb
> complexes/WW4-HECT_nb.C11 Complex/3.1A Map/Color maps/Recoloring of
> domains/lightseagreen_peru_seagreen.cxs"

——— End of log from Mon Jan 29 22:44:44 2024 ———

opened ChimeraX session  

> ui tool show "Model Panel"

> hide #!7 models

> hide #!2 models

> show #!2 models

> show #!7 models

> select #7:468-504, 514-526

426 atoms, 441 bonds, 50 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel sea green

[Repeated 3 time(s)]

> hide #!7 models

> select add #7

4433 atoms, 4552 bonds, 539 residues, 1 model selected  

> hide #!2 models

> select subtract #7

Nothing selected  

> show #!7 models

> select add #7

4433 atoms, 4552 bonds, 539 residues, 1 model selected  

> select subtract #7

Nothing selected  

> ui tool show "Color Zone"

> color zone #2 near #7 distance 1.03

> show #!2 models

> color zone #2 near #7 distance 4.22

> color zone #2 near #7 distance 4.1

> color zone #2 near #7 distance 8.77

[Repeated 1 time(s)]

> save "/Users/emmanuelafriyie/Documents/Cryo-EM/Cryo-EM Maps/WW4-HECT_nb
> complexes/WW4-HECT_nb.C11 Complex/3.1A Map/Color maps/Recoloring of
> domains/lightseagreen_peru_seagreen_1.cxs"

> ui tool show "Color Actions"

> select #7/b

3483 atoms, 3580 bonds, 417 residues, 1 model selected  

> select #7/b:1-527

434 atoms, 449 bonds, 51 residues, 1 model selected  

> select #7/b:1-527

434 atoms, 449 bonds, 51 residues, 1 model selected  

> hide #!2 models

> select clear

> select #7/b:1-527

434 atoms, 449 bonds, 51 residues, 1 model selected  

> select #7/b:527-end

3057 atoms, 3138 bonds, 367 residues, 1 model selected  

> color sel thistle

> show #!2 models

> ui tool show "Color Zone"

> color zone #2 near #7 distance 1.03

[Repeated 1 time(s)]

> color zone #2 near #7 distance 10.17

> color zone #2 near #7 distance 10.37

> color zone #2 near #7 distance 19.33

> ui tool show "Color Actions"

[Repeated 1 time(s)]

> save "/Users/emmanuelafriyie/Documents/Cryo-EM/Cryo-EM Maps/WW4-HECT_nb
> complexes/WW4-HECT_nb.C11 Complex/3.1A Map/Color maps/Recoloring of
> domains/lightseagreen_Thistle_seagreen.cxs"

> select add #7

4433 atoms, 4552 bonds, 539 residues, 1 model selected  

> hide #!7 models

> select subtract #7

Nothing selected  

> hide #!2 models

> show #!7 models

> preset "overall look" "publication 1 (silhouettes)"

Using preset: Overall Look / Publication 1 (Silhouettes)  
Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t
    lighting depthCue f

  

> select #7/b:527-end

3057 atoms, 3138 bonds, 367 residues, 1 model selected  

> color sel rosy brown

> select clear

> ui tool show "Color Zone"

> color zone #2 near #7 distance 1.03

[Repeated 1 time(s)]

> show #!2 models

> color zone #2 near #7 distance 4.57

> color zone #2 near #7 distance 4.43

> color zone #2 near #7 distance 5.4

> save "/Users/emmanuelafriyie/Documents/Cryo-EM/Cryo-EM Maps/WW4-HECT_nb
> complexes/WW4-HECT_nb.C11 Complex/3.1A Map/Color maps/Recoloring of
> domains/lightseagreen_Rosybrown_seagreen.cxs"

> hide #!2 models

> select #7/b:527-end

3057 atoms, 3138 bonds, 367 residues, 1 model selected  

> color sel peru

> undo

> color sel lightblue peru

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

> color sel peru

> select clear

> color medium purple

> undo

[Repeated 1 time(s)]

> select clear

> select #7/b:527-end

3057 atoms, 3138 bonds, 367 residues, 1 model selected  

> color sel medium purple

> color sel cornflower blue

> select clear

> ui tool show "Color Zone"

> color zone #2 near #7 distance 1.03

[Repeated 1 time(s)]

> show #!2 models

> color zone #2 near #7 distance 6.33

> save "/Users/emmanuelafriyie/Documents/Cryo-EM/Cryo-EM Maps/WW4-HECT_nb
> complexes/WW4-HECT_nb.C11 Complex/3.1A Map/Color maps/Recoloring of
> domains/lightseagreen_cauliflower_seagreen.cxs"

> hide #!7 models

> show #!7 models

> hide #!2 models

> show #!2 models

> select #7/b:1-526

426 atoms, 441 bonds, 50 residues, 1 model selected  

> ui tool show "Color Actions"

[Repeated 1 time(s)]

> color sel medium purple

> hide #!2 models

> show #!2 models

> ui tool show "Color Zone"

> color zone #2 near #7 distance 1.03

[Repeated 1 time(s)]

> color zone #2 near #7 distance 5.04

> color zone #2 near #7 distance 4.89

> color zone #2 near #7 distance 6.39

> color zone #2 near #7 distance 6.33

> color zone #2 near #7 distance 7.86

> color zone #2 near #7 distance 8.02

> color zone #2 near #7 distance 9.3

> ui tool show "Color Actions"

> save "/Users/emmanuelafriyie/Documents/Cryo-EM/Cryo-EM Maps/WW4-HECT_nb
> complexes/WW4-HECT_nb.C11 Complex/3.1A Map/Color maps/Recoloring of
> domains/lightseagreen_corniflower_seagreen.cxs"

> save "/Users/emmanuelafriyie/Documents/Cryo-EM/Cryo-EM Maps/WW4-HECT_nb
> complexes/WW4-HECT_nb.C11 Complex/3.1A Map/Color maps/Recoloring of
> domains/lightseagreen_corniflower_medium purple.cxs"

——— End of log from Tue Jan 30 08:55:37 2024 ———

opened ChimeraX session  

> ui tool show "Color Actions"

> ui tool show "Model Panel"

> select #7/a

950 atoms, 972 bonds, 122 residues, 1 model selected  

> hide #!2 models

> color sel orange

> select clear

> ui tool show "Color Zone"

> color zone #2 near #7 distance 1.03

> show #!2 models

> color zone #2 near #7 distance 1.03

> color zone #2 near #7 distance 11.33

> color zone #2 near #7 distance 11.45

> color zone #2 near #7 distance 28.42

> save "/Users/emmanuelafriyie/Documents/Cryo-EM/Cryo-EM Maps/WW4-HECT_nb
> complexes/WW4-HECT_nb.C11 Complex/3.1A Map/Color maps/Recoloring of
> domains/orange_corniflower_medium purple.cxs"

——— End of log from Tue Jan 30 09:08:53 2024 ———

opened ChimeraX session  

> ui tool show "Model Panel"

> hide #!2 models

> show #!2 models

> hide #!2 models

> 468-504, 514-520

Unknown command: 468-504, 514-520  

> select #7:468-504, 514-520

367 atoms, 380 bonds, 44 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel salmon

> select clear

> select #7:521-end

3116 atoms, 3199 bonds, 373 residues, 1 model selected  

> color sel cornflower blue

> select clear

> select #7 468-504

Expected a keyword  

> select #7: 468-504

313 atoms, 324 bonds, 37 residues, 1 model selected  

> ui tool show "Show Sequence Viewer"

> sequence chain #1/B #3/B #5/B #6/B #7/B

Alignment identifier is 1  

> select #7: 468-504

313 atoms, 324 bonds, 37 residues, 1 model selected  

> select clear

> select #7: 468-504

313 atoms, 324 bonds, 37 residues, 1 model selected  

> select #7:514-521

63 atoms, 65 bonds, 8 residues, 1 model selected  

> select #7:514-520

54 atoms, 56 bonds, 7 residues, 1 model selected  

> show sel atoms

> hide sel atoms

> select #7:785-end

902 atoms, 930 bonds, 109 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel salmon

> select clear

> select #7:785-end

902 atoms, 930 bonds, 109 residues, 1 model selected  

> color sel forest green

> select clear

> select #7:468-504

313 atoms, 324 bonds, 37 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel salmon

> select clear

> select #7:514-520

54 atoms, 56 bonds, 7 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel cornflower blue

> select clear

> ui tool show "Model Panel"

> show #!6 models

> hide #!6 models

> show #!2 models

> ui tool show "Model Panel"

> ui tool show "Color Zone"

> color zone #2 near #7 distance 1.03

> ui tool show "Model Panel"

> hide #!2 models

> save "/Users/emmanuelafriyie/Documents/Cryo-EM/Cryo-EM Maps/WW4-HECT_nb
> complexes/WW4-HECT_nb.C11 Complex/3.1A Map/Color maps/Recoloring of
> domains/Selected color_further coloring of NLobe and
> CLobe/orange_corniflowerblue_Forestgreen_salmon.cxs"

——— End of log from Sat Feb 3 20:12:39 2024 ———

opened ChimeraX session  

> ui tool show "Color Zone"

> color zone #2 near #7 distance 1.03

[Repeated 1 time(s)]

> ui tool show "Model Panel"

> show #!2 models

> color zone #2 near #7 distance 1.03

> color zone #2 near #7 distance 8.43

> save "/Users/emmanuelafriyie/Documents/Cryo-EM/Cryo-EM Maps/WW4-HECT_nb
> complexes/WW4-HECT_nb.C11 Complex/3.1A Map/Color maps/Recoloring of
> domains/Selected color_further coloring of NLobe and
> CLobe/orange_corniflowerblue_Forestgreen_salmon_1.cxs"

> color zone #2 near #7 distance 8.43

> ui tool show "Model Panel"

> hide #!2 models

> show #!2 models

> hide #!7 models

> save "/Users/emmanuelafriyie/Documents/Cryo-EM/Cryo-EM Maps/WW4-HECT_nb
> complexes/WW4-HECT_nb.C11 Complex/3.1A Map/Color maps/Recoloring of
> domains/Selected color_further coloring of NLobe and
> CLobe/orange_corniflowerblue_Forestgreen_salmon_2.cxs"

——— End of log from Sat Feb 3 20:20:01 2024 ———

opened ChimeraX session  




OpenGL version: 4.1 Metal - 83
OpenGL renderer: Apple M1
OpenGL vendor: Apple

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Air
      Model Identifier: MacBookAir10,1
      Model Number: Z125000HMLL/A
      Chip: Apple M1
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 16 GB
      System Firmware Version: 8419.41.10
      OS Loader Version: 8419.41.10

Software:

    System Software Overview:

      System Version: macOS 13.0.1 (22A400)
      Kernel Version: Darwin 22.1.0
      Time since boot: 3 minutes, 13 seconds

Graphics/Displays:

    Apple M1:

      Chipset Model: Apple M1
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 8
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 2.4.1
    Babel: 2.14.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.0.3
    certifi: 2023.11.17
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.15
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.3
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.4
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.53
    ChimeraX-AtomicLibrary: 12.1.11
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.11
    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: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.3.2
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.8.dev202402080317
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.9
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    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: 2.1.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6.2
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12.2
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.15
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.1
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.2
    ChimeraX-PDB: 2.7.3
    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
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.2.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.2
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.15
    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: 2.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.33.7
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.2
    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: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.1
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.8
    debugpy: 1.8.0
    decorator: 5.1.1
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.1
    fonttools: 4.48.1
    funcparserlib: 2.0.0a0
    glfw: 2.6.5
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2020.1.16
    idna: 3.6
    ihm: 0.43
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.1
    jedi: 0.19.1
    Jinja2: 3.1.3
    jupyter-client: 8.6.0
    jupyter-core: 5.7.1
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    lxml: 5.1.0
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.7
    ndindex: 1.7
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.2.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.9.0
    numpy: 1.26.3
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.2.0
    pip: 23.3.2
    pkginfo: 1.9.6
    platformdirs: 4.2.0
    prompt-toolkit: 3.0.43
    psutil: 5.9.8
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.3.0
    pygments: 2.17.2
    pynmrstar: 3.3.2
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3301
    pyparsing: 3.1.1
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2024.1
    pyzmq: 25.1.2
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.11.4
    setuptools: 69.0.3
    setuptools-scm: 8.0.4
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 7.2.6
    sphinx-autodoc-typehints: 1.25.3
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.6.1
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2023.12.9
    tinyarray: 1.2.4
    tornado: 6.4
    traitlets: 5.14.1
    typing-extensions: 4.9.0
    tzdata: 2023.4
    urllib3: 2.2.0
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.42.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9

Change History (2)

comment:1 by Eric Pettersen, 21 months 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 → Qt fatal error: Failed to initialize graphics backend for OpenGL

comment:2 by Eric Pettersen, 21 months ago

Status: accepted → feedback

Hi Emmanuel,

Thanks for reporting this problem. Did ChimeraX crash at startup? But it started up at other times okay?

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

Note: See TracTickets for help on using tickets.