Context Navigation

← Previous Ticket
Next Ticket →

#16422 closed defect

Crash on Mac waking from sleep — at Version 1

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

Description (last modified by Eric Pettersen)

The following bug report has been submitted:
Platform:        macOS-14.6.1-arm64-arm-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Current thread 0x00000001f40f0f40 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 in 
  File "", line 88 in _run_code
  File "", line 198 in _run_module_as_main

Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.pdb_lib._load_libs, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, openmm._openmm, openmm.app.internal.compiled, PIL._imagingmath, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, psutil._psutil_osx, psutil._psutil_posix (total: 63)


{"app_name":"ChimeraX","timestamp":"2024-12-05 01:25:10.00 +0100","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":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 14.6.1 (23G93)","roots_installed":0,"name":"ChimeraX","incident_id":"1A45BAC7-6FFC-4440-B61D-232BFACB799D"}
{
  "uptime" : 740000,
  "procRole" : "Background",
  "version" : 2,
  "userID" : 502,
  "deployVersion" : 210,
  "modelCode" : "Mac14,7",
  "coalitionID" : 1763,
  "osVersion" : {
    "train" : "macOS 14.6.1",
    "build" : "23G93",
    "releaseType" : "User"
  },
  "captureTime" : "2024-12-05 00:19:36.6742 +0100",
  "codeSigningMonitor" : 1,
  "incident" : "1A45BAC7-6FFC-4440-B61D-232BFACB799D",
  "pid" : 231,
  "translated" : false,
  "cpuType" : "ARM-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2024-12-04 19:39:56.2755 +0100",
  "procStartAbsTime" : 17373257614560,
  "procExitAbsTime" : 17775986940482,
  "procName" : "ChimeraX",
  "procPath" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
  "bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
  "storeInfo" : {"deviceIdentifierForVendor":"28FE279B-5C00-53B3-BED9-B0F9D96FA4E2","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "3610094C-FE23-95D2-FA43-F569A7A5CF1F",
  "lowPowerMode" : 1,
  "codeSigningID" : "edu.ucsf.cgl.ChimeraX",
  "codeSigningTeamID" : "LWV8X224YF",
  "codeSigningFlags" : 570491649,
  "codeSigningValidationCategory" : 6,
  "codeSigningTrustLevel" : 4294967295,
  "instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRd+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkWzg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
  "wakeTime" : 22019,
  "sleepWakeUUID" : "8819E196-7082-49CC-AD74-8CF1DB73C047",
  "sip" : "enabled",
  "vmRegionInfo" : "0x6e703f3a25d8 is not in any region.  Bytes after previous region: 15872038675929  \n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      MALLOC_NANO              6000a0000000-6000c0000000 [512.0M] rw-\/rwx SM=PRV  \n--->  \n      UNUSED SPACE AT END",
  "exception" : {"codes":"0x0000000000000001, 0x0000ee703f3a25d8","rawCodes":[1,262165864523224],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000ee703f3a25d8 -> 0x00006e703f3a25d8 (possible pointer authentication failure)"},
  "termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":231},
  "vmregioninfo" : "0x6e703f3a25d8 is not in any region.  Bytes after previous region: 15872038675929  \n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      MALLOC_NANO              6000a0000000-6000c0000000 [512.0M] rw-\/rwx SM=PRV  \n--->  \n      UNUSED SPACE AT END",
  "extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
  "faultingThread" : 0,
  "threads" : [{"threadState":{"x":[{"value":0},{"value":0},{"value":1},{"value":4966415000},{"value":112},{"value":116},{"value":2305948562347500224},{"value":0},{"value":7701468002353644955},{"value":7701468010205973211},{"value":14757395258967641293},{"value":4294967286},{"value":4966414930},{"value":0},{"value":54},{"value":4294967280},{"value":328},{"value":8564712680},{"value":0},{"value":11},{"value":8389594944,"symbolLocation":0,"symbol":"_main_thread"},{"value":259},{"value":8389595168,"symbolLocation":224,"symbol":"_main_thread"},{"value":1},{"value":4386539056,"symbolLocation":0,"symbol":"faulthandler_handlers"},{"value":8395169792,"symbolLocation":0,"symbol":"OBJC_IVAR_$_NSCGSStatusItem._selectedContentFrame"},{"value":8395169792,"symbolLocation":0,"symbol":"OBJC_IVAR_$_NSCGSStatusItem._selectedContentFrame"},{"value":5},{"value":0}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6646537248},"cpsr":{"value":1073745920},"fp":{"value":4966415072},"sp":{"value":4966415040},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6646306288,"matchesCrashFrame":1},"far":{"value":0}},"id":8565434,"triggered":true,"name":"CrBrowserMain","queue":"com.apple.main-thread","frames":[{"imageOffset":38384,"symbol":"__pthread_kill","symbolLocation":8,"imageIndex":183},{"imageOffset":27680,"symbol":"pthread_kill","symbolLocation":288,"imageIndex":184},{"imageOffset":262624,"symbol":"raise","symbolLocation":32,"imageIndex":185},{"imageOffset":2417160,"symbol":"faulthandler_fatal_error","symbolLocation":392,"imageIndex":181},{"imageOffset":17796,"symbol":"_sigtramp","symbolLocation":56,"imageIndex":186},{"imageOffset":343184,"imageIndex":113},{"imageOffset":343184,"imageIndex":113},{"imageOffset":380316,"symbol":"_NSViewHierarchyDidChangeBackingProperties","symbolLocation":244,"imageIndex":187},{"imageOffset":11486732,"symbol":"-[NSWindow _postWindowDidChangeBackingPropertiesAndDisplayWindowForPreviousBackingScaleFactor:previousColorSpace:]","symbolLocation":192,"imageIndex":187},{"imageOffset":2095464,"symbol":"__67-[NSWindow _updateSettingsSendingScreenChangeNotificationToScreen:]_block_invoke","symbolLocation":448,"imageIndex":187},{"imageOffset":510204,"symbol":"NSPerformVisuallyAtomicChange","symbolLocation":108,"imageIndex":187},{"imageOffset":2095004,"symbol":"-[NSWindow _updateSettingsSendingScreenChangeNotificationToScreen:]","symbolLocation":96,"imageIndex":187},{"imageOffset":3405336,"symbol":"-[NSWindow _screenChanged:]","symbolLocation":136,"imageIndex":187},{"imageOffset":3405168,"symbol":"-[NSWindow _displayChangedSoAdjustWindows:]","symbolLocation":112,"imageIndex":187},{"imageOffset":14668244,"symbol":"___NSApplicationPerformScreenInvalidationReactions_block_invoke","symbolLocation":72,"imageIndex":187},{"imageOffset":216096,"symbol":"-[NSApplication enumerateWindowsWithOptions:usingBlock:]","symbolLocation":236,"imageIndex":187},{"imageOffset":14667004,"symbol":"___NSApplicationReactToScreenInvalidation_block_invoke","symbolLocation":856,"imageIndex":187},{"imageOffset":14665396,"symbol":"_NSApplicationReactToScreenInvalidation","symbolLocation":280,"imageIndex":187},{"imageOffset":14665868,"symbol":"-[NSApplication(ScreenHandling) _reactToDisplayChanges:]","symbolLocation":372,"imageIndex":187},{"imageOffset":8139332,"symbol":"_NSCGSDisplayConfigurationUpdateAndInvokeObservers","symbolLocation":416,"imageIndex":187},{"imageOffset":8140236,"symbol":"_NSCGSDisplayConfigurationDidReconfigureNotificationHandler","symbolLocation":308,"imageIndex":187},{"imageOffset":46152,"symbol":"(anonymous namespace)::notify_datagram_handler(unsigned int, CGSDatagramType, void*, unsigned long, void*)","symbolLocation":876,"imageIndex":188},{"imageOffset":3844700,"symbol":"CGSDatagramReadStream::dispatchMainQueueDatagrams()","symbolLocation":228,"imageIndex":188},{"imageOffset":3844440,"symbol":"invocation function for block in CGSDatagramReadStream::mainQueueWakeup()","symbolLocation":28,"imageIndex":188},{"imageOffset":10064,"symbol":"_dispatch_call_block_and_release","symbolLocation":32,"imageIndex":189},{"imageOffset":17384,"symbol":"_dispatch_client_callout","symbolLocation":20,"imageIndex":189},{"imageOffset":76728,"symbol":"_dispatch_main_queue_drain","symbolLocation":988,"imageIndex":189},{"imageOffset":75724,"symbol":"_dispatch_main_queue_callback_4CF","symbolLocation":44,"imageIndex":189},{"imageOffset":785108,"symbol":"__CFRUNLOOP_IS_SERVICING_THE_MAIN_DISPATCH_QUEUE__","symbolLocation":16,"imageIndex":190},{"imageOffset":512600,"symbol":"__CFRunLoopRun","symbolLocation":1996,"imageIndex":190},{"imageOffset":508980,"symbol":"CFRunLoopRunSpecific","symbolLocation":608,"imageIndex":190},{"imageOffset":209308,"symbol":"RunCurrentEventLoopInMode","symbolLocation":292,"imageIndex":191},{"imageOffset":208856,"symbol":"ReceiveNextEventCommon","symbolLocation":648,"imageIndex":191},{"imageOffset":208176,"symbol":"_BlockUntilNextEventMatchingListInModeWithFilter","symbolLocation":76,"imageIndex":191},{"imageOffset":236744,"symbol":"_DPSNextEvent","symbolLocation":660,"imageIndex":187},{"imageOffset":8586448,"symbol":"-[NSApplication(NSEventRouting) _nextEventMatchingEventMask:untilDate:inMode:dequeue:]","symbolLocation":700,"imageIndex":187},{"imageOffset":184316,"symbol":"-[NSApplication run]","symbolLocation":476,"imageIndex":187},{"imageOffset":81772,"imageIndex":113},{"imageOffset":573772,"symbol":"QEventLoop::exec(QFlags)","symbolLocation":540,"imageIndex":138},{"imageOffset":535260,"symbol":"QCoreApplication::exec()","symbolLocation":112,"imageIndex":138},{"imageOffset":2507676,"symbol":"meth_QApplication_exec(_object*, _object*)","symbolLocation":96,"imageIndex":131},{"imageOffset":1004504,"symbol":"cfunction_call","symbolLocation":96,"imageIndex":181},{"imageOffset":594156,"symbol":"_PyObject_MakeTpCall","symbolLocation":128,"imageIndex":181},{"imageOffset":1789244,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":54984,"imageIndex":181},{"imageOffset":1729512,"symbol":"PyEval_EvalCode","symbolLocation":276,"imageIndex":181},{"imageOffset":1707120,"symbol":"builtin_exec","symbolLocation":428,"imageIndex":181},{"imageOffset":1007044,"symbol":"cfunction_vectorcall_FASTCALL_KEYWORDS","symbolLocation":80,"imageIndex":181},{"imageOffset":1788292,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":54032,"imageIndex":181},{"imageOffset":1811404,"symbol":"_PyEval_Vector","symbolLocation":156,"imageIndex":181},{"imageOffset":2389028,"symbol":"pymain_run_module","symbolLocation":256,"imageIndex":181},{"imageOffset":2387652,"symbol":"Py_RunMain","symbolLocation":1784,"imageIndex":181},{"imageOffset":2392180,"symbol":"pymain_main","symbolLocation":52,"imageIndex":181},{"imageOffset":2392116,"symbol":"Py_Main","symbolLocation":36,"imageIndex":181},{"imageOffset":15700,"symbol":"main","symbolLocation":128,"imageIndex":182},{"imageOffset":24916,"symbol":"start","symbolLocation":2476,"imageIndex":192}]},{"id":8565713,"name":"ThreadPoolServiceThread","threadState":{"x":[{"value":4},{"value":0},{"value":0},{"value":105553155100032},{"value":4},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":3},{"value":2},{"value":6282529440},{"value":64771},{"value":1},{"value":1},{"value":369},{"value":12918681600},{"value":0},{"value":6416223464},{"value":5224911152},{"value":0},{"value":12918680912},{"value":12297829382473034411},{"value":1},{"value":0},{"value":0},{"value":0},{"value":0}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6175873464},"cpsr":{"value":2684358656},"fp":{"value":12918680896},"sp":{"value":12918680832},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6646320160},"far":{"value":0}},"frames":[{"imageOffset":52256,"symbol":"kevent64","symbolLocation":8,"imageIndex":183},{"imageOffset":66705848,"imageIndex":121},{"imageOffset":66705328,"imageIndex":121},{"imageOffset":66336288,"imageIndex":121},{"imageOffset":66064512,"imageIndex":121},{"imageOffset":66483648,"imageIndex":121},{"imageOffset":66384288,"imageIndex":121},{"imageOffset":66484032,"imageIndex":121},{"imageOffset":66589352,"imageIndex":121},{"imageOffset":28564,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":184},{"imageOffset":7476,"symbol":"thread_start","symbolLocation":8,"imageIndex":184}]},{"id":8565714,"name":"ThreadPoolForegroundWorker","threadState":{"x":[{"value":268451845},{"value":17179869442},{"value":0},{"value":193526931390464},{"value":0},{"value":193526931390464},{"value":32},{"value":33000},{"value":18446744073709550527},{"value":45059},{"value":0},{"value":1},{"value":45059},{"value":2045},{"value":2359492694},{"value":86},{"value":18446744073709551569},{"value":196608},{"value":0},{"value":33000},{"value":32},{"value":193526931390464},{"value":0},{"value":193526931390464},{"value":12927102224},{"value":0},{"value":17179870466},{"value":17179869442},{"value":1282}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6646347236},"cpsr":{"value":4096},"fp":{"value":12927101568},"sp":{"value":12927101488},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6646271476},"far":{"value":0}},"frames":[{"imageOffset":3572,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":183},{"imageOffset":79332,"symbol":"mach_msg2_internal","symbolLocation":80,"imageIndex":183},{"imageOffset":39364,"symbol":"mach_msg_overwrite","symbolLocation":476,"imageIndex":183},{"imageOffset":4472,"symbol":"mach_msg","symbolLocation":24,"imageIndex":183},{"imageOffset":66741424,"imageIndex":121},{"imageOffset":66197236,"imageIndex":121},{"imageOffset":66429892,"imageIndex":121},{"imageOffset":66433464,"imageIndex":121},{"imageOffset":66432016,"imageIndex":121},{"imageOffset":66431744,"imageIndex":121},{"imageOffset":66589352,"imageIndex":121},{"imageOffset":28564,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":184},{"imageOffset":7476,"symbol":"thread_start","symbolLocation":8,"imageIndex":184}]},{"id":8565715,"name":"ThreadPoolBackgroundWorker","threadState":{"x":[{"value":268451845},{"value":17179869442},{"value":0},{"value":194626443018240},{"value":0},{"value":194626443018240},{"value":32},{"value":33000},{"value":18446744073709550527},{"value":45315},{"value":0},{"value":1},{"value":45315},{"value":2045},{"value":3686844663},{"value":247},{"value":18446744073709551569},{"value":51200},{"value":0},{"value":33000},{"value":32},{"value":194626443018240},{"value":0},{"value":194626443018240},{"value":12935523600},{"value":0},{"value":17179870466},{"value":17179869442},{"value":1282}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6646347236},"cpsr":{"value":4096},"fp":{"value":12935522944},"sp":{"value":12935522864},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6646271476},"far":{"value":0}},"frames":[{"imageOffset":3572,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":183},{"imageOffset":79332,"symbol":"mach_msg2_internal","symbolLocation":80,"imageIndex":183},{"imageOffset":39364,"symbol":"mach_msg_overwrite","symbolLocation":476,"imageIndex":183},{"imageOffset":4472,"symbol":"mach_msg","symbolLocation":24,"imageIndex":183},{"imageOffset":66741424,"imageIndex":121},{"imageOffset":66197236,"imageIndex":121},{"imageOffset":66429892,"imageIndex":121},{"imageOffset":66433464,"imageIndex":121},{"imageOffset":66431884,"imageIndex":121},{"imageOffset":66431792,"imageIndex":121},{"imageOffset":66589352,"imageIndex":121},{"imageOffset":28564,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":184},{"imageOffset":7476,"symbol":"thread_start","symbolLocation":8,"imageIndex":184}]},{"id":8565716,"name":"Chrome_IOThread","threadState":{"x":[{"value":4},{"value":0},{"value":0},{"value":105553155319936},{"value":3},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":9223372036854775809},{"value":6282529488},{"value":62467},{"value":1},{"value":1},{"value":369},{"value":12943945728},{"value":0},{"value":6416215560},{"value":6411338496},{"value":0},{"value":12943945024},{"value":12297829382473034411},{"value":1},{"value":0},{"value":0},{"value":0},{"value":0}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6175873464},"cpsr":{"value":1610616832},"fp":{"value":12943945008},"sp":{"value":12943944944},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6646320160},"far":{"value":0}},"frames":[{"imageOffset":52256,"symbol":"kevent64","symbolLocation":8,"imageIndex":183},{"imageOffset":66705848,"imageIndex":121},{"imageOffset":66705328,"imageIndex":121},{"imageOffset":66336288,"imageIndex":121},{"imageOffset":66064512,"imageIndex":121},{"imageOffset":66483648,"imageIndex":121},{"imageOffset":42148336,"imageIndex":121},{"imageOffset":66484032,"imageIndex":121},{"imageOffset":66589352,"imageIndex":121},{"imageOffset":28564,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":184},{"imageOffset":7476,"symbol":"thread_start","symbolLocation":8,"imageIndex":184}]},{"id":8565717,"name":"NetworkConfigWatcher","threadState":{"x":[{"value":268451845},{"value":17179869186},{"value":0},{"value":202323024412672},{"value":0},{"value":202323024412672},{"value":32},{"value":0},{"value":18446744073709550527},{"value":47107},{"value":0},{"value":1},{"value":47107},{"value":61187},{"value":1},{"value":1},{"value":18446744073709551569},{"value":12952367104},{"value":0},{"value":0},{"value":32},{"value":202323024412672},{"value":0},{"value":202323024412672},{"value":12952366160},{"value":0},{"value":17179869186},{"value":17179869186},{"value":2}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6646347236},"cpsr":{"value":4096},"fp":{"value":12952365504},"sp":{"value":12952365424},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6646271476},"far":{"value":0}},"frames":[{"imageOffset":3572,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":183},{"imageOffset":79332,"symbol":"mach_msg2_internal","symbolLocation":80,"imageIndex":183},{"imageOffset":39364,"symbol":"mach_msg_overwrite","symbolLocation":476,"imageIndex":183},{"imageOffset":4472,"symbol":"mach_msg","symbolLocation":24,"imageIndex":183},{"imageOffset":66741424,"imageIndex":121},{"imageOffset":66197236,"imageIndex":121},{"imageOffset":66197084,"imageIndex":121},{"imageOffset":65870644,"imageIndex":121},{"imageOffset":66336288,"imageIndex":121},{"imageOffset":66064512,"imageIndex":121},{"imageOffset":66483648,"imageIndex":121},{"imageOffset":66484032,"imageIndex":121},{"imageOffset":66589352,"imageIndex":121},{"imageOffset":28564,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":184},{"imageOffset":7476,"symbol":"thread_start","symbolLocation":8,"imageIndex":184}]},{"id":8565721,"name":"Chrome_InProcGpuThread","threadState":{"x":[{"value":268451845},{"value":17179869186},{"value":0},{"value":256199094173696},{"value":0},{"value":256199094173696},{"value":32},{"value":0},{"value":18446744073709550527},{"value":59651},{"value":0},{"value":1},{"value":59651},{"value":59907},{"value":1},{"value":1},{"value":18446744073709551569},{"value":12986052608},{"value":0},{"value":0},{"value":32},{"value":256199094173696},{"value":0},{"value":256199094173696},{"value":12986051664},{"value":0},{"value":17179869186},{"value":17179869186},{"value":2}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6646347236},"cpsr":{"value":4096},"fp":{"value":12986051008},"sp":{"value":12986050928},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6646271476},"far":{"value":0}},"frames":[{"imageOffset":3572,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":183},{"imageOffset":79332,"symbol":"mach_msg2_internal","symbolLocation":80,"imageIndex":183},{"imageOffset":39364,"symbol":"mach_msg_overwrite","symbolLocation":476,"imageIndex":183},{"imageOffset":4472,"symbol":"mach_msg","symbolLocation":24,"imageIndex":183},{"imageOffset":66741424,"imageIndex":121},{"imageOffset":66197236,"imageIndex":121},{"imageOffset":66197084,"imageIndex":121},{"imageOffset":65870644,"imageIndex":121},{"imageOffset":66336288,"imageIndex":121},{"imageOffset":66064512,"imageIndex":121},{"imageOffset":66483648,"imageIndex":121},{"imageOffset":66484032,"imageIndex":121},{"imageOffset":66589352,"imageIndex":121},{"imageOffset":28564,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":184},{"imageOffset":7476,"symbol":"thread_start","symbolLocation":8,"imageIndex":184}]},{"id":8565722,"name":"Chrome_ChildIOThread","threadState":{"x":[{"value":4},{"value":0},{"value":0},{"value":105553148038576},{"value":1},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":1},{"value":2},{"value":6282529584},{"value":59395},{"value":1},{"value":1},{"value":369},{"value":12994473984},{"value":0},{"value":6418869896},{"value":6416233968},{"value":0},{"value":12994473280},{"value":12297829382473034411},{"value":1},{"value":0},{"value":0},{"value":0},{"value":0}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6175873464},"cpsr":{"value":2684358656},"fp":{"value":12994473264},"sp":{"value":12994473200},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6646320160},"far":{"value":0}},"frames":[{"imageOffset":52256,"symbol":"kevent64","symbolLocation":8,"imageIndex":183},{"imageOffset":66705848,"imageIndex":121},{"imageOffset":66705328,"imageIndex":121},{"imageOffset":66336288,"imageIndex":121},{"imageOffset":66064512,"imageIndex":121},{"imageOffset":66483648,"imageIndex":121},{"imageOffset":107949588,"imageIndex":121},{"imageOffset":66484032,"imageIndex":121},{"imageOffset":66589352,"imageIndex":121},{"imageOffset":28564,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":184},{"imageOffset":7476,"symbol":"thread_start","symbolLocation":8,"imageIndex":184}]},{"id":8565723,"name":"CompositorTileWorker1","threadState":{"x":[{"value":260},{"value":0},{"value":512},{"value":0},{"value":0},{"value":161},{"value":0},{"value":0},{"value":13002894936},{"value":0},{"value":4399256032},{"value":2},{"value":0},{"value":0},{"value":0},{"value":0},{"value":305},{"value":8564712608},{"value":0},{"value":4399256008},{"value":4399256136},{"value":13002895584},{"value":0},{"value":0},{"value":512},{"value":513},{"value":768},{"value":0},{"value":0}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6646539612},"cpsr":{"value":1610616832},"fp":{"value":13002895056},"sp":{"value":13002894912},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6646285804},"far":{"value":0}},"frames":[{"imageOffset":17900,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":183},{"imageOffset":30044,"symbol":"_pthread_cond_wait","symbolLocation":1228,"imageIndex":184},{"imageOffset":66586532,"imageIndex":121},{"imageOffset":99447652,"imageIndex":121},{"imageOffset":66589352,"imageIndex":121},{"imageOffset":28564,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":184},{"imageOffset":7476,"symbol":"thread_start","symbolLocation":8,"imageIndex":184}]},{"id":8565724,"name":"ThreadPoolSingleThreadSharedForeground0","threadState":{"x":[{"value":268451845},{"value":17179869186},{"value":0},{"value":250701536034816},{"value":0},{"value":250701536034816},{"value":32},{"value":0},{"value":18446744073709550527},{"value":58371},{"value":0},{"value":1},{"value":58371},{"value":2045},{"value":2734707019},{"value":331},{"value":18446744073709551569},{"value":20480},{"value":0},{"value":0},{"value":32},{"value":250701536034816},{"value":0},{"value":250701536034816},{"value":13011315984},{"value":0},{"value":17179869186},{"value":17179869186},{"value":2}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6646347236},"cpsr":{"value":4096},"fp":{"value":13011315328},"sp":{"value":13011315248},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6646271476},"far":{"value":0}},"frames":[{"imageOffset":3572,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":183},{"imageOffset":79332,"symbol":"mach_msg2_internal","symbolLocation":80,"imageIndex":183},{"imageOffset":39364,"symbol":"mach_msg_overwrite","symbolLocation":476,"imageIndex":183},{"imageOffset":4472,"symbol":"mach_msg","symbolLocation":24,"imageIndex":183},{"imageOffset":66741424,"imageIndex":121},{"imageOffset":66197236,"imageIndex":121},{"imageOffset":66429892,"imageIndex":121},{"imageOffset":66432404,"imageIndex":121},{"imageOffset":66432060,"imageIndex":121},{"imageOffset":66431816,"imageIndex":121},{"imageOffset":66589352,"imageIndex":121},{"imageOffset":28564,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":184},{"imageOffset":7476,"symbol":"thread_start","symbolLocation":8,"imageIndex":184}]},{"id":8565725,"name":"NetworkConfigWatcher","threadState":{"x":[{"value":268451845},{"value":17179869186},{"value":0},{"value":241905443012608},{"value":0},{"value":241905443012608},{"value":32},{"value":0},{"value":18446744073709550527},{"value":56323},{"value":0},{"value":1},{"value":56323},{"value":52995},{"value":1},{"value":1},{"value":18446744073709551569},{"value":13027487744},{"value":0},{"value":0},{"value":32},{"value":241905443012608},{"value":0},{"value":241905443012608},{"value":13027486800},{"value":0},{"value":17179869186},{"value":17179869186},{"value":2}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6646347236},"cpsr":{"value":4096},"fp":{"value":13027486144},"sp":{"value":13027486064},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6646271476},"far":{"value":0}},"frames":[{"imageOffset":3572,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":183},{"imageOffset":79332,"symbol":"mach_msg2_internal","symbolLocation":80,"imageIndex":183},{"imageOffset":39364,"symbol":"mach_msg_overwrite","symbolLocation":476,"imageIndex":183},{"imageOffset":4472,"symbol":"mach_msg","symbolLocation":24,"imageIndex":183},{"imageOffset":66741424,"imageIndex":121},{"imageOffset":66197236,"imageIndex":121},{"imageOffset":66197084,"imageIndex":121},{"imageOffset":65870644,"imageIndex":121},{"imageOffset":66336288,"imageIndex":121},{"imageOffset":66064512,"imageIndex":121},{"imageOffset":66483648,"imageIndex":121},{"imageOffset":66484032,"imageIndex":121},{"imageOffset":66589352,"imageIndex":121},{"imageOffset":28564,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":184},{"imageOffset":7476,"symbol":"thread_start","symbolLocation":8,"imageIndex":184}]},{"id":8565726,"name":"VizCompositorThread","threadState":{"x":[{"value":268451843},{"value":17179869442},{"value":0},{"value":234208861618176},{"value":0},{"value":234208861618176},{"value":32},{"value":3},{"value":18446744073709550527},{"value":54531},{"value":0},{"value":1},{"value":54531},{"value":55811},{"value":1},{"value":1},{"value":18446744073709551569},{"value":13035909120},{"value":0},{"value":3},{"value":32},{"value":234208861618176},{"value":0},{"value":234208861618176},{"value":13035908192},{"value":0},{"value":17179870466},{"value":17179869442},{"value":1282}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6646347236},"cpsr":{"value":4096},"fp":{"value":13035907536},"sp":{"value":13035907456},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6646271476},"far":{"value":0}},"frames":[{"imageOffset":3572,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":183},{"imageOffset":79332,"symbol":"mach_msg2_internal","symbolLocation":80,"imageIndex":183},{"imageOffset":39364,"symbol":"mach_msg_overwrite","symbolLocation":476,"imageIndex":183},{"imageOffset":4472,"symbol":"mach_msg","symbolLocation":24,"imageIndex":183},{"imageOffset":66741424,"imageIndex":121},{"imageOffset":66197236,"imageIndex":121},{"imageOffset":65870544,"imageIndex":121},{"imageOffset":66336288,"imageIndex":121},{"imageOffset":66064512,"imageIndex":121},{"imageOffset":66483648,"imageIndex":121},{"imageOffset":66484032,"imageIndex":121},{"imageOffset":66589352,"imageIndex":121},{"imageOffset":28564,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":184},{"imageOffset":7476,"symbol":"thread_start","symbolLocation":8,"imageIndex":184}]},{"id":8565727,"name":"NetworkService","threadState":{"x":[{"value":4},{"value":0},{"value":0},{"value":105553170923712},{"value":2},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":9223372036854775807},{"value":740637210250},{"value":6282529776},{"value":55299},{"value":1},{"value":1},{"value":369},{"value":13061074944},{"value":0},{"value":6419268360},{"value":12892686016},{"value":0},{"value":13061074288},{"value":12297829382473034411},{"value":1},{"value":0},{"value":0},{"value":0},{"value":0}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6175873464},"cpsr":{"value":2684358656},"fp":{"value":13061074272},"sp":{"value":13061074208},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6646320160},"far":{"value":0}},"frames":[{"imageOffset":52256,"symbol":"kevent64","symbolLocation":8,"imageIndex":183},{"imageOffset":66705848,"imageIndex":121},{"imageOffset":66705328,"imageIndex":121},{"imageOffset":66336288,"imageIndex":121},{"imageOffset":66064512,"imageIndex":121},{"imageOffset":66483648,"imageIndex":121},{"imageOffset":66484032,"imageIndex":121},{"imageOffset":66589352,"imageIndex":121},{"imageOffset":28564,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":184},{"imageOffset":7476,"symbol":"thread_start","symbolLocation":8,"imageIndex":184}]},{"id":8565728,"name":"NetworkConfigWatcher","threadState":{"x":[{"value":268451845},{"value":17179869186},{"value":0},{"value":283686884868096},{"value":0},{"value":283686884868096},{"value":32},{"value":0},{"value":18446744073709550527},{"value":66051},{"value":0},{"value":1},{"value":66051},{"value":86531},{"value":1},{"value":1},{"value":18446744073709551569},{"value":13069496320},{"value":0},{"value":0},{"value":32},{"value":283686884868096},{"value":0},{"value":283686884868096},{"value":13069495376},{"value":0},{"value":17179869186},{"value":17179869186},{"value":2}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6646347236},"cpsr":{"value":4096},"fp":{"value":13069494720},"sp":{"value":13069494640},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6646271476},"far":{"value":0}},"frames":[{"imageOffset":3572,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":183},{"imageOffset":79332,"symbol":"mach_msg2_internal","symbolLocation":80,"imageIndex":183},{"imageOffset":39364,"symbol":"mach_msg_overwrite","symbolLocation":476,"imageIndex":183},{"imageOffset":4472,"symbol":"mach_msg","symbolLocation":24,"imageIndex":183},{"imageOffset":66741424,"imageIndex":121},{"imageOffset":66197236,"imageIndex":121},{"imageOffset":66197084,"imageIndex":121},{"imageOffset":65870644,"imageIndex":121},{"imageOffset":66336288,"imageIndex":121},{"imageOffset":66064512,"imageIndex":121},{"imageOffset":66483648,"imageIndex":121},{"imageOffset":66484032,"imageIndex":121},{"imageOffset":66589352,"imageIndex":121},{"imageOffset":28564,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":184},{"imageOffset":7476,"symbol":"thread_start","symbolLocation":8,"imageIndex":184}]},{"id":8565729,"name":"ThreadPoolSingleThreadForegroundBlocking1","threadState":{"x":[{"value":268451845},{"value":17179869186},{"value":0},{"value":369448791834624},{"value":0},{"value":369448791834624},{"value":32},{"value":0},{"value":18446744073709550527},{"value":86019},{"value":0},{"value":1},{"value":86019},{"value":0},{"value":72057602427648497,"symbolLocation":72057594037927937,"symbol":"OBJC_CLASS_$_NSAutoreleasePool"},{"value":8389720560,"symbolLocation":0,"symbol":"OBJC_CLASS_$_NSAutoreleasePool"},{"value":18446744073709551569},{"value":8565075592},{"value":0},{"value":0},{"value":32},{"value":369448791834624},{"value":0},{"value":369448791834624},{"value":13077916944},{"value":0},{"value":17179869186},{"value":17179869186},{"value":2}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6646347236},"cpsr":{"value":4096},"fp":{"value":13077916288},"sp":{"value":13077916208},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6646271476},"far":{"value":0}},"frames":[{"imageOffset":3572,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":183},{"imageOffset":79332,"symbol":"mach_msg2_internal","symbolLocation":80,"imageIndex":183},{"imageOffset":39364,"symbol":"mach_msg_overwrite","symbolLocation":476,"imageIndex":183},{"imageOffset":4472,"symbol":"mach_msg","symbolLocation":24,"imageIndex":183},{"imageOffset":66741424,"imageIndex":121},{"imageOffset":66197236,"imageIndex":121},{"imageOffset":66429892,"imageIndex":121},{"imageOffset":66433464,"imageIndex":121},{"imageOffset":66432104,"imageIndex":121},{"imageOffset":66431804,"imageIndex":121},{"imageOffset":66589352,"imageIndex":121},{"imageOffset":28564,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":184},{"imageOffset":7476,"symbol":"thread_start","symbolLocation":8,"imageIndex":184}]},{"id":8565751,"name":"NetworkConfigWatcher","threadState":{"x":[{"value":268451845},{"value":17179869186},{"value":0},{"value":316672233701376},{"value":0},{"value":316672233701376},{"value":32},{"value":0},{"value":18446744073709550527},{"value":73731},{"value":0},{"value":1},{"value":73731},{"value":73475},{"value":1},{"value":1},{"value":18446744073709551569},{"value":13185888256},{"value":0},{"value":0},{"value":32},{"value":316672233701376},{"value":0},{"value":316672233701376},{"value":13185887312},{"value":0},{"value":17179869186},{"value":17179869186},{"value":2}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6646347236},"cpsr":{"value":4096},"fp":{"value":13185886656},"sp":{"value":13185886576},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6646271476},"far":{"value":0}},"frames":[{"imageOffset":3572,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":183},{"imageOffset":79332,"symbol":"mach_msg2_internal","symbolLocation":80,"imageIndex":183},{"imageOffset":39364,"symbol":"mach_msg_overwrite","symbolLocation":476,"imageIndex":183},{"imageOffset":4472,"symbol":"mach_msg","symbolLocation":24,"imageIndex":183},{"imageOffset":66741424,"imageIndex":121},{"imageOffset":66197236,"imageIndex":121},{"imageOffset":66197084,"imageIndex":121},{"imageOffset":65870644,"imageIndex":121},{"imageOffset":66336288,"imageIndex":121},{"imageOffset":66064512,"imageIndex":121},{"imageOffset":66483648,"imageIndex":121},{"imageOffset":66484032,"imageIndex":121},{"imageOffset":66589352,"imageIndex":121},{"imageOffset":28564,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":184},{"imageOffset":7476,"symbol":"thread_start","symbolLocation":8,"imageIndex":184}]},{"id":8565832,"frames":[{"imageOffset":17900,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":183},{"imageOffset":30044,"symbol":"_pthread_cond_wait","symbolLocation":1228,"imageIndex":184},{"imageOffset":1502040,"symbol":"blas_thread_server","symbolLocation":360,"imageIndex":161},{"imageOffset":28564,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":184},{"imageOffset":7476,"symbol":"thread_start","symbolLocation":8,"imageIndex":184}],"threadState":{"x":[{"value":260},{"value":0},{"value":184064},{"value":0},{"value":0},{"value":160},{"value":0},{"value":0},{"value":6104542920},{"value":0},{"value":4425736232,"symbolLocation":40,"symbol":"thread_status"},{"value":2},{"value":0},{"value":0},{"value":0},{"value":0},{"value":305},{"value":8564712608},{"value":0},{"value":4425736208,"symbolLocation":16,"symbol":"thread_status"},{"value":4425736272,"symbolLocation":80,"symbol":"thread_status"},{"value":6104543456},{"value":0},{"value":0},{"value":184064},{"value":184065},{"value":184320},{"value":4425650176,"symbolLocation":16,"symbol":"gemm_driver.level3_lock"},{"value":1}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6646539612},"cpsr":{"value":1610616832},"fp":{"value":6104543040},"sp":{"value":6104542896},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6646285804},"far":{"value":0}}},{"id":8565833,"frames":[{"imageOffset":17900,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":183},{"imageOffset":30044,"symbol":"_pthread_cond_wait","symbolLocation":1228,"imageIndex":184},{"imageOffset":1502040,"symbol":"blas_thread_server","symbolLocation":360,"imageIndex":161},{"imageOffset":28564,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":184},{"imageOffset":7476,"symbol":"thread_start","symbolLocation":8,"imageIndex":184}],"threadState":{"x":[{"value":260},{"value":0},{"value":184064},{"value":0},{"value":0},{"value":160},{"value":0},{"value":0},{"value":6105116360},{"value":0},{"value":4425736360,"symbolLocation":168,"symbol":"thread_status"},{"value":2},{"value":0},{"value":0},{"value":0},{"value":0},{"value":305},{"value":8564712608},{"value":0},{"value":4425736336,"symbolLocation":144,"symbol":"thread_status"},{"value":4425736400,"symbolLocation":208,"symbol":"thread_status"},{"value":6105116896},{"value":0},{"value":0},{"value":184064},{"value":184065},{"value":184320},{"value":4425650176,"symbolLocation":16,"symbol":"gemm_driver.level3_lock"},{"value":1}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6646539612},"cpsr":{"value":1610616832},"fp":{"value":6105116480},"sp":{"value":6105116336},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6646285804},"far":{"value":0}}},{"id":8565834,"frames":[{"imageOffset":17900,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":183},{"imageOffset":30044,"symbol":"_pthread_cond_wait","symbolLocation":1228,"imageIndex":184},{"imageOffset":1502040,"symbol":"blas_thread_server","symbolLocation":360,"imageIndex":161},{"imageOffset":28564,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":184},{"imageOffset":7476,"symbol":"thread_start","symbolLocation":8,"imageIndex":184}],"threadState":{"x":[{"value":260},{"value":0},{"value":0},{"value":0},{"value":0},{"value":160},{"value":0},{"value":0},{"value":6105689800},{"value":0},{"value":4425736488,"symbolLocation":296,"symbol":"thread_status"},{"value":2},{"value":0},{"value":0},{"value":0},{"value":0},{"value":305},{"value":8564712608},{"value":0},{"value":4425736464,"symbolLocation":272,"symbol":"thread_status"},{"value":4425736528,"symbolLocation":336,"symbol":"thread_status"},{"value":6105690336},{"value":0},{"value":0},{"value":0},{"value":1},{"value":256},{"value":4425650176,"symbolLocation":16,"symbol":"gemm_driver.level3_lock"},{"value":1}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6646539612},"cpsr":{"value":1610616832},"fp":{"value":6105689920},"sp":{"value":6105689776},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6646285804},"far":{"value":0}}},{"id":8565835,"frames":[{"imageOffset":17900,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":183},{"imageOffset":30044,"symbol":"_pthread_cond_wait","symbolLocation":1228,"imageIndex":184},{"imageOffset":1502040,"symbol":"blas_thread_server","symbolLocation":360,"imageIndex":161},{"imageOffset":28564,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":184},{"imageOffset":7476,"symbol":"thread_start","symbolLocation":8,"imageIndex":184}],"threadState":{"x":[{"value":260},{"value":0},{"value":0},{"value":0},{"value":0},{"value":160},{"value":0},{"value":0},{"value":6106263240},{"value":0},{"value":4425736616,"symbolLocation":424,"symbol":"thread_status"},{"value":2},{"value":0},{"value":0},{"value":0},{"value":0},{"value":305},{"value":8564712608},{"value":0},{"value":4425736592,"symbolLocation":400,"symbol":"thread_status"},{"value":4425736656,"symbolLocation":464,"symbol":"thread_status"},{"value":6106263776},{"value":0},{"value":0},{"value":0},{"value":1},{"value":256},{"value":4425650176,"symbolLocation":16,"symbol":"gemm_driver.level3_lock"},{"value":1}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6646539612},"cpsr":{"value":1610616832},"fp":{"value":6106263360},"sp":{"value":6106263216},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6646285804},"far":{"value":0}}},{"id":8565836,"frames":[{"imageOffset":17900,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":183},{"imageOffset":30044,"symbol":"_pthread_cond_wait","symbolLocation":1228,"imageIndex":184},{"imageOffset":1502040,"symbol":"blas_thread_server","symbolLocation":360,"imageIndex":161},{"imageOffset":28564,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":184},{"imageOffset":7476,"symbol":"thread_start","symbolLocation":8,"imageIndex":184}],"threadState":{"x":[{"value":260},{"value":0},{"value":0},{"value":0},{"value":0},{"value":160},{"value":0},{"value":0},{"value":6106836680},{"value":0},{"value":4425736744,"symbolLocation":552,"symbol":"thread_status"},{"value":2},{"value":0},{"value":0},{"value":0},{"value":0},{"value":305},{"value":8564712608},{"value":0},{"value":4425736720,"symbolLocation":528,"symbol":"thread_status"},{"value":4425736784,"symbolLocation":592,"symbol":"thread_status"},{"value":6106837216},{"value":0},{"value":0},{"value":0},{"value":1},{"value":256},{"value":4425650176,"symbolLocation":16,"symbol":"gemm_driver.level3_lock"},{"value":1}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6646539612},"cpsr":{"value":1610616832},"fp":{"value":6106836800},"sp":{"value":6106836656},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6646285804},"far":{"value":0}}},{"id":8565837,"frames":[{"imageOffset":17900,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":183},{"imageOffset":30044,"symbol":"_pthread_cond_wait","symbolLocation":1228,"imageIndex":184},{"imageOffset":1502040,"symbol":"blas_thread_server","symbolLocation":360,"imageIndex":161},{"imageOffset":28564,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":184},{"imageOffset":7476,"symbol":"thread_start","symbolLocation":8,"imageIndex":184}],"threadState":{"x":[{"value":260},{"value":0},{"value":0},{"value":0},{"value":0},{"value":160},{"value":0},{"value":0},{"value":13270920904},{"value":0},{"value":4425736872,"symbolLocation":680,"symbol":"thread_status"},{"value":2},{"value":0},{"value":0},{"value":0},{"value":0},{"value":305},{"value":8564712608},{"value":0},{"value":4425736848,"symbolLocation":656,"symbol":"thread_status"},{"value":4425736912,"symbolLocation":720,"symbol":"thread_status"},{"value":13270921440},{"value":0},{"value":0},{"value":0},{"value":1},{"value":256},{"value":4425650176,"symbolLocation":16,"symbol":"gemm_driver.level3_lock"},{"value":1}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6646539612},"cpsr":{"value":1610616832},"fp":{"value":13270921024},"sp":{"value":13270920880},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6646285804},"far":{"value":0}}},{"id":8565838,"frames":[{"imageOffset":17900,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":183},{"imageOffset":30044,"symbol":"_pthread_cond_wait","symbolLocation":1228,"imageIndex":184},{"imageOffset":1502040,"symbol":"blas_thread_server","symbolLocation":360,"imageIndex":161},{"imageOffset":28564,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":184},{"imageOffset":7476,"symbol":"thread_start","symbolLocation":8,"imageIndex":184}],"threadState":{"x":[{"value":260},{"value":0},{"value":0},{"value":0},{"value":0},{"value":160},{"value":0},{"value":0},{"value":13451013832},{"value":0},{"value":4425737000,"symbolLocation":808,"symbol":"thread_status"},{"value":2},{"value":0},{"value":0},{"value":0},{"value":0},{"value":305},{"value":8564712608},{"value":0},{"value":4425736976,"symbolLocation":784,"symbol":"thread_status"},{"value":4425737040,"symbolLocation":848,"symbol":"thread_status"},{"value":13451014368},{"value":0},{"value":0},{"value":0},{"value":1},{"value":256},{"value":4425650176,"symbolLocation":16,"symbol":"gemm_driver.level3_lock"},{"value":1}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6646539612},"cpsr":{"value":1610616832},"fp":{"value":13451013952},"sp":{"value":13451013808},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6646285804},"far":{"value":0}}},{"id":8565842,"name":"com.apple.NSEventThread","threadState":{"x":[{"value":268451845},{"value":21592279046},{"value":8589934592},{"value":477218111225856},{"value":0},{"value":477218111225856},{"value":2},{"value":4294967295},{"value":18446744073709550527},{"value":111111},{"value":0},{"value":1},{"value":111111},{"value":234967},{"value":0},{"value":6597069766656},{"value":18446744073709551569},{"value":8564696808},{"value":0},{"value":4294967295},{"value":2},{"value":477218111225856},{"value":0},{"value":477218111225856},{"value":13273981032},{"value":8589934592},{"value":21592279046},{"value":21592279046},{"value":4412409862,"symbolLocation":2450,"symbol":"dtrsm_kernel_RT_ARMV8SVE"}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6646347236},"cpsr":{"value":4096},"fp":{"value":13273980880},"sp":{"value":13273980800},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6646271476},"far":{"value":0}},"frames":[{"imageOffset":3572,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":183},{"imageOffset":79332,"symbol":"mach_msg2_internal","symbolLocation":80,"imageIndex":183},{"imageOffset":39364,"symbol":"mach_msg_overwrite","symbolLocation":476,"imageIndex":183},{"imageOffset":4472,"symbol":"mach_msg","symbolLocation":24,"imageIndex":183},{"imageOffset":517760,"symbol":"__CFRunLoopServiceMachPort","symbolLocation":160,"imageIndex":190},{"imageOffset":511812,"symbol":"__CFRunLoopRun","symbolLocation":1208,"imageIndex":190},{"imageOffset":508980,"symbol":"CFRunLoopRunSpecific","symbolLocation":608,"imageIndex":190},{"imageOffset":1458816,"symbol":"_NSEventThread","symbolLocation":144,"imageIndex":187},{"imageOffset":28564,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":184},{"imageOffset":7476,"symbol":"thread_start","symbolLocation":8,"imageIndex":184}]},{"id":8565843,"name":"MemoryInfra","threadState":{"x":[{"value":268451845},{"value":17179869186},{"value":0},{"value":570659419717632},{"value":0},{"value":570659419717632},{"value":32},{"value":0},{"value":18446744073709550527},{"value":132867},{"value":0},{"value":1},{"value":132867},{"value":132355},{"value":1},{"value":1},{"value":18446744073709551569},{"value":13282406400},{"value":0},{"value":0},{"value":32},{"value":570659419717632},{"value":0},{"value":570659419717632},{"value":13282405456},{"value":0},{"value":17179869186},{"value":17179869186},{"value":2}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6646347236},"cpsr":{"value":4096},"fp":{"value":13282404800},"sp":{"value":13282404720},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6646271476},"far":{"value":0}},"frames":[{"imageOffset":3572,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":183},{"imageOffset":79332,"symbol":"mach_msg2_internal","symbolLocation":80,"imageIndex":183},{"imageOffset":39364,"symbol":"mach_msg_overwrite","symbolLocation":476,"imageIndex":183},{"imageOffset":4472,"symbol":"mach_msg","symbolLocation":24,"imageIndex":183},{"imageOffset":66741424,"imageIndex":121},{"imageOffset":66197236,"imageIndex":121},{"imageOffset":66197084,"imageIndex":121},{"imageOffset":65870644,"imageIndex":121},{"imageOffset":66336288,"imageIndex":121},{"imageOffset":66064512,"imageIndex":121},{"imageOffset":66483648,"imageIndex":121},{"imageOffset":66484032,"imageIndex":121},{"imageOffset":66589352,"imageIndex":121},{"imageOffset":28564,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":184},{"imageOffset":7476,"symbol":"thread_start","symbolLocation":8,"imageIndex":184}]},{"id":8565844,"name":"ThreadPoolSingleThreadSharedBackgroundBlocking2","threadState":{"x":[{"value":268451845},{"value":17179869186},{"value":0},{"value":569559908089856},{"value":0},{"value":569559908089856},{"value":32},{"value":0},{"value":18446744073709550527},{"value":132611},{"value":0},{"value":1},{"value":132611},{"value":2045},{"value":2271901702},{"value":6},{"value":18446744073709551569},{"value":686080},{"value":0},{"value":0},{"value":32},{"value":569559908089856},{"value":0},{"value":569559908089856},{"value":13630008592},{"value":0},{"value":17179869186},{"value":17179869186},{"value":2}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6646347236},"cpsr":{"value":4096},"fp":{"value":13630007936},"sp":{"value":13630007856},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6646271476},"far":{"value":0}},"frames":[{"imageOffset":3572,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":183},{"imageOffset":79332,"symbol":"mach_msg2_internal","symbolLocation":80,"imageIndex":183},{"imageOffset":39364,"symbol":"mach_msg_overwrite","symbolLocation":476,"imageIndex":183},{"imageOffset":4472,"symbol":"mach_msg","symbolLocation":24,"imageIndex":183},{"imageOffset":66741424,"imageIndex":121},{"imageOffset":66197236,"imageIndex":121},{"imageOffset":66429892,"imageIndex":121},{"imageOffset":66432404,"imageIndex":121},{"imageOffset":66431928,"imageIndex":121},{"imageOffset":66431840,"imageIndex":121},{"imageOffset":66589352,"imageIndex":121},{"imageOffset":28564,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":184},{"imageOffset":7476,"symbol":"thread_start","symbolLocation":8,"imageIndex":184}]},{"id":8644423,"frames":[{"imageOffset":7456,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":184}],"threadState":{"x":[{"value":13594832896},{"value":159247},{"value":13594296320},{"value":13594831744},{"value":5193730},{"value":1},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0}],"flavor":"ARM_THREAD_STATE64","lr":{"value":0},"cpsr":{"value":4096},"fp":{"value":0},"sp":{"value":13594831728},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6646517024},"far":{"value":0}}},{"id":8645777,"frames":[{"imageOffset":7456,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":184}],"threadState":{"x":[{"value":13565702144},{"value":157531},{"value":13565165568},{"value":0},{"value":409604},{"value":18446744073709551615},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0}],"flavor":"ARM_THREAD_STATE64","lr":{"value":0},"cpsr":{"value":4096},"fp":{"value":0},"sp":{"value":13565702144},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6646517024},"far":{"value":0}}},{"id":8647027,"threadState":{"x":[{"value":105553151276960},{"value":8263578949,"objc-selector":"_decodeAndInvokeMessageWithEvent:reply:flags:"},{"value":105556186154640},{"value":0},{"value":1},{"value":0},{"value":13084139392},{"value":132097},{"value":4916514888},{"value":2711724449},{"value":460},{"value":240},{"value":105556155182012},{"value":2095104},{"value":2043},{"value":3089168392},{"value":6642503680,"symbolLocation":0,"symbol":"objc_msgSend"},{"value":8418076056},{"value":0},{"value":105553151276960},{"value":105556186154640},{"value":1},{"value":0},{"value":4916514880},{"value":4916514872},{"value":13084143840},{"value":13084141008},{"value":105553122278056},{"value":0}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6674019560},"cpsr":{"value":536875008},"fp":{"value":13084140352},"sp":{"value":13084140304},"esr":{"value":2449473543,"description":"(Data Abort) byte read Translation fault"},"pc":{"value":6642503688},"far":{"value":105553151276960}},"queue":"com.apple.NSXPCConnection.m-user.com.apple.windowmanager.server","frames":[{"imageOffset":36872,"symbol":"objc_msgSend","symbolLocation":8,"imageIndex":194},{"imageOffset":8910056,"symbol":"message_handler_message","symbolLocation":88,"imageIndex":195},{"imageOffset":129204,"symbol":"message_handler","symbolLocation":152,"imageIndex":195},{"imageOffset":61300,"symbol":"_xpc_connection_call_event_handler","symbolLocation":144,"imageIndex":196},{"imageOffset":55016,"symbol":"_xpc_connection_mach_event","symbolLocation":1404,"imageIndex":196},{"imageOffset":17576,"symbol":"_dispatch_client_callout4","symbolLocation":20,"imageIndex":189},{"imageOffset":133256,"symbol":"_dispatch_mach_msg_invoke","symbolLocation":468,"imageIndex":189},{"imageOffset":47256,"symbol":"_dispatch_lane_serial_drain","symbolLocation":368,"imageIndex":189},{"imageOffset":136664,"symbol":"_dispatch_mach_invoke","symbolLocation":444,"imageIndex":189},{"imageOffset":47256,"symbol":"_dispatch_lane_serial_drain","symbolLocation":368,"imageIndex":189},{"imageOffset":50552,"symbol":"_dispatch_lane_invoke","symbolLocation":432,"imageIndex":189},{"imageOffset":94928,"symbol":"_dispatch_root_queue_drain_deferred_wlh","symbolLocation":288,"imageIndex":189},{"imageOffset":92996,"symbol":"_dispatch_workloop_worker_thread","symbolLocation":404,"imageIndex":189},{"imageOffset":12300,"symbol":"_pthread_wqthread","symbolLocation":288,"imageIndex":184},{"imageOffset":7464,"symbol":"start_wqthread","symbolLocation":8,"imageIndex":184}]},{"id":8647028,"threadState":{"x":[{"value":13245165344},{"value":17402511360},{"value":196608},{"value":0},{"value":409605},{"value":0},{"value":0},{"value":0},{"value":2711724449},{"value":2711724449},{"value":4294967294},{"value":2147483648},{"value":0},{"value":0},{"value":0},{"value":0},{"value":6642513356,"symbolLocation":0,"symbol":"objc_autoreleasePoolPush"},{"value":8472602096},{"value":0},{"value":13245165792},{"value":8389611968,"symbolLocation":1536,"symbol":"_dispatch_root_queues"},{"value":0},{"value":409605},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":13245165792}],"flavor":"ARM_THREAD_STATE64","lr":{"value":2962664874012775308},"cpsr":{"value":1610616832},"fp":{"value":13245165280},"sp":{"value":13245165264},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6642722524},"far":{"value":0}},"queue":"com.apple.root.user-initiated-qos","frames":[{"imageOffset":255708,"symbol":"AutoreleasePoolPage::push()","symbolLocation":204,"imageIndex":194},{"imageOffset":17292,"symbol":"_dispatch_last_resort_autorelease_pool_push","symbolLocation":36,"imageIndex":189},{"imageOffset":89516,"symbol":"_dispatch_root_queue_drain","symbolLocation":140,"imageIndex":189},{"imageOffset":91832,"symbol":"_dispatch_worker_thread2","symbolLocation":156,"imageIndex":189},{"imageOffset":12240,"symbol":"_pthread_wqthread","symbolLocation":228,"imageIndex":184},{"imageOffset":7464,"symbol":"start_wqthread","symbolLocation":8,"imageIndex":184}]},{"id":8753894,"frames":[{"imageOffset":7456,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":184}],"threadState":{"x":[{"value":13468741632},{"value":154063},{"value":13468205056},{"value":0},{"value":409604},{"value":18446744073709551615},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0}],"flavor":"ARM_THREAD_STATE64","lr":{"value":0},"cpsr":{"value":4096},"fp":{"value":0},"sp":{"value":13468741632},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6646517024},"far":{"value":0}}}],
  "usedImages" : [
[deleted to fit within ticket limits]
],
  "sharedCache" : {
  "base" : 6642040832,
  "size" : 4214358016,
  "uuid" : "bb3df3d3-38bd-304c-9233-e43de95f1903"
},
  "vmSummary" : "ReadOnly portion of Libraries: Total=1.5G resident=0K(0%) swapped_out_or_unallocated=1.5G(100%)\nWritable regions: Total=8.4G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=8.4G(100%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nAccelerate framework               384K        3 \nActivity Tracing                   256K        1 \nCG image                           880K       43 \nColorSync                          640K       30 \nCoreAnimation                     3072K      189 \nCoreGraphics                        48K        3 \nCoreUI image data                 5776K       63 \nFoundation                          32K        2 \nKernel Alloc Once                   32K        1 \nMALLOC                             7.6G      171 \nMALLOC guard page                  192K       12 \nMach message                        64K        2 \nOpenGL GLSL                        256K        3 \nSTACK GUARD                        480K       30 \nStack                            151.2M       31 \nStack Guard                       56.0M        1 \nVM_ALLOCATE                      531.3M      331 \nVM_ALLOCATE (reserved)            96.0M        2         reserved VM address space (unallocated)\n__AUTH                            2199K      404 \n__AUTH_CONST                      31.8M      622 \n__CTF                               824        1 \n__DATA                            22.9M      803 \n__DATA_CONST                      43.0M      811 \n__DATA_DIRTY                      2024K      232 \n__FONT_DATA                        2352        1 \n__GLSLBUILTINS                    5174K        1 \n__INFO_FILTER                         8        1 \n__LINKEDIT                       562.0M      184 \n__OBJC_RO                         71.9M        1 \n__OBJC_RW                         2200K        1 \n__TEXT                           960.3M      828 \ndyld private memory                320K        4 \nmapped file                      546.2M       91 \nshared memory                     3184K       27 \n===========                     =======  ======= \nTOTAL                             10.6G     4930 \nTOTAL, minus reserved VM space    10.5G     4930 \n",
  "legacyInfo" : {
  "threadTriggered" : {
    "name" : "CrBrowserMain",
    "queue" : "com.apple.main-thread"
  }
},
  "logWritingSignature" : "a1db39312f991c6da151b762603b61f2b5cae364",
  "trialInfo" : {
  "rollouts" : [
    {
      "rolloutId" : "648a2601f74c42732876cb5b",
      "factorPackIds" : {
        "SIRI_TEXT_TO_SPEECH" : "6733fcb357a33f0bf26912cf"
      },
      "deploymentId" : 240000272
    },
    {
      "rolloutId" : "5ffde50ce2aacd000d47a95f",
      "factorPackIds" : {

      },
      "deploymentId" : 240000451
    }
  ],
  "experiments" : [
    {
      "treatmentId" : "45f4e2a5-551b-4bc2-a2dc-19c244dda8f8",
      "experimentId" : "6643969b3099cf28e049862f",
      "deploymentId" : 400000007
    }
  ]
}
}
===== Log before crash start =====
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Chimera sessions/20241125_chimera_for_figures.cxs"

Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292,
pixel 1.71, shown at level 0.005, step 1, values float32  
Opened emd_3720_2017_leaf.map as #56, grid size 128,128,128, pixel 1.78, shown
at level 0.155, step 1, values float32  
Opened relion_locres_filtered_20240326_GT_colorset2.mrc as #63, grid size
292,292,292, pixel 1.71, shown at level 0.0053, step 1, values float32  
Log from Tue Nov 26 17:24:46 2024UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Figures/2024_Nov/20241122_chimera_for_figures.cxs"

Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292,
pixel 1.71, shown at level 0.008, step 1, values float32  
Opened emd_3720_2017_leaf.map as #56, grid size 128,128,128, pixel 1.78, shown
at level 0.155, step 1, values float32  
Opened relion_locres_filtered_20240326_GT_colorset2.mrc as #63, grid size
292,292,292, pixel 1.71, shown at level 0.0053, step 1, values float32  
Log from Fri Nov 22 15:12:25 2024UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Figures/2024_Nov/Figure1/20241114_v2.cxs"

Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292,
pixel 1.71, shown at level 0.008, step 1, values float32  
Opened emd_3720_2017_leaf.map as #56, grid size 128,128,128, pixel 1.78, shown
at level 0.155, step 1, values float32  
Opened relion_locres_filtered_20240326_GT_colorset2.mrc as #63, grid size
292,292,292, pixel 1.71, shown at level 0.0053, step 1, values float32  
Log from Thu Nov 14 15:28:36 2024UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Chimera sessions/20241017_COPI_leaf_all_AF3_results_aligned.cxs"

Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292,
pixel 1.71, shown at level 0.008, step 1, values float32  
Opened emd_3720_2017_leaf.map as #56, grid size 128,128,128, pixel 1.78, shown
at level 0.155, step 1, values float32  
Opened relion_locres_filtered_20240326_GT_colorset2.mrc as #63, grid size
292,292,292, pixel 1.71, shown at level 0.008, step 1, values float32  
Log from Thu Oct 17 14:08:25 2024UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Chimera sessions/20241009_COPI_leaf_AF3_for_figs_v8.cxs"

Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292,
pixel 1.71, shown at level 0.008, step 1, values float32  
Opened emd_3720_2017_leaf.map as #56, grid size 128,128,128, pixel 1.78, shown
at level 0.155, step 1, values float32  
Opened relion_locres_filtered_20240326_GT_colorset1.mrc as #58, grid size
292,292,292, pixel 1.71, shown at level 0.005, step 1, values float32  
Opened relion_locres_filtered_20240326_GT_colorset2.mrc as #60, grid size
292,292,292, pixel 1.71, shown at level 0.008, step 1, values float32  
Opened relion_locres_filtered_20240326_GT_colorset2.mrc as #62, grid size
292,292,292, pixel 1.71, shown at level 0.008, step 1, values float32  
Opened relion_locres_filtered_20240326_GT_colorset2.mrc as #63, grid size
292,292,292, pixel 1.71, shown at level 0.008, step 1, values float32  
Log from Wed Oct 9 16:21:15 2024UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Chimera sessions/20240808_COPI_leaf_AF3_for_figs_v7_with_files.cxs"

Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292,
pixel 1.71, shown at level 0.008, step 1, values float32  
Opened emd_3720_2017_leaf.map as #56, grid size 128,128,128, pixel 1.78, shown
at level 0.155, step 1, values float32  
Opened relion_locres_filtered_20240326_GT_colorset1.mrc as #58, grid size
292,292,292, pixel 1.71, shown at level 0.005, step 1, values float32  
Opened relion_locres_filtered_20240326_GT_colorset2.mrc as #60, grid size
292,292,292, pixel 1.71, shown at level 0.008, step 1, values float32  
Opened relion_locres_filtered_20240326_GT_colorset2.mrc as #62, grid size
292,292,292, pixel 1.71, shown at level 0.008, step 1, values float32  
Opened relion_locres_filtered_20240326_GT_colorset2.mrc as #63, grid size
292,292,292, pixel 1.71, shown at level 0.008, step 1, values float32  
Log from Wed Sep 25 22:56:27 2024UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Chimera sessions/20240808_COPI_leaf_AF3_for_figs_v7.cxs"

Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292,
pixel 1.71, shown at level 0.008, step 1, values float32  
Opened emd_3720_2017_leaf.map as #56, grid size 128,128,128, pixel 1.78, shown
at level 0.155, step 1, values float32  
Opened relion_locres_filtered_20240326_GT_colorset1.mrc as #58, grid size
292,292,292, pixel 1.71, shown at level 0.005, step 1, values float32  
Opened relion_locres_filtered_20240326_GT_colorset2.mrc as #60, grid size
292,292,292, pixel 1.71, shown at level 0.008, step 1, values float32  
Opened relion_locres_filtered_20240326_GT_colorset2.mrc as #62, grid size
292,292,292, pixel 1.71, shown at level 0.008, step 1, values float32  
Opened relion_locres_filtered_20240326_GT_colorset2.mrc as #63, grid size
292,292,292, pixel 1.71, shown at level 0.008, step 1, values float32  
Log from Fri Aug 9 13:21:55 2024UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Chimera sessions/20240806_COPI_leaf_AF3_for_figs_v2.cxs"

Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292,
pixel 1.71, shown at level 0.008, step 1, values float32  
Opened emd_3720_2017_leaf.map as #56, grid size 128,128,128, pixel 1.78, shown
at level 0.155, step 1, values float32  
Opened relion_locres_filtered_20240326_GT.mrc as #58, grid size 292,292,292,
pixel 1.71, shown at level 0.005, step 1, values float32  
Opened relion_locres_filtered_20240326_GT.mrc copy as #61, grid size
292,292,292, pixel 1.71, shown at level 0.008, step 1, values float32  
Log from Tue Aug 6 15:17:45 2024UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240715_leaf_fitting_AF3_only_v4.cxs"

Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292,
pixel 1.71, shown at level 0.00585, step 1, values float32  
Log from Wed Jul 24 16:40:43 2024UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Structure files/alphafold 3
> /fold_20240711_copi_golph3/20240711_leaf_fitting_alphafold_withGolph3AF3_v2.cxs"

Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292,
pixel 1.71, shown at level 0.00736, step 1, values float32  
Log from Sat Jul 13 09:14:12 2024UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Structure files/alphafold 3 /GT 20240604
> /fold_2024_06_04_12_31/20240710_leaf_fitting_alphafold_only_withAF3_v5.cxs"

Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292,
pixel 1.71, shown at level 0.00736, step 1, values float32  
Log from Fri Jul 12 14:16:12 2024UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Structure files/alphafold 3 /GT 20240604
> /fold_2024_06_04_12_31/20240710_leaf_fitting_alphafold_only_withAF3_v4.cxs"

Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292,
pixel 1.71, shown at level 0.00465, step 1, values float32  
Log from Wed Jul 10 18:08:13 2024UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Structure files/alphafold 3 /GT 20240604
> /fold_2024_06_04_12_31/20240710_leaf_fitting_alphafold_only_withAF3_v2.cxs"

Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292,
pixel 1.71, shown at level 0.00465, step 1, values float32  
Log from Wed Jul 10 17:31:38 2024UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240710_leaf_fitting_alphafold_only_fitting.cxs"

Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292,
pixel 1.71, shown at level 0.00404, step 1, values float32  
Log from Wed Jul 10 16:36:09 2024UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240710_leaf_fitting_alphafold_only_fitting.cxs"

Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292,
pixel 1.71, shown at level 0.00404, step 1, values float32  
Log from Wed Jul 10 16:07:37 2024UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240709_leaf_fitting_v39_labelled.cxs"

Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292,
pixel 1.71, shown at level 0.00473, step 1, values float32  
Log from Tue Jul 9 17:02:08 2024UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240708_leaf_fitting_v36_labelled.cxs"

Opened emdb 3720 as #2, grid size 128,128,128, pixel 1.78, shown at level
0.12, step 1, values float32  
Opened COPI_golph_linkage1_postprocess.mrc as #13, grid size 128,128,128,
pixel 3.4, shown at level 0.368, step 1, values float32  
Opened emd_2986_2015_linkage1.map as #14, grid size 200,200,200, pixel 2.02,
shown at level 2.05, step 1, values float32  
Opened emd_3722_2017_linkage1.map as #15, grid size 212,212,212, pixel 1.78,
shown at level 0.0358, step 1, values float32  
Opened COPI_golph_linkage2_postprocess.mrc as #16, grid size 150,150,150,
pixel 3.4, shown at level 0.475, step 1, values float32  
Opened emd_2987_2015_linkage2.map as #17, grid size 200,200,200, pixel 2.02,
shown at level 1.91, step 1, values float32  
Opened emd_3723_2017_linkage2.map as #18, grid size 212,212,212, pixel 1.78,
shown at level 0.0556, step 1, values float32  
Opened COPI_golph_linkage3_postprocess.mrc as #19, grid size 160,160,160,
pixel 3.4, shown at level 0.54, step 1, values float32  
Opened emd_2988_2015_linkage3.map as #20, grid size 200,200,200, pixel 2.02,
shown at level 1.01, step 1, values float32  
Opened COPI_golph_linkage4_postprocess.mrc as #21, grid size 160,160,160,
pixel 3.4, shown at level 0.5, step 1, values float32  
Opened emd_2989_2015_linkage4.map as #22, grid size 200,200,200, pixel 2.02,
shown at level 1.74, step 1, values float32  
Opened emd_3724_2017_linkage4.map as #23, grid size 212,212,212, pixel 1.78,
shown at level 0.0393, step 1, values float32  
Opened relion_locres_filtered_20240325_GT.mrc as #33, grid size 292,292,292,
pixel 1.71, shown at level 0.0083, step 1, values float32  
Opened relion_locres_filtered_20240326_GT.mrc as #34, grid size 292,292,292,
pixel 1.71, shown at level 0.00463, step 1, values float32  
Log from Mon Jul 8 16:31:05 2024UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240522_leaf_fitting_v32_labelled.cxs"

Opened emdb 3720 as #2, grid size 128,128,128, pixel 1.78, shown at level
0.12, step 1, values float32  
Opened postprocess_20231221.mrc as #1, grid size 156,156,156, pixel 2.55,
shown at level 0.0037, step 1, values float32  
Opened COPI_golph_linkage1_postprocess.mrc as #13, grid size 128,128,128,
pixel 3.4, shown at level 0.368, step 1, values float32  
Opened emd_2986_2015_linkage1.map as #14, grid size 200,200,200, pixel 2.02,
shown at level 2.05, step 1, values float32  
Opened emd_3722_2017_linkage1.map as #15, grid size 212,212,212, pixel 1.78,
shown at level 0.0358, step 1, values float32  
Opened COPI_golph_linkage2_postprocess.mrc as #16, grid size 150,150,150,
pixel 3.4, shown at level 0.475, step 1, values float32  
Opened emd_2987_2015_linkage2.map as #17, grid size 200,200,200, pixel 2.02,
shown at level 1.91, step 1, values float32  
Opened emd_3723_2017_linkage2.map as #18, grid size 212,212,212, pixel 1.78,
shown at level 0.0556, step 1, values float32  
Opened COPI_golph_linkage3_postprocess.mrc as #19, grid size 160,160,160,
pixel 3.4, shown at level 0.54, step 1, values float32  
Opened emd_2988_2015_linkage3.map as #20, grid size 200,200,200, pixel 2.02,
shown at level 1.01, step 1, values float32  
Opened COPI_golph_linkage4_postprocess.mrc as #21, grid size 160,160,160,
pixel 3.4, shown at level 0.5, step 1, values float32  
Opened emd_2989_2015_linkage4.map as #22, grid size 200,200,200, pixel 2.02,
shown at level 1.74, step 1, values float32  
Opened emd_3724_2017_linkage4.map as #23, grid size 212,212,212, pixel 1.78,
shown at level 0.0393, step 1, values float32  
Opened relion_locres_filtered_20240325_GT.mrc as #33, grid size 292,292,292,
pixel 1.71, shown at level 0.0083, step 1, values float32  
Opened relion_locres_filtered_20240326_GT.mrc as #34, grid size 292,292,292,
pixel 1.71, shown at level 0.00733, step 1, values float32  
Log from Mon Jun 3 13:56:09 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera
> sessions/20240521_leaf_fitting_v31_mutations_interactions_labeled.cxs"

Opened emdb 3720 as #2, grid size 128,128,128, pixel 1.78, shown at level
0.12, step 1, values float32  
Opened postprocess_20231221.mrc as #1, grid size 156,156,156, pixel 2.55,
shown at level 0.0037, step 1, values float32  
Opened COPI_golph_linkage1_postprocess.mrc as #13, grid size 128,128,128,
pixel 3.4, shown at level 0.368, step 1, values float32  
Opened emd_2986_2015_linkage1.map as #14, grid size 200,200,200, pixel 2.02,
shown at level 2.05, step 1, values float32  
Opened emd_3722_2017_linkage1.map as #15, grid size 212,212,212, pixel 1.78,
shown at level 0.0358, step 1, values float32  
Opened COPI_golph_linkage2_postprocess.mrc as #16, grid size 150,150,150,
pixel 3.4, shown at level 0.475, step 1, values float32  
Opened emd_2987_2015_linkage2.map as #17, grid size 200,200,200, pixel 2.02,
shown at level 1.91, step 1, values float32  
Opened emd_3723_2017_linkage2.map as #18, grid size 212,212,212, pixel 1.78,
shown at level 0.0556, step 1, values float32  
Opened COPI_golph_linkage3_postprocess.mrc as #19, grid size 160,160,160,
pixel 3.4, shown at level 0.54, step 1, values float32  
Opened emd_2988_2015_linkage3.map as #20, grid size 200,200,200, pixel 2.02,
shown at level 1.01, step 1, values float32  
Opened COPI_golph_linkage4_postprocess.mrc as #21, grid size 160,160,160,
pixel 3.4, shown at level 0.5, step 1, values float32  
Opened emd_2989_2015_linkage4.map as #22, grid size 200,200,200, pixel 2.02,
shown at level 1.74, step 1, values float32  
Opened emd_3724_2017_linkage4.map as #23, grid size 212,212,212, pixel 1.78,
shown at level 0.0393, step 1, values float32  
Opened relion_locres_filtered_20240325_GT.mrc as #33, grid size 292,292,292,
pixel 1.71, shown at level 0.0083, step 1, values float32  
Opened relion_locres_filtered_20240326_GT.mrc as #34, grid size 292,292,292,
pixel 1.71, shown at level 0.00733, step 1, values float32  
Log from Tue May 21 23:56:29 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240406_leaf_fitting_v25.cxs"

Opened emdb 3720 as #2, grid size 128,128,128, pixel 1.78, shown at level
0.187, step 1, values float32  
Opened postprocess_20231221.mrc as #1, grid size 156,156,156, pixel 2.55,
shown at level 0.0037, step 1, values float32  
Opened COPI_golph_linkage1_postprocess.mrc as #13, grid size 128,128,128,
pixel 3.4, shown at level 0.368, step 1, values float32  
Opened emd_2986_2015_linkage1.map as #14, grid size 200,200,200, pixel 2.02,
shown at level 2.05, step 1, values float32  
Opened emd_3722_2017_linkage1.map as #15, grid size 212,212,212, pixel 1.78,
shown at level 0.0358, step 1, values float32  
Opened COPI_golph_linkage2_postprocess.mrc as #16, grid size 150,150,150,
pixel 3.4, shown at level 0.475, step 1, values float32  
Opened emd_2987_2015_linkage2.map as #17, grid size 200,200,200, pixel 2.02,
shown at level 1.91, step 1, values float32  
Opened emd_3723_2017_linkage2.map as #18, grid size 212,212,212, pixel 1.78,
shown at level 0.0556, step 1, values float32  
Opened COPI_golph_linkage3_postprocess.mrc as #19, grid size 160,160,160,
pixel 3.4, shown at level 0.54, step 1, values float32  
Opened emd_2988_2015_linkage3.map as #20, grid size 200,200,200, pixel 2.02,
shown at level 1.01, step 1, values float32  
Opened COPI_golph_linkage4_postprocess.mrc as #21, grid size 160,160,160,
pixel 3.4, shown at level 0.5, step 1, values float32  
Opened emd_2989_2015_linkage4.map as #22, grid size 200,200,200, pixel 2.02,
shown at level 1.74, step 1, values float32  
Opened emd_3724_2017_linkage4.map as #23, grid size 212,212,212, pixel 1.78,
shown at level 0.0393, step 1, values float32  
Opened relion_locres_filtered_20240325_GT.mrc as #33, grid size 292,292,292,
pixel 1.71, shown at level 0.0083, step 1, values float32  
Opened relion_locres_filtered_20240326_GT.mrc as #34, grid size 292,292,292,
pixel 1.71, shown at level 0.00645, step 1, values float32  
Log from Mon Apr 15 16:36:47 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240406_leaf_fitting_v21.cxs"

Opened emdb 3720 as #2, grid size 128,128,128, pixel 1.78, shown at level
0.187, step 1, values float32  
Opened postprocess_20231221.mrc as #1, grid size 156,156,156, pixel 2.55,
shown at level 0.0037, step 1, values float32  
Opened COPI_golph_linkage1_postprocess.mrc as #13, grid size 128,128,128,
pixel 3.4, shown at level 0.368, step 1, values float32  
Opened emd_2986_2015_linkage1.map as #14, grid size 200,200,200, pixel 2.02,
shown at level 2.05, step 1, values float32  
Opened emd_3722_2017_linkage1.map as #15, grid size 212,212,212, pixel 1.78,
shown at level 0.0358, step 1, values float32  
Opened COPI_golph_linkage2_postprocess.mrc as #16, grid size 150,150,150,
pixel 3.4, shown at level 0.475, step 1, values float32  
Opened emd_2987_2015_linkage2.map as #17, grid size 200,200,200, pixel 2.02,
shown at level 1.91, step 1, values float32  
Opened emd_3723_2017_linkage2.map as #18, grid size 212,212,212, pixel 1.78,
shown at level 0.0556, step 1, values float32  
Opened COPI_golph_linkage3_postprocess.mrc as #19, grid size 160,160,160,
pixel 3.4, shown at level 0.54, step 1, values float32  
Opened emd_2988_2015_linkage3.map as #20, grid size 200,200,200, pixel 2.02,
shown at level 1.01, step 1, values float32  
Opened COPI_golph_linkage4_postprocess.mrc as #21, grid size 160,160,160,
pixel 3.4, shown at level 0.5, step 1, values float32  
Opened emd_2989_2015_linkage4.map as #22, grid size 200,200,200, pixel 2.02,
shown at level 1.74, step 1, values float32  
Opened emd_3724_2017_linkage4.map as #23, grid size 212,212,212, pixel 1.78,
shown at level 0.0393, step 1, values float32  
Opened relion_locres_filtered_20240325_GT.mrc as #33, grid size 292,292,292,
pixel 1.71, shown at level 0.0083, step 1, values float32  
Opened relion_locres_filtered_20240326_GT.mrc as #34, grid size 292,292,292,
pixel 1.71, shown at level 0.00645, step 1, values float32  
Log from Mon Apr 15 15:35:58 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240328_leaf_fitting_v17.cxs"

Opened emdb 3720 as #2, grid size 128,128,128, pixel 1.78, shown at level
0.187, step 1, values float32  
Opened postprocess_20231221.mrc as #1, grid size 156,156,156, pixel 2.55,
shown at level 0.0037, step 1, values float32  
Opened COPI_golph_linkage1_postprocess.mrc as #13, grid size 128,128,128,
pixel 3.4, shown at level 0.368, step 1, values float32  
Opened emd_2986_2015_linkage1.map as #14, grid size 200,200,200, pixel 2.02,
shown at level 2.05, step 1, values float32  
Opened emd_3722_2017_linkage1.map as #15, grid size 212,212,212, pixel 1.78,
shown at level 0.0358, step 1, values float32  
Opened COPI_golph_linkage2_postprocess.mrc as #16, grid size 150,150,150,
pixel 3.4, shown at level 0.475, step 1, values float32  
Opened emd_2987_2015_linkage2.map as #17, grid size 200,200,200, pixel 2.02,
shown at level 1.91, step 1, values float32  
Opened emd_3723_2017_linkage2.map as #18, grid size 212,212,212, pixel 1.78,
shown at level 0.0556, step 1, values float32  
Opened COPI_golph_linkage3_postprocess.mrc as #19, grid size 160,160,160,
pixel 3.4, shown at level 0.54, step 1, values float32  
Opened emd_2988_2015_linkage3.map as #20, grid size 200,200,200, pixel 2.02,
shown at level 1.01, step 1, values float32  
Opened COPI_golph_linkage4_postprocess.mrc as #21, grid size 160,160,160,
pixel 3.4, shown at level 0.5, step 1, values float32  
Opened emd_2989_2015_linkage4.map as #22, grid size 200,200,200, pixel 2.02,
shown at level 1.74, step 1, values float32  
Opened emd_3724_2017_linkage4.map as #23, grid size 212,212,212, pixel 1.78,
shown at level 0.0393, step 1, values float32  
Opened relion_locres_filtered_20240325_GT.mrc as #33, grid size 292,292,292,
pixel 1.71, shown at level 0.0083, step 1, values float32  
Opened relion_locres_filtered_20240326_GT.mrc as #34, grid size 292,292,292,
pixel 1.71, shown at level 0.00645, step 1, values float32  
Opened cryosparc_P126_J1413_005_volume_map.mrc as #35, grid size 480,480,480,
pixel 0.953, shown at level 0.136, step 1, values float32  
Opened cryosparc_P126_J1449_008_volume_map_sharp.mrc as #36, grid size
480,480,480, pixel 0.953, shown at level 0.227, step 1, values float32  
Log from Fri Mar 29 15:25:34 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240326_leaf_fitting_v13.cxs"

Opened emdb 3720 as #2, grid size 128,128,128, pixel 1.78, shown at level
0.153, step 1, values float32  
Opened postprocess_20231221.mrc as #1, grid size 156,156,156, pixel 2.55,
shown at level 0.0037, step 1, values float32  
Opened COPI_golph_linkage1_postprocess.mrc as #13, grid size 128,128,128,
pixel 3.4, shown at level 0.368, step 1, values float32  
Opened emd_2986_2015_linkage1.map as #14, grid size 200,200,200, pixel 2.02,
shown at level 2.05, step 1, values float32  
Opened emd_3722_2017_linkage1.map as #15, grid size 212,212,212, pixel 1.78,
shown at level 0.0358, step 1, values float32  
Opened COPI_golph_linkage2_postprocess.mrc as #16, grid size 150,150,150,
pixel 3.4, shown at level 0.475, step 1, values float32  
Opened emd_2987_2015_linkage2.map as #17, grid size 200,200,200, pixel 2.02,
shown at level 1.91, step 1, values float32  
Opened emd_3723_2017_linkage2.map as #18, grid size 212,212,212, pixel 1.78,
shown at level 0.0556, step 1, values float32  
Opened COPI_golph_linkage3_postprocess.mrc as #19, grid size 160,160,160,
pixel 3.4, shown at level 0.54, step 1, values float32  
Opened emd_2988_2015_linkage3.map as #20, grid size 200,200,200, pixel 2.02,
shown at level 1.01, step 1, values float32  
Opened COPI_golph_linkage4_postprocess.mrc as #21, grid size 160,160,160,
pixel 3.4, shown at level 0.5, step 1, values float32  
Opened emd_2989_2015_linkage4.map as #22, grid size 200,200,200, pixel 2.02,
shown at level 1.74, step 1, values float32  
Opened emd_3724_2017_linkage4.map as #23, grid size 212,212,212, pixel 1.78,
shown at level 0.0393, step 1, values float32  
Opened relion_locres_filtered_20240325_GT.mrc as #33, grid size 292,292,292,
pixel 1.71, shown at level 0.0083, step 1, values float32  
Opened relion_locres_filtered_20240326_GT.mrc as #34, grid size 292,292,292,
pixel 1.71, shown at level 0.00747, step 1, values float32  
Log from Tue Mar 26 13:48:19 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240212_leaf_fitting_v10.cxs"

Opened emdb 3720 as #2, grid size 128,128,128, pixel 1.78, shown at level
0.153, step 1, values float32  
Opened postprocess_20231221.mrc as #1, grid size 156,156,156, pixel 2.55,
shown at level 0.0037, step 1, values float32  
Opened COPI_golph_linkage1_postprocess.mrc as #13, grid size 128,128,128,
pixel 3.4, shown at level 0.368, step 1, values float32  
Opened emd_2986_2015_linkage1.map as #14, grid size 200,200,200, pixel 2.02,
shown at level 2.05, step 1, values float32  
Opened emd_3722_2017_linkage1.map as #15, grid size 212,212,212, pixel 1.78,
shown at level 0.0358, step 1, values float32  
Opened COPI_golph_linkage2_postprocess.mrc as #16, grid size 150,150,150,
pixel 3.4, shown at level 0.475, step 1, values float32  
Opened emd_2987_2015_linkage2.map as #17, grid size 200,200,200, pixel 2.02,
shown at level 1.91, step 1, values float32  
Opened emd_3723_2017_linkage2.map as #18, grid size 212,212,212, pixel 1.78,
shown at level 0.0556, step 1, values float32  
Opened COPI_golph_linkage3_postprocess.mrc as #19, grid size 160,160,160,
pixel 3.4, shown at level 0.54, step 1, values float32  
Opened emd_2988_2015_linkage3.map as #20, grid size 200,200,200, pixel 2.02,
shown at level 1.01, step 1, values float32  
Opened COPI_golph_linkage4_postprocess.mrc as #21, grid size 160,160,160,
pixel 3.4, shown at level 0.5, step 1, values float32  
Opened emd_2989_2015_linkage4.map as #22, grid size 200,200,200, pixel 2.02,
shown at level 1.74, step 1, values float32  
Opened emd_3724_2017_linkage4.map as #23, grid size 212,212,212, pixel 1.78,
shown at level 0.0393, step 1, values float32  
Log from Thu Feb 15 12:14:52 2024UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240212_leaf_fitting_v2.cxs"

Opened emdb 3720 as #2, grid size 128,128,128, pixel 1.78, shown at level
0.153, step 1, values float32  
Opened postprocess_20231221.mrc as #1, grid size 156,156,156, pixel 2.55,
shown at level 0.00338, step 1, values float32  
Opened COPI_golph_linkage1_postprocess.mrc as #13, grid size 128,128,128,
pixel 3.4, shown at level 0.368, step 1, values float32  
Opened emd_2986_2015_linkage1.map as #14, grid size 200,200,200, pixel 2.02,
shown at level 2.05, step 1, values float32  
Opened emd_3722_2017_linkage1.map as #15, grid size 212,212,212, pixel 1.78,
shown at level 0.0358, step 1, values float32  
Opened COPI_golph_linkage2_postprocess.mrc as #16, grid size 150,150,150,
pixel 3.4, shown at level 0.475, step 1, values float32  
Opened emd_2987_2015_linkage2.map as #17, grid size 200,200,200, pixel 2.02,
shown at level 1.91, step 1, values float32  
Opened emd_3723_2017_linkage2.map as #18, grid size 212,212,212, pixel 1.78,
shown at level 0.0556, step 1, values float32  
Opened COPI_golph_linkage3_postprocess.mrc as #19, grid size 160,160,160,
pixel 3.4, shown at level 0.54, step 1, values float32  
Opened emd_2988_2015_linkage3.map as #20, grid size 200,200,200, pixel 2.02,
shown at level 1.01, step 1, values float32  
Opened COPI_golph_linkage4_postprocess.mrc as #21, grid size 160,160,160,
pixel 3.4, shown at level 0.5, step 1, values float32  
Opened emd_2989_2015_linkage4.map as #22, grid size 200,200,200, pixel 2.02,
shown at level 1.74, step 1, values float32  
Opened emd_3724_2017_linkage4.map as #23, grid size 212,212,212, pixel 1.78,
shown at level 0.0393, step 1, values float32  
Log from Mon Feb 12 10:40:16 2024UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240126_linkage_3_fitting_v1.cxs"

Opened emdb 3720 as #2, grid size 128,128,128, pixel 1.78, shown at level
0.153, step 1, values float32  
Opened emd_3720_2017_leaf.map as #25, grid size 128,128,128, pixel 1.78, shown
at level 0.145, step 1, values float32  
Opened postprocess_20231221.mrc as #1, grid size 156,156,156, pixel 2.55,
shown at level 0.00369, step 1, values float32  
Opened COPI_golph_linkage1_postprocess.mrc as #13, grid size 128,128,128,
pixel 3.4, shown at level 0.368, step 1, values float32  
Opened emd_2986_2015_linkage1.map as #14, grid size 200,200,200, pixel 2.02,
shown at level 2.05, step 1, values float32  
Opened emd_3722_2017_linkage1.map as #15, grid size 212,212,212, pixel 1.78,
shown at level 0.0358, step 1, values float32  
Opened COPI_golph_linkage2_postprocess.mrc as #16, grid size 150,150,150,
pixel 3.4, shown at level 0.475, step 1, values float32  
Opened emd_2987_2015_linkage2.map as #17, grid size 200,200,200, pixel 2.02,
shown at level 1.91, step 1, values float32  
Opened emd_3723_2017_linkage2.map as #18, grid size 212,212,212, pixel 1.78,
shown at level 0.0556, step 1, values float32  
Opened COPI_golph_linkage3_postprocess.mrc as #19, grid size 160,160,160,
pixel 3.4, shown at level 0.54, step 1, values float32  
Opened emd_2988_2015_linkage3.map as #20, grid size 200,200,200, pixel 2.02,
shown at level 1.01, step 1, values float32  
Opened COPI_golph_linkage4_postprocess.mrc as #21, grid size 160,160,160,
pixel 3.4, shown at level 0.5, step 1, values float32  
Opened emd_2989_2015_linkage4.map as #22, grid size 200,200,200, pixel 2.02,
shown at level 1.74, step 1, values float32  
Opened emd_3724_2017_linkage4.map as #23, grid size 212,212,212, pixel 1.78,
shown at level 0.0393, step 1, values float32  
Opened postprocess_20231221.mrc as #24, grid size 156,156,156, pixel 2.55,
shown at level 0.00376, step 1, values float32  
Opened postprocess_20231221.mrc as #36, grid size 156,156,156, pixel 2.55,
shown at level 0.00396, step 1, values float32  
Opened emd_3720_2017_leaf.map as #37, grid size 128,128,128, pixel 1.78, shown
at level 0.115, step 1, values float32  
Opened postprocess_20231221.mrc as #48, grid size 156,156,156, pixel 2.55,
shown at level 0.00387, step 1, values float32  
Opened emd_3720_2017_leaf.map as #49, grid size 128,128,128, pixel 1.78, shown
at level 0.226, step 1, values float32  
Log from Fri Jan 26 14:05:24 2024UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240125_linkage_3_fitting.cxs"

Opened emdb 3720 as #2, grid size 128,128,128, pixel 1.78, shown at level
0.153, step 1, values float32  
Opened emd_3720_2017_leaf.map as #25, grid size 128,128,128, pixel 1.78, shown
at level 0.145, step 1, values float32  
Opened postprocess_20231221.mrc as #1, grid size 156,156,156, pixel 2.55,
shown at level 0.00369, step 1, values float32  
Opened COPI_golph_linkage1_postprocess.mrc as #13, grid size 128,128,128,
pixel 3.4, shown at level 0.368, step 1, values float32  
Opened emd_2986_2015_linkage1.map as #14, grid size 200,200,200, pixel 2.02,
shown at level 2.05, step 1, values float32  
Opened emd_3722_2017_linkage1.map as #15, grid size 212,212,212, pixel 1.78,
shown at level 0.0358, step 1, values float32  
Opened COPI_golph_linkage2_postprocess.mrc as #16, grid size 150,150,150,
pixel 3.4, shown at level 0.475, step 1, values float32  
Opened emd_2987_2015_linkage2.map as #17, grid size 200,200,200, pixel 2.02,
shown at level 1.91, step 1, values float32  
Opened emd_3723_2017_linkage2.map as #18, grid size 212,212,212, pixel 1.78,
shown at level 0.0556, step 1, values float32  
Opened COPI_golph_linkage3_postprocess.mrc as #19, grid size 160,160,160,
pixel 3.4, shown at level 0.54, step 1, values float32  
Opened emd_2988_2015_linkage3.map as #20, grid size 200,200,200, pixel 2.02,
shown at level 1.01, step 1, values float32  
Opened COPI_golph_linkage4_postprocess.mrc as #21, grid size 160,160,160,
pixel 3.4, shown at level 0.5, step 1, values float32  
Opened emd_2989_2015_linkage4.map as #22, grid size 200,200,200, pixel 2.02,
shown at level 1.74, step 1, values float32  
Opened emd_3724_2017_linkage4.map as #23, grid size 212,212,212, pixel 1.78,
shown at level 0.0393, step 1, values float32  
Opened postprocess_20231221.mrc as #24, grid size 156,156,156, pixel 2.55,
shown at level 0.0033, step 1, values float32  
Opened postprocess_20231221.mrc as #36, grid size 156,156,156, pixel 2.55,
shown at level 0.00303, step 1, values float32  
Opened emd_3720_2017_leaf.map as #37, grid size 128,128,128, pixel 1.78, shown
at level 0.115, step 1, values float32  
Log from Thu Jan 25 18:04:25 2024UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240125_linkage_1_fitting.cxs"

Opened emdb 3720 as #2, grid size 128,128,128, pixel 1.78, shown at level
0.153, step 1, values float32  
Opened emd_3720_2017_leaf.map as #25, grid size 128,128,128, pixel 1.78, shown
at level 0.145, step 1, values float32  
Opened postprocess_20231221.mrc as #1, grid size 156,156,156, pixel 2.55,
shown at level 0.00369, step 1, values float32  
Opened COPI_golph_linkage1_postprocess.mrc as #13, grid size 128,128,128,
pixel 3.4, shown at level 0.368, step 1, values float32  
Opened emd_2986_2015_linkage1.map as #14, grid size 200,200,200, pixel 2.02,
shown at level 2.05, step 1, values float32  
Opened emd_3722_2017_linkage1.map as #15, grid size 212,212,212, pixel 1.78,
shown at level 0.0358, step 1, values float32  
Opened COPI_golph_linkage2_postprocess.mrc as #16, grid size 150,150,150,
pixel 3.4, shown at level 0.475, step 1, values float32  
Opened emd_2987_2015_linkage2.map as #17, grid size 200,200,200, pixel 2.02,
shown at level 1.91, step 1, values float32  
Opened emd_3723_2017_linkage2.map as #18, grid size 212,212,212, pixel 1.78,
shown at level 0.0556, step 1, values float32  
Opened COPI_golph_linkage3_postprocess.mrc as #19, grid size 160,160,160,
pixel 3.4, shown at level 0.606, step 1, values float32  
Opened emd_2988_2015_linkage3.map as #20, grid size 200,200,200, pixel 2.02,
shown at level 3.38, step 1, values float32  
Opened COPI_golph_linkage4_postprocess.mrc as #21, grid size 160,160,160,
pixel 3.4, shown at level 0.5, step 1, values float32  
Opened emd_2989_2015_linkage4.map as #22, grid size 200,200,200, pixel 2.02,
shown at level 1.74, step 1, values float32  
Opened emd_3724_2017_linkage4.map as #23, grid size 212,212,212, pixel 1.78,
shown at level 0.0393, step 1, values float32  
Opened postprocess_20231221.mrc as #24, grid size 156,156,156, pixel 2.55,
shown at level 0.0033, step 1, values float32  
Opened postprocess_20231221.mrc as #36, grid size 156,156,156, pixel 2.55,
shown at level 0.00453, step 1, values float32  
Opened emd_3720_2017_leaf.map as #37, grid size 128,128,128, pixel 1.78, shown
at level 0.115, step 1, values float32  
Log from Thu Jan 25 16:06:42 2024UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240124_Golph3_fitting.cxs"

Opened emdb 3720 as #2, grid size 128,128,128, pixel 1.78, shown at level
0.153, step 1, values float32  
Opened COPI_golph_linkage1_postprocess.mrc as #15, grid size 128,128,128,
pixel 3.4, shown at level 0.368, step 1, values float32  
Opened emd_2986_2015_linkage1.map as #16, grid size 200,200,200, pixel 2.02,
shown at level 2.05, step 1, values float32  
Opened emd_3722_2017_linkage1.map as #17, grid size 212,212,212, pixel 1.78,
shown at level 0.0358, step 1, values float32  
Opened COPI_golph_linkage2_postprocess.mrc as #18, grid size 150,150,150,
pixel 3.4, shown at level 0.475, step 1, values float32  
Opened emd_2987_2015_linkage2.map as #19, grid size 200,200,200, pixel 2.02,
shown at level 1.91, step 1, values float32  
Opened emd_3723_2017_linkage2.map as #20, grid size 212,212,212, pixel 1.78,
shown at level 0.0556, step 1, values float32  
Opened COPI_golph_linkage3_postprocess.mrc as #21, grid size 160,160,160,
pixel 3.4, shown at level 0.606, step 1, values float32  
Opened COPI_golph_linkage4_postprocess.mrc as #22, grid size 160,160,160,
pixel 3.4, shown at level 0.5, step 1, values float32  
Opened emd_2989_2015_linkage4.map as #23, grid size 200,200,200, pixel 2.02,
shown at level 1.74, step 1, values float32  
Opened emd_3724_2017_linkage4.map as #24, grid size 212,212,212, pixel 1.78,
shown at level 0.0393, step 1, values float32  
Opened emd_3720_2017_leaf.map as #25, grid size 128,128,128, pixel 1.78, shown
at level 0.145, step 1, values float32  
Opened emd_3720_2017_leaf.map as #26, grid size 128,128,128, pixel 1.78, shown
at level 0.115, step 1, values float32  
Opened postprocess_20231221.mrc as #27, grid size 156,156,156, pixel 2.55,
shown at level 0.00356, step 1, values float32  
Opened postprocess_20231221.mrc as #1, grid size 156,156,156, pixel 2.55,
shown at level 0.00402, step 1, values float32  
Log from Wed Jan 24 14:57:19 2024UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/COPI-Golph_GT/All_Linkages_fitting_Golph_AF_RT.cxs"

Opened postprocess.mrc as #1, grid size 244,244,244, pixel 2.55, shown at
level 0.01, step 1, values float32  
Opened emdb 3720 as #2, grid size 128,128,128, pixel 1.78, shown at level
0.153, step 1, values float32  
Opened COPI_golph_linkage1_postprocess.mrc as #15, grid size 128,128,128,
pixel 3.4, shown at level 0.368, step 1, values float32  
Opened emd_2986_2015_linkage1.map as #16, grid size 200,200,200, pixel 2.02,
shown at level 2.05, step 1, values float32  
Opened emd_3722_2017_linkage1.map as #17, grid size 212,212,212, pixel 1.78,
shown at level 0.0358, step 1, values float32  
Opened COPI_golph_linkage2_postprocess.mrc as #18, grid size 150,150,150,
pixel 3.4, shown at level 0.475, step 1, values float32  
Opened emd_2987_2015_linkage2.map as #19, grid size 200,200,200, pixel 2.02,
shown at level 1.91, step 1, values float32  
Opened emd_3723_2017_linkage2.map as #20, grid size 212,212,212, pixel 1.78,
shown at level 0.0556, step 1, values float32  
Opened COPI_golph_linkage3_postprocess.mrc as #21, grid size 160,160,160,
pixel 3.4, shown at level 0.606, step 1, values float32  
Opened COPI_golph_linkage4_postprocess.mrc as #22, grid size 160,160,160,
pixel 3.4, shown at level 0.5, step 1, values float32  
Opened emd_2989_2015_linkage4.map as #23, grid size 200,200,200, pixel 2.02,
shown at level 1.74, step 1, values float32  
Opened emd_3724_2017_linkage4.map as #24, grid size 212,212,212, pixel 1.78,
shown at level 0.0393, step 1, values float32  
Opened emd_3720_2017_leaf.map as #25, grid size 128,128,128, pixel 1.78, shown
at level 0.145, step 1, values float32  
Opened emd_3720_2017_leaf.map as #26, grid size 128,128,128, pixel 1.78, shown
at level 0.115, step 1, values float32  
Log from Tue Dec 5 16:56:09 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/COPI-Golph_GT/Linkage_1_fitting_Golph_AF_RT.cxs" format
> session

Opened postprocess.mrc as #1, grid size 244,244,244, pixel 2.55, shown at
level 0.00761, step 1, values float32  
Opened emdb 3720 as #2, grid size 128,128,128, pixel 1.78, shown at level
0.193, step 1, values float32  
Opened COPI_golph_linkage1_postprocess.mrc as #15, grid size 128,128,128,
pixel 3.4, shown at level 0.372, step 1, values float32  
Opened emd_2986_2015_linkage1.map as #16, grid size 200,200,200, pixel 2.02,
shown at level 2.05, step 1, values float32  
Opened emd_3722_2017_linkage1.map as #17, grid size 212,212,212, pixel 1.78,
shown at level 0.0358, step 1, values float32  
Log from Tue Dec 5 14:45:54 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Users/becca/Desktop/Postdoc/COPI-GOLPH
> dataset/Chimera_COPI_golph/alphafold_copi_colored_RT_4.cxs"

Opened postprocess.mrc as #1, grid size 244,244,244, pixel 2.55, shown at
level 0.00761, step 1, values float32  
Opened emdb 3720 as #2, grid size 128,128,128, pixel 1.78, shown at level
0.109, step 1, values float32  
Log from Tue Nov 7 12:35:14 2023UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> open alphafold_copi_colored_RT_2.cxs

Opened postprocess.mrc as #1, grid size 244,244,244, pixel 2.55, shown at
level 0.00761, step 1, values float32  
Opened emdb 3720 as #2, grid size 128,128,128, pixel 1.78, shown at level
0.109, step 1, values float32  
Log from Tue Nov 7 08:56:24 2023UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> open /fs/gpfs41/lv09/fileset01/pool/pool-
> briggs/taylor/em_data/20220715_COPI_Golph/alignments/alphafold_copi_colored_RT.cxs
> format session

Opened postprocess.mrc as #1, grid size 244,244,244, pixel 2.55, shown at
level 0.00761, step 1, values float32  
Opened emdb 3720 as #2, grid size 128,128,128, pixel 1.78, shown at level
0.109, step 1, values float32  
Log from Mon Nov 6 14:26:30 2023UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> open alphafold_copi_gt_colored.cxs

Opened postprocess.mrc as #1, grid size 244,244,244, pixel 2.55, shown at
level 0.00914, step 1, values float32  
Opened emdb 3720 as #2, grid size 128,128,128, pixel 1.78, shown at level
0.155, step 1, values float32  
Log from Sun Nov 5 21:56:53 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open alphafold_copi_gt.cxs

Opened postprocess.mrc as #1, grid size 244,244,244, pixel 2.55, shown at
level 0.012, step 1, values float32  
Opened emdb 3720 as #2, grid size 128,128,128, pixel 1.78, shown at level
0.155, step 1, values float32  
Log from Sun Nov 5 03:35:04 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 /fs/gpfs41/lv09/fileset01/pool/pool-
> briggs/tagiltsev/warp_4becca/warpV1_erase/relion/PostProcess/job062/postprocess.mrc

Opened postprocess.mrc as #1, grid size 244,244,244, pixel 2.55, shown at
level 0.00604, step 1, values float32  

> open 5nzr

Summary of feedback from opening 5nzr fetched from pdb  
---  
note | Fetching compressed mmCIF 5nzr from http://files.rcsb.org/download/5nzr.cif  
  
5nzr title:  
The structure of the COPI coat leaf [more info...]  
  
Chain information for 5nzr #2  
---  
Chain | Description | UniProt  
A | Coatomer subunit alpha | COPA_MOUSE 1-1224  
B | Coatomer subunit beta | COPB_MOUSE 16-968  
C | Coatomer subunit beta' | COPB2_MOUSE 1-905  
D | Coatomer subunit delta | COPD_MOUSE 1-511  
F M R | ADP-ribosylation factor 1 | ARF1_YEAST 1-181  
G K | Coatomer subunit gamma-1 | COPG1_MOUSE 1-874  
L Z | Coatomer subunit zeta-1 | COPZ1_MOUSE 1-177  
  

> select add #2

18970 atoms, 18952 bonds, 7 pseudobonds, 4746 residues, 2 models selected  

> select subtract #2

Nothing selected  

> select add #2

18970 atoms, 18952 bonds, 7 pseudobonds, 4746 residues, 2 models selected  

> volume #1 level 0.0087

> ui mousemode right "translate selected models"

[Repeated 1 time(s)]

> view matrix models #2,1,0,0,-37.882,0,1,0,64.414,0,0,1,202.79

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.52562,-0.43202,0.73286,-19.37,-0.17024,0.79062,0.58817,39.912,-0.83351,-0.43392,0.34202,421.68

> view matrix models
> #2,0.7,0.68406,-0.20508,-62.275,0.0068065,0.28077,0.95975,37.92,0.71411,-0.67322,0.19188,297.56

> view matrix models
> #2,0.28224,0.88452,-0.37142,-20.952,-0.65525,0.46053,0.5988,130.99,0.7007,0.074371,0.70957,150.66

> view matrix models
> #2,0.49213,0.75481,-0.43366,-21.427,-0.82839,0.25296,-0.49979,301.54,-0.26755,0.6052,0.74977,189.39

> view matrix models
> #2,0.36057,0.92393,-0.12783,-62.367,-0.57964,0.11459,-0.80677,326.12,-0.73076,0.365,0.57687,288.65

> view matrix models
> #2,-0.61475,0.27359,-0.73975,192.39,-0.35757,-0.93266,-0.047782,338.05,-0.70301,0.23514,0.67118,290.08

> view matrix models
> #2,-0.91301,0.40193,0.069771,116.36,-0.4071,-0.9087,-0.092394,345.81,0.026265,-0.11276,0.99328,214.04

> view matrix models
> #2,-0.88167,0.40879,0.2357,92.928,-0.40453,-0.91196,0.068457,327.32,0.24293,-0.034992,0.96941,183.81

> view matrix models
> #2,-0.5303,0.84267,0.093238,19.456,-0.82612,-0.53832,0.16656,317.99,0.19054,0.011299,0.98161,182.67

> ui mousemode right "translate selected models"

> view matrix models
> #2,-0.5303,0.84267,0.093238,263.37,-0.82612,-0.53832,0.16656,455.06,0.19054,0.011299,0.98161,199.63

> fitmap #1 #2

Missing required "in_map" argument  

> fitmap #2 inMap #1

Fit molecule 5nzr (#2) to map postprocess.mrc (#1) using 18970 atoms  
average map value = 0.01091, steps = 116  
shifted from previous position = 7.15  
rotated from previous position = 12 degrees  
atoms outside contour = 7834, contour level = 0.0087005  
  
Position of 5nzr (#2) relative to postprocess.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.53470562 0.84443643 -0.03189051 278.17154273  
-0.84484986 -0.53500265 -0.00093313 482.55400590  
-0.01784948 0.02644375 0.99949093 224.67222139  
Axis 0.01620349 -0.00831044 -0.99983418  
Axis point 273.19248819 162.79104531 0.00000000  
Rotation angle (degrees) 122.35128157  
Shift along axis -224.13785000  
  

> select subtract #2

Nothing selected  

> close #2

> open 3720

Fetching url http://files.rcsb.org/download/3720.cif failed:  
HTTP Error 404: Not Found  

> open emdb3720

'emdb3720' has no suffix  

> open 3720 fromDatabase emdb

Summary of feedback from opening 3720 fetched from emdb  
---  
note | Fetching compressed map 3720 from ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-3720/map/emd_3720.map.gz  
  
Opened emdb 3720 as #2, grid size 128,128,128, pixel 1.78, shown at level
0.226, step 1, values float32  

> volume #2 level 0.09618

> select add #2

2 models selected  

> ui mousemode right "translate selected models"

> view matrix models #2,1,0,0,223.78,0,1,0,-35.337,0,0,1,158.95

> view matrix models #2,1,0,0,225.18,0,1,0,9.8187,0,0,1,170.58

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.76316,0.27646,-0.58409,288.27,-0.32541,0.94531,0.022268,51.04,0.5583,0.17307,0.81138,108.15

> view matrix models
> #2,0.95657,0.056083,-0.28607,257.23,-0.28053,-0.089841,-0.95563,285,-0.079296,0.99438,-0.070206,187.24

> view matrix models
> #2,-0.25273,0.83078,0.49592,211.05,-0.38627,0.3833,-0.83897,226.83,-0.88708,-0.4036,0.22403,412.13

> view matrix models
> #2,-0.051655,0.96539,0.25564,200.28,-0.9833,-0.093889,0.15587,234.85,0.17448,-0.24332,0.95412,185.06

> view matrix models
> #2,0.02585,0.7816,-0.62325,317.1,-0.70553,-0.42742,-0.56528,327.98,-0.70821,0.45433,0.54039,251.79

> view matrix models
> #2,-0.58335,0.28587,0.76025,282.85,-0.81203,-0.1846,-0.55366,309.81,-0.017932,-0.94032,0.33982,362.91

> view matrix models
> #2,-0.98042,-0.17156,0.096691,461.36,-0.048228,-0.26686,-0.96253,280.32,0.19094,-0.94834,0.25336,350.12

> view matrix models
> #2,-0.92285,0.28368,-0.26051,442.55,-0.18618,-0.92069,-0.34304,301.1,-0.33716,-0.26807,0.90248,252.78

> view matrix models
> #2,-0.93117,0.30503,-0.1997,433.78,-0.29572,-0.95227,-0.07566,285.87,-0.21324,-0.011399,0.97693,199.12

> ui mousemode right "translate selected models"

> view matrix models
> #2,-0.93117,0.30503,-0.1997,397.2,-0.29572,-0.95227,-0.07566,498.67,-0.21324,-0.011399,0.97693,255.17

> fitmap #2 inMap #1

Fit map emdb 3720 in map postprocess.mrc using 114393 points  
correlation = 0.6691, correlation about mean = 0.05303, overlap = 91.28  
steps = 100, shift = 27.4, angle = 14.2 degrees  
  
Position of emdb 3720 (#2) relative to postprocess.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.90384624 0.23353058 -0.35850446 426.60125938  
-0.28809092 -0.95167357 0.10640039 474.89273455  
-0.31633147 0.19945147 0.92744462 222.06398803  
Axis 0.17506212 -0.07934236 -0.98135521  
Axis point 264.85851560 196.87446978 0.00000000  
Rotation angle (degrees) 164.58753247  
Shift along axis -180.92104267  
  

> volume #2 level 0.136

> select clear

> ui mousemode right "translate selected models"

> select #2

2 models selected  

> view matrix models
> #2,-0.90385,0.23353,-0.3585,425.99,-0.28809,-0.95167,0.1064,430.09,-0.31633,0.19945,0.92744,249.04

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.93137,0.093427,-0.35189,445.01,-0.15388,-0.97696,0.14789,412.92,-0.32997,0.19189,0.92428,251.87

> view matrix models
> #2,-0.3246,0.87931,-0.3485,282.32,-0.83775,-0.43832,-0.32566,483.27,-0.43911,0.18625,0.87892,270.36

> view matrix models
> #2,-0.71374,0.63847,-0.28798,347.66,-0.6764,-0.73504,0.046791,455.31,-0.18181,0.22819,0.95649,226.9

> view matrix models
> #2,-0.30923,0.92464,-0.22232,259.88,-0.94209,-0.32976,-0.06112,450.03,-0.12982,0.19054,0.97306,223.52

> view matrix models
> #2,-0.79733,0.57614,-0.1798,351.42,-0.59927,-0.79112,0.1225,444.11,-0.071665,0.20542,0.97605,214.81

> view matrix models
> #2,-0.58975,0.77816,-0.21604,308.27,-0.80056,-0.59852,0.029561,455.12,-0.1063,0.19039,0.97594,220.53

> view matrix models
> #2,-0.86768,0.45921,-0.1904,374.6,-0.48592,-0.8643,0.12984,439.16,-0.10494,0.20518,0.97308,218.96

> view matrix models
> #2,-0.74473,0.62297,-0.23933,347.11,-0.64295,-0.76587,0.0071296,460.02,-0.17885,0.15918,0.97091,233.05

> ui mousemode right "translate selected models"

> view matrix models
> #2,-0.74473,0.62297,-0.23933,342.91,-0.64295,-0.76587,0.0071296,479.3,-0.17885,0.15918,0.97091,239.3

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.79959,0.57272,-0.1807,347.99,-0.59537,-0.79538,0.11357,464.54,-0.078687,0.19839,0.97696,222.58

> view matrix models
> #2,-0.67006,0.71251,-0.20821,320.02,-0.73726,-0.67144,0.074925,470.46,-0.086418,0.20371,0.97521,223.03

> view matrix models
> #2,-0.91364,0.36722,-0.17437,384.62,-0.37083,-0.92862,-0.012671,470.39,-0.16657,0.053082,0.9846,248.92

> view matrix models
> #2,-0.75132,0.63901,-0.16488,332.72,-0.64038,-0.76631,-0.051852,486.21,-0.15948,0.066629,0.98495,246.46

> view matrix models
> #2,-0.77803,0.62815,-0.010172,318.27,-0.62601,-0.77654,-0.071466,488.18,-0.052791,-0.049235,0.99739,246.73

> view matrix models
> #2,-0.65763,0.75315,0.017269,286.44,-0.75149,-0.65422,-0.085182,489.42,-0.052856,-0.068995,0.99622,249.24

> ui mousemode right "translate selected models"

> view matrix models
> #2,-0.65763,0.75315,0.017269,300.45,-0.75149,-0.65422,-0.085182,488.98,-0.052856,-0.068995,0.99622,232.81

> view matrix models
> #2,-0.65763,0.75315,0.017269,297.73,-0.75149,-0.65422,-0.085182,497.05,-0.052856,-0.068995,0.99622,233.9

> fitmap #2 inMap #1

Fit map emdb 3720 in map postprocess.mrc using 73589 points  
correlation = 0.8646, correlation about mean = 0.3064, overlap = 147.1  
steps = 96, shift = 6.01, angle = 10.4 degrees  
  
Position of emdb 3720 (#2) relative to postprocess.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.53666347 0.84316340 -0.03267727 278.66671757  
-0.84365691 -0.53687633 0.00261266 482.08926923  
-0.01534075 0.02897052 0.99946254 223.65484556  
Axis 0.01562303 -0.01027584 -0.99982515  
Axis point 272.76166410 162.45158774 0.00000000  
Rotation angle (degrees) 122.48227196  
Shift along axis -224.21599001  
  

> select clear

> volume #2 level 0.1256

> volume #1 level 0.007442

> volume #2 level 0.07023

> volume #2 level 0.1775

> volume #1 level 0.005345

> volume #1 level 0.009819

> ui tool show AlphaFold

> alphafold match
> MLTKFETKSARVKGLSFHPKRPWILTSLHNGVIQLWDYRMCTLIDKFDEHDGPVRGIDFHKQQPLFVSGGDDYKIKVWNYKLRRCLFTLLGHLDYIRTTFFHHEYPWILSASDDQTIRVWNWQSRTCVCVLTGHNHYVMCAQFHPSEDLVVSASLDQTVRVWDISGLRKKNLSPGAVESDVRGITGVDLFGTTDAVVKHVLEGHDRGVNWAAFHPTMPLIVSGADDRQVKIWRMNESKAWEVDTCRGHYNNVSCAVFHPRQELILSNSEDKSIRVWDMSKRTGVQTFRRDHDRFWVLAAHPNLNLFAAGHDGGMIVFKLERERPAYAVHGNMLHYVKDRFLRQLDFNSSKDVAVMQLRSGSKFPVFNMSYNPAENAVLLCTRASNLENSTYDLYTIPKDADSQNPDAPEGKRSSGLTAVWVARNRFAVLDRMHSLLIKNLKNEITKKIQVPNCDEIFYAGTGNLLLRDADSITLFDVQQKRTLASVKISKVKYVIWSADMSHVALLAKHEHSCPLPLTAIVICNRKLDALCNIHENIRVKSGAWDESGVFIYTTSNHIKYAVTTGDHGIIRTLDLPIYVTRVKGNNVYCLDRECRPRVLTIDPTEFKFKLALINRKYDEVLHMVRNAKLVGQSIIAYLQKKGYPEVALHFVKDEKTRFSLALECGNIEIALEAAKALDDKNCWEKLGEVALLQGNHQIVEMCYQRTKNFDKLSFLYLITGNLEKLRKMMKIAEIRKDMSGHYQNALYLGDVSERVRILKNCGQKSLAYLSAATHGLDEEAESLKETFDPEKETIPDIDPNAKLLQPPAPIMPLDTNWPLLTVSKGFFEGSIASKGKGGALAADIDIDTVGTEGWGEDAELQLDEDGFVEAPEGLGEDVLGKGQEEGGGWDVEEDLELPPELDVPSGVSGSAEDGFFVPPTKGTSPTQIWCNNSQLPVDHILAGSFETAMRLLHDQVGVIQFGPYKQLFLQTYARGRTTYQALPCLPSMYSYPNRNWKDAGLKNGVPAVGLKLNDLIQRLQLCYQLTTVGKFEEAVEKFRSILLSVPLLVVDNKQEIAEAQQLITICREYIVGLCMEIERKKLPKETLDQQKRICEMAAYFTHSNLQPVHMILVLRTALNLFFKLKNFKTAATFARRLLELGPKPEVAQQTRKILSACEKNPTDACQLNYDMHNPFDICAASYRPIYRGKPVEKCPLSGACYSPEFKGQICRVTTVTEIGKDVIGLRISPLQFR

AlphaFold sequence search web service failed (404) "Not Found"  
  
https://www.rbvi.ucsf.edu/chimerax/cgi-bin/alphafold_search3_cgi.py  

No AlphaFold model with similar sequence for 1 sequences  

Opened 0 AlphaFold model  
Fetching compressed F8WHL2 UniProt info from
https://www.uniprot.org/uniprot/F8WHL2.xml  

> alphafold match F8WHL2

Fetching compressed AlphaFold F8WHL2 from
https://alphafold.ebi.ac.uk/files/AF-F8WHL2-F1-model_v4.cif  
1 AlphaFold model found using UniProt identifier: F8WHL2 (UniProt F8WHL2)  
Sequence Similarity  
---  
AlphaFold Model| Query Sequence| Identity %| Coverage %  
F8WHL2 | F8WHL2 | 100.0 | 100.0    
Opened 1 AlphaFold model  
> select add #39810 atoms, 10032 bonds, 1233 residues, 1 model selected  
> ui mousemode right "translate selected models"> view matrix models
> #3,1,0,0,303.28,0,1,0,304.96,0,0,1,11.166> view matrix models
> #3,1,0,0,324.74,0,1,0,283.74,0,0,1,319.33> view matrix models
> #3,1,0,0,209.64,0,1,0,387.4,0,0,1,429.36> ui mousemode right "translate
> selected models"[Repeated 1 time(s)]> view matrix models
> #3,1,0,0,222.42,0,1,0,405.56,0,0,1,420.95> ui mousemode right "rotate
> selected models"> view matrix models
> #3,0.32639,-0.23212,-0.91629,218.55,-0.93865,-0.1938,-0.28526,399.27,-0.11137,0.95319,-0.28113,421.32>
> view matrix models
> #3,-0.60439,0.30546,-0.7358,196.12,-0.51637,-0.85352,0.069815,409.29,-0.60669,0.42214,0.67359,409.09>
> view matrix models
> #3,-0.96723,0.14467,-0.20868,186.74,-0.15733,-0.9865,0.045344,417.05,-0.1993,0.076689,0.97693,416.89>
> view matrix models
> #3,-0.9522,0.23336,-0.19714,186.28,-0.23562,-0.97177,-0.01224,415.93,-0.19443,0.034795,0.9803,417.26>
> view matrix models
> #3,-0.97348,-0.079573,-0.21447,188.33,0.038436,-0.98112,0.18956,419.54,-0.2255,0.17629,0.95816,415.81>
> view matrix models
> #3,-0.22693,-0.37305,-0.89963,209.3,0.58137,0.68921,-0.43244,421.75,0.78135,-0.62115,0.060477,446.87>
> view matrix models
> #3,0.21155,-0.58135,-0.78567,218.06,0.9196,-0.15386,0.36146,428.33,-0.33102,-0.79897,0.50207,424.47>
> view matrix models
> #3,-0.12158,-0.084379,-0.98899,209.76,-0.25211,-0.96108,0.11299,414.62,-0.96003,0.26307,0.095579,408.05>
> view matrix models
> #3,0.84817,0.13727,0.51163,214.82,-0.089352,-0.91493,0.3936,415.19,0.52213,-0.37955,-0.76375,446.42>
> view matrix models
> #3,0.32531,0.49583,-0.80518,212.31,0.69626,0.45057,0.55876,418.28,0.63984,-0.74239,-0.19865,447.08>
> view matrix models
> #3,0.4134,0.56919,-0.71072,212.69,0.6828,0.32261,0.65552,418.27,0.6024,-0.75627,-0.25528,446.92>
> view matrix models
> #3,-0.13517,-0.24305,-0.96055,210.47,0.45069,0.84827,-0.27806,417.02,0.88239,-0.4705,-0.0051158,448.09>
> view matrix models
> #3,-0.8766,0.28966,-0.38428,188.63,0.43236,0.82468,-0.36465,417.5,0.21128,-0.4858,-0.84815,442.12>
> view matrix models
> #3,-0.75554,0.47772,0.44827,183.3,-0.087054,0.60499,-0.79146,412.75,-0.6493,-0.637,-0.4155,424.22>
> view matrix models
> #3,-0.17993,0.68527,0.70571,190.43,-0.77714,0.3408,-0.52907,400.08,-0.60306,-0.64363,0.47123,418.55>
> view matrix models
> #3,0.38482,0.64397,0.66123,201.45,-0.54337,0.73715,-0.40169,400.49,-0.7461,-0.20471,0.63358,411.47>
> ui mousemode right "translate selected models"> view matrix models
> #3,0.38482,0.64397,0.66123,209.11,-0.54337,0.73715,-0.40169,352.77,-0.7461,-0.20471,0.63358,346.78>
> view matrix models
> #3,0.38482,0.64397,0.66123,272.84,-0.54337,0.73715,-0.40169,341.51,-0.7461,-0.20471,0.63358,359.04>
> view matrix models
> #3,0.38482,0.64397,0.66123,275.5,-0.54337,0.73715,-0.40169,343.71,-0.7461,-0.20471,0.63358,340.28>
> volume #1 level 0.009245> volume #1 transparency .5> view matrix models
> #3,0.38482,0.64397,0.66123,277.74,-0.54337,0.73715,-0.40169,343.45,-0.7461,-0.20471,0.63358,342.76>
> view matrix models
> #3,0.38482,0.64397,0.66123,274.73,-0.54337,0.73715,-0.40169,335.94,-0.7461,-0.20471,0.63358,326.51>
> view matrix models
> #3,0.38482,0.64397,0.66123,273,-0.54337,0.73715,-0.40169,338.08,-0.7461,-0.20471,0.63358,327.8>
> ui mousemode right "rotate selected models"> view matrix models
> #3,0.2206,0.77424,0.5932,269.52,-0.66437,0.56456,-0.48978,337.79,-0.7141,-0.28606,0.63893,328.95>
> view matrix models
> #3,0.46242,0.64706,0.60621,274.81,-0.30974,0.75851,-0.57335,343.48,-0.8308,0.077362,0.55116,324.76>
> view matrix models
> #3,0.1596,0.83662,0.52402,268.45,-0.68532,0.47596,-0.55117,338.51,-0.71054,-0.27116,0.64932,328.83>
> view matrix models
> #3,0.48141,0.60575,0.63349,275.26,-0.24765,0.78731,-0.56464,344.35,-0.84078,0.11494,0.52903,324.46>
> view matrix models
> #3,0.22271,0.44453,0.86764,269.97,-0.69434,0.69705,-0.1789,333.95,-0.68431,-0.56259,0.4639,332.84>
> view matrix models
> #3,0.25107,0.90985,0.33037,271.02,-0.74263,0.39997,-0.53714,337.92,-0.62085,-0.11048,0.7761,328.35>
> view matrix models
> #3,0.60545,0.57661,0.54859,278.39,-0.6801,0.73285,-0.01969,332.77,-0.41339,-0.36117,0.83586,333.57>
> view matrix models
> #3,0.5141,0.75687,0.40355,276.45,-0.8383,0.54295,0.049627,330.76,-0.18154,-0.3638,0.91361,337.28>
> view matrix models
> #3,0.68948,0.49522,0.52856,280.68,-0.57485,0.81809,-0.016621,334.05,-0.44064,-0.29238,0.84873,332.47>
> view matrix models
> #3,0.76356,0.52587,0.37475,282.96,-0.51319,0.84643,-0.14212,335.9,-0.39194,-0.083795,0.91617,331.32>
> view matrix models
> #3,0.20308,0.96515,0.16504,270.96,-0.89543,0.25126,-0.36754,334.96,-0.3962,-0.073139,0.91525,331.17>
> select clear> volume #1 level 0.007668> volume #1 level 0.008528> select add
> #39810 atoms, 10032 bonds, 1233 residues, 1 model selected  
> select subtract #3Nothing selected  
> select add #39810 atoms, 10032 bonds, 1233 residues, 1 model selected  
> view matrix models
> #3,0.24506,0.95994,0.13585,271.98,-0.89492,0.27787,-0.34914,334.63,-0.3729,-0.036017,0.92717,331.23>
> view matrix models
> #3,0.1572,0.79158,0.5905,268.25,-0.72926,0.49624,-0.47109,336.96,-0.66593,-0.35657,0.65528,330.24>
> view matrix models
> #3,0.28322,0.87764,0.3867,271.44,-0.81992,0.43074,-0.37709,335.08,-0.49751,-0.21027,0.84159,330.87>
> view matrix models
> #3,-0.017812,0.84232,0.53868,265.04,-0.76613,0.33468,-0.54867,338.06,-0.64244,-0.42247,0.63937,331.27>
> view matrix models
> #3,-0.0031655,0.85903,0.51192,265.38,-0.72124,0.35264,-0.5962,339.1,-0.69268,-0.37111,0.61845,330.13>
> view matrix models
> #3,-0.27124,0.8759,0.39904,261.17,-0.68704,0.11416,-0.7176,342.39,-0.67409,-0.4688,0.57081,331.54>
> view matrix models
> #3,0.13566,0.93162,0.33715,268.69,-0.77565,0.31159,-0.54889,338.05,-0.61641,-0.18705,0.76489,329.08>
> select clear> select /A:7789 atoms, 8 bonds, 1 residue, 1 model selected  
> select clear> select /A:19910 atoms, 10 bonds, 1 residue, 1 model selected  
> select add /A:78015 atoms, 14 bonds, 2 residues, 1 model selected  
> select up111 atoms, 110 bonds, 14 residues, 1 model selected  
> select up9810 atoms, 10032 bonds, 1233 residues, 1 model selected  
> select down111 atoms, 110 bonds, 14 residues, 1 model selected  
> ui mousemode right "translate selected models"> view matrix models
> #3,0.13566,0.93162,0.33715,267.62,-0.77565,0.31159,-0.54889,339.05,-0.61641,-0.18705,0.76489,326.53>
> view matrix models
> #3,0.13566,0.93162,0.33715,263.83,-0.77565,0.31159,-0.54889,331.53,-0.61641,-0.18705,0.76489,323.99>
> view matrix models
> #3,0.13566,0.93162,0.33715,264.39,-0.77565,0.31159,-0.54889,331.73,-0.61641,-0.18705,0.76489,323.13>
> view matrix models
> #3,0.13566,0.93162,0.33715,264.12,-0.77565,0.31159,-0.54889,329.56,-0.61641,-0.18705,0.76489,322.14>
> ui mousemode right "rotate selected models"> view matrix models
> #3,0.27221,0.90106,0.33763,266.85,-0.73533,0.42111,-0.531,329.36,-0.62064,-0.10372,0.77721,321.36>
> view matrix models
> #3,0.2643,0.91061,0.31769,266.78,-0.70061,0.40766,-0.58563,330.5,-0.66279,-0.0678,0.74573,320.55>
> ui mousemode right "translate selected models"> view matrix models
> #3,0.2643,0.91061,0.31769,268.7,-0.70061,0.40766,-0.58563,332.37,-0.66279,-0.0678,0.74573,325.34>
> view matrix models
> #3,0.2643,0.91061,0.31769,268.14,-0.70061,0.40766,-0.58563,333.45,-0.66279,-0.0678,0.74573,326.51>
> ui mousemode right "rotate selected models"> view matrix models
> #3,0.41107,0.83158,0.37349,271.01,-0.59062,0.55504,-0.58574,334.38,-0.6944,0.02019,0.71931,325.47>
> ui mousemode right "translate selected models"> view matrix models
> #3,0.41107,0.83158,0.37349,268.91,-0.59062,0.55504,-0.58574,338.04,-0.6944,0.02019,0.71931,328.38>
> view matrix models
> #3,0.41107,0.83158,0.37349,266.29,-0.59062,0.55504,-0.58574,340.47,-0.6944,0.02019,0.71931,325.69>
> view matrix models
> #3,0.41107,0.83158,0.37349,266.62,-0.59062,0.55504,-0.58574,340.35,-0.6944,0.02019,0.71931,326.17>
> view matrix models
> #3,0.41107,0.83158,0.37349,266.32,-0.59062,0.55504,-0.58574,341.97,-0.6944,0.02019,0.71931,326.79>
> ui mousemode right "rotate selected models"> view matrix models
> #3,0.57049,0.67618,0.46618,269.71,-0.47052,0.73431,-0.4893,342.13,-0.67317,0.05979,0.73706,326.76>
> ui mousemode right "translate selected models"> view matrix models
> #3,0.57049,0.67618,0.46618,257.51,-0.47052,0.73431,-0.4893,347.5,-0.67317,0.05979,0.73706,322.97>
[deleted to fit within ticket limits]

> color sel betapv3

> show #42 models

> select add #42

6695 atoms, 6846 bonds, 838 residues, 2 models selected  

> color sel betapv3

> select subtract #42

4686 atoms, 4798 bonds, 586 residues, 1 model selected  

> select subtract #41

Nothing selected  

> hide #41 models

> hide #42 models

> show #!43 models

> show #!44 models

> show #!45 models

> select add #45

2879 atoms, 2928 bonds, 1 pseudobond, 362 residues, 2 models selected  

> select add #44

5367 atoms, 5446 bonds, 2 pseudobonds, 675 residues, 4 models selected  

> select add #43

7239 atoms, 7350 bonds, 2 pseudobonds, 918 residues, 5 models selected  

> color sel betav3

> select subtract #45

4360 atoms, 4422 bonds, 1 pseudobond, 556 residues, 3 models selected  

> select subtract #44

1872 atoms, 1904 bonds, 243 residues, 1 model selected  

> select subtract #43

Nothing selected  

> hide #!45 models

> show #!45 models

> hide #!44 models

> hide #!43 models

> hide #!45 models

> show #!46 models

> color sel deltav3

> select add #46

1681 atoms, 1700 bonds, 1 pseudobond, 209 residues, 2 models selected  

> color sel deltav3

> select subtract #46

Nothing selected  

> hide #!46 models

> show #47 models

> show #48 models

> show #!49 models

> color sel gammav3

> select add #47

1163 atoms, 1177 bonds, 149 residues, 1 model selected  

> select add #48

3496 atoms, 3549 bonds, 448 residues, 2 models selected  

> select add #49

4560 atoms, 4629 bonds, 1 pseudobond, 583 residues, 4 models selected  

> color sel gammav3

> select subtract #49

3496 atoms, 3549 bonds, 448 residues, 2 models selected  

> select subtract #48

1163 atoms, 1177 bonds, 149 residues, 1 model selected  

> select subtract #47

Nothing selected  

> hide #47 models

> hide #48 models

> hide #!49 models

> show #50 models

> color sel zetav3

> select add #50

1200 atoms, 1218 bonds, 150 residues, 1 model selected  

> color sel zetav3

> select subtract #50

Nothing selected  

> hide #50 models

> show #51 models

> show #52 models

> show #53 models

> select add #53

1350 atoms, 1373 bonds, 167 residues, 1 model selected  

> select add #52

2700 atoms, 2746 bonds, 334 residues, 2 models selected  

> select add #51

4050 atoms, 4119 bonds, 501 residues, 3 models selected  

> color sel arf1v3

> select subtract #51

2700 atoms, 2746 bonds, 334 residues, 2 models selected  

> select subtract #52

1350 atoms, 1373 bonds, 167 residues, 1 model selected  

> select subtract #53

Nothing selected  

> hide #53 models

> hide #52 models

> hide #51 models

> show #!54 models

> show #55 models

> color sel label_purple_v3

> select add #54

229 atoms, 228 bonds, 31 residues, 1 model selected  

> select add #55

2200 atoms, 2230 bonds, 275 residues, 2 models selected  

> color sel label_purple_v3

> select subtract #55

229 atoms, 228 bonds, 31 residues, 1 model selected  

> select subtract #54

Nothing selected  

> hide #!54 models

> hide #55 models

> show #!57 models

> color #57/a alphav3

> color #57/b betav3

> color #57/c betapv3

> color #57/d deltav3

> color #57/e gammav3

> color #57/f gammav3

> color #57/f arf1v3

> color #57/g arf1v3

> color #57/g gammav3

> color #57/h arf1v3

> color #57/i arf1v3

> color #57/j arf1v3

> color #57/k arf1v3

> color #57/k gammav3

> color #57/l zetav3

> color #57/m zetav3

> color #57/m arf1v3

> color #57/n arf1v3

> color #57/o arf1v3

> color #57/p arf1v3

> color #57/q arf1v3

> color #57/r arf1v3

> color #57/a zetav3

> undo

> color #57/z zetav3

> hide #!57 models

> show #!61 models

> color #58/d alphav3

> color #61/d alphav3

> color #61/e alphav3

> color #61/f betapv3

> color #61/g betapv3

> color #61/h betav3

> color #61/i betav3

> color #61/j betav3

> color #61/k deltav3

> color #61/l gammav3

> color #61/m gammav3

> color #61/n gammav3

> color #61/o zetav3

> color #61/p arf1v3

> color #61/q arf1v3

> color #61/q label_purple_v3

> color #61/a label_purple_v3

> color #61/b arf1v3

> color #61/c arf1v3

> show #!63 models

> hide #!63 models

> show #!63 models

> hide #!63 models

> ui tool show "Color Zone"

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

[Repeated 1 time(s)]

> color zone #63 near #61 distance 8.31

> show #!63 models

> hide #!63 models

> show #!63 models

> hide #!63 models

> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Figures/2024_Nov/Figure1/20241114_v3.cxs"

> show #!1 models

> color #1 #d6d6d680 models

> color #1 #d6d6d669 models

> view view1

[Repeated 4 time(s)]

> view view2

> volume #1 level 0.005

> 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

  

> cd "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Figures/2024_Nov/Figure1"

Current working directory is: /Users/becca/Desktop/Postdoc/Grants and paper
drafts/Golph3 paper/Figures/2024_Nov/Figure1  

> volume #1 level 0.008

> save overview_wout_membrane_v3.png supersample 3 transparentBackground true

> view view2

[Repeated 1 time(s)]

> volume #1 level 0.005

> save overview_w_membrane_v2.png supersample 3 transparentBackground true

> volume #1 level 0.008

> save overview_w_membrane_v3.png supersample 3 transparentBackground true

> view view3

[Repeated 1 time(s)]

> save zoomed_view_with_no_bkgd_v2.png supersample 3 transparentBackground
> true

> view view4

> save zoomed_view_with_bkgd_v2.png supersample 3 transparentBackground true

> view view5

> save zoomed_view_with_full_bkgd_v2.png supersample 3 transparentBackground
> true

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Figures/2024_Nov/20241122_chimera_for_figures.cxs"

——— End of log from Fri Nov 22 15:12:25 2024 ———

opened ChimeraX session  

> view view5

> view

> view view5

> ui tool show "Side View"

> view name view6

> view view6

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> view name view7

> view view5

> hide #!1 models

> show #!43 models

> hide #!43 models

> hide #!61 models

> show #!43 models

> show #!40 models

> hide #!43 models

> hide #!40 models

> show #!61 models

> show #!1 models

> hide #!1 models

> show #!1 models

> view view5

> view view6

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> cd "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Figures/2024_Nov/Figure1"

Current working directory is: /Users/becca/Desktop/Postdoc/Grants and paper
drafts/Golph3 paper/Figures/2024_Nov/Figure1  

> save zoomed_view_GOLPH3_alpha.png supersample 3 transparentBackground true

> hide #!1 models

> ui mousemode right select

> select #61/D:136

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

> select #61/D:135

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

> select #61/D:136

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

> select clear

> select #61/D:135

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

> style sel stick

Changed 8 atom styles  

> show sel atoms

> color sel byhetero

> select #61/D:136

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

> show sel atoms

> color sel byhetero

> select #61/D:137

12 atoms, 12 bonds, 1 residue, 1 model selected  

> show sel atoms

> style sel stick

Changed 12 atom styles  

> color sel byhetero

> select clear

> select #61/D:94

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

> show sel atoms

> style sel stick

Changed 8 atom styles  

> color sel byhetero

> select #61/Q:56

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

> show sel atoms

> style sel stick

Changed 9 atom styles  

> color sel byhetero

> select #61/D:290

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

> color sel byhetero

> show sel atoms

> style sel stick

Changed 8 atom styles  

> select #61/D:292

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

> select #61/D:291

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

> select clear

> select #61/D:292

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

> show sel atoms

> style sel stick

Changed 8 atom styles  

> color sel byhetero

> select #61/Q:200

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

> show sel atoms

> style sel stick

Changed 7 atom styles  

> color sel byhetero

> select #61/Q:191

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

> style sel stick

Changed 9 atom styles  

> color sel byhetero

> show sel atoms

> select #61/Q:189

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

> show sel atoms

> style sel stick

Changed 7 atom styles  

> color sel byhetero

> select #61/Q:182

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

> select #61/Q:183

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

> color sel byhetero

> show sel atoms

> style sel stick

Changed 9 atom styles  

> select #61/Q:167

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

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> select #61/Q:179

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

> show sel atoms

> style sel stick

Changed 9 atom styles  

> color sel byhetero

> select #61/Q:176

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

> select #61/Q:175

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

> color sel byhetero

> show sel atoms

> style sel stick

Changed 9 atom styles  

> select clear

> view view6

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> select clear

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> select clear

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

Drag select of 1 residues  

> select #61/D:243

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

> select clear

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> volume #1 level 0.005

> hide #!1 models

> volume #1 level 0.008

> select clear

> select #61/Q:183

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

> hide sel atoms

> select clear

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> select clear

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> select clear

> select #61/D:135

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

> view name view8

> select clear

> select #61/D:135

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

> hide sel atoms

> view view8

> select clear

> select #61/D:211

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

> select clear

> view name view9

> view view9

> view view8

> show #!1 models

> view name view10

> save zoomed_view_GOLPH3_alpha_residues.png supersample 3
> transparentBackground true

> volume #1 level 0.005

> volume #1 level 0.006

> save zoomed_view_GOLPH3_alpha_G-K56_A-290-292.png supersample 3
> transparentBackground true

> save zoomed_view_GOLPH3_alpha_G-K56_A-290-292_v2.png supersample 3
> transparentBackground true

> view view8

> view view9

> hide #!1 models

> select #61/Q:175

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

> hide sel atoms

> select clear

> view view9

> show #!1 models

> volume #1 level 0.0065

> volume #1 level 0.006

> volume #1 level 0.007

> volume #1 level 0.006

> save zoomed_view_GOLPH3_alpha_G-K56_A-290-292_v3.png supersample 3
> transparentBackground true

> volume #1 level 0.008

> hide #!1 models

> select #61/D:94@CB

1 atom, 1 residue, 1 model selected  

> select #61/D:94@CB

1 atom, 1 residue, 1 model selected  

> select #61/D:94

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

> select #61/D:93

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

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> select #61/D:94

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

> select #61/D:94@CB

1 atom, 1 residue, 1 model selected  

> select #61/Q:179

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

> hide sel atoms

> select clear

> select #61/D:94

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

> hide sel atoms

> select clear

[Repeated 1 time(s)]

> show #!1 models

> select #1

4 models selected  

> select subtract #1

Nothing selected  

> hide #!1 models

> select clear

> select #61/Q:200

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

> show sel atoms

> style sel stick

Changed 7 atom styles  

> style sel stick

Changed 7 atom styles  

> select #61/Q:200

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

> select #61/Q:191

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

> show sel atoms

> select #61/Q:189

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

> select #61/Q:191

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

> select #61/Q:200

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

> show #!1 models

> select clear

[Repeated 1 time(s)]

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

[Repeated 3 time(s)]

> volume #63 color #ffffff00

> volume #1 color #ebebeb

> volume #1 color #ebebeb00

> volume #1 color #ebebeb22

> volume #1 color #ebebeb23

> volume #1 color #ebebeb32

> volume #1 color #ebebeb40

> volume #1 color white

> volume #1 color #ffffff00

> lighting simple

> volume #1 color #ffffff4d

> ui tool show "Side View"

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

[Repeated 1 time(s)]

> hide #!1 models

> show #!1 models

> hide #!1 models

> select #61/D:135

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

> show sel atoms

> style sel stick

Changed 8 atom styles  

> style sel stick

Changed 8 atom styles  

> hide sel atoms

> show #!1 models

> save zoomed_view_GOLPH3_alpha_G-T189_K191_T200_A-136-137.png supersample 3
> transparentBackground true

> select clear

> save zoomed_view_GOLPH3_alpha_G-T189_K191_T200_A-136-137.png supersample 3
> transparentBackground true

> view view10

> volume #1 level 0.006

> view view5

> save zoomed_view_GOLPH3_alpha_G-K56_A-290-292_v4.png supersample 3
> transparentBackground true

> view view5

> view name view11

[Repeated 1 time(s)]

> save zoomed_view_GOLPH3_alpha_G-T189_K191_T200_A-136-137_v2.png supersample
> 3 transparentBackground true

> hide #!1 models

> select #61/Q:189

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

> hide sel atoms

> select #61/Q:191

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

> hide sel atoms

Drag select of 1 residues  

> hide sel atoms

> select #61/D:136@CA

1 atom, 1 residue, 1 model selected  

> select #61/D:136

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

> hide sel atoms

> select #61/D:137

12 atoms, 12 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select #61/Q:200

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

> hide sel atoms

> view view11

> select #61/Q:199

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

> select #61/Q:179

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

> show sel atoms

> select #61/D:205

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

> select #61/D:94

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

> show sel atoms

> select clear

> show #!1 models

> volume #1 level 0.008

> lighting simple

> lighting soft

> lighting simple

> lighting soft

> lighting full

> lighting soft

> lighting simple

> save zoomed_view_GOLPH3_alpha_G-K179_A-94.png supersample 3
> transparentBackground true

> view name view12

> hide #!1 models

> view view5

> select #61/Q:191

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

> show sel atoms

> select #61/Q:190

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

> select #61/Q:189

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

> show sel atoms

> select #61/Q:192

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

> select #61/Q:191

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

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> select #61/Q:199

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

> select #61/Q:198

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

> select #61/Q:200

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

> show sel atoms

> select #61/D:137

12 atoms, 12 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #61/D:136

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

> show sel atoms

> view view5

> view view6

> view view7

> view view8

> show #!1 models

> volume #1 level 0.006

> volume #1 level 0.007

> volume #1 level 0.0067

> volume #1 level 0.0065

> select clear

> view view5

> view view11

> volume #1 level 0.008

> volume #1 level 0.008491

> volume #1 level 0.008

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/Files from csparc/J3101/J3101_alignments_20241125.py"

Failed opening file /Users/becca/Desktop/Postdoc/COPI notebooks and
resources/Processing/Files from csparc/J3101/J3101_alignments_20241125.py:  
ChimeraX cannot open a regular Chimera session. An exporter from Chimera to  
ChimeraX is available in the latest Chimera release. Use its File->Export
Scene  
menu item, and change the resulting dialog's "File Type" to ChimeraX.  

> show #!49 models

> hide #!49 models

> view view1

> show #!49 models

> hide #!49 models

> show #48 models

> hide #48 models

> show #!56 models

> hide #!56 models

> show #!57 models

> hide #!57 models

> show #39 models

> hide #39 models

> show #39 models

> hide #!61 models

> show #38 models

> hide #39 models

> hide #38 models

> show #!61 models

> view view1

> volume #1 level 0.005

> hide #!1 models

Drag select of 57 atoms, 463 residues, 1 pseudobonds, 49 bonds  

> hide sel atoms

> select clear

> view view1

> show #!1 models

> view view2

[Repeated 1 time(s)]

> view view3

[Repeated 1 time(s)]

> view name view12

> hide #!1 models

> select #61/Q:81

14 atoms, 15 bonds, 1 residue, 1 model selected  

> show sel atoms

> style sel stick

Changed 14 atom styles  

> color sel byhetero

> select #61/Q:90

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

> show sel atoms

> style sel stick

Changed 11 atom styles  

> color sel byhetero

> select #61/Q:171

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

> color sel byhetero

> show sel atoms

> style sel stick

Changed 11 atom styles  

> select #61/Q:174

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

> show sel atoms

> style sel stick

Changed 11 atom styles  

> color sel byhetero

> select clear

> select #61/Q:172

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

> show sel atoms

> show sel cartoons

> style sel stick

Changed 8 atom styles  

> color sel byhetero

> view view12

> select #61/Q:81

14 atoms, 15 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select clear

> view view12

> show #!1 models

> cd "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Figures/2024_Nov/Figure 2"

Current working directory is: /Users/becca/Desktop/Postdoc/Grants and paper
drafts/Golph3 paper/Figures/2024_Nov/Figure 2  

> save zoomed_view_GOLPH3_membrane_PI4P_site_sticks_v1.png supersample 3
> transparentBackground true

> volume #1 level 0.008

> view view12

> volume #1 level 0.005

> volume #1 level 0.008

> hide #!61 models

> show #55 models

> hide #!1 models

> show #!61 models

> select #55/A:171

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

> show sel atoms

> style sel stick

Changed 11 atom styles  

> color sel byhetero

> select #55/A:175

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

> select #55/A:175

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

> select #55/A:174

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

> show sel atoms

> style sel stick

Changed 11 atom styles  

> color sel byhetero

> select #61/Q:173

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

> select #55/A:173

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

> select #55/A:172

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

> select #55/A:172

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

> select #61/Q:172

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

> show sel atoms

> style sel stick

Changed 8 atom styles  

> select add #61

34068 atoms, 34686 bonds, 4 pseudobonds, 4274 residues, 2 models selected  

> select subtract #61

Nothing selected  

> select add #61

34068 atoms, 34686 bonds, 4 pseudobonds, 4274 residues, 2 models selected  

> select subtract #61

Nothing selected  

> hide #!61 models

> select #55/A:172

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

> show sel atoms

> style sel stick

Changed 8 atom styles  

> color sel byhetero

> select add #55

1971 atoms, 2002 bonds, 244 residues, 1 model selected  

> show #!61 models

> select #61/Q:90

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

> select add #61

34068 atoms, 34686 bonds, 4 pseudobonds, 4274 residues, 2 models selected  

> hide #!61 models

> select #55/A:90

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

> show sel atoms

> style sel stick

Changed 11 atom styles  

> color sel byhetero

> select add #55

1971 atoms, 2002 bonds, 244 residues, 1 model selected  

> select subtract #55

Nothing selected  

> hide #55 models

> select add #61

34068 atoms, 34686 bonds, 4 pseudobonds, 4274 residues, 2 models selected  

> show #!61 models

> hide sel atoms

> select subtract #61

Nothing selected  

> hide #!61 models

> show #!61 models

> show #!1 models

> show #55 models

> view view12

> volume #1 level 0.005

> hide #55 models

> save zoomed_view_GOLPH3_membrane_PI4P_site_v2.png supersample 3
> transparentBackground true

> show #55 models

> volume #1 level 0.008

> hide #!61 models

> view name view13

> view view13

> view name view14

> save zoomed_view_GOLPH3_membrane_PI4P_site_rotate_v4.png supersample 3
> transparentBackground true

> view view13

> save zoomed_view_GOLPH3_membrane_PI4P_site_rotate_v3.png supersample 3
> transparentBackground true

> volume #1 level 0.005

> view name view15

> save zoomed_view_GOLPH3_membrane_PI4P_site_rotate_wmembrane_v5.png
> supersample 3 transparentBackground true

> view view14

> volume #1 level 0.008

> volume #1 level 0.006

> volume #1 level 0.005

> volume #1 level 0.008

> color #1 #ffffff23 models

> color #1 #ffffff24 models

> color #1 #ffffff26 models

> view name view16

> save zoomed_view_GOLPH3_membrane_PI4P_site_rotate_zoomed_v6.png supersample
> 3 transparentBackground true

> hide #!1 models

> view view1

> show #!1 models

> hide #55 models

> show #!61 models

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> select ~sel & ##selected

Nothing selected  

> view view2

> view view3

> view view4

> view view5

> view view6

> view view7

> view view8

> view view9

> view view10

> view view11

> view view10

> cd "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Figures/2024_Nov/Figure 3"

Current working directory is: /Users/becca/Desktop/Postdoc/Grants and paper
drafts/Golph3 paper/Figures/2024_Nov/Figure 3  

> color #1 #ffffff4c models

> color #1 #ffffff4d models

> lighting simple

> lighting soft

> lighting simple

> lighting full

> lighting simple

> lighting soft

> lighting simple

> lighting full

> lighting soft

> lighting simple

> volume #1 level 0.006

> volume #1 level 0.007

> volume #1 level 0.008

> save zoomed_view_GOLPH3_alpha_overview.png supersample 3
> transparentBackground true

> view name view17

> hide #!1 models

> select #61/Q:56

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

> show sel atoms

> select #61/D:290

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

> show sel atoms

> select #61/D:291

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

> select #61/D:292

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

> show sel atoms

> show #!1 models

> volume #1 level 0.006

[Repeated 1 time(s)]

> color #1 #ffffff22 models

> color #1 #ffffff23 models

> color #1 #ffffff24 models

> color #1 #ffffff26 models

> lighting soft

> lighting simple

> color #1 #ffffff34 models

> color #1 #ffffff37 models

> color #1 #ffffff48 models

> color #1 #ffffff51 models

> color #1 #ffffff4e models

> color #1 #ffffff4d models

> color #1 white models

> select clear

> save zoomed_view_GOLPH3_alpha_K56-D290D292_v5.png supersample 3
> transparentBackground true

> hide #!1 models

> view view7

> show #!1 models

> hide #!1 models

> select #61/O:73

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

> show sel atoms

> style sel stick

Changed 8 atom styles  

> color sel byhetero

> select #61/O:72

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

> select #61/O:73

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

> color sel byhetero

> select #61/O:72

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

> show sel atoms

> style sel stick

Changed 6 atom styles  

> color sel byhetero

> select #61/O:74

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

> color sel byhetero

> show sel atoms

> style sel stick

Changed 8 atom styles  

> select #61/Q:224

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

> show sel atoms

> show sel cartoons

> style sel stick

Changed 9 atom styles  

> color sel byhetero

> select #61/Q:223

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

> color sel byhetero

> show sel atoms

> style sel stick

Changed 8 atom styles  

> select clear

> select #61/Q:222

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

> select #61/Q:224

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

> select #61/Q:225

14 atoms, 15 bonds, 1 residue, 1 model selected  

> show sel atoms

> style sel stick

Changed 14 atom styles  

> color sel byhetero

> select #61/Q:226

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

> color sel byhetero

> select #61/Q:227

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

> color sel bynucleotide

> color sel byhetero

> show sel atoms

> select clear

> select #61/Q:226

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

> show sel atoms

> select #61/Q:223

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

> hide sel atoms

> view view7

> show #!1 models

> hide #!1 models

> select #61/Q:224

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

> hide sel atoms

> show #!1 models

> view view7

> save zoomed_view_GOLPH3_zewta.png supersample 3 transparentBackground true

[Repeated 1 time(s)]

> cd "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Figures/2024_Nov/Figure4"

Current working directory is: /Users/becca/Desktop/Postdoc/Grants and paper
drafts/Golph3 paper/Figures/2024_Nov/Figure4  

> save zoomed_view_GOLPH3_zeta.png supersample 3 transparentBackground true

> select clear

> save zoomed_view_GOLPH3_zeta_v2.png supersample 3 transparentBackground true

[Repeated 1 time(s)]

> hide #!1 models

> view view5

> show #!1 models

> volume #1 level 0.008

> hide #!1 models

> select #61/A:14

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

> show sel atoms

> style sel stick

Changed 11 atom styles  

> color sel byhetero

> select clear

> select #61/A:14

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

> hide sel atoms

> select clear

> show #!1 models

> save zoomed_view_GOLPH3_beta_gamma.png supersample 3 transparentBackground
> true

> hide #!1 models

> select #61/A:14

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

> show sel atoms

> select #61/L:445

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

> show sel atoms

> color sel byhetero

> select #61/L:447

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

> color sel byhetero

> show sel atoms

> show #!1 models

> select clear

> volume #1 level 0.007

> volume #1 level 0.008

> save zoomed_view_GOLPH3_gamma_sticks.png supersample 3 transparentBackground
> true

> view view7

> hide #!1 models

> select #61/Q:228

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

> view view7

> view view1

> show #!1 models

> volume #1 level 0.005

> volume #1 level 0.008

> volume #1 level 0.005

> volume #1 level 0.008

> volume #1 level 0.007

> volume #1 level 0.006

> volume #1 level 0.005

> volume #1 level 0.004

> volume #1 level 0.008

> volume #1 level 0.007

> volume #1 level 0.006

> lighting simple

> volume #1 level 0.004772

> volume #1 level 0.00428

> view view13

> select add #61

34068 atoms, 34686 bonds, 4 pseudobonds, 4274 residues, 2 models selected  

> select subtract #61

Nothing selected  

> hide #!61 models

> show #55 models

> show #!61 models

> view view13

> volume #1 level 0.004

> volume #1 level 0.007

> view view5

> volume #1 level 0.008

> volume #1 level 0.007

> volume #1 level 0.008

> volume #1 level 0.005

> volume #1 level 0.008

> volume #1 level 0.005

> volume #1 level 0.008

> volume #1 level 0.005

> view view13

> view view14

> view view15

> view view16

> view view5

> volume #1 level 0.004

> volume #1 level 0.005

> view view5

> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Figures/2024_Nov/20241125_chimera_for_figures.cxs"

——— End of log from Tue Nov 26 17:24:46 2024 ———

opened ChimeraX session  

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> select add #61

34068 atoms, 34686 bonds, 4 pseudobonds, 4274 residues, 2 models selected  

> hide sel atoms

> select subtract #61

Nothing selected  

> show #!63 models

> hide #!63 models

> show #!63 models

> hide #!63 models

> show #!63 models

> hide #!63 models

> show #!63 models

> hide #!1 models

> hide #!63 models

> show #!63 models

> volume #63 level 0.004

> ui tool show "Side View"

> ui tool show "Map Filter"

> volume gaussian #63 sDev 1.5

Opened relion_locres_filtered_20240326_GT_colorset2.mrc gaussian as #2, grid
size 292,292,292, pixel 1.71, shown at step 1, values float32  

> color #2 white models

> color #2 #ffffff00 models

> graphics silhouettes false

> graphics silhouettes true

> volume gaussian #63 sDev 2.1 modelId #2

Opened relion_locres_filtered_20240326_GT_colorset2.mrc gaussian as #2, grid
size 292,292,292, pixel 1.71, shown at step 1, values float32  

> volume gaussian #63 sDev 2.79 modelId #2

Opened relion_locres_filtered_20240326_GT_colorset2.mrc gaussian as #2, grid
size 292,292,292, pixel 1.71, shown at step 1, values float32  

> volume gaussian #63 sDev 3.55 modelId #2

Opened relion_locres_filtered_20240326_GT_colorset2.mrc gaussian as #2, grid
size 292,292,292, pixel 1.71, shown at step 1, values float32  

> color #2 #ffffff8c models

> volume gaussian #63 sDev 3.5 modelId #2

Opened relion_locres_filtered_20240326_GT_colorset2.mrc gaussian as #2, grid
size 292,292,292, pixel 1.71, shown at step 1, values float32  

> color #2 #ffffff00 models

> volume gaussian #63 sDev 1.5 modelId #2

Opened relion_locres_filtered_20240326_GT_colorset2.mrc gaussian as #2, grid
size 292,292,292, pixel 1.71, shown at step 1, values float32  

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> close #2

> show #!1 models

> volume #1 level 0.006

> hide #!61 models

> hide #55 models

> show #55 models

> hide #55 models

> show #!63 models

> hide #!63 models

> close #63

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Structure
> files/leaf_maps/postprocess/relion_locres_filtered_20240325_GT.mrc"

Opened relion_locres_filtered_20240325_GT.mrc as #2, grid size 292,292,292,
pixel 1.71, shown at level 0.00475, step 2, values float32  

> color #2 #ebebebff models

> color #2 darkgrey models

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> volume #2 step 1

> select add #2

2 models selected  

> ui mousemode right "translate selected models"

> view matrix models #2,1,0,0,60.559,0,1,0,12.615,0,0,1,89.849

> view matrix models #2,1,0,0,60.961,0,1,0,65.494,0,0,1,66.73

> view matrix models #2,1,0,0,60.741,0,1,0,65.531,0,0,1,66.879

> view matrix models #2,1,0,0,60.201,0,1,0,65.945,0,0,1,68.739

> view matrix models #2,1,0,0,61.693,0,1,0,68.054,0,0,1,78.697

> ui tool show "Fit in Map"

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> fitmap #2 inMap #1

Fit map relion_locres_filtered_20240325_GT.mrc in map
relion_locres_filtered_20240326_GT.mrc using 247574 points  
correlation = 0.5776, correlation about mean = 0.1585, overlap = 12.09  
steps = 104, shift = 3.7, angle = 3.43 degrees  
  
Position of relion_locres_filtered_20240325_GT.mrc (#2) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99906191 0.00800065 0.04255917 -16.84417788  
-0.00693201 0.99965844 -0.02519806 -1.48444089  
-0.04274624 0.02487940 0.99877614 8.42119695  
Axis 0.50058073 0.85272375 -0.14926870  
Axis point 151.01302871 0.00000000 270.26195011  
Rotation angle (degrees) 2.86709508  
Shift along axis -10.95471000  
  

> select subtract #2

Nothing selected  

> hide #!1 models

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Structure files/leaf_maps/postprocess/postprocess_20231221.mrc"

Opened postprocess_20231221.mrc as #3, grid size 156,156,156, pixel 2.55,
shown at level 0.00309, step 1, values float32  

> color #3 #d6d6d6ff models

> color #3 silver models

> select add #3

3 models selected  

> view matrix models #3,1,0,0,112.33,0,1,0,23.983,0,0,1,141.92

> view matrix models #3,1,0,0,114.32,0,1,0,92.543,0,0,1,105.62

> view matrix models #3,1,0,0,103.11,0,1,0,95.885,0,0,1,130.81

> fitmap #3 inMap #1

Fit map postprocess_20231221.mrc in map relion_locres_filtered_20240326_GT.mrc
using 37871 points  
correlation = 0.5352, correlation about mean = 0.1111, overlap = 1.056  
steps = 176, shift = 20, angle = 6.83 degrees  
  
Position of postprocess_20231221.mrc (#3) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99751059 0.06991241 0.00921266 27.35560896  
-0.06875146 0.99325284 -0.09339179 71.61173506  
-0.01567974 0.09252592 0.99558681 26.73581423  
Axis 0.79702261 0.10671282 -0.59444709  
Axis point 0.00000000 -339.01817829 775.79602219  
Rotation angle (degrees) 6.69780267  
Shift along axis 13.55190198  
  

> view matrix models
> #3,0.99819,0.058024,0.016064,86.369,-0.056065,0.99307,-0.10324,139.24,-0.021943,0.10216,0.99453,104.3

> fitmap #3 inMap #1

Fit map postprocess_20231221.mrc in map relion_locres_filtered_20240326_GT.mrc
using 37871 points  
correlation = 0.5352, correlation about mean = 0.1111, overlap = 1.056  
steps = 92, shift = 9.15, angle = 0.00108 degrees  
  
Position of postprocess_20231221.mrc (#3) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99751078 0.06990804 0.00922575 27.35667632  
-0.06874570 0.99325206 -0.09340440 71.61659488  
-0.01569322 0.09253767 0.99558551 26.73719253  
Axis 0.79707159 0.10681931 -0.59436228  
Axis point 0.00000000 -339.04603471 775.71927260  
Rotation angle (degrees) 6.69827053  
Shift along axis 13.56368605  
  

> select subtract #3

Nothing selected  

> hide #!2 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> volume #3 level 0.004246

> hide #!1 models

> volume #3 level 0.004102

> close #3

> show #!2 models

> volume #2 level 0.00795

> volume #2 level 0.009987

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Structure
> files/leaf_maps/postprocess/COPGolph_20200121_bin2_ref9_bf300.mrc"

Opened COPGolph_20200121_bin2_ref9_bf300.mrc as #3, grid size 128,128,128,
pixel 3.4, shown at level 0.129, step 1, values float32  

> select add #3

3 models selected  

> select subtract #3

Nothing selected  

> close #3

> view view1

> hide #!2 models

> show #!2 models

> show #!1 models

> hide #!1 models

> show #!1 models

> fitmap #2 inMap #1

Fit map relion_locres_filtered_20240325_GT.mrc in map
relion_locres_filtered_20240326_GT.mrc using 54122 points  
correlation = 0.5268, correlation about mean = 0.1559, overlap = 7.027  
steps = 44, shift = 0.309, angle = 0.235 degrees  
  
Position of relion_locres_filtered_20240325_GT.mrc (#2) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99902778 0.01210431 0.04239090 -17.80684422  
-0.01103402 0.99961668 -0.02539190 -0.36777814  
-0.04268200 0.02489947 0.99877839 8.70044806  
Axis 0.49548740 0.83816672 -0.22796661  
Axis point 136.08540377 -0.00000000 293.26901725  
Rotation angle (degrees) 2.90897539  
Shift along axis -11.11473805  
  

> select add #2

2 models selected  

> view matrix models
> #2,0.99883,-0.00024469,0.048407,49.131,0.0019347,0.99939,-0.034868,86.429,-0.048369,0.034921,0.99822,81.672

> fitmap #2 inMap #1

Fit map relion_locres_filtered_20240325_GT.mrc in map
relion_locres_filtered_20240326_GT.mrc using 54122 points  
correlation = 0.9995, correlation about mean = 0.9987, overlap = 22.52  
steps = 60, shift = 3.01, angle = 2.92 degrees  
  
Position of relion_locres_filtered_20240325_GT.mrc (#2) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99999997 0.00014454 -0.00020656 0.02230057  
-0.00014454 0.99999999 -0.00000418 0.02620686  
0.00020656 0.00000421 0.99999998 -0.02948238  
Axis 0.01665653 -0.81921023 -0.57325139  
Axis point 154.38656054 0.00000000 108.27488169  
Rotation angle (degrees) 0.01444704  
Shift along axis -0.00419666  
  

> select subtract #2

Nothing selected  

> hide #!2 models

> hide #!1 models

> show #!1 models

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Structure
> files/leaf_maps/LocalRes_jobs_leaf/job073/relion_locres_filtered.mrc"

Opened relion_locres_filtered.mrc as #3, grid size 292,292,292, pixel 1.71,
shown at level 0.00473, step 2, values float32  

> rename #3 relion_locres_filtered_job072.mrc

> color #3 silver models

> select add #3

3 models selected  

> view matrix models #3,1,0,0,30.539,0,1,0,-15.667,0,0,1,78.206

> view matrix models #3,1,0,0,54.166,0,1,0,45.183,0,0,1,34.056

> view matrix models #3,1,0,0,54.587,0,1,0,50.812,0,0,1,76.198

> view matrix models #3,1,0,0,56.131,0,1,0,58.42,0,0,1,66.709

> fitmap #3 inMap #1

Fit map relion_locres_filtered_job072.mrc in map
relion_locres_filtered_20240326_GT.mrc using 30984 points  
correlation = 0.6121, correlation about mean = 0.1178, overlap = 1.264  
steps = 244, shift = 12.2, angle = 2.78 degrees  
  
Position of relion_locres_filtered_job072.mrc (#3) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99900846 0.01613693 -0.04149329 0.32501303  
-0.01436556 0.99898722 0.04264000 -14.82959067  
0.04213934 -0.04200165 0.99822850 -3.51967302  
Axis -0.68905437 -0.68084012 -0.24831594  
Axis point 0.00000000 -27.66742894 175.53564929  
Rotation angle (degrees) 3.52124839  
Shift along axis 10.74661948  
  

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> volume #3 step 1

> volume #3 level 0.006009

> view matrix models
> #3,0.99933,0.0034134,-0.036322,74.839,-0.0022469,0.99948,0.032108,64.226,0.036413,-0.032005,0.99882,77.163

> fitmap #3 inMap #1

Fit map relion_locres_filtered_job072.mrc in map
relion_locres_filtered_20240326_GT.mrc using 104109 points  
correlation = 0.9694, correlation about mean = 0.9204, overlap = 18.06  
steps = 68, shift = 5.13, angle = 3.52 degrees  
  
Position of relion_locres_filtered_job072.mrc (#3) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99999985 0.00032727 -0.00043305 0.12443189  
-0.00032746 0.99999985 -0.00044412 0.17911073  
0.00043290 0.00044426 0.99999981 -0.20153574  
Axis 0.63330421 -0.61731536 -0.46674139  
Axis point 0.00000000 388.40421450 489.76047590  
Rotation angle (degrees) 0.04018615  
Shift along axis 0.06230051  
  

> select subtract #3

Nothing selected  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Structure
> files/leaf_maps/LocalRes_jobs_leaf/job076/relion_locres_filtered.mrc"

Opened relion_locres_filtered.mrc as #4, grid size 292,292,292, pixel 1.71,
shown at level 0.00472, step 2, values float32  

> rename #3 relion_locres_filtered_job073.mrc

> rename #4 relion_locres_filtered_job076.mrc

> select add #4

2 models selected  

> view matrix models #4,1,0,0,16.92,0,1,0,24.499,0,0,1,-17.193

> view matrix models #4,1,0,0,55.723,0,1,0,11.772,0,0,1,75.251

> view matrix models #4,1,0,0,62.536,0,1,0,67.084,0,0,1,60.553

> view matrix models #4,1,0,0,67.827,0,1,0,64.316,0,0,1,70.509

> view matrix models #4,1,0,0,58.535,0,1,0,64.656,0,0,1,73.258

> fitmap #4 inMap #1

Fit map relion_locres_filtered_job076.mrc in map
relion_locres_filtered_20240326_GT.mrc using 30955 points  
correlation = 0.6078, correlation about mean = 0.1074, overlap = 1.267  
steps = 64, shift = 2.8, angle = 0.688 degrees  
  
Position of relion_locres_filtered_job076.mrc (#4) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99988799 0.00486326 -0.01415478 -0.00653699  
-0.00467298 0.99989869 0.01344490 -12.25906211  
0.01421873 -0.01337725 0.99980942 -4.97528219  
Axis -0.66734489 -0.70594336 -0.23726521  
Axis point 191.91942423 0.00000000 461.89280026  
Rotation angle (degrees) 1.15150302  
Shift along axis 9.83902726  
  

> view matrix models
> #4,0.99993,-0.0077072,-0.0086124,61.953,0.0077353,0.99996,0.0032435,68.699,0.0085871,-0.0033099,0.99996,69.366

> view matrix models
> #4,0.99993,-0.0077072,-0.0086124,56.218,0.0077353,0.99996,0.0032435,68.574,0.0085871,-0.0033099,0.99996,68.917

> fitmap #4 inMap #1

Fit map relion_locres_filtered_job076.mrc in map
relion_locres_filtered_20240326_GT.mrc using 30955 points  
correlation = 0.6108, correlation about mean = 0.1251, overlap = 1.279  
steps = 104, shift = 1.78, angle = 1.12 degrees  
  
Position of relion_locres_filtered_job076.mrc (#4) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99997231 0.00555723 -0.00494882 -9.73830653  
-0.00557589 0.99997737 -0.00376441 -1.39875088  
0.00492779 0.00379190 0.99998067 -6.79486943  
Axis 0.45271595 -0.59173011 -0.66701105  
Axis point -157.33116793 1829.07450339 0.00000000  
Rotation angle (degrees) 0.47816945  
Shift along axis 0.95124929  
  

> view matrix models
> #4,0.99998,-0.0069162,0.00080869,64.023,0.0069267,0.99988,-0.01385,78.472,-0.00071281,0.013855,0.9999,68.833

> view matrix models
> #4,0.99998,-0.0069162,0.00080869,64.971,0.0069267,0.99988,-0.01385,76.867,-0.00071281,0.013855,0.9999,73.048

> fitmap #4 inMap #1

Fit map relion_locres_filtered_job076.mrc in map
relion_locres_filtered_20240326_GT.mrc using 30955 points  
correlation = 0.982, correlation about mean = 0.9627, overlap = 2.853  
steps = 84, shift = 1.03, angle = 0.447 degrees  
  
Position of relion_locres_filtered_job076.mrc (#4) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99999991 0.00030155 -0.00029701 0.06745018  
-0.00030166 0.99999988 -0.00038573 0.14319029  
0.00029689 0.00038582 0.99999988 -0.16137842  
Axis 0.67363056 -0.51851584 -0.52665281  
Axis point 0.00000000 341.71992784 446.62796416  
Rotation angle (degrees) 0.03281253  
Shift along axis 0.05618047  
  

> select subtract #4

Nothing selected  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Structure
> files/leaf_maps/LocalRes_jobs_leaf/job092/relion_locres_filtered.mrc"

Opened relion_locres_filtered.mrc as #5, grid size 292,292,292, pixel 1.71,
shown at level 0.00475, step 2, values float32  

> rename #5 relion_locres_filtered_job092.mrc

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> volume #4 step 1

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> volume #5 step 1

> select add #5

2 models selected  

> color #5 darkgrey models

> view matrix models #5,1,0,0,78.04,0,1,0,9.8449,0,0,1,60.259

> view matrix models #5,1,0,0,61.825,0,1,0,76.575,0,0,1,72.243

> view matrix models #5,1,0,0,62.283,0,1,0,77.072,0,0,1,76.941

> fitmap #5 inMap #1

Fit map relion_locres_filtered_job092.mrc in map
relion_locres_filtered_20240326_GT.mrc using 247574 points  
correlation = 0.9988, correlation about mean = 0.999, overlap = 29.14  
steps = 88, shift = 1.22, angle = 0.968 degrees  
  
Position of relion_locres_filtered_job092.mrc (#5) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99999999 0.00015944 0.00001109 -0.05484775  
-0.00015944 0.99999999 0.00003740 0.02924308  
-0.00001108 -0.00003741 1.00000000 0.01335645  
Axis -0.22787236 0.06752846 -0.97134654  
Axis point 182.74280768 341.86651106 0.00000000  
Rotation angle (degrees) 0.00940494  
Shift along axis 0.00149928  
  

> select subtract #5

Nothing selected  

> hide #!5 models

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Structure
> files/triad_maps/PostProcess_jobs_triad/job020/postprocess.mrc"

Opened postprocess.mrc as #6, grid size 192,192,192, pixel 2.55, shown at
level 0.418, step 1, values float32  

> rename #6 postprocess_triad_job020.mrc

> color #6 #929292ff models

> select add #6

2 models selected  

> view matrix models #6,1,0,0,104.36,0,1,0,15.431,0,0,1,0.51008

> view matrix models #6,1,0,0,93.734,0,1,0,37.225,0,0,1,90.332

> view matrix models #6,1,0,0,128.14,0,1,0,64.539,0,0,1,90.582

> view matrix models #6,1,0,0,134.94,0,1,0,70.79,0,0,1,81.862

> ui tool show "Fit in Map"

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> fitmap #6 inMap #1

Fit map postprocess_triad_job020.mrc in map
relion_locres_filtered_20240326_GT.mrc using 70711 points  
correlation = 0.673, correlation about mean = 0.2053, overlap = 223.4  
steps = 108, shift = 5.92, angle = 1.12 degrees  
  
Position of postprocess_triad_job020.mrc (#6) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99982486 0.01846854 0.00302814 66.76160543  
-0.01844906 0.99980970 -0.00633944 -4.37708384  
-0.00314464 0.00628246 0.99997532 1.62612945  
Axis 0.31953420 0.15626921 -0.93460036  
Axis point -365.37120016 -3287.39016242 0.00000000  
Rotation angle (degrees) 1.13169211  
Shift along axis 19.12883189  
  

> volume #6 level 0.2964

> volume #6 level 0.2721

> select add #6

3 models selected  

> select subtract #6

Nothing selected  

> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Structure
> files/triad_maps/PostProcess_jobs_triad/job007/postprocess.mrc"

Opened postprocess.mrc as #7, grid size 168,168,168, pixel 3.4, shown at level
0.444, step 1, values float32  

> color #7 #929292ff models

> select add #7

2 models selected  

> view matrix models #7,1,0,0,91.521,0,1,0,23.197,0,0,1,24.065

> view matrix models #7,1,0,0,96.402,0,1,0,26.264,0,0,1,33.056

> fitmap #7 inMap #1

Fit map postprocess.mrc in map relion_locres_filtered_20240326_GT.mrc using
47389 points  
correlation = 0.6617, correlation about mean = 0.09379, overlap = 140.4  
steps = 116, shift = 4.6, angle = 1.3 degrees  
  
Position of postprocess.mrc (#7) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99961800 0.02680029 0.00675246 21.33370946  
-0.02678389 0.99963810 -0.00250708 -42.94662361  
-0.00681720 0.00232526 0.99997406 -45.51754509  
Axis 0.08709040 0.24455780 -0.96571566  
Axis point -1916.30172591 -708.58915302 0.00000000  
Rotation angle (degrees) 1.58977516  
Shift along axis 35.31203555  
  

> select subtract #7

Nothing selected  

> rename #7 postprocess_triad_job007.mrc

> hide #!6 models

> volume #7 level 0.3932

> show #!6 models

> hide #!6 models

> hide #!7 models

> hide #!4 models

> hide #!3 models

> show #!5 models

> hide #!1 models

> volume #5 level 0.008164

> volume #5 level 0.008

> volume #5 level 0.005

> volume #4 level 0.005

> show #!4 models

> volume #4 level 0.006

> hide #!4 models

> show #!3 models

> volume #3 level 0.006

> volume #3 level 0.005

> ui tool show "Side View"

> volume #2 level 0.005

> volume #4 level 0.005

> volume #4 level 0.006

> volume #3 level 0.006

> show #!6 models

> color #6 white models

> color #6 #ffffff00 models

> color #6 #ffffff54 models

> color #6 #ffffff4d models

> view view1

> view view2

> hide #!4 models

> hide #!3 models

> color #6 #ffffff00 models

> color #6 #ffffff15 models

> color #6 #ffffff11 models

> color #6 #ffffff12 models

> view view2

> hide #!6 models

> show #!6 models

> show #!1 models

> hide #!6 models

> show #!2 models

> hide #!2 models

> hide #!1 models

> show #!1 models

> show #!2 models

> hide #!2 models

> ui tool show "Map Filter"

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> hide #!1 models

> show #!3 models

> volume gaussian #3 sDev 1.5

Opened relion_locres_filtered_job073.mrc gaussian as #8, grid size
292,292,292, pixel 1.71, shown at step 1, values float32  

> volume #8 level 0.004637

> volume #8 level 0.004706

> volume gaussian #3 sDev 2 modelId #8

Opened relion_locres_filtered_job073.mrc gaussian as #8, grid size
292,292,292, pixel 1.71, shown at step 1, values float32  

> volume #8 level 0.004247

> volume gaussian #3 sDev 2.5 modelId #8

Opened relion_locres_filtered_job073.mrc gaussian as #8, grid size
292,292,292, pixel 1.71, shown at step 1, values float32  

> volume #8 level 0.004296

> volume gaussian #3 sDev 3 modelId #8

Opened relion_locres_filtered_job073.mrc gaussian as #8, grid size
292,292,292, pixel 1.71, shown at step 1, values float32  

> volume #8 level 0.004258

> ui tool show "Side View"

> hide #!8 models

> show #!4 models

> volume gaussian #4 sDev 3

Opened relion_locres_filtered_job076.mrc gaussian as #9, grid size
292,292,292, pixel 1.71, shown at step 1, values float32  

> volume #9 level 0.004378

> hide #!9 models

> volume gaussian #5 sDev 3

Opened relion_locres_filtered_job092.mrc gaussian as #10, grid size
292,292,292, pixel 1.71, shown at step 1, values float32  

> volume #10 level 0.004746

> show #!1 models

> hide #!1 models

> hide #!10 models

> show #!6 models

> color #6 #d6d6d6ff models

> show #!1 models

> show #!61 models

> color #6 #d6d6d684 models

> color #6 #d6d6d685 models

> volume gaussian #6 sDev 3

Opened postprocess_triad_job020.mrc gaussian as #11, grid size 192,192,192,
pixel 2.55, shown at step 1, values float32  

> volume #11 color #b2b2b29c

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!11 models

> show #!7 models

> hide #!7 models

> show #!7 models

> color #7 white models

> color #7 #ffffff3b models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!7 models

> color #6 white models

> color #6 #ffffff00 models

> hide #!61 models

> show #!61 models

> hide #!61 models

> hide #!1 models

> color #6 #ffffff80 models

> hide #!6 models

> show #!7 models

> volume #7 level 0.3477

> show #!61 models

> volume #7 level 0.3337

> volume gaussian #7 sDev 3

Opened postprocess_triad_job007.mrc gaussian as #12, grid size 168,168,168,
pixel 3.4, shown at step 1, values float32  

> color #12 white models

> color #12 #ffffff22 models

> color #12 #ffffff21 models

> show #!1 models

> color #1 #ffffffca models

> color #1 #ffffffc9 models

> color #1 darkgrey models

> hide #!1 models

> hide #!61 models

> show #!61 models

> view view2

> view view5

> hide #!12 models

> show #!25 models

> hide #!25 models

> hide #!61 models

> color #25.1 alphav3

> color #25.2 betav3

> color #25.3 betapv3

> color #25.4 deltav3

> color #25.5 gammav3

> color #25.6 zetav3

> color arf1v3 #25.7

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

> color #25.7 arf1v3

> color #25.8 arf1v3

> show #!25 models

> close #25

> show #!34 models

> show #34.1 models

> show #34.2 models

> show #34.3 models

> show #34.4 models

> show #34.5 models

> show #34.6 models

> show #34.7 models

> show #34.8 models

> show #34.9 models

> color #34.1 label_purple_v3

> color #34.2 arf1v3

> color #34.3 arf1v3

> color #34.4 alphav3

> color #34.5 betav3

> color #34.6 betapv3

> color #34.7 deltav3


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

Log:
Startup Messages  
---  
warning | No presets found in custom preset folder /Users/becca/Desktop/Postdoc/Computational references/ChimeraX_presets  
note | available bundle cache has not been initialized yet  
  

> color name alphav1 #5786F5

Color 'alphav1' is opaque: rgb(34.1%, 52.5%, 96.1%) hex: #5786f5

  

> color name alphav2 #2A4B9B

Color 'alphav2' is opaque: rgb(16.5%, 29.4%, 60.8%) hex: #2a4b9b

  

> color name betapv1 #53EAF3

Color 'betapv1' is opaque: rgb(32.5%, 91.8%, 95.3%) hex: #53eaf3

  

> color name betapv2 #759ED9

Color 'betapv2' is opaque: rgb(45.9%, 62%, 85.1%) hex: #759ed9

  

> color name betav1 #37863D

Color 'betav1' is opaque: rgb(21.6%, 52.5%, 23.9%) hex: #37863d

  

> color name betav2 #207B35

Color 'betav2' is opaque: rgb(12.5%, 48.2%, 20.8%) hex: #207b35

  

> color name deltav1 #CE8041

Color 'deltav1' is opaque: rgb(80.8%, 50.2%, 25.5%) hex: #ce8041

  

> color name deltav2 #E97408

Color 'deltav2' is opaque: rgb(91.4%, 45.5%, 3.14%) hex: #e97408

  

> color name epsilonv1 #F06969

Color 'epsilonv1' is opaque: rgb(94.1%, 41.2%, 41.2%) hex: #f06969

  

> color name gammav1 #2AFF3C

Color 'gammav1' is opaque: rgb(16.5%, 100%, 23.5%) hex: #2aff3c

  

> color name gammav2 #61B230

Color 'gammav2' is opaque: rgb(38%, 69.8%, 18.8%) hex: #61b230

  

> color name zetav1 #E0C819

Color 'zetav1' is opaque: rgb(87.8%, 78.4%, 9.8%) hex: #e0c819

  

> color name zetav2 #EFE30C

Color 'zetav2' is opaque: rgb(93.7%, 89%, 4.71%) hex: #efe30c

  

> color name arf1v1 #FF76AF

Color 'arf1v1' is opaque: rgb(100%, 46.3%, 68.6%) hex: #ff76af

  

> color name arf1v2 #EB70A8

Color 'arf1v2' is opaque: rgb(92.2%, 43.9%, 65.9%) hex: #eb70a8

  

> color name label_red #E32723

Color 'label_red' is opaque: rgb(89%, 15.3%, 13.7%) hex: #e32723

  

> color name label_purple #6C4896

Color 'label_purple' is opaque: rgb(42.4%, 28.2%, 58.8%) hex: #6c4896

  

> color name alphav3 #57679E

Color 'alphav3' is opaque: rgb(34.1%, 40.4%, 62%) hex: #57679e

  

> color name betapv3 #7ACADA

Color 'betapv3' is opaque: rgb(47.8%, 79.2%, 85.5%) hex: #7acada

  

> color name betav3 #447A57

Color 'betav3' is opaque: rgb(26.7%, 47.8%, 34.1%) hex: #447a57

  

> color name gammav3 #ADE57C

Color 'gammav3' is opaque: rgb(67.8%, 89.8%, 48.6%) hex: #ade57c

  

> color name deltav3 #E5AF76

Color 'deltav3' is opaque: rgb(89.8%, 68.6%, 46.3%) hex: #e5af76

  

> color name epsilonv3 #EB8675

Color 'epsilonv3' is opaque: rgb(92.2%, 52.5%, 45.9%) hex: #eb8675

  

> color name zetav3 #F0E07B

Color 'zetav3' is opaque: rgb(94.1%, 87.8%, 48.2%) hex: #f0e07b

  

> color name arf1v3 #EB8BCA

Color 'arf1v3' is opaque: rgb(92.2%, 54.5%, 79.2%) hex: #eb8bca

  

> color name label_red_v3 #E51A16

Color 'label_red_v3' is opaque: rgb(89.8%, 10.2%, 8.63%) hex: #e51a16

  

> color name label_purple_v3 #691099

Color 'label_purple_v3' is opaque: rgb(41.2%, 6.27%, 60%) hex: #691099

  

> color name lable_purple_v4 #9057AD

Color 'lable_purple_v4' is opaque: rgb(56.5%, 34.1%, 67.8%) hex: #9057ad

  
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  




OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M2
OpenGL vendor: Apple

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: Mac14,7
      Model Number: Z16S000N6D/A
      Chip: Apple M2
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 16 GB
      System Firmware Version: 10151.140.19
      OS Loader Version: 10151.140.19

Software:

    System Software Overview:

      System Version: macOS 14.6.1 (23G93)
      Kernel Version: Darwin 23.6.0
      Time since boot: 37 days, 4 hours, 13 minutes

Graphics/Displays:

    Apple M2:

      Chipset Model: Apple M2
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 10
      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
        DELL P2422H:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported


Installed Packages:
    alabaster: 0.7.16
    annotated-types: 0.7.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 2.4.1
    Babel: 2.15.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.7
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-ArtiaX: 0.4.7
    ChimeraX-Atomic: 1.57.1
    ChimeraX-AtomicLibrary: 14.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.6
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.7
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.23.1
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.8
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.4
    ChimeraX-DiffPlot: 1.0
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.8
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.10
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.1
    ChimeraX-MedicalToolbar: 1.0.3
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.17
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.5
    ChimeraX-PDB: 2.7.5
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PhenixUI: 1.3.5
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.1
    ChimeraX-PubChem: 2.2
    ChimeraX-QScore: 1.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.4.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.0.15
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.16.5
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.39.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.3
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-XMAS: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.2.1
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.1
    decorator: 5.1.1
    docutils: 0.20.1
    et-xmlfile: 1.1.0
    executing: 2.0.1
    filelock: 3.13.4
    fonttools: 4.53.0
    funcparserlib: 2.0.0a0
    geomdl: 5.3.1
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.11.0
    html2text: 2024.2.26
    idna: 3.7
    ihm: 1.0
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.3
    jedi: 0.19.1
    jinja2: 3.1.4
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.11
    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    lxml: 5.2.1
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.4
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.0
    numpy: 1.26.4
    openpyxl: 3.1.5
    openvr: 1.26.701
    packaging: 23.2
    pandas: 2.2.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.3.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.2
    prompt-toolkit: 3.0.47
    psutil: 5.9.8
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pyarrow: 16.1.0
    pycollada: 0.8
    pydantic: 2.8.2
    pydantic-core: 2.20.1
    pydicom: 2.4.4
    pygments: 2.17.2
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.1.2
    pyproject-hooks: 1.1.0
    PyQt6-commercial: 6.6.1
    PyQt6-Qt6: 6.6.3
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.3
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pyzmq: 26.0.3
    qtconsole: 5.5.1
    QtPy: 2.4.1
    QtRangeSlider: 0.1.5
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.13.0
    seaborn: 0.13.2
    setuptools: 69.5.1
    setuptools-scm: 8.0.4
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 7.2.6
    sphinx-autodoc-typehints: 2.0.1
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    starfile: 0.5.8
    superqt: 0.6.3
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    tornado: 6.4.1
    traitlets: 5.14.2
    typing-extensions: 4.12.2
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.11

Change History (1)

comment:1 by Eric Pettersen, 11 months ago

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

Note: See TracTickets for help on using tickets.

Download in other formats: