![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 3 weeks ago
Last modified 3 weeks ago
#19911 closed defect
Crash destroying OpenGL context on exit — at Version 1
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Graphics | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: macOS-15.6.1-arm64-arm-64bit
ChimeraX Version: 1.10.dev202503130118 (2025-03-13 01:18:56 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 0x000000020560a0c0 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 440 in quit
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 805 in closeEvent
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 302 in event
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 339 in event_loop
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, cython.cimports.libc.math, scipy._lib._ccallback_c, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.linalg._propack._spropack, scipy.sparse.linalg._propack._dpropack, scipy.sparse.linalg._propack._cpropack, scipy.sparse.linalg._propack._zpropack, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, scipy.spatial._ckdtree, scipy._lib.messagestream, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.special._ufuncs_cxx, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, markupsafe._speedups, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, chimerax.pdb_lib._load_libs, chimerax.surface._surface, openmm._openmm, openmm.app.internal.xtc_utils, openmm.app.internal.compiled, psutil._psutil_osx, psutil._psutil_posix, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, PIL._imaging, 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, PIL._imagingmath (total: 100)
{"app_name":"ChimeraX","timestamp":"2026-02-27 15:24:33.00 -0800","app_version":"1.10.0","slice_uuid":"9cf8124a-d876-34ad-b7ee-c011183ebc15","build_version":"1.10.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 15.6.1 (24G90)","roots_installed":0,"name":"ChimeraX","incident_id":"2510DE5B-D6C3-4A1D-AAE3-ABA015D1D8C7"}
{
"uptime" : 140000,
"procRole" : "Background",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "Mac16,1",
"coalitionID" : 2752,
"osVersion" : {
"train" : "macOS 15.6.1",
"build" : "24G90",
"releaseType" : "User"
},
"captureTime" : "2026-02-27 15:24:28.4085 -0800",
"codeSigningMonitor" : 2,
"incident" : "2510DE5B-D6C3-4A1D-AAE3-ABA015D1D8C7",
"pid" : 48086,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2026-02-27 11:26:19.9945 -0800",
"procStartAbsTime" : 3317802885036,
"procExitAbsTime" : 3431724170526,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.10.0","CFBundleVersion":"1.10.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"6EB36192-985F-52AF-B8E6-46C6ECBF748E","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "E2796449-E3BF-8B60-EBDE-A5CD5F936DBB",
"appleIntelligenceStatus" : {"state":"available"},
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRm+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkZDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"bootSessionUUID" : "DDD027C3-EF99-45D7-9673-1A4E7CF8B2CA",
"wakeTime" : 4122,
"sleepWakeUUID" : "F946FB0B-9576-45F6-8E14-9B60A9FAA828",
"sip" : "enabled",
"vmRegionInfo" : "0 is not in any region. Bytes before following region: 4311384064\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 100fa8000-100fac000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000000","rawCodes":[1,0],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000000"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":48086},
"vmregioninfo" : "0 is not in any region. Bytes before following region: 4311384064\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 100fa8000-100fac000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
"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":4429478552},{"value":80},{"value":95},{"value":0},{"value":0},{"value":7479097512625543673},{"value":7479097504125761849},{"value":14757395258967641293},{"value":4294967286},{"value":4429478481},{"value":0},{"value":49},{"value":4294967280},{"value":328},{"value":8697288024},{"value":0},{"value":11},{"value":259},{"value":8680153504,"symbolLocation":224,"symbol":"_main_thread"},{"value":316},{"value":1},{"value":4332258864,"symbolLocation":0,"symbol":"faulthandler_handlers"},{"value":4638048256,"symbolLocation":0,"symbol":"init_type_QFontComboBox(_sipSimpleWrapper*, _object*, _object*, _object**, _object**, _object**)::sipKwdList"},{"value":1},{"value":4327136080},{"value":6155483960}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6835107980},"cpsr":{"value":1073741824},"fp":{"value":4429478624},"sp":{"value":4429478592},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6834873224,"matchesCrashFrame":1},"far":{"value":0}},"id":2631097,"triggered":true,"name":"CrBrowserMain","queue":"com.apple.main-thread","frames":[{"imageOffset":37768,"symbol":"__pthread_kill","symbolLocation":8,"imageIndex":212},{"imageOffset":26764,"symbol":"pthread_kill","symbolLocation":296,"imageIndex":213},{"imageOffset":265476,"symbol":"raise","symbolLocation":32,"imageIndex":214},{"imageOffset":2417160,"symbol":"faulthandler_fatal_error","symbolLocation":392,"imageIndex":1},{"imageOffset":13988,"symbol":"_sigtramp","symbolLocation":56,"imageIndex":215},{"imageOffset":2246160,"symbol":"QThreadStorageData::get() const","symbolLocation":28,"imageIndex":45},{"imageOffset":3750212,"symbol":"QOpenGLContext::currentContext()","symbolLocation":72,"imageIndex":50},{"imageOffset":3751564,"symbol":"QOpenGLContext::destroy()","symbolLocation":220,"imageIndex":50},{"imageOffset":3753236,"symbol":"QOpenGLContext::~QOpenGLContext()","symbolLocation":32,"imageIndex":50},{"imageOffset":252664,"symbol":"sipQOpenGLContext::~sipQOpenGLContext()","symbolLocation":52,"imageIndex":52},{"imageOffset":890164,"symbol":"QObject::event(QEvent*)","symbolLocation":696,"imageIndex":45},{"imageOffset":253236,"symbol":"sipQOpenGLContext::event(QEvent*)","symbolLocation":224,"imageIndex":52},{"imageOffset":66200,"symbol":"QApplicationPrivate::notify_helper(QObject*, QEvent*)","symbolLocation":336,"imageIndex":49},{"imageOffset":70228,"symbol":"QApplication::notify(QObject*, QEvent*)","symbolLocation":504,"imageIndex":49},{"imageOffset":1430992,"symbol":"sipQApplication::notify(QObject*, QEvent*)","symbolLocation":248,"imageIndex":48},{"imageOffset":598928,"symbol":"QCoreApplication::notifyInternal2(QObject*, QEvent*)","symbolLocation":200,"imageIndex":45},{"imageOffset":603292,"symbol":"QCoreApplicationPrivate::sendPostedEvents(QObject*, int, QThreadData*)","symbolLocation":532,"imageIndex":45},{"imageOffset":2193460,"imageIndex":45},{"imageOffset":2196804,"imageIndex":45},{"imageOffset":162116,"symbol":"__cxa_finalize_ranges","symbolLocation":480,"imageIndex":214},{"imageOffset":161540,"symbol":"exit","symbolLocation":44,"imageIndex":214},{"imageOffset":2364216,"symbol":"-[NSApplication terminate:]","symbolLocation":2084,"imageIndex":216},{"imageOffset":3565120,"symbol":"-[NSApplication _terminateFromSender:askIfShouldTerminate:saveWindows:]","symbolLocation":124,"imageIndex":216},{"imageOffset":2363324,"symbol":"-[NSApplication terminate:]","symbolLocation":1192,"imageIndex":216},{"imageOffset":137888,"imageIndex":71},{"imageOffset":1169464,"symbol":"meth_QCoreApplication_quit(_object*, _object*)","symbolLocation":64,"imageIndex":44},{"imageOffset":1004504,"symbol":"cfunction_call","symbolLocation":96,"imageIndex":1},{"imageOffset":594156,"symbol":"_PyObject_MakeTpCall","symbolLocation":128,"imageIndex":1},{"imageOffset":1789244,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":54984,"imageIndex":1},{"imageOffset":1811404,"symbol":"_PyEval_Vector","symbolLocation":156,"imageIndex":1},{"imageOffset":611268,"symbol":"method_vectorcall","symbolLocation":164,"imageIndex":1},{"imageOffset":22868,"symbol":"sip_api_call_procedure_method","symbolLocation":100,"imageIndex":46},{"imageOffset":693720,"symbol":"sipQMainWindow::closeEvent(QCloseEvent*)","symbolLocation":132,"imageIndex":48},{"imageOffset":396772,"symbol":"QWidget::event(QEvent*)","symbolLocation":128,"imageIndex":49},{"imageOffset":1623176,"symbol":"QMainWindow::event(QEvent*)","symbolLocation":716,"imageIndex":49},{"imageOffset":689016,"symbol":"sipQMainWindow::event(QEvent*)","symbolLocation":224,"imageIndex":48},{"imageOffset":66200,"symbol":"QApplicationPrivate::notify_helper(QObject*, QEvent*)","symbolLocation":336,"imageIndex":49},{"imageOffset":72984,"symbol":"QApplication::notify(QObject*, QEvent*)","symbolLocation":3260,"imageIndex":49},{"imageOffset":1430992,"symbol":"sipQApplication::notify(QObject*, QEvent*)","symbolLocation":248,"imageIndex":48},{"imageOffset":598928,"symbol":"QCoreApplication::notifyInternal2(QObject*, QEvent*)","symbolLocation":200,"imageIndex":45},{"imageOffset":396164,"symbol":"QWidgetPrivate::handleClose(QWidgetPrivate::CloseMode)","symbolLocation":372,"imageIndex":49},{"imageOffset":503468,"imageIndex":49},{"imageOffset":944912,"symbol":"QWindow::event(QEvent*)","symbolLocation":484,"imageIndex":50},{"imageOffset":66200,"symbol":"QApplicationPrivate::notify_helper(QObject*, QEvent*)","symbolLocation":336,"imageIndex":49},{"imageOffset":70228,"symbol":"QApplication::notify(QObject*, QEvent*)","symbolLocation":504,"imageIndex":49},{"imageOffset":1430992,"symbol":"sipQApplication::notify(QObject*, QEvent*)","symbolLocation":248,"imageIndex":48},{"imageOffset":598928,"symbol":"QCoreApplication::notifyInternal2(QObject*, QEvent*)","symbolLocation":200,"imageIndex":45},{"imageOffset":568784,"symbol":"QGuiApplicationPrivate::processWindowSystemEvent(QWindowSystemInterfacePrivate::WindowSystemEvent*)","symbolLocation":2456,"imageIndex":50},{"imageOffset":1001596,"imageIndex":50},{"imageOffset":941652,"symbol":"QWindow::close()","symbolLocation":132,"imageIndex":50},{"imageOffset":58828,"symbol":"QApplicationPrivate::tryCloseAllWidgetWindows(QList*)","symbolLocation":372,"imageIndex":49},{"imageOffset":59632,"symbol":"QApplication::event(QEvent*)","symbolLocation":376,"imageIndex":49},{"imageOffset":2508756,"symbol":"meth_QApplication_event(_object*, _object*)","symbolLocation":180,"imageIndex":48},{"imageOffset":1004504,"symbol":"cfunction_call","symbolLocation":96,"imageIndex":1},{"imageOffset":594156,"symbol":"_PyObject_MakeTpCall","symbolLocation":128,"imageIndex":1},{"imageOffset":1789244,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":54984,"imageIndex":1},{"imageOffset":1811404,"symbol":"_PyEval_Vector","symbolLocation":156,"imageIndex":1},{"imageOffset":611268,"symbol":"method_vectorcall","symbolLocation":164,"imageIndex":1},{"imageOffset":22668,"symbol":"sip_api_call_method","symbolLocation":88,"imageIndex":46},{"imageOffset":1431168,"symbol":"sipQApplication::event(QEvent*)","symbolLocation":148,"imageIndex":48},{"imageOffset":66200,"symbol":"QApplicationPrivate::notify_helper(QObject*, QEvent*)","symbolLocation":336,"imageIndex":49},{"imageOffset":70228,"symbol":"QApplication::notify(QObject*, QEvent*)","symbolLocation":504,"imageIndex":49},{"imageOffset":1430992,"symbol":"sipQApplication::notify(QObject*, QEvent*)","symbolLocation":248,"imageIndex":48},{"imageOffset":598928,"symbol":"QCoreApplication::notifyInternal2(QObject*, QEvent*)","symbolLocation":200,"imageIndex":45},{"imageOffset":567368,"symbol":"QGuiApplicationPrivate::processWindowSystemEvent(QWindowSystemInterfacePrivate::WindowSystemEvent*)","symbolLocation":1040,"imageIndex":50},{"imageOffset":979856,"symbol":"bool QWindowSystemInterface::handleApplicationTermination()","symbolLocation":204,"imageIndex":50},{"imageOffset":44440,"imageIndex":71},{"imageOffset":2419276,"symbol":"-[NSApplication _docController:shouldTerminate:]","symbolLocation":144,"imageIndex":216},{"imageOffset":2418736,"symbol":"__91-[NSDocumentController(NSInternal) _closeAllDocumentsWithDelegate:shouldTerminateSelector:]_block_invoke","symbolLocation":404,"imageIndex":216},{"imageOffset":2417548,"symbol":"-[NSDocumentController(NSInternal) _closeAllDocumentsWithDelegate:shouldTerminateSelector:]","symbolLocation":1156,"imageIndex":216},{"imageOffset":2416272,"symbol":"-[NSDocumentController(NSInternal) __closeAllDocumentsWithDelegate:shouldTerminateSelector:]","symbolLocation":236,"imageIndex":216},{"imageOffset":2415160,"symbol":"-[NSApplication _shouldTerminate]","symbolLocation":1076,"imageIndex":216},{"imageOffset":3564184,"symbol":"-[NSApplication(NSAppleEventHandling) _handleAEQuit]","symbolLocation":420,"imageIndex":216},{"imageOffset":266800,"symbol":"-[NSApplication(NSAppleEventHandling) _handleCoreEvent:withReplyEvent:]","symbolLocation":668,"imageIndex":216},{"imageOffset":204352,"symbol":"-[NSAppleEventManager dispatchRawAppleEvent:withRawReply:handlerRefCon:]","symbolLocation":316,"imageIndex":217},{"imageOffset":203832,"symbol":"_NSAppleEventManagerGenericHandler","symbolLocation":80,"imageIndex":217},{"imageOffset":45372,"imageIndex":218},{"imageOffset":43644,"imageIndex":218},{"imageOffset":16452,"symbol":"aeProcessAppleEvent","symbolLocation":484,"imageIndex":218},{"imageOffset":92200,"symbol":"AEProcessAppleEvent","symbolLocation":68,"imageIndex":219},{"imageOffset":240952,"symbol":"_DPSNextEvent","symbolLocation":1456,"imageIndex":216},{"imageOffset":10328384,"symbol":"-[NSApplication(NSEventRouting) _nextEventMatchingEventMask:untilDate:inMode:dequeue:]","symbolLocation":688,"imageIndex":216},{"imageOffset":187364,"symbol":"-[NSApplication run]","symbolLocation":480,"imageIndex":216},{"imageOffset":97412,"imageIndex":71},{"imageOffset":639864,"symbol":"QEventLoop::exec(QFlags)","symbolLocation":596,"imageIndex":45},{"imageOffset":600940,"symbol":"QCoreApplication::exec()","symbolLocation":144,"imageIndex":45},{"imageOffset":2508944,"symbol":"meth_QApplication_exec(_object*, _object*)","symbolLocation":96,"imageIndex":48},{"imageOffset":1004504,"symbol":"cfunction_call","symbolLocation":96,"imageIndex":1},{"imageOffset":594156,"symbol":"_PyObject_MakeTpCall","symbolLocation":128,"imageIndex":1},{"imageOffset":1789244,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":54984,"imageIndex":1},{"imageOffset":1729512,"symbol":"PyEval_EvalCode","symbolLocation":276,"imageIndex":1},{"imageOffset":1707120,"symbol":"builtin_exec","symbolLocation":428,"imageIndex":1},{"imageOffset":1007044,"symbol":"cfunction_vectorcall_FASTCALL_KEYWORDS","symbolLocation":80,"imageIndex":1},{"imageOffset":1788292,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":54032,"imageIndex":1},{"imageOffset":1811404,"symbol":"_PyEval_Vector","symbolLocation":156,"imageIndex":1},{"imageOffset":2389028,"symbol":"pymain_run_module","symbolLocation":256,"imageIndex":1},{"imageOffset":2387652,"symbol":"Py_RunMain","symbolLocation":1784,"imageIndex":1},{"imageOffset":2392180,"symbol":"pymain_main","symbolLocation":52,"imageIndex":1},{"imageOffset":2392116,"symbol":"Py_Main","symbolLocation":36,"imageIndex":1},{"imageOffset":15764,"symbol":"main","symbolLocation":128,"imageIndex":0},{"imageOffset":27544,"symbol":"start","symbolLocation":6076,"imageIndex":220}]},{"id":2631255,"name":"ThreadPoolServiceThread","threadState":{"x":[{"value":4},{"value":0},{"value":0},{"value":105553144984320},{"value":4},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":3},{"value":2},{"value":44035},{"value":0},{"value":3779229761},{"value":3777130555},{"value":369},{"value":13287501824},{"value":0},{"value":13254155392},{"value":13203125072},{"value":0},{"value":13287501096},{"value":12297829382473034411},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0}],"flavor":"ARM_THREAD_STATE64","lr":{"value":5916567428},"cpsr":{"value":2684354560},"fp":{"value":13287501072},"sp":{"value":13287500976},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6834887004},"far":{"value":0}},"frames":[{"imageOffset":51548,"symbol":"kevent64","symbolLocation":8,"imageIndex":212},{"imageOffset":77670276,"imageIndex":56},{"imageOffset":77669752,"imageIndex":56},{"imageOffset":77272856,"imageIndex":56},{"imageOffset":77019148,"imageIndex":56},{"imageOffset":77432160,"imageIndex":56},{"imageOffset":77324944,"imageIndex":56},{"imageOffset":77432544,"imageIndex":56},{"imageOffset":77536044,"imageIndex":56},{"imageOffset":27660,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":213},{"imageOffset":7040,"symbol":"thread_start","symbolLocation":8,"imageIndex":213}]},{"id":2631256,"name":"ThreadPoolForegroundWorker","threadState":{"x":[{"value":268451845},{"value":17179869186},{"value":0},{"value":280388349984768},{"value":0},{"value":280388349984768},{"value":32},{"value":0},{"value":0},{"value":17179869184},{"value":32},{"value":0},{"value":0},{"value":0},{"value":65283},{"value":2043},{"value":18446744073709551569},{"value":235},{"value":0},{"value":0},{"value":32},{"value":280388349984768},{"value":0},{"value":280388349984768},{"value":13295922480},{"value":0},{"value":17179869186},{"value":18446744073709550527},{"value":2}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6834914208},"cpsr":{"value":0},"fp":{"value":13295921824},"sp":{"value":13295921744},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6834838580},"far":{"value":0}},"frames":[{"imageOffset":3124,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":212},{"imageOffset":78752,"symbol":"mach_msg2_internal","symbolLocation":76,"imageIndex":212},{"imageOffset":38756,"symbol":"mach_msg_overwrite","symbolLocation":484,"imageIndex":212},{"imageOffset":4008,"symbol":"mach_msg","symbolLocation":24,"imageIndex":212},{"imageOffset":77644624,"imageIndex":56},{"imageOffset":77143240,"imageIndex":56},{"imageOffset":77377520,"imageIndex":56},{"imageOffset":77374852,"imageIndex":56},{"imageOffset":77374288,"imageIndex":56},{"imageOffset":77374004,"imageIndex":56},{"imageOffset":77536044,"imageIndex":56},{"imageOffset":27660,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":213},{"imageOffset":7040,"symbol":"thread_start","symbolLocation":8,"imageIndex":213}]},{"id":2631257,"name":"ThreadPoolBackgroundWorker","threadState":{"x":[{"value":268451845},{"value":17179869186},{"value":0},{"value":191327908134912},{"value":0},{"value":191327908134912},{"value":32},{"value":0},{"value":0},{"value":17179869184},{"value":32},{"value":0},{"value":0},{"value":0},{"value":44547},{"value":2043},{"value":18446744073709551569},{"value":241},{"value":0},{"value":0},{"value":32},{"value":191327908134912},{"value":0},{"value":191327908134912},{"value":13304343856},{"value":0},{"value":17179869186},{"value":18446744073709550527},{"value":2}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6834914208},"cpsr":{"value":0},"fp":{"value":13304343200},"sp":{"value":13304343120},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6834838580},"far":{"value":0}},"frames":[{"imageOffset":3124,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":212},{"imageOffset":78752,"symbol":"mach_msg2_internal","symbolLocation":76,"imageIndex":212},{"imageOffset":38756,"symbol":"mach_msg_overwrite","symbolLocation":484,"imageIndex":212},{"imageOffset":4008,"symbol":"mach_msg","symbolLocation":24,"imageIndex":212},{"imageOffset":77644624,"imageIndex":56},{"imageOffset":77143240,"imageIndex":56},{"imageOffset":77377520,"imageIndex":56},{"imageOffset":77374852,"imageIndex":56},{"imageOffset":77374156,"imageIndex":56},{"imageOffset":77374064,"imageIndex":56},{"imageOffset":77536044,"imageIndex":56},{"imageOffset":27660,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":213},{"imageOffset":7040,"symbol":"thread_start","symbolLocation":8,"imageIndex":213}]},{"id":2631258,"name":"Chrome_IOThread","threadState":{"x":[{"value":4},{"value":0},{"value":0},{"value":105553144678272},{"value":3},{"value":0},{"value":0},{"value":1},{"value":0},{"value":0},{"value":0},{"value":9223372036854775809},{"value":62979},{"value":0},{"value":2405607451},{"value":2403508392},{"value":369},{"value":13312765952},{"value":0},{"value":13202871568},{"value":13215352992},{"value":0},{"value":13312765208},{"value":12297829382473034411},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0}],"flavor":"ARM_THREAD_STATE64","lr":{"value":5916567428},"cpsr":{"value":1610612736},"fp":{"value":13312765184},"sp":{"value":13312765088},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6834887004},"far":{"value":0}},"frames":[{"imageOffset":51548,"symbol":"kevent64","symbolLocation":8,"imageIndex":212},{"imageOffset":77670276,"imageIndex":56},{"imageOffset":77669752,"imageIndex":56},{"imageOffset":77272856,"imageIndex":56},{"imageOffset":77019148,"imageIndex":56},{"imageOffset":77432160,"imageIndex":56},{"imageOffset":49839956,"imageIndex":56},{"imageOffset":77432544,"imageIndex":56},{"imageOffset":77536044,"imageIndex":56},{"imageOffset":27660,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":213},{"imageOffset":7040,"symbol":"thread_start","symbolLocation":8,"imageIndex":213}]},{"id":2631259,"name":"NetworkConfigWatcher","threadState":{"x":[{"value":268451845},{"value":17179869186},{"value":0},{"value":200124001157120},{"value":0},{"value":200124001157120},{"value":32},{"value":0},{"value":0},{"value":17179869184},{"value":32},{"value":0},{"value":0},{"value":0},{"value":46595},{"value":3772932158},{"value":18446744073709551569},{"value":13321187328},{"value":0},{"value":0},{"value":32},{"value":200124001157120},{"value":0},{"value":200124001157120},{"value":13321186320},{"value":0},{"value":17179869186},{"value":18446744073709550527},{"value":2}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6834914208},"cpsr":{"value":0},"fp":{"value":13321185664},"sp":{"value":13321185584},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6834838580},"far":{"value":0}},"frames":[{"imageOffset":3124,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":212},{"imageOffset":78752,"symbol":"mach_msg2_internal","symbolLocation":76,"imageIndex":212},{"imageOffset":38756,"symbol":"mach_msg_overwrite","symbolLocation":484,"imageIndex":212},{"imageOffset":4008,"symbol":"mach_msg","symbolLocation":24,"imageIndex":212},{"imageOffset":77644624,"imageIndex":56},{"imageOffset":77143240,"imageIndex":56},{"imageOffset":77143120,"imageIndex":56},{"imageOffset":76806856,"imageIndex":56},{"imageOffset":77272856,"imageIndex":56},{"imageOffset":77019148,"imageIndex":56},{"imageOffset":77432160,"imageIndex":56},{"imageOffset":77432544,"imageIndex":56},{"imageOffset":77536044,"imageIndex":56},{"imageOffset":27660,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":213},{"imageOffset":7040,"symbol":"thread_start","symbolLocation":8,"imageIndex":213}]},{"id":2631260,"name":"ThreadPoolForegroundWorker","threadState":{"x":[{"value":268451845},{"value":17179869186},{"value":0},{"value":202357384151040},{"value":0},{"value":202357384151040},{"value":32},{"value":0},{"value":0},{"value":17179869184},{"value":32},{"value":0},{"value":0},{"value":0},{"value":47115},{"value":2043},{"value":18446744073709551569},{"value":239},{"value":0},{"value":0},{"value":32},{"value":202357384151040},{"value":0},{"value":202357384151040},{"value":13329607984},{"value":0},{"value":17179869186},{"value":18446744073709550527},{"value":2}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6834914208},"cpsr":{"value":0},"fp":{"value":13329607328},"sp":{"value":13329607248},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6834838580},"far":{"value":0}},"frames":[{"imageOffset":3124,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":212},{"imageOffset":78752,"symbol":"mach_msg2_internal","symbolLocation":76,"imageIndex":212},{"imageOffset":38756,"symbol":"mach_msg_overwrite","symbolLocation":484,"imageIndex":212},{"imageOffset":4008,"symbol":"mach_msg","symbolLocation":24,"imageIndex":212},{"imageOffset":77644624,"imageIndex":56},{"imageOffset":77143240,"imageIndex":56},{"imageOffset":77377520,"imageIndex":56},{"imageOffset":77374852,"imageIndex":56},{"imageOffset":77374288,"imageIndex":56},{"imageOffset":77374004,"imageIndex":56},{"imageOffset":77536044,"imageIndex":56},{"imageOffset":27660,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":213},{"imageOffset":7040,"symbol":"thread_start","symbolLocation":8,"imageIndex":213}]},{"id":2631261,"name":"ThreadPoolForegroundWorker","threadState":{"x":[{"value":268451845},{"value":17179869186},{"value":0},{"value":264995187195904},{"value":0},{"value":264995187195904},{"value":32},{"value":0},{"value":0},{"value":17179869184},{"value":32},{"value":0},{"value":0},{"value":0},{"value":61699},{"value":4255195374},{"value":18446744073709551569},{"value":47},{"value":0},{"value":0},{"value":32},{"value":264995187195904},{"value":0},{"value":264995187195904},{"value":13338029360},{"value":0},{"value":17179869186},{"value":18446744073709550527},{"value":2}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6834914208},"cpsr":{"value":0},"fp":{"value":13338028704},"sp":{"value":13338028624},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6834838580},"far":{"value":0}},"frames":[{"imageOffset":3124,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":212},{"imageOffset":78752,"symbol":"mach_msg2_internal","symbolLocation":76,"imageIndex":212},{"imageOffset":38756,"symbol":"mach_msg_overwrite","symbolLocation":484,"imageIndex":212},{"imageOffset":4008,"symbol":"mach_msg","symbolLocation":24,"imageIndex":212},{"imageOffset":77644624,"imageIndex":56},{"imageOffset":77143240,"imageIndex":56},{"imageOffset":77377520,"imageIndex":56},{"imageOffset":77374852,"imageIndex":56},{"imageOffset":77374288,"imageIndex":56},{"imageOffset":77374004,"imageIndex":56},{"imageOffset":77536044,"imageIndex":56},{"imageOffset":27660,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":213},{"imageOffset":7040,"symbol":"thread_start","symbolLocation":8,"imageIndex":213}]},{"id":2631262,"name":"ThreadPoolForegroundWorker","threadState":{"x":[{"value":268451845},{"value":17179869186},{"value":0},{"value":262796163940352},{"value":0},{"value":262796163940352},{"value":32},{"value":0},{"value":0},{"value":17179869184},{"value":32},{"value":0},{"value":0},{"value":0},{"value":61187},{"value":3873554550},{"value":18446744073709551569},{"value":60},{"value":0},{"value":0},{"value":32},{"value":262796163940352},{"value":0},{"value":262796163940352},{"value":13346450736},{"value":0},{"value":17179869186},{"value":18446744073709550527},{"value":2}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6834914208},"cpsr":{"value":0},"fp":{"value":13346450080},"sp":{"value":13346450000},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6834838580},"far":{"value":0}},"frames":[{"imageOffset":3124,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":212},{"imageOffset":78752,"symbol":"mach_msg2_internal","symbolLocation":76,"imageIndex":212},{"imageOffset":38756,"symbol":"mach_msg_overwrite","symbolLocation":484,"imageIndex":212},{"imageOffset":4008,"symbol":"mach_msg","symbolLocation":24,"imageIndex":212},{"imageOffset":77644624,"imageIndex":56},{"imageOffset":77143240,"imageIndex":56},{"imageOffset":77377520,"imageIndex":56},{"imageOffset":77374852,"imageIndex":56},{"imageOffset":77374288,"imageIndex":56},{"imageOffset":77374004,"imageIndex":56},{"imageOffset":77536044,"imageIndex":56},{"imageOffset":27660,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":213},{"imageOffset":7040,"symbol":"thread_start","symbolLocation":8,"imageIndex":213}]},{"id":2631263,"name":"Chrome_InProcGpuThread","threadState":{"x":[{"value":268451845},{"value":17179869186},{"value":0},{"value":257298605801472},{"value":0},{"value":257298605801472},{"value":32},{"value":0},{"value":0},{"value":17179869184},{"value":32},{"value":0},{"value":0},{"value":0},{"value":59907},{"value":3613567012},{"value":18446744073709551569},{"value":13354872832},{"value":0},{"value":0},{"value":32},{"value":257298605801472},{"value":0},{"value":257298605801472},{"value":13354871824},{"value":0},{"value":17179869186},{"value":18446744073709550527},{"value":2}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6834914208},"cpsr":{"value":0},"fp":{"value":13354871168},"sp":{"value":13354871088},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6834838580},"far":{"value":0}},"frames":[{"imageOffset":3124,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":212},{"imageOffset":78752,"symbol":"mach_msg2_internal","symbolLocation":76,"imageIndex":212},{"imageOffset":38756,"symbol":"mach_msg_overwrite","symbolLocation":484,"imageIndex":212},{"imageOffset":4008,"symbol":"mach_msg","symbolLocation":24,"imageIndex":212},{"imageOffset":77644624,"imageIndex":56},{"imageOffset":77143240,"imageIndex":56},{"imageOffset":77143120,"imageIndex":56},{"imageOffset":76806856,"imageIndex":56},{"imageOffset":77272856,"imageIndex":56},{"imageOffset":77019148,"imageIndex":56},{"imageOffset":77432160,"imageIndex":56},{"imageOffset":77432544,"imageIndex":56},{"imageOffset":77536044,"imageIndex":56},{"imageOffset":27660,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":213},{"imageOffset":7040,"symbol":"thread_start","symbolLocation":8,"imageIndex":213}]},{"id":2631264,"name":"Chrome_ChildIOThread","threadState":{"x":[{"value":4},{"value":0},{"value":0},{"value":105553149937824},{"value":1},{"value":0},{"value":0},{"value":13363291776},{"value":0},{"value":0},{"value":1},{"value":1099511628034},{"value":49923},{"value":0},{"value":2799724632},{"value":2797625417},{"value":369},{"value":13363294208},{"value":0},{"value":13253098384},{"value":6355098688},{"value":0},{"value":13363293464},{"value":12297829382473034411},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0}],"flavor":"ARM_THREAD_STATE64","lr":{"value":5916567428},"cpsr":{"value":2684354560},"fp":{"value":13363293440},"sp":{"value":13363293344},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6834887004},"far":{"value":0}},"frames":[{"imageOffset":51548,"symbol":"kevent64","symbolLocation":8,"imageIndex":212},{"imageOffset":77670276,"imageIndex":56},{"imageOffset":77669752,"imageIndex":56},{"imageOffset":77272856,"imageIndex":56},{"imageOffset":77019148,"imageIndex":56},{"imageOffset":77432160,"imageIndex":56},{"imageOffset":120628144,"imageIndex":56},{"imageOffset":77432544,"imageIndex":56},{"imageOffset":77536044,"imageIndex":56},{"imageOffset":27660,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":213},{"imageOffset":7040,"symbol":"thread_start","symbolLocation":8,"imageIndex":213}]},{"id":2631265,"name":"CompositorTileWorker1","threadState":{"x":[{"value":260},{"value":0},{"value":512},{"value":0},{"value":0},{"value":161},{"value":0},{"value":0},{"value":13371715144},{"value":0},{"value":0},{"value":2},{"value":2},{"value":0},{"value":0},{"value":0},{"value":305},{"value":8697287952},{"value":0},{"value":4316840280},{"value":4316840408},{"value":13371715808},{"value":0},{"value":0},{"value":512},{"value":513},{"value":768},{"value":0},{"value":0}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6835110112},"cpsr":{"value":1610612736},"fp":{"value":13371715264},"sp":{"value":13371715120},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6834852812},"far":{"value":0}},"frames":[{"imageOffset":17356,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":212},{"imageOffset":28896,"symbol":"_pthread_cond_wait","symbolLocation":984,"imageIndex":213},{"imageOffset":77533976,"imageIndex":56},{"imageOffset":110943884,"imageIndex":56},{"imageOffset":77536044,"imageIndex":56},{"imageOffset":27660,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":213},{"imageOffset":7040,"symbol":"thread_start","symbolLocation":8,"imageIndex":213}]},{"id":2631266,"name":"ThreadPoolSingleThreadSharedForeground0","threadState":{"x":[{"value":268451845},{"value":17179869186},{"value":0},{"value":254000070918144},{"value":0},{"value":254000070918144},{"value":32},{"value":0},{"value":0},{"value":17179869184},{"value":32},{"value":0},{"value":0},{"value":0},{"value":59139},{"value":2607337467},{"value":18446744073709551569},{"value":59},{"value":0},{"value":0},{"value":32},{"value":254000070918144},{"value":0},{"value":254000070918144},{"value":13380136240},{"value":0},{"value":17179869186},{"value":18446744073709550527},{"value":2}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6834914208},"cpsr":{"value":0},"fp":{"value":13380135584},"sp":{"value":13380135504},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6834838580},"far":{"value":0}},"frames":[{"imageOffset":3124,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":212},{"imageOffset":78752,"symbol":"mach_msg2_internal","symbolLocation":76,"imageIndex":212},{"imageOffset":38756,"symbol":"mach_msg_overwrite","symbolLocation":484,"imageIndex":212},{"imageOffset":4008,"symbol":"mach_msg","symbolLocation":24,"imageIndex":212},{"imageOffset":77644624,"imageIndex":56},{"imageOffset":77143240,"imageIndex":56},{"imageOffset":77377520,"imageIndex":56},{"imageOffset":77374852,"imageIndex":56},{"imageOffset":77374332,"imageIndex":56},{"imageOffset":77374088,"imageIndex":56},{"imageOffset":77536044,"imageIndex":56},{"imageOffset":27660,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":213},{"imageOffset":7040,"symbol":"thread_start","symbolLocation":8,"imageIndex":213}]},{"id":2631267,"name":"VizCompositorThread","threadState":{"x":[{"value":268451845},{"value":17179869442},{"value":0},{"value":248502512779264},{"value":0},{"value":248502512779264},{"value":32},{"value":13},{"value":0},{"value":17179869184},{"value":32},{"value":0},{"value":0},{"value":0},{"value":57859},{"value":4088574229},{"value":18446744073709551569},{"value":13396373504},{"value":0},{"value":13},{"value":32},{"value":248502512779264},{"value":0},{"value":248502512779264},{"value":13396372512},{"value":0},{"value":17179870466},{"value":18446744073709550527},{"value":1282}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6834914208},"cpsr":{"value":0},"fp":{"value":13396371856},"sp":{"value":13396371776},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6834838580},"far":{"value":0}},"frames":[{"imageOffset":3124,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":212},{"imageOffset":78752,"symbol":"mach_msg2_internal","symbolLocation":76,"imageIndex":212},{"imageOffset":38756,"symbol":"mach_msg_overwrite","symbolLocation":484,"imageIndex":212},{"imageOffset":4008,"symbol":"mach_msg","symbolLocation":24,"imageIndex":212},{"imageOffset":77644624,"imageIndex":56},{"imageOffset":77143240,"imageIndex":56},{"imageOffset":76806888,"imageIndex":56},{"imageOffset":77272856,"imageIndex":56},{"imageOffset":77019148,"imageIndex":56},{"imageOffset":77432160,"imageIndex":56},{"imageOffset":77432544,"imageIndex":56},{"imageOffset":77536044,"imageIndex":56},{"imageOffset":27660,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":213},{"imageOffset":7040,"symbol":"thread_start","symbolLocation":8,"imageIndex":213}]},{"id":2631268,"name":"NetworkConfigWatcher","threadState":{"x":[{"value":268451845},{"value":17179869186},{"value":0},{"value":233109349990400},{"value":0},{"value":233109349990400},{"value":32},{"value":0},{"value":0},{"value":17179869184},{"value":32},{"value":0},{"value":0},{"value":0},{"value":54275},{"value":3758237786},{"value":18446744073709551569},{"value":13404794880},{"value":0},{"value":0},{"value":32},{"value":233109349990400},{"value":0},{"value":233109349990400},{"value":13404793872},{"value":0},{"value":17179869186},{"value":18446744073709550527},{"value":2}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6834914208},"cpsr":{"value":0},"fp":{"value":13404793216},"sp":{"value":13404793136},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6834838580},"far":{"value":0}},"frames":[{"imageOffset":3124,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":212},{"imageOffset":78752,"symbol":"mach_msg2_internal","symbolLocation":76,"imageIndex":212},{"imageOffset":38756,"symbol":"mach_msg_overwrite","symbolLocation":484,"imageIndex":212},{"imageOffset":4008,"symbol":"mach_msg","symbolLocation":24,"imageIndex":212},{"imageOffset":77644624,"imageIndex":56},{"imageOffset":77143240,"imageIndex":56},{"imageOffset":77143120,"imageIndex":56},{"imageOffset":76806856,"imageIndex":56},{"imageOffset":77272856,"imageIndex":56},{"imageOffset":77019148,"imageIndex":56},{"imageOffset":77432160,"imageIndex":56},{"imageOffset":77432544,"imageIndex":56},{"imageOffset":77536044,"imageIndex":56},{"imageOffset":27660,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":213},{"imageOffset":7040,"symbol":"thread_start","symbolLocation":8,"imageIndex":213}]},{"id":2631271,"name":"NetworkService","threadState":{"x":[{"value":4},{"value":0},{"value":0},{"value":105553126781408},{"value":2},{"value":0},{"value":0},{"value":13419096048},{"value":0},{"value":0},{"value":2},{"value":4398046512130},{"value":55043},{"value":0},{"value":2420285608},{"value":2418186267},{"value":369},{"value":13419098112},{"value":0},{"value":13249660048},{"value":13254736320},{"value":0},{"value":13419097416},{"value":12297829382473034411},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0}],"flavor":"ARM_THREAD_STATE64","lr":{"value":5916567428},"cpsr":{"value":2684354560},"fp":{"value":13419097392},"sp":{"value":13419097296},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6834887004},"far":{"value":0}},"frames":[{"imageOffset":51548,"symbol":"kevent64","symbolLocation":8,"imageIndex":212},{"imageOffset":77670276,"imageIndex":56},{"imageOffset":77669752,"imageIndex":56},{"imageOffset":77272856,"imageIndex":56},{"imageOffset":77019148,"imageIndex":56},{"imageOffset":77432160,"imageIndex":56},{"imageOffset":77432544,"imageIndex":56},{"imageOffset":77536044,"imageIndex":56},{"imageOffset":27660,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":213},{"imageOffset":7040,"symbol":"thread_start","symbolLocation":8,"imageIndex":213}]},{"id":2631272,"name":"NetworkNotificationThreadMac","threadState":{"x":[{"value":268451845},{"value":21592279046},{"value":8589934592},{"value":281487861612544},{"value":0},{"value":281487861612544},{"value":2},{"value":4294967295},{"value":0},{"value":17179869184},{"value":0},{"value":2},{"value":0},{"value":0},{"value":65539},{"value":0},{"value":18446744073709551569},{"value":8697289832},{"value":0},{"value":4294967295},{"value":2},{"value":281487861612544},{"value":0},{"value":281487861612544},{"value":13427514824},{"value":8589934592},{"value":21592279046},{"value":18446744073709550527},{"value":4412409862}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6834914208},"cpsr":{"value":0},"fp":{"value":13427514672},"sp":{"value":13427514592},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6834838580},"far":{"value":0}},"frames":[{"imageOffset":3124,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":212},{"imageOffset":78752,"symbol":"mach_msg2_internal","symbolLocation":76,"imageIndex":212},{"imageOffset":38756,"symbol":"mach_msg_overwrite","symbolLocation":484,"imageIndex":212},{"imageOffset":4008,"symbol":"mach_msg","symbolLocation":24,"imageIndex":212},{"imageOffset":511164,"symbol":"__CFRunLoopServiceMachPort","symbolLocation":160,"imageIndex":222},{"imageOffset":505304,"symbol":"__CFRunLoopRun","symbolLocation":1208,"imageIndex":222},{"imageOffset":502424,"symbol":"CFRunLoopRunSpecific","symbolLocation":572,"imageIndex":222},{"imageOffset":367736,"symbol":"-[NSRunLoop(NSRunLoop) runMode:beforeDate:]","symbolLocation":212,"imageIndex":217},{"imageOffset":77876416,"imageIndex":56},{"imageOffset":77870672,"imageIndex":56},{"imageOffset":77272856,"imageIndex":56},{"imageOffset":77019148,"imageIndex":56},{"imageOffset":77432160,"imageIndex":56},{"imageOffset":77432544,"imageIndex":56},{"imageOffset":77536044,"imageIndex":56},{"imageOffset":27660,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":213},{"imageOffset":7040,"symbol":"thread_start","symbolLocation":8,"imageIndex":213}]},{"id":2631273,"name":"NetworkConfigWatcher","threadState":{"x":[{"value":268451845},{"value":17179869186},{"value":0},{"value":370548303462400},{"value":0},{"value":370548303462400},{"value":32},{"value":0},{"value":0},{"value":17179869184},{"value":32},{"value":0},{"value":0},{"value":0},{"value":86275},{"value":3768733756},{"value":18446744073709551569},{"value":13435940864},{"value":0},{"value":0},{"value":32},{"value":370548303462400},{"value":0},{"value":370548303462400},{"value":13435939856},{"value":0},{"value":17179869186},{"value":18446744073709550527},{"value":2}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6834914208},"cpsr":{"value":0},"fp":{"value":13435939200},"sp":{"value":13435939120},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6834838580},"far":{"value":0}},"frames":[{"imageOffset":3124,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":212},{"imageOffset":78752,"symbol":"mach_msg2_internal","symbolLocation":76,"imageIndex":212},{"imageOffset":38756,"symbol":"mach_msg_overwrite","symbolLocation":484,"imageIndex":212},{"imageOffset":4008,"symbol":"mach_msg","symbolLocation":24,"imageIndex":212},{"imageOffset":77644624,"imageIndex":56},{"imageOffset":77143240,"imageIndex":56},{"imageOffset":77143120,"imageIndex":56},{"imageOffset":76806856,"imageIndex":56},{"imageOffset":77272856,"imageIndex":56},{"imageOffset":77019148,"imageIndex":56},{"imageOffset":77432160,"imageIndex":56},{"imageOffset":77432544,"imageIndex":56},{"imageOffset":77536044,"imageIndex":56},{"imageOffset":27660,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":213},{"imageOffset":7040,"symbol":"thread_start","symbolLocation":8,"imageIndex":213}]},{"id":2631274,"name":"ThreadPoolSingleThreadForegroundBlocking1","threadState":{"x":[{"value":268451845},{"value":17179869186},{"value":0},{"value":365050745323520},{"value":0},{"value":365050745323520},{"value":32},{"value":0},{"value":0},{"value":17179869184},{"value":32},{"value":0},{"value":0},{"value":0},{"value":84995},{"value":3466592364},{"value":18446744073709551569},{"value":4417702400},{"value":0},{"value":0},{"value":32},{"value":365050745323520},{"value":0},{"value":365050745323520},{"value":13444361520},{"value":0},{"value":17179869186},{"value":18446744073709550527},{"value":2}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6834914208},"cpsr":{"value":0},"fp":{"value":13444360864},"sp":{"value":13444360784},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6834838580},"far":{"value":0}},"frames":[{"imageOffset":3124,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":212},{"imageOffset":78752,"symbol":"mach_msg2_internal","symbolLocation":76,"imageIndex":212},{"imageOffset":38756,"symbol":"mach_msg_overwrite","symbolLocation":484,"imageIndex":212},{"imageOffset":4008,"symbol":"mach_msg","symbolLocation":24,"imageIndex":212},{"imageOffset":77644624,"imageIndex":56},{"imageOffset":77143240,"imageIndex":56},{"imageOffset":77377520,"imageIndex":56},{"imageOffset":77374852,"imageIndex":56},{"imageOffset":77374376,"imageIndex":56},{"imageOffset":77374076,"imageIndex":56},{"imageOffset":77536044,"imageIndex":56},{"imageOffset":27660,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":213},{"imageOffset":7040,"symbol":"thread_start","symbolLocation":8,"imageIndex":213}]},{"id":2631290,"name":"NetworkConfigWatcher","threadState":{"x":[{"value":268451845},{"value":17179869186},{"value":0},{"value":329866373234688},{"value":0},{"value":329866373234688},{"value":32},{"value":0},{"value":0},{"value":17179869184},{"value":32},{"value":0},{"value":0},{"value":0},{"value":76803},{"value":3754039405},{"value":18446744073709551569},{"value":13626208256},{"value":0},{"value":0},{"value":32},{"value":329866373234688},{"value":0},{"value":329866373234688},{"value":13626207248},{"value":0},{"value":17179869186},{"value":18446744073709550527},{"value":2}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6834914208},"cpsr":{"value":0},"fp":{"value":13626206592},"sp":{"value":13626206512},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6834838580},"far":{"value":0}},"frames":[{"imageOffset":3124,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":212},{"imageOffset":78752,"symbol":"mach_msg2_internal","symbolLocation":76,"imageIndex":212},{"imageOffset":38756,"symbol":"mach_msg_overwrite","symbolLocation":484,"imageIndex":212},{"imageOffset":4008,"symbol":"mach_msg","symbolLocation":24,"imageIndex":212},{"imageOffset":77644624,"imageIndex":56},{"imageOffset":77143240,"imageIndex":56},{"imageOffset":77143120,"imageIndex":56},{"imageOffset":76806856,"imageIndex":56},{"imageOffset":77272856,"imageIndex":56},{"imageOffset":77019148,"imageIndex":56},{"imageOffset":77432160,"imageIndex":56},{"imageOffset":77432544,"imageIndex":56},{"imageOffset":77536044,"imageIndex":56},{"imageOffset":27660,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":213},{"imageOffset":7040,"symbol":"thread_start","symbolLocation":8,"imageIndex":213}]},{"id":2631309,"frames":[{"imageOffset":17356,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":212},{"imageOffset":28896,"symbol":"_pthread_cond_wait","symbolLocation":984,"imageIndex":213},{"imageOffset":1502040,"symbol":"blas_thread_server","symbolLocation":360,"imageIndex":19},{"imageOffset":27660,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":213},{"imageOffset":7040,"symbol":"thread_start","symbolLocation":8,"imageIndex":213}],"threadState":{"x":[{"value":260},{"value":0},{"value":25088},{"value":0},{"value":0},{"value":160},{"value":0},{"value":0},{"value":6357020360},{"value":0},{"value":0},{"value":2},{"value":2},{"value":0},{"value":0},{"value":0},{"value":305},{"value":8697287952},{"value":0},{"value":4408664080,"symbolLocation":16,"symbol":"thread_status"},{"value":4408664144,"symbolLocation":80,"symbol":"thread_status"},{"value":6357020896},{"value":0},{"value":0},{"value":25088},{"value":25089},{"value":25344},{"value":4408578048,"symbolLocation":16,"symbol":"gemm_driver.level3_lock"},{"value":1}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6835110112},"cpsr":{"value":1610612736},"fp":{"value":6357020480},"sp":{"value":6357020336},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6834852812},"far":{"value":0}}},{"id":2631310,"frames":[{"imageOffset":17356,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":212},{"imageOffset":28896,"symbol":"_pthread_cond_wait","symbolLocation":984,"imageIndex":213},{"imageOffset":1502040,"symbol":"blas_thread_server","symbolLocation":360,"imageIndex":19},{"imageOffset":27660,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":213},{"imageOffset":7040,"symbol":"thread_start","symbolLocation":8,"imageIndex":213}],"threadState":{"x":[{"value":260},{"value":0},{"value":25088},{"value":0},{"value":0},{"value":160},{"value":0},{"value":0},{"value":6361919176},{"value":0},{"value":0},{"value":2},{"value":2},{"value":0},{"value":0},{"value":0},{"value":305},{"value":8697287952},{"value":0},{"value":4408664208,"symbolLocation":144,"symbol":"thread_status"},{"value":4408664272,"symbolLocation":208,"symbol":"thread_status"},{"value":6361919712},{"value":0},{"value":0},{"value":25088},{"value":25089},{"value":25344},{"value":4408578048,"symbolLocation":16,"symbol":"gemm_driver.level3_lock"},{"value":1}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6835110112},"cpsr":{"value":1610612736},"fp":{"value":6361919296},"sp":{"value":6361919152},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6834852812},"far":{"value":0}}},{"id":2631311,"frames":[{"imageOffset":17356,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":212},{"imageOffset":28896,"symbol":"_pthread_cond_wait","symbolLocation":984,"imageIndex":213},{"imageOffset":1502040,"symbol":"blas_thread_server","symbolLocation":360,"imageIndex":19},{"imageOffset":27660,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":213},{"imageOffset":7040,"symbol":"thread_start","symbolLocation":8,"imageIndex":213}],"threadState":{"x":[{"value":260},{"value":0},{"value":0},{"value":0},{"value":0},{"value":160},{"value":0},{"value":0},{"value":6362623688},{"value":0},{"value":0},{"value":2},{"value":2},{"value":0},{"value":0},{"value":0},{"value":305},{"value":8697287952},{"value":0},{"value":4408664336,"symbolLocation":272,"symbol":"thread_status"},{"value":4408664400,"symbolLocation":336,"symbol":"thread_status"},{"value":6362624224},{"value":0},{"value":0},{"value":0},{"value":1},{"value":256},{"value":4408578048,"symbolLocation":16,"symbol":"gemm_driver.level3_lock"},{"value":1}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6835110112},"cpsr":{"value":1610612736},"fp":{"value":6362623808},"sp":{"value":6362623664},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6834852812},"far":{"value":0}}},{"id":2631312,"frames":[{"imageOffset":17356,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":212},{"imageOffset":28896,"symbol":"_pthread_cond_wait","symbolLocation":984,"imageIndex":213},{"imageOffset":1502040,"symbol":"blas_thread_server","symbolLocation":360,"imageIndex":19},{"imageOffset":27660,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":213},{"imageOffset":7040,"symbol":"thread_start","symbolLocation":8,"imageIndex":213}],"threadState":{"x":[{"value":260},{"value":0},{"value":0},{"value":0},{"value":0},{"value":160},{"value":0},{"value":0},{"value":6363868872},{"value":0},{"value":0},{"value":2},{"value":2},{"value":0},{"value":0},{"value":0},{"value":305},{"value":8697287952},{"value":0},{"value":4408664464,"symbolLocation":400,"symbol":"thread_status"},{"value":4408664528,"symbolLocation":464,"symbol":"thread_status"},{"value":6363869408},{"value":0},{"value":0},{"value":0},{"value":1},{"value":256},{"value":4408578048,"symbolLocation":16,"symbol":"gemm_driver.level3_lock"},{"value":1}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6835110112},"cpsr":{"value":1610612736},"fp":{"value":6363868992},"sp":{"value":6363868848},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6834852812},"far":{"value":0}}},{"id":2631313,"frames":[{"imageOffset":17356,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":212},{"imageOffset":28896,"symbol":"_pthread_cond_wait","symbolLocation":984,"imageIndex":213},{"imageOffset":1502040,"symbol":"blas_thread_server","symbolLocation":360,"imageIndex":19},{"imageOffset":27660,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":213},{"imageOffset":7040,"symbol":"thread_start","symbolLocation":8,"imageIndex":213}],"threadState":{"x":[{"value":260},{"value":0},{"value":0},{"value":0},{"value":0},{"value":160},{"value":0},{"value":0},{"value":6364442312},{"value":0},{"value":0},{"value":2},{"value":2},{"value":0},{"value":0},{"value":0},{"value":305},{"value":8697287952},{"value":0},{"value":4408664592,"symbolLocation":528,"symbol":"thread_status"},{"value":4408664656,"symbolLocation":592,"symbol":"thread_status"},{"value":6364442848},{"value":0},{"value":0},{"value":0},{"value":1},{"value":256},{"value":4408578048,"symbolLocation":16,"symbol":"gemm_driver.level3_lock"},{"value":1}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6835110112},"cpsr":{"value":1610612736},"fp":{"value":6364442432},"sp":{"value":6364442288},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6834852812},"far":{"value":0}}},{"id":2631314,"frames":[{"imageOffset":17356,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":212},{"imageOffset":28896,"symbol":"_pthread_cond_wait","symbolLocation":984,"imageIndex":213},{"imageOffset":1502040,"symbol":"blas_thread_server","symbolLocation":360,"imageIndex":19},{"imageOffset":27660,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":213},{"imageOffset":7040,"symbol":"thread_start","symbolLocation":8,"imageIndex":213}],"threadState":{"x":[{"value":260},{"value":0},{"value":0},{"value":0},{"value":0},{"value":160},{"value":0},{"value":0},{"value":6365015752},{"value":0},{"value":0},{"value":2},{"value":2},{"value":0},{"value":0},{"value":0},{"value":305},{"value":8697287952},{"value":0},{"value":4408664720,"symbolLocation":656,"symbol":"thread_status"},{"value":4408664784,"symbolLocation":720,"symbol":"thread_status"},{"value":6365016288},{"value":0},{"value":0},{"value":0},{"value":1},{"value":256},{"value":4408578048,"symbolLocation":16,"symbol":"gemm_driver.level3_lock"},{"value":1}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6835110112},"cpsr":{"value":1610612736},"fp":{"value":6365015872},"sp":{"value":6365015728},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6834852812},"far":{"value":0}}},{"id":2631315,"frames":[{"imageOffset":17356,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":212},{"imageOffset":28896,"symbol":"_pthread_cond_wait","symbolLocation":984,"imageIndex":213},{"imageOffset":1502040,"symbol":"blas_thread_server","symbolLocation":360,"imageIndex":19},{"imageOffset":27660,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":213},{"imageOffset":7040,"symbol":"thread_start","symbolLocation":8,"imageIndex":213}],"threadState":{"x":[{"value":260},{"value":0},{"value":0},{"value":0},{"value":0},{"value":160},{"value":0},{"value":0},{"value":14038888136},{"value":0},{"value":0},{"value":2},{"value":2},{"value":0},{"value":0},{"value":0},{"value":305},{"value":8697287952},{"value":0},{"value":4408664848,"symbolLocation":784,"symbol":"thread_status"},{"value":4408664912,"symbolLocation":848,"symbol":"thread_status"},{"value":14038888672},{"value":0},{"value":0},{"value":0},{"value":1},{"value":256},{"value":4408578048,"symbolLocation":16,"symbol":"gemm_driver.level3_lock"},{"value":1}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6835110112},"cpsr":{"value":1610612736},"fp":{"value":14038888256},"sp":{"value":14038888112},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6834852812},"far":{"value":0}}},{"id":2631316,"frames":[{"imageOffset":17356,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":212},{"imageOffset":28896,"symbol":"_pthread_cond_wait","symbolLocation":984,"imageIndex":213},{"imageOffset":1502040,"symbol":"blas_thread_server","symbolLocation":360,"imageIndex":19},{"imageOffset":27660,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":213},{"imageOffset":7040,"symbol":"thread_start","symbolLocation":8,"imageIndex":213}],"threadState":{"x":[{"value":260},{"value":0},{"value":0},{"value":0},{"value":0},{"value":160},{"value":0},{"value":0},{"value":14284451528},{"value":0},{"value":0},{"value":2},{"value":2},{"value":0},{"value":0},{"value":0},{"value":305},{"value":8697287952},{"value":0},{"value":4408664976,"symbolLocation":912,"symbol":"thread_status"},{"value":4408665040,"symbolLocation":976,"symbol":"thread_status"},{"value":14284452064},{"value":0},{"value":0},{"value":0},{"value":1},{"value":256},{"value":4408578048,"symbolLocation":16,"symbol":"gemm_driver.level3_lock"},{"value":1}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6835110112},"cpsr":{"value":1610612736},"fp":{"value":14284451648},"sp":{"value":14284451504},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6834852812},"far":{"value":0}}},{"id":2631317,"frames":[{"imageOffset":17356,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":212},{"imageOffset":28896,"symbol":"_pthread_cond_wait","symbolLocation":984,"imageIndex":213},{"imageOffset":1502040,"symbol":"blas_thread_server","symbolLocation":360,"imageIndex":19},{"imageOffset":27660,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":213},{"imageOffset":7040,"symbol":"thread_start","symbolLocation":8,"imageIndex":213}],"threadState":{"x":[{"value":260},{"value":0},{"value":0},{"value":0},{"value":0},{"value":160},{"value":0},{"value":0},{"value":14285024968},{"value":0},{"value":0},{"value":2},{"value":2},{"value":0},{"value":0},{"value":0},{"value":305},{"value":8697287952},{"value":0},{"value":4408665104,"symbolLocation":1040,"symbol":"thread_status"},{"value":4408665168,"symbolLocation":1104,"symbol":"thread_status"},{"value":14285025504},{"value":0},{"value":0},{"value":0},{"value":1},{"value":256},{"value":4408578048,"symbolLocation":16,"symbol":"gemm_driver.level3_lock"},{"value":1}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6835110112},"cpsr":{"value":1610612736},"fp":{"value":14285025088},"sp":{"value":14285024944},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6834852812},"far":{"value":0}}},{"id":2631569,"name":"com.apple.NSEventThread","threadState":{"x":[{"value":268451845},{"value":21592279046},{"value":8589934592},{"value":393758306729984},{"value":0},{"value":393758306729984},{"value":2},{"value":4294967295},{"value":0},{"value":17179869184},{"value":0},{"value":2},{"value":0},{"value":0},{"value":91679},{"value":0},{"value":18446744073709551569},{"value":8697289832},{"value":0},{"value":4294967295},{"value":2},{"value":393758306729984},{"value":0},{"value":393758306729984},{"value":13627842696},{"value":8589934592},{"value":21592279046},{"value":18446744073709550527},{"value":4412409862}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6834914208},"cpsr":{"value":0},"fp":{"value":13627842544},"sp":{"value":13627842464},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6834838580},"far":{"value":0}},"frames":[{"imageOffset":3124,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":212},{"imageOffset":78752,"symbol":"mach_msg2_internal","symbolLocation":76,"imageIndex":212},{"imageOffset":38756,"symbol":"mach_msg_overwrite","symbolLocation":484,"imageIndex":212},{"imageOffset":4008,"symbol":"mach_msg","symbolLocation":24,"imageIndex":212},{"imageOffset":511164,"symbol":"__CFRunLoopServiceMachPort","symbolLocation":160,"imageIndex":222},{"imageOffset":505304,"symbol":"__CFRunLoopRun","symbolLocation":1208,"imageIndex":222},{"imageOffset":502424,"symbol":"CFRunLoopRunSpecific","symbolLocation":572,"imageIndex":222},{"imageOffset":1435532,"symbol":"_NSEventThread","symbolLocation":140,"imageIndex":216},{"imageOffset":27660,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":213},{"imageOffset":7040,"symbol":"thread_start","symbolLocation":8,"imageIndex":213}]},{"id":2631572,"name":"ThreadPoolBackgroundWorker","threadState":{"x":[{"value":268451845},{"value":17179869186},{"value":0},{"value":726824430600192},{"value":0},{"value":726824430600192},{"value":32},{"value":0},{"value":0},{"value":17179869184},{"value":32},{"value":0},{"value":0},{"value":0},{"value":169227},{"value":2043},{"value":18446744073709551569},{"value":8},{"value":0},{"value":0},{"value":32},{"value":726824430600192},{"value":0},{"value":726824430600192},{"value":14318021936},{"value":0},{"value":17179869186},{"value":18446744073709550527},{"value":2}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6834914208},"cpsr":{"value":0},"fp":{"value":14318021280},"sp":{"value":14318021200},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6834838580},"far":{"value":0}},"frames":[{"imageOffset":3124,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":212},{"imageOffset":78752,"symbol":"mach_msg2_internal","symbolLocation":76,"imageIndex":212},{"imageOffset":38756,"symbol":"mach_msg_overwrite","symbolLocation":484,"imageIndex":212},{"imageOffset":4008,"symbol":"mach_msg","symbolLocation":24,"imageIndex":212},{"imageOffset":77644624,"imageIndex":56},{"imageOffset":77143240,"imageIndex":56},{"imageOffset":77377520,"imageIndex":56},{"imageOffset":77374852,"imageIndex":56},{"imageOffset":77374156,"imageIndex":56},{"imageOffset":77374064,"imageIndex":56},{"imageOffset":77536044,"imageIndex":56},{"imageOffset":27660,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":213},{"imageOffset":7040,"symbol":"thread_start","symbolLocation":8,"imageIndex":213}]},{"id":2631573,"name":"MemoryInfra","threadState":{"x":[{"value":268451845},{"value":17179869186},{"value":0},{"value":495909808898048},{"value":0},{"value":495909808898048},{"value":32},{"value":0},{"value":0},{"value":17179869184},{"value":32},{"value":0},{"value":0},{"value":0},{"value":115463},{"value":3762436154},{"value":18446744073709551569},{"value":13995831296},{"value":0},{"value":0},{"value":32},{"value":495909808898048},{"value":0},{"value":495909808898048},{"value":13995830288},{"value":0},{"value":17179869186},{"value":18446744073709550527},{"value":2}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6834914208},"cpsr":{"value":0},"fp":{"value":13995829632},"sp":{"value":13995829552},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6834838580},"far":{"value":0}},"frames":[{"imageOffset":3124,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":212},{"imageOffset":78752,"symbol":"mach_msg2_internal","symbolLocation":76,"imageIndex":212},{"imageOffset":38756,"symbol":"mach_msg_overwrite","symbolLocation":484,"imageIndex":212},{"imageOffset":4008,"symbol":"mach_msg","symbolLocation":24,"imageIndex":212},{"imageOffset":77644624,"imageIndex":56},{"imageOffset":77143240,"imageIndex":56},{"imageOffset":77143120,"imageIndex":56},{"imageOffset":76806856,"imageIndex":56},{"imageOffset":77272856,"imageIndex":56},{"imageOffset":77019148,"imageIndex":56},{"imageOffset":77432160,"imageIndex":56},{"imageOffset":77432544,"imageIndex":56},{"imageOffset":77536044,"imageIndex":56},{"imageOffset":27660,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":213},{"imageOffset":7040,"symbol":"thread_start","symbolLocation":8,"imageIndex":213}]},{"id":2631574,"name":"ThreadPoolSingleThreadSharedBackgroundBlocking2","threadState":{"x":[{"value":268451845},{"value":17179869186},{"value":0},{"value":494810297270272},{"value":0},{"value":494810297270272},{"value":32},{"value":0},{"value":0},{"value":17179869184},{"value":32},{"value":0},{"value":0},{"value":0},{"value":115207},{"value":3509194773},{"value":18446744073709551569},{"value":231},{"value":0},{"value":0},{"value":32},{"value":494810297270272},{"value":0},{"value":494810297270272},{"value":14004251952},{"value":0},{"value":17179869186},{"value":18446744073709550527},{"value":2}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6834914208},"cpsr":{"value":0},"fp":{"value":14004251296},"sp":{"value":14004251216},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6834838580},"far":{"value":0}},"frames":[{"imageOffset":3124,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":212},{"imageOffset":78752,"symbol":"mach_msg2_internal","symbolLocation":76,"imageIndex":212},{"imageOffset":38756,"symbol":"mach_msg_overwrite","symbolLocation":484,"imageIndex":212},{"imageOffset":4008,"symbol":"mach_msg","symbolLocation":24,"imageIndex":212},{"imageOffset":77644624,"imageIndex":56},{"imageOffset":77143240,"imageIndex":56},{"imageOffset":77377520,"imageIndex":56},{"imageOffset":77374852,"imageIndex":56},{"imageOffset":77374200,"imageIndex":56},{"imageOffset":77374112,"imageIndex":56},{"imageOffset":77536044,"imageIndex":56},{"imageOffset":27660,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":213},{"imageOffset":7040,"symbol":"thread_start","symbolLocation":8,"imageIndex":213}]},{"id":2665993,"name":"ThreadPoolForegroundWorker","threadState":{"x":[{"value":268451845},{"value":17179869186},{"value":0},{"value":432035055271936},{"value":0},{"value":432035055271936},{"value":32},{"value":0},{"value":0},{"value":17179869184},{"value":32},{"value":0},{"value":0},{"value":0},{"value":100591},{"value":3871635727},{"value":18446744073709551569},{"value":14329615872},{"value":0},{"value":0},{"value":32},{"value":432035055271936},{"value":0},{"value":432035055271936},{"value":14079733040},{"value":0},{"value":17179869186},{"value":18446744073709550527},{"value":2}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6834914208},"cpsr":{"value":0},"fp":{"value":14079732384},"sp":{"value":14079732304},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6834838580},"far":{"value":0}},"frames":[{"imageOffset":3124,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":212},{"imageOffset":78752,"symbol":"mach_msg2_internal","symbolLocation":76,"imageIndex":212},{"imageOffset":38756,"symbol":"mach_msg_overwrite","symbolLocation":484,"imageIndex":212},{"imageOffset":4008,"symbol":"mach_msg","symbolLocation":24,"imageIndex":212},{"imageOffset":77644624,"imageIndex":56},{"imageOffset":77143240,"imageIndex":56},{"imageOffset":77377520,"imageIndex":56},{"imageOffset":77374852,"imageIndex":56},{"imageOffset":77374288,"imageIndex":56},{"imageOffset":77374004,"imageIndex":56},{"imageOffset":77536044,"imageIndex":56},{"imageOffset":27660,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":213},{"imageOffset":7040,"symbol":"thread_start","symbolLocation":8,"imageIndex":213}]},{"id":2667286,"frames":[{"imageOffset":7020,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":213}],"threadState":{"x":[{"value":13520891904},{"value":132951},{"value":13520355328},{"value":0},{"value":409603},{"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":0},"fp":{"value":0},"sp":{"value":13520891904},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6835088236},"far":{"value":0}}},{"id":2698463,"frames":[{"imageOffset":7020,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":213}],"threadState":{"x":[{"value":13570240512},{"value":147307},{"value":13569703936},{"value":0},{"value":409603},{"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":0},"fp":{"value":0},"sp":{"value":13570240512},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6835088236},"far":{"value":0}}},{"id":2730065,"frames":[{"imageOffset":7020,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":213}],"threadState":{"x":[{"value":13564407808},{"value":172863},{"value":13563871232},{"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":0},"fp":{"value":0},"sp":{"value":13564407808},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6835088236},"far":{"value":0}}},{"id":2730066,"frames":[{"imageOffset":7020,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":213}],"threadState":{"x":[{"value":13570813952},{"value":0},{"value":13570277376},{"value":0},{"value":278532},{"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":0},"fp":{"value":0},"sp":{"value":13570813952},"esr":{"value":0,"description":" Address size fault"},"pc":{"value":6835088236},"far":{"value":0}}},{"id":2730067,"frames":[{"imageOffset":7020,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":213}],"threadState":{"x":[{"value":13571387392},{"value":0},{"value":13570850816},{"value":0},{"value":278532},{"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":0},"fp":{"value":0},"sp":{"value":13571387392},"esr":{"value":0,"description":" Address size fault"},"pc":{"value":6835088236},"far":{"value":0}}}],
"usedImages" : [
[deleted to fit within ticket limits]
],
"sharedCache" : {
"base" : 6830440448,
"size" : 5040898048,
"uuid" : "4c1223e5-cace-3982-a003-6110a7a8a25c"
},
"vmSummary" : "ReadOnly portion of Libraries: Total=2.0G resident=0K(0%) swapped_out_or_unallocated=2.0G(100%)\nWritable regions: Total=4.7G written=148.7M(3%) resident=2708K(0%) swapped_out=146.0M(3%) unallocated=4.5G(97%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 1280K 10 \nActivity Tracing 256K 1 \nCG image 176K 9 \nColorSync 608K 32 \nCoreAnimation 1728K 108 \nCoreGraphics 48K 3 \nCoreUI image data 4288K 32 \nFoundation 16K 1 \nKernel Alloc Once 32K 1 \nMALLOC 4.0G 120 \nMALLOC guard page 288K 18 \nMach message 64K 2 \nOpenGL GLSL 384K 4 \nSTACK GUARD 608K 38 \nStack 200.3M 39 \nStack Guard 56.0M 1 \nVM_ALLOCATE 409.4M 160 \nVM_ALLOCATE (reserved) 128.0M 2 reserved VM address space (unallocated)\n__AUTH 5441K 690 \n__AUTH_CONST 76.8M 937 \n__CTF 824 1 \n__DATA 39.6M 1149 \n__DATA_CONST 38.2M 1155 \n__DATA_DIRTY 2776K 341 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 658.9M 213 \n__OBJC_RO 61.4M 1 \n__OBJC_RW 2396K 1 \n__TEXT 1.3G 1176 \n__TPRO_CONST 128K 2 \ndyld private memory 8400K 67 \nmapped file 270.3M 52 \npage table in kernel 2708K 1 \nshared memory 3696K 24 \n=========== ======= ======= \nTOTAL 7.2G 6394 \nTOTAL, minus reserved VM space 7.1G 6394 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"logWritingSignature" : "766e6a6e920b82d5d9e7313caf6f7c45a3f4394d",
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "6410af69ed1e1e7ab93ed169",
"factorPackIds" : {
},
"deploymentId" : 240000011
},
{
"rolloutId" : "6434420a89ec2e0a7a38bf5a",
"factorPackIds" : {
},
"deploymentId" : 240000011
}
],
"experiments" : [
]
}
}
===== Log before crash start =====
UCSF ChimeraX version: 1.10.dev202503130118 (2025-03-13)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/Ward lab work/364
> fab and CSP.cxs"
Opened emdb 27789 as #2, grid size 220,220,220, pixel 1.15, shown at level
0.3, step 1, values float32
Opened J138_005_volume_map_emready2.mrc as #3, grid size 637,637,637, pixel
0.5, shown at level 3.78, step 1, values float32
Opened J138_005_volume_map_emready2.mrc z flip as #4, grid size 637,637,637,
pixel 0.5, shown at level 4.4, step 1, values float32
Log from Thu Feb 12 17:06:40 2026UCSF ChimeraX version: 1.10.dev202503130118
(2025-03-13)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/zrizvi/Downloads/8DZ5.cif
8DZ5.cif title:
Cryo-EM structure of 364 Fab in complex with recombinant shortened Plasmodium
falciparum circumsporozoite protein (rsCSP) [more info...]
Chain information for 8DZ5.cif #1
---
Chain | Description
A C E H M | 364 Fab heavy chain
B D F L N | 364 Fab light chain
I | Circumsporozoite protein
> open EMDB:27789
Opened emdb 27789 as #2, grid size 220,220,220, pixel 1.15, shown at level
0.3, step 1, values float32, fit PDB 8dz5
> hide atoms
> show cartoons
> open /Users/zrizvi/Desktop/J138_005_volume_map_emready2.mrc
Opened J138_005_volume_map_emready2.mrc as #3, grid size 637,637,637, pixel
0.5, shown at level 0.082, step 4, values float32
> volume #3 step 1
> volume #3 level 1.727
> volume #3 level 3.448
> vop flip #3
Opened J138_005_volume_map_emready2.mrc z flip as #4, grid size 637,637,637,
pixel 0.5, shown at step 1, values float32
> hide #1 models
> set bgColor white
> graphics silhouettes true
> lighting shadows false
> lighting soft
> lighting full
> hide #!4 models
> show #!4 models
> select add #4
2 models selected
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.99607,-0.080169,0.037668,327.4,0.067721,-0.96335,-0.25955,350.65,0.057095,-0.25598,0.965,38.156
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.99607,-0.080169,0.037668,325.57,0.067721,-0.96335,-0.25955,327.43,0.057095,-0.25598,0.965,11.263
> ui mousemode right translate
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.99607,-0.080169,0.037668,297.17,0.067721,-0.96335,-0.25955,331.06,0.057095,-0.25598,0.965,15.212
> ui mousemode right translate
> select up
8950 atoms, 9174 bonds, 1155 residues, 7 models selected
> fitmap #4 inMap #2
Fit map J138_005_volume_map_emready2.mrc z flip in map emdb 27789 using 722271
points
correlation = 0.7375, correlation about mean = 0.04011, overlap = 9.945e+05
steps = 136, shift = 5.32, angle = 14.3 degrees
Position of J138_005_volume_map_emready2.mrc z flip (#4) relative to emdb
27789 (#2) coordinates:
Matrix rotation and translation
-0.99337646 0.10058286 0.05555444 264.91651700
-0.11457169 -0.90384363 -0.41223782 369.68694887
0.00874847 -0.41587231 0.90938094 55.13871083
Axis -0.01650415 0.21254486 -0.97701192
Axis point 142.31803628 183.34485876 0.00000000
Rotation angle (degrees) 173.67843250
Shift along axis 20.33165992
> select subtract #1
6 models selected
> select subtract #2
4 models selected
> hide #!2 models
> show #1 models
> select subtract #3
2 models selected
> fitmap #1 inMap #4
Fit molecule 8DZ5.cif (#1) to map J138_005_volume_map_emready2.mrc z flip (#4)
using 8950 atoms
average map value = 2.582, steps = 2000
shifted from previous position = 3.12
rotated from previous position = 6.67 degrees
atoms outside contour = 6103, contour level = 3.4477
Position of 8DZ5.cif (#1) relative to J138_005_volume_map_emready2.mrc z flip
(#4) coordinates:
Matrix rotation and translation
-0.99477432 -0.09896582 0.02509620 304.20449803
0.08642159 -0.94707885 -0.30914875 323.81417332
0.05436324 -0.30536439 0.95068251 69.72705585
Axis 0.02015947 -0.15590668 0.98756605
Axis point 143.58853154 174.64329383 0.00000000
Rotation angle (degrees) 174.61424657
Shift along axis 24.50788175
> color #4 #ffffb2ab models
> lighting full
> select subtract #4
Nothing selected
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
Drag select of 2 residues
> select up
280 atoms, 289 bonds, 40 residues, 1 model selected
> color sel black
> select clear
> show #!4 models
> show #!2 models
> hide #!4 models
> color #2 #b2b2b2b1 models
> color #2 #b2b2b2b0 models
> hide #!2 models
> show #!4 models
> volume #3 level 3.781
> hide #!3 models
> volume #4 level 4.397
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #1 models
> show #1 models
> hide #!2 models
> fitmap #1 inMap #4
Fit molecule 8DZ5.cif (#1) to map J138_005_volume_map_emready2.mrc z flip (#4)
using 8950 atoms
average map value = 2.581, steps = 2000
shifted from previous position = 0.242
rotated from previous position = 0.0941 degrees
atoms outside contour = 6767, contour level = 4.3974
Position of 8DZ5.cif (#1) relative to J138_005_volume_map_emready2.mrc z flip
(#4) coordinates:
Matrix rotation and translation
-0.99482591 -0.09809147 0.02644767 303.97868662
0.08519576 -0.94730131 -0.30880722 324.17704316
0.05534526 -0.30495620 0.95075687 69.63647307
Axis 0.02075004 -0.15570561 0.98758554
Axis point 143.53604341 174.72210576 0.00000000
Rotation angle (degrees) 174.67554238
Shift along axis 24.60336188
> fitmap #2 inMap #4
Fit map emdb 27789 in map J138_005_volume_map_emready2.mrc z flip using 67102
points
correlation = 0.7187, correlation about mean = 0.1659, overlap = 8.451e+04
steps = 96, shift = 0.377, angle = 0.608 degrees
Position of emdb 27789 (#2) relative to J138_005_volume_map_emready2.mrc z
flip (#4) coordinates:
Matrix rotation and translation
-0.99393761 -0.10858956 0.01721448 303.06956338
0.09152362 -0.90395157 -0.41772596 331.71968624
0.06092174 -0.41361801 0.90840997 87.47175308
Axis 0.02005131 -0.21333946 0.97677235
Axis point 141.80065823 183.36819890 0.00000000
Rotation angle (degrees) 174.12053987
Shift along axis 20.74803338
> show #!2 models
> hide #1 models
> show #1 models
> save "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/Ward lab work/364
> fab and CSP.cxs" includeMaps true
——— End of log from Thu Feb 12 17:06:40 2026 ———
> view name session-start
opened ChimeraX session
> hide #!2 models
> show #!2 models
> hide #1 models
> show #1 models
> hide #!2 models
> show #!2 models
> hide #1 models
> hide #!4 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!2 models
> show #1 models
> fitmap #1 inMap #4
Fit molecule 8DZ5.cif (#1) to map J138_005_volume_map_emready2.mrc z flip (#4)
using 8950 atoms
average map value = 2.582, steps = 2000
shifted from previous position = 0.108
rotated from previous position = 0.145 degrees
atoms outside contour = 6785, contour level = 4.3974
Position of 8DZ5.cif (#1) relative to J138_005_volume_map_emready2.mrc z flip
(#4) coordinates:
Matrix rotation and translation
-0.99459702 -0.10017085 0.02724993 304.11905575
0.08699560 -0.94749088 -0.30772195 323.74569560
0.05664383 -0.30368871 0.95108603 69.18569866
Axis 0.02128319 -0.15511012 0.98766790
Axis point 143.44028428 174.60330984 0.00000000
Rotation angle (degrees) 174.56297062
Shift along axis 24.58888421
> select add #4
2 models selected
> select subtract #4
Nothing selected
> select add #1
8950 atoms, 9174 bonds, 1155 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.6314,-0.73868,-0.23597,167.23,0.74572,0.49495,0.44601,-94.609,-0.21267,-0.45758,0.86336,102.65
> view matrix models
> #1,-0.98558,-0.15069,0.077003,272.57,-0.010092,0.50657,0.86214,-47.02,-0.16892,0.84893,-0.50079,108.09
> view matrix models
> #1,-0.94088,-0.28361,-0.18525,316.03,-0.28544,0.36925,0.88441,4.0657,-0.18242,0.885,-0.42837,96.327
> fitmap #1 inMap #4
Fit molecule 8DZ5.cif (#1) to map J138_005_volume_map_emready2.mrc z flip (#4)
using 8950 atoms
average map value = 4.14, steps = 540
shifted from previous position = 2.77
rotated from previous position = 11.8 degrees
atoms outside contour = 4982, contour level = 4.3974
Position of 8DZ5.cif (#1) relative to J138_005_volume_map_emready2.mrc z flip
(#4) coordinates:
Matrix rotation and translation
0.99019989 0.13963739 -0.00236196 11.48961637
0.08976090 -0.64928916 -0.75522616 342.31421032
-0.10699140 0.74761285 -0.65546004 161.48976063
Axis 0.99703892 0.06941504 -0.03308991
Axis point 0.00000000 133.70365955 158.52805012
Rotation angle (degrees) 131.09235241
Shift along axis 29.87366836
> hide #1 models
> show #1 models
> volume #4 level 4.141
> hide #!4 models
> show #!4 models
> hide #1 models
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.10.dev202503130118 (2025-03-13)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN-
> inhibitor/Figures/Fig 2b final EMready fig maps/0. figure 2 making .cxs"
Opened 2. cryosparc_P341_J1614_localrefine. selected.mrc as #4, grid size
300,300,300, pixel 0.833, shown at level 0.304, step 1, values float32
Opened 1. cryosparc_P341_J1735_NUrefine selected.mrc as #9, grid size
300,300,300, pixel 0.833, shown at level 0.158, step 1, values float32
Opened 3a. composite_map on EMReady2 maps of 1735 and 1614.ccp4 as #10, grid
size 300,300,300, pixel 0.833, shown at level 9.26, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 0 as #13.1, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 1 as #13.2, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 2 as #13.3, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 3 as #13.4, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 4 as #13.5, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 5 as #13.6, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 6 as #13.7, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 7 as #13.8, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 8 as #13.9, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 9 as #13.10, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 10 as #13.11, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 11 as #13.12, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened 4. open- vvd+imid NU J2526_map_emready2.mrc as #1, grid size
443,443,443, pixel 0.5, shown at level 1.01, step 1, values float32
Opened 5. open- vvd+imid local J2540_005_volume_map_emready2.mrc as #2, grid
size 443,443,443, pixel 0.5, shown at level 1.2, step 1, values float32
Opened 6a. combination of 2526 and 2540 emready2 as #3, grid size 443,443,443,
pixel 0.5, shown at level 3.48, step 1, values float32
Opened 7. Clsoed- vvd+imid NU J2528_map_emready2.mrc as #5, grid size
443,443,443, pixel 0.5, shown at level 2.31, step 1, values float32
Opened 8. Closed- vvd+imid local J2544_007_volume_map_emready2.mrc as #7, grid
size 443,443,443, pixel 0.5, shown at level 2.03, step 1, values float32
Opened 9a. combination of 2528 and 2544 emready2 as #8, grid size 443,443,443,
pixel 0.5, shown at level 5.07, step 1, values float32
Opened 6b. combination of 2526 and 2540 emready2 copy as #16, grid size
443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32
Opened 6a. combination of 2526 and 2540 emready2 0 as #14.1, grid size
443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32
Opened 6a. combination of 2526 and 2540 emready2 1 as #14.2, grid size
443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32
Opened 6a. combination of 2526 and 2540 emready2 2 as #14.3, grid size
443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32
Opened 6a. combination of 2526 and 2540 emready2 3 as #14.4, grid size
443,443,443, pixel 0.5, shown at level 4.95, step 1, values float32
Opened 6a. combination of 2526 and 2540 emready2 4 as #14.5, grid size
443,443,443, pixel 0.5, shown at level 3.46, step 1, values float32
Opened 6a. combination of 2526 and 2540 emready2 5 as #14.6, grid size
443,443,443, pixel 0.5, shown at level 4.45, step 1, values float32
Opened 6a. combination of 2526 and 2540 emready2 6 as #14.7, grid size
443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32
Opened 6a. combination of 2526 and 2540 emready2 7 as #14.8, grid size
443,443,443, pixel 0.5, shown at level 2.27, step 1, values float32
Opened 6b. combination of 2526 and 2540 emready2 copy 0 as #17.1, grid size
443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32
Opened 6b. combination of 2526 and 2540 emready2 copy 1 as #17.2, grid size
443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32
Opened 6b. combination of 2526 and 2540 emready2 copy 2 as #17.3, grid size
443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32
Opened 6b. combination of 2526 and 2540 emready2 copy 3 as #17.4, grid size
443,443,443, pixel 0.5, shown at level 2.89, step 1, values float32
Opened 6b. combination of 2526 and 2540 emready2 copy 4 as #17.5, grid size
443,443,443, pixel 0.5, shown at level 2.84, step 1, values float32
Opened 6b. combination of 2526 and 2540 emready2 copy 5 as #17.6, grid size
443,443,443, pixel 0.5, shown at level 2.85, step 1, values float32
Opened 6b. combination of 2526 and 2540 emready2 copy 6 as #17.7, grid size
443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32
Opened 6b. combination of 2526 and 2540 emready2 copy 7 as #17.8, grid size
443,443,443, pixel 0.5, shown at level 2.11, step 1, values float32
Opened 10. int1 vvd+imid NU J2527_map_emready2.mrc as #18, grid size
443,443,443, pixel 0.5, shown at level 0.9, step 1, values float32
Opened 11. int1 vvd+imid local J2541_004_volume_map_emready2.mrc as #19, grid
size 443,443,443, pixel 0.5, shown at level 1.16, step 1, values float32
Opened 12. combination of 10 and 11 as #20, grid size 443,443,443, pixel 0.5,
shown at level 6.81, step 1, values float32
Opened 14. int2 vvd+imid NU J2612_map_emready2.mrc as #21, grid size
438,438,438, pixel 0.5, shown at level 3.83, step 1, values float32
Opened 15. int2 vvd+imid local J2614_004_volume_map_emready2.mrc as #23, grid
size 438,438,438, pixel 0.5, shown at level 1.74, step 1, values float32
Opened 16. combination of 2612 and 2614 as #24, grid size 438,438,438, pixel
0.5, shown at level 5.92, step 1, values float32
Opened 18. frustrated vvd+imid NU J2438_map_emready2.mrc as #26, grid size
443,443,443, pixel 0.5, shown at level 1.18, step 1, values float32
Opened 19. frustrated vvd+imid local J2456_004_volume_map_emready2.mrc as #27,
grid size 443,443,443, pixel 0.5, shown at level 0.895, step 1, values float32
Opened 20 combination of 18 and 19 as #28, grid size 443,443,443, pixel 0.5,
shown at level 6.9, step 1, values float32
Opened 12. combination of 10 and 11 0 as #29.1, grid size 443,443,443, pixel
0.5, shown at level 5.05, step 1, values float32
Opened 12. combination of 10 and 11 1 as #29.2, grid size 443,443,443, pixel
0.5, shown at level 5.67, step 1, values float32
Opened 12. combination of 10 and 11 2 as #29.3, grid size 443,443,443, pixel
0.5, shown at level 5.87, step 1, values float32
Opened 12. combination of 10 and 11 3 as #29.4, grid size 443,443,443, pixel
0.5, shown at level 5.62, step 1, values float32
Opened 12. combination of 10 and 11 4 as #29.5, grid size 443,443,443, pixel
0.5, shown at level 3.84, step 1, values float32
Opened 12. combination of 10 and 11 5 as #29.6, grid size 443,443,443, pixel
0.5, shown at level 4.7, step 1, values float32
Opened 12. combination of 10 and 11 6 as #29.7, grid size 443,443,443, pixel
0.5, shown at level 1.29, step 1, values float32
Opened 12. combination of 10 and 11 7 as #29.8, grid size 443,443,443, pixel
0.5, shown at level 0.584, step 1, values float32
Opened 22. intT NU J2618_map_emready2.mrc as #31, grid size 438,438,438, pixel
0.5, shown at level 1.39, step 1, values float32
Opened 23. intT local J2619_004_volume_map_emready2.mrc as #32, grid size
438,438,438, pixel 0.5, shown at level 1.71, step 1, values float32
Opened combination of 22 and 23 as #33, grid size 438,438,438, pixel 0.5,
shown at level 3.68, step 1, values float32
Opened combination of 22 and 23 0 as #34.1, grid size 438,438,438, pixel 0.5,
shown at level 6.34, step 1, values float32
Opened combination of 22 and 23 1 as #34.2, grid size 438,438,438, pixel 0.5,
shown at level 6.71, step 1, values float32
Opened combination of 22 and 23 2 as #34.3, grid size 438,438,438, pixel 0.5,
shown at level 5.88, step 1, values float32
Opened combination of 22 and 23 3 as #34.4, grid size 438,438,438, pixel 0.5,
shown at level 4.06, step 1, values float32
Opened combination of 22 and 23 4 as #34.5, grid size 438,438,438, pixel 0.5,
shown at level 5.07, step 1, values float32
Opened combination of 22 and 23 5 as #34.6, grid size 438,438,438, pixel 0.5,
shown at level 3.33, step 1, values float32
Opened combination of 22 and 23 6 as #34.7, grid size 438,438,438, pixel 0.5,
shown at level 3.11, step 1, values float32
Opened combination of 22 and 23 7 as #34.8, grid size 438,438,438, pixel 0.5,
shown at level 7.44, step 1, values float32
Opened combination of 22 and 23 7 copy as #37, grid size 438,438,438, pixel
0.5, shown at level 1.65, step 1, values float32
Opened cryosparc_P341_J2527_map (3).mrc as #36, grid size 300,300,300, pixel
0.74, shown at level 0.00303, step 1, values float32
Opened cryosparc_P341_J2527_map (3).mrc 0 as #38.1, grid size 300,300,300,
pixel 0.74, shown at level 0.00303, step 1, values float32
Opened cryosparc_P341_J2527_map (3).mrc 1 as #38.2, grid size 300,300,300,
pixel 0.74, shown at level 0.00303, step 1, values float32
Opened cryosparc_P341_J2527_map (3).mrc 2 as #38.3, grid size 300,300,300,
pixel 0.74, shown at level 0.00303, step 1, values float32
Opened cryosparc_P341_J2527_map (3).mrc 3 as #38.4, grid size 300,300,300,
pixel 0.74, shown at level 0.00288, step 1, values float32
Opened cryosparc_P341_J2527_map (3).mrc 4 as #38.5, grid size 300,300,300,
pixel 0.74, shown at level 0.00217, step 1, values float32
Opened cryosparc_P341_J2527_map (3).mrc 5 as #38.6, grid size 300,300,300,
pixel 0.74, shown at level 0.00284, step 1, values float32
Opened cryosparc_P341_J2527_map (3).mrc 6 as #38.7, grid size 300,300,300,
pixel 0.74, shown at level 0.00303, step 1, values float32
Opened cryosparc_P341_J2527_map (3).mrc 7 as #38.8, grid size 300,300,300,
pixel 0.74, shown at level 0.00903, step 1, values float32
Opened cryosparc_P341_J2527_map (3).mrc 7 copy as #39, grid size 300,300,300,
pixel 0.74, shown at level 0.00381, step 1, values float32
Opened cryosparc_P341_J2574_006_volume_map (4).mrc as #40, grid size
300,300,300, pixel 0.731, shown at level 0.0303, step 1, values float32
Opened cryosparc_P341_J2574_006_volume_map (4).mrc 0 as #41.1, grid size
300,300,300, pixel 0.731, shown at level 0.0303, step 1, values float32
Opened cryosparc_P341_J2574_006_volume_map (4).mrc 1 as #41.2, grid size
300,300,300, pixel 0.731, shown at level 0.0303, step 1, values float32
Opened cryosparc_P341_J2574_006_volume_map (4).mrc 2 as #41.3, grid size
300,300,300, pixel 0.731, shown at level 0.0303, step 1, values float32
Opened cryosparc_P341_J2574_006_volume_map (4).mrc 3 as #41.4, grid size
300,300,300, pixel 0.731, shown at level 0.0175, step 1, values float32
Opened cryosparc_P341_J2574_006_volume_map (4).mrc 4 as #41.5, grid size
300,300,300, pixel 0.731, shown at level 0.0363, step 1, values float32
Opened cryosparc_P341_J2574_006_volume_map (4).mrc 5 as #41.6, grid size
300,300,300, pixel 0.731, shown at level 0.0168, step 1, values float32
Opened cryosparc_P341_J2574_006_volume_map (4).mrc 6 as #41.7, grid size
300,300,300, pixel 0.731, shown at level 0.0303, step 1, values float32
Opened cryosparc_P341_J2574_006_volume_map (4).mrc 7 as #41.8, grid size
300,300,300, pixel 0.731, shown at level 0.0303, step 1, values float32
Opened cryosparc_P341_J2574_006_volume_map (4).mrc 8 as #41.9, grid size
300,300,300, pixel 0.731, shown at level 0.0303, step 1, values float32
Opened cryosparc_P341_J2526_map (3).mrc as #42, grid size 300,300,300, pixel
0.74, shown at level 0.00917, step 1, values float32
Opened INT1 cryosparc_P341_J2527_map (3).mrc as #43, grid size 300,300,300,
pixel 0.74, shown at level 0.00274, step 1, values float32
Log from Fri Feb 27 10:44:17 2026UCSF ChimeraX version: 1.10.dev202503130118
(2025-03-13)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN-
> inhibitor/Figures/Fig 2b final EMready fig maps/0. figure 2 making .cxs"
Opened 2. cryosparc_P341_J1614_localrefine. selected.mrc as #4, grid size
300,300,300, pixel 0.833, shown at level 0.304, step 1, values float32
Opened 1. cryosparc_P341_J1735_NUrefine selected.mrc as #9, grid size
300,300,300, pixel 0.833, shown at level 0.158, step 1, values float32
Opened 3a. composite_map on EMReady2 maps of 1735 and 1614.ccp4 as #10, grid
size 300,300,300, pixel 0.833, shown at level 9.26, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 0 as #13.1, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 1 as #13.2, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 2 as #13.3, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 3 as #13.4, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 4 as #13.5, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 5 as #13.6, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 6 as #13.7, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 7 as #13.8, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 8 as #13.9, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 9 as #13.10, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 10 as #13.11, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 11 as #13.12, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened 4. open- vvd+imid NU J2526_map_emready2.mrc as #1, grid size
443,443,443, pixel 0.5, shown at level 1.01, step 1, values float32
Opened 5. open- vvd+imid local J2540_005_volume_map_emready2.mrc as #2, grid
size 443,443,443, pixel 0.5, shown at level 1.2, step 1, values float32
Opened 6a. combination of 2526 and 2540 emready2 as #3, grid size 443,443,443,
pixel 0.5, shown at level 3.48, step 1, values float32
Opened 7. Clsoed- vvd+imid NU J2528_map_emready2.mrc as #5, grid size
443,443,443, pixel 0.5, shown at level 2.31, step 1, values float32
Opened 8. Closed- vvd+imid local J2544_007_volume_map_emready2.mrc as #7, grid
size 443,443,443, pixel 0.5, shown at level 2.03, step 1, values float32
Opened 9a. combination of 2528 and 2544 emready2 as #8, grid size 443,443,443,
pixel 0.5, shown at level 5.07, step 1, values float32
Opened 6b. combination of 2526 and 2540 emready2 copy as #16, grid size
443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32
Opened 6a. combination of 2526 and 2540 emready2 0 as #14.1, grid size
443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32
Opened 6a. combination of 2526 and 2540 emready2 1 as #14.2, grid size
443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32
Opened 6a. combination of 2526 and 2540 emready2 2 as #14.3, grid size
443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32
Opened 6a. combination of 2526 and 2540 emready2 3 as #14.4, grid size
443,443,443, pixel 0.5, shown at level 4.95, step 1, values float32
Opened 6a. combination of 2526 and 2540 emready2 4 as #14.5, grid size
443,443,443, pixel 0.5, shown at level 3.46, step 1, values float32
Opened 6a. combination of 2526 and 2540 emready2 5 as #14.6, grid size
443,443,443, pixel 0.5, shown at level 4.45, step 1, values float32
Opened 6a. combination of 2526 and 2540 emready2 6 as #14.7, grid size
443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32
Opened 6a. combination of 2526 and 2540 emready2 7 as #14.8, grid size
443,443,443, pixel 0.5, shown at level 2.27, step 1, values float32
Opened 6b. combination of 2526 and 2540 emready2 copy 0 as #17.1, grid size
443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32
Opened 6b. combination of 2526 and 2540 emready2 copy 1 as #17.2, grid size
443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32
Opened 6b. combination of 2526 and 2540 emready2 copy 2 as #17.3, grid size
443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32
Opened 6b. combination of 2526 and 2540 emready2 copy 3 as #17.4, grid size
443,443,443, pixel 0.5, shown at level 2.89, step 1, values float32
Opened 6b. combination of 2526 and 2540 emready2 copy 4 as #17.5, grid size
443,443,443, pixel 0.5, shown at level 2.84, step 1, values float32
Opened 6b. combination of 2526 and 2540 emready2 copy 5 as #17.6, grid size
443,443,443, pixel 0.5, shown at level 2.85, step 1, values float32
Opened 6b. combination of 2526 and 2540 emready2 copy 6 as #17.7, grid size
443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32
Opened 6b. combination of 2526 and 2540 emready2 copy 7 as #17.8, grid size
443,443,443, pixel 0.5, shown at level 2.11, step 1, values float32
Opened 10. int1 vvd+imid NU J2527_map_emready2.mrc as #18, grid size
443,443,443, pixel 0.5, shown at level 0.9, step 1, values float32
Opened 11. int1 vvd+imid local J2541_004_volume_map_emready2.mrc as #19, grid
size 443,443,443, pixel 0.5, shown at level 1.16, step 1, values float32
Opened 12. combination of 10 and 11 as #20, grid size 443,443,443, pixel 0.5,
shown at level 5.05, step 1, values float32
Opened 14. int2 vvd+imid NU J2612_map_emready2.mrc as #21, grid size
438,438,438, pixel 0.5, shown at level 3.83, step 1, values float32
Opened 15. int2 vvd+imid local J2614_004_volume_map_emready2.mrc as #23, grid
size 438,438,438, pixel 0.5, shown at level 1.74, step 1, values float32
Opened 16. combination of 2612 and 2614 as #24, grid size 438,438,438, pixel
0.5, shown at level 5.92, step 1, values float32
Opened 18. frustrated vvd+imid NU J2438_map_emready2.mrc as #26, grid size
443,443,443, pixel 0.5, shown at level 1.18, step 1, values float32
Opened 19. frustrated vvd+imid local J2456_004_volume_map_emready2.mrc as #27,
grid size 443,443,443, pixel 0.5, shown at level 0.895, step 1, values float32
Opened 20 combination of 18 and 19 as #28, grid size 443,443,443, pixel 0.5,
shown at level 6.9, step 1, values float32
Opened 12. combination of 10 and 11 0 as #29.1, grid size 443,443,443, pixel
0.5, shown at level 5.05, step 1, values float32
Opened 12. combination of 10 and 11 1 as #29.2, grid size 443,443,443, pixel
0.5, shown at level 5.67, step 1, values float32
Opened 12. combination of 10 and 11 2 as #29.3, grid size 443,443,443, pixel
0.5, shown at level 5.87, step 1, values float32
Opened 12. combination of 10 and 11 3 as #29.4, grid size 443,443,443, pixel
0.5, shown at level 5.62, step 1, values float32
Opened 12. combination of 10 and 11 4 as #29.5, grid size 443,443,443, pixel
0.5, shown at level 3.84, step 1, values float32
Opened 12. combination of 10 and 11 5 as #29.6, grid size 443,443,443, pixel
0.5, shown at level 4.7, step 1, values float32
Opened 12. combination of 10 and 11 6 as #29.7, grid size 443,443,443, pixel
0.5, shown at level 1.29, step 1, values float32
Opened 12. combination of 10 and 11 7 as #29.8, grid size 443,443,443, pixel
0.5, shown at level 0.584, step 1, values float32
Opened 22. intT NU J2618_map_emready2.mrc as #31, grid size 438,438,438, pixel
0.5, shown at level 1.39, step 1, values float32
Opened 23. intT local J2619_004_volume_map_emready2.mrc as #32, grid size
438,438,438, pixel 0.5, shown at level 1.71, step 1, values float32
Opened combination of 22 and 23 as #33, grid size 438,438,438, pixel 0.5,
shown at level 3.68, step 1, values float32
Opened combination of 22 and 23 0 as #34.1, grid size 438,438,438, pixel 0.5,
shown at level 6.34, step 1, values float32
Opened combination of 22 and 23 1 as #34.2, grid size 438,438,438, pixel 0.5,
shown at level 6.71, step 1, values float32
Opened combination of 22 and 23 2 as #34.3, grid size 438,438,438, pixel 0.5,
shown at level 5.88, step 1, values float32
Opened combination of 22 and 23 3 as #34.4, grid size 438,438,438, pixel 0.5,
shown at level 4.06, step 1, values float32
Opened combination of 22 and 23 4 as #34.5, grid size 438,438,438, pixel 0.5,
shown at level 5.07, step 1, values float32
Opened combination of 22 and 23 5 as #34.6, grid size 438,438,438, pixel 0.5,
shown at level 3.33, step 1, values float32
Opened combination of 22 and 23 6 as #34.7, grid size 438,438,438, pixel 0.5,
shown at level 3.11, step 1, values float32
Opened combination of 22 and 23 7 as #34.8, grid size 438,438,438, pixel 0.5,
shown at level 7.44, step 1, values float32
Opened combination of 22 and 23 7 copy as #37, grid size 438,438,438, pixel
0.5, shown at level 1.65, step 1, values float32
Log from Thu Feb 26 15:13:55 2026UCSF ChimeraX version: 1.10.dev202503130118
(2025-03-13)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN-
> inhibitor/Figures/Fig 2b final EMready fig maps/0. figure 2 making .cxs"
Opened 2. cryosparc_P341_J1614_localrefine. selected.mrc as #4, grid size
300,300,300, pixel 0.833, shown at level 0.304, step 1, values float32
Opened 1. cryosparc_P341_J1735_NUrefine selected.mrc as #9, grid size
300,300,300, pixel 0.833, shown at level 0.158, step 1, values float32
Opened 3a. composite_map on EMReady2 maps of 1735 and 1614.ccp4 as #10, grid
size 300,300,300, pixel 0.833, shown at level 9.26, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 0 as #13.1, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 1 as #13.2, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 2 as #13.3, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 3 as #13.4, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 4 as #13.5, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 5 as #13.6, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 6 as #13.7, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 7 as #13.8, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 8 as #13.9, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 9 as #13.10, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 10 as #13.11, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 11 as #13.12, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened 4. open- vvd+imid NU J2526_map_emready2.mrc as #1, grid size
443,443,443, pixel 0.5, shown at level 1.01, step 1, values float32
Opened 5. open- vvd+imid local J2540_005_volume_map_emready2.mrc as #2, grid
size 443,443,443, pixel 0.5, shown at level 1.2, step 1, values float32
Opened 6a. combination of 2526 and 2540 emready2 as #3, grid size 443,443,443,
pixel 0.5, shown at level 3.48, step 1, values float32
Opened 7. Clsoed- vvd+imid NU J2528_map_emready2.mrc as #5, grid size
443,443,443, pixel 0.5, shown at level 2.31, step 1, values float32
Opened 8. Closed- vvd+imid local J2544_007_volume_map_emready2.mrc as #7, grid
size 443,443,443, pixel 0.5, shown at level 2.03, step 1, values float32
Opened 9a. combination of 2528 and 2544 emready2 as #8, grid size 443,443,443,
pixel 0.5, shown at level 5.07, step 1, values float32
Opened 6b. combination of 2526 and 2540 emready2 copy as #16, grid size
443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32
Opened 6a. combination of 2526 and 2540 emready2 0 as #14.1, grid size
443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32
Opened 6a. combination of 2526 and 2540 emready2 1 as #14.2, grid size
443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32
Opened 6a. combination of 2526 and 2540 emready2 2 as #14.3, grid size
443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32
Opened 6a. combination of 2526 and 2540 emready2 3 as #14.4, grid size
443,443,443, pixel 0.5, shown at level 4.95, step 1, values float32
Opened 6a. combination of 2526 and 2540 emready2 4 as #14.5, grid size
443,443,443, pixel 0.5, shown at level 3.46, step 1, values float32
Opened 6a. combination of 2526 and 2540 emready2 5 as #14.6, grid size
443,443,443, pixel 0.5, shown at level 4.45, step 1, values float32
Opened 6a. combination of 2526 and 2540 emready2 6 as #14.7, grid size
443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32
Opened 6a. combination of 2526 and 2540 emready2 7 as #14.8, grid size
443,443,443, pixel 0.5, shown at level 2.27, step 1, values float32
Opened 6b. combination of 2526 and 2540 emready2 copy 0 as #17.1, grid size
443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32
Opened 6b. combination of 2526 and 2540 emready2 copy 1 as #17.2, grid size
443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32
Opened 6b. combination of 2526 and 2540 emready2 copy 2 as #17.3, grid size
443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32
Opened 6b. combination of 2526 and 2540 emready2 copy 3 as #17.4, grid size
443,443,443, pixel 0.5, shown at level 2.89, step 1, values float32
Opened 6b. combination of 2526 and 2540 emready2 copy 4 as #17.5, grid size
443,443,443, pixel 0.5, shown at level 2.84, step 1, values float32
Opened 6b. combination of 2526 and 2540 emready2 copy 5 as #17.6, grid size
443,443,443, pixel 0.5, shown at level 2.85, step 1, values float32
Opened 6b. combination of 2526 and 2540 emready2 copy 6 as #17.7, grid size
443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32
Opened 6b. combination of 2526 and 2540 emready2 copy 7 as #17.8, grid size
443,443,443, pixel 0.5, shown at level 2.11, step 1, values float32
Opened 10. int1 vvd+imid NU J2527_map_emready2.mrc as #18, grid size
443,443,443, pixel 0.5, shown at level 0.9, step 1, values float32
Opened 11. int1 vvd+imid local J2541_004_volume_map_emready2.mrc as #19, grid
size 443,443,443, pixel 0.5, shown at level 1.16, step 1, values float32
Opened 12. combination of 10 and 11 as #20, grid size 443,443,443, pixel 0.5,
shown at level 5.05, step 1, values float32
Opened 14. int2 vvd+imid NU J2612_map_emready2.mrc as #21, grid size
438,438,438, pixel 0.5, shown at level 3.83, step 1, values float32
Opened 15. int2 vvd+imid local J2614_004_volume_map_emready2.mrc as #23, grid
size 438,438,438, pixel 0.5, shown at level 1.74, step 1, values float32
Opened 16. combination of 2612 and 2614 as #24, grid size 438,438,438, pixel
0.5, shown at level 5.92, step 1, values float32
Opened 18. frustrated vvd+imid NU J2438_map_emready2.mrc as #26, grid size
443,443,443, pixel 0.5, shown at level 1.18, step 1, values float32
Opened 19. frustrated vvd+imid local J2456_004_volume_map_emready2.mrc as #27,
grid size 443,443,443, pixel 0.5, shown at level 0.895, step 1, values float32
Opened 20 combination of 18 and 19 as #28, grid size 443,443,443, pixel 0.5,
shown at level 6.9, step 1, values float32
Opened 12. combination of 10 and 11 0 as #29.1, grid size 443,443,443, pixel
0.5, shown at level 5.05, step 1, values float32
Opened 12. combination of 10 and 11 1 as #29.2, grid size 443,443,443, pixel
0.5, shown at level 5.67, step 1, values float32
Opened 12. combination of 10 and 11 2 as #29.3, grid size 443,443,443, pixel
0.5, shown at level 5.87, step 1, values float32
Opened 12. combination of 10 and 11 3 as #29.4, grid size 443,443,443, pixel
0.5, shown at level 5.62, step 1, values float32
Opened 12. combination of 10 and 11 4 as #29.5, grid size 443,443,443, pixel
0.5, shown at level 3.84, step 1, values float32
Opened 12. combination of 10 and 11 5 as #29.6, grid size 443,443,443, pixel
0.5, shown at level 4.7, step 1, values float32
Opened 12. combination of 10 and 11 6 as #29.7, grid size 443,443,443, pixel
0.5, shown at level 1.29, step 1, values float32
Opened 12. combination of 10 and 11 7 as #29.8, grid size 443,443,443, pixel
0.5, shown at level 0.584, step 1, values float32
Opened 22. intT NU J2618_map_emready2.mrc as #31, grid size 438,438,438, pixel
0.5, shown at level 1.39, step 1, values float32
Opened 23. intT local J2619_004_volume_map_emready2.mrc as #32, grid size
438,438,438, pixel 0.5, shown at level 1.71, step 1, values float32
Opened combination of 22 and 23 as #33, grid size 438,438,438, pixel 0.5,
shown at level 4.67, step 1, values float32
Log from Thu Feb 26 14:52:15 2026UCSF ChimeraX version: 1.10.dev202503130118
(2025-03-13)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN-
> inhibitor/Figures/Fig 2b final EMready fig maps/0. figure 2 making .cxs"
Opened 2. cryosparc_P341_J1614_localrefine. selected.mrc as #4, grid size
300,300,300, pixel 0.833, shown at level 0.304, step 1, values float32
Opened 1. cryosparc_P341_J1735_NUrefine selected.mrc as #9, grid size
300,300,300, pixel 0.833, shown at level 0.158, step 1, values float32
Opened 3a. composite_map on EMReady2 maps of 1735 and 1614.ccp4 as #10, grid
size 300,300,300, pixel 0.833, shown at level 14, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 0 as #13.1, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 1 as #13.2, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 2 as #13.3, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 3 as #13.4, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 4 as #13.5, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 5 as #13.6, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 6 as #13.7, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 7 as #13.8, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 8 as #13.9, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 9 as #13.10, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 10 as #13.11, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 11 as #13.12, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened 4. open- vvd+imid NU J2526_map_emready2.mrc as #1, grid size
443,443,443, pixel 0.5, shown at level 1.01, step 1, values float32
Opened 5. open- vvd+imid local J2540_005_volume_map_emready2.mrc as #2, grid
size 443,443,443, pixel 0.5, shown at level 1.2, step 1, values float32
Opened 6a. combination of 2526 and 2540 emready2 as #3, grid size 443,443,443,
pixel 0.5, shown at level 6.02, step 1, values float32
Opened 7. Clsoed- vvd+imid NU J2528_map_emready2.mrc as #5, grid size
443,443,443, pixel 0.5, shown at level 2.31, step 1, values float32
Opened 8. Closed- vvd+imid local J2544_007_volume_map_emready2.mrc as #7, grid
size 443,443,443, pixel 0.5, shown at level 2.03, step 1, values float32
Opened 9a. combination of 2528 and 2544 emready2 as #8, grid size 443,443,443,
pixel 0.5, shown at level 5.07, step 1, values float32
[deleted to fit within ticket limits]
> fitmap sel inMap #28
Fit molecule copy of 9b. 5v3o- closed vvd+imid C (#29.2) to map 20 combination
of 18 and 19 (#28) using 2902 atoms
average map value = 4.105, steps = 100
shifted from previous position = 1.88
rotated from previous position = 4.04 degrees
atoms outside contour = 2438, contour level = 7.4224
Position of copy of 9b. 5v3o- closed vvd+imid C (#29.2) relative to 20
combination of 18 and 19 (#28) coordinates:
Matrix rotation and translation
0.27233221 0.52177145 0.80844897 123.48841484
-0.49550931 -0.64417995 0.58266862 177.43691566
0.82480646 -0.55927342 0.08311166 122.12419648
Axis -0.74664500 -0.01069515 -0.66513672
Axis point 0.00000000 89.54887059 -48.61646436
Rotation angle (degrees) 130.11830986
Shift along axis -175.32900958
> select clear
> select add #29
8879 atoms, 9055 bonds, 16 pseudobonds, 1140 residues, 6 models selected
> combine sel
> close #29
> rename #30 "21. model for frustrated"
> color zone #28 near #30 distance 10
> hide #!30 models
> color zone #28 near #30 distance 15
> select clear
> volume #28 level 6.67
> volume #28 level 6.933
> volume #28 level 6.896
> ui mousemode right "map eraser"
> volume erase #28 center 146.05,96.223,129.13 radius 3.8053
> view
> save "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN-
> inhibitor/Figures/Fig 2b final EMready fig maps/frustrated/frustrated.png"
> width 1800 height 1592 supersample 4 transparentBackground true
> hide #!28 models
> show #!28 models
> show #!24 models
> show #!20 models
> hide #!20 models
> show #!3 models
> hide #!3 models
> show #!8 models
> show #!20 models
> volume #20 level 4.956
> show #!16 models
> hide #!16 models
> save "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN-
> inhibitor/Figures/Fig 2b final EMready fig maps/0. figure 2 making .cxs"
> includeMaps true
——— End of log from Wed Feb 25 16:06:42 2026 ———
> view name session-start
opened ChimeraX session
> show #!14 models
> hide #!8 models
> hide #!24 models
> hide #!28 models
> hide #!20 models
> show #!3 models
> hide #!3 models
> show #!14.4 models
> show #!14.5 models
> show #!14.6 models
> show #!14.7 models
> show #!14.8 models
> volume #14.4 level 4.654
> volume #14.8 level 2.274
> volume #14.6 level 4.453
> volume #14.5 level 3.458
> volume #14.4 level 4.954
> save "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN-
> inhibitor/Figures/Fig 2b final EMready fig maps/open/fig2b.open.png" width
> 1800 height 1532 supersample 4 transparentBackground true
> save "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN-
> inhibitor/Figures/Fig 2b final EMready fig maps/0. figure 2 making .cxs"
> includeMaps true
——— End of log from Wed Feb 25 16:20:52 2026 ———
> view name session-start
opened ChimeraX session
> hide #!14 models
> show #!20 models
> hide #!20 models
> show #!18 models
> show #!19 models
> show #!20 models
> hide #!19 models
> hide #!18 models
> show #!22 models
> hide #!22 models
> volume #20 level 0.9846
> volume #20 level 5.052
> show #!22 models
> fitmap #22 inMap #20
Fit molecule 13. vvd+iberdo int1.pdb (#22) to map 12. combination of 10 and 11
(#20) using 8572 atoms
average map value = 10.26, steps = 80
shifted from previous position = 2.39
rotated from previous position = 0.5 degrees
atoms outside contour = 1849, contour level = 5.0525
Position of 13. vvd+iberdo int1.pdb (#22) relative to 12. combination of 10
and 11 (#20) coordinates:
Matrix rotation and translation
0.45290121 -0.60806549 0.65202519 66.30022263
0.65359924 -0.27095091 -0.70667789 185.29085499
0.60637325 0.74621844 0.27471715 -70.50773735
Axis 0.75483642 0.02371797 0.65548413
Axis point 0.00000000 129.65147482 28.74738650
Rotation angle (degrees) 105.76344401
Shift along axis 8.22384205
> ui tool show "Color Zone"
> volume splitbyzone #20
Opened 12. combination of 10 and 11 0 as #29.1, grid size 443,443,443, pixel
0.5, shown at level 5.05, step 1, values float32
Opened 12. combination of 10 and 11 1 as #29.2, grid size 443,443,443, pixel
0.5, shown at level 5.05, step 1, values float32
Opened 12. combination of 10 and 11 2 as #29.3, grid size 443,443,443, pixel
0.5, shown at level 5.05, step 1, values float32
Opened 12. combination of 10 and 11 3 as #29.4, grid size 443,443,443, pixel
0.5, shown at level 5.05, step 1, values float32
Opened 12. combination of 10 and 11 4 as #29.5, grid size 443,443,443, pixel
0.5, shown at level 5.05, step 1, values float32
Opened 12. combination of 10 and 11 5 as #29.6, grid size 443,443,443, pixel
0.5, shown at level 5.05, step 1, values float32
Opened 12. combination of 10 and 11 6 as #29.7, grid size 443,443,443, pixel
0.5, shown at level 5.05, step 1, values float32
Opened 12. combination of 10 and 11 7 as #29.8, grid size 443,443,443, pixel
0.5, shown at level 5.05, step 1, values float32
> volume #29.2 level 5.983
> volume #29.2 level 5.673
> volume #29.3 level 5.872
> hide #!22 models
> volume #29.4 level 5.623
> volume #29.5 level 3.84
> volume #29.6 level 4.849
> volume #29.7 level 1.294
> volume #29.8 level 0.5091
> volume #29.6 level 4.704
> volume #29.8 level 0.5836
[Repeated 1 time(s)]
> surface dust #29.1 size 5
> surface dust #29.2 size 5
> surface dust #29.3 size 5
> surface dust #29.4 size 5
> surface dust #29.5 size 5
> surface dust #29.6 size 5
> surface dust #29.7 size 5
> surface dust #29.8 size 5
> view
> save "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN-
> inhibitor/Figures/Fig 2b final EMready fig maps/int 1/int1.png" width 1800
> height 1536 supersample 4 transparentBackground true
> save "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN-
> inhibitor/Figures/Fig 2b final EMready fig maps/0. figure 2 making .cxs"
> includeMaps true
——— End of log from Wed Feb 25 16:39:20 2026 ———
> view name session-start
opened ChimeraX session
> open /Users/zrizvi/Desktop/J2618_map_emready2.mrc
Opened J2618_map_emready2.mrc as #31, grid size 438,438,438, pixel 0.5, shown
at level 1.39, step 2, values float32
> open /Users/zrizvi/Desktop/J2619_004_volume_map_emready2.mrc
Opened J2619_004_volume_map_emready2.mrc as #32, grid size 438,438,438, pixel
0.5, shown at level 1.71, step 2, values float32
> volume #31 step 1
> volume #32 step 1
> hide #!29 models
> vop max #31 #32
Opened volume maximum as #33, grid size 438,438,438, pixel 0.5, shown at step
1, values float32
> rename #31 "22. intT NU J2618_map_emready2.mrc"
> rename #32 "23. intT local J2619_004_volume_map_emready2.mrc"
> rename #33 "combination of 22 and 23"
> volume #33 level 2.381
> show #!22 models
> color #33 darkgrey models
> color #33 #a9a9a9c7 models
> volume #33 level 5.874
> volume #33 level 4.545
> show #!20 models
> hide #!22 models
> volume #33 level 2.913
> fitmap #33 inMap #20
Fit map combination of 22 and 23 in map 12. combination of 10 and 11 using
652899 points
correlation = 0.9014, correlation about mean = 0.6876, overlap = 3.196e+07
steps = 68, shift = 1.94, angle = 2.29 degrees
Position of combination of 22 and 23 (#33) relative to 12. combination of 10
and 11 (#20) coordinates:
Matrix rotation and translation
0.99985638 0.01511052 -0.00767438 -0.38329162
-0.01537770 0.99923205 -0.03603929 7.26333600
0.00712391 0.03615212 0.99932091 -4.77174349
Axis 0.90521734 -0.18555763 -0.38229561
Axis point 0.00000000 134.36592659 199.34294276
Rotation angle (degrees) 2.28528549
Shift along axis 0.12948695
> show #!22 models
> hide #!20 models
> fitmap #13 inMap #33
Multiple maps for #13
> fitmap #22 inMap #33
Fit molecule 13. vvd+iberdo int1.pdb (#22) to map combination of 22 and 23
(#33) using 8572 atoms
average map value = 7.743, steps = 48
shifted from previous position = 0.0492
rotated from previous position = 0.175 degrees
atoms outside contour = 1479, contour level = 2.9126
Position of 13. vvd+iberdo int1.pdb (#22) relative to combination of 22 and 23
(#33) coordinates:
Matrix rotation and translation
0.44794773 -0.59759499 0.66499854 63.25832983
0.68016505 -0.25496860 -0.68728925 177.00102643
0.58027436 0.76017843 0.29225062 -72.48259428
Axis 0.74896737 0.04383907 0.66115506
Axis point 0.00000000 126.28354268 26.48493941
Rotation angle (degrees) 104.91496081
Shift along axis 7.21575224
> volume #33 level 2.799
> combine #22 close false modelId #34
> hide #!22 models
> split #34
Split copy of 13. vvd+iberdo int1.pdb (#34) into 3 models
Chain information for copy of 13. vvd+iberdo int1.pdb F #34.1
---
Chain | Description
F | No description available
Chain information for copy of 13. vvd+iberdo int1.pdb G #34.2
---
Chain | Description
G | No description available
> select add #34
8572 atoms, 8732 bonds, 4 pseudobonds, 1176 residues, 5 models selected
> select subtract #34
Nothing selected
> select add #34.1
6318 atoms, 6434 bonds, 824 residues, 1 model selected
> fitmap sel inMap #33
Fit molecule copy of 13. vvd+iberdo int1.pdb F (#34.1) to map combination of
22 and 23 (#33) using 6318 atoms
average map value = 8.754, steps = 48
shifted from previous position = 0.0938
rotated from previous position = 0.438 degrees
atoms outside contour = 663, contour level = 2.7987
Position of copy of 13. vvd+iberdo int1.pdb F (#34.1) relative to combination
of 22 and 23 (#33) coordinates:
Matrix rotation and translation
0.44720607 -0.59287065 0.66970973 62.36924831
0.68026524 -0.26069452 -0.68503838 177.34741034
0.58072880 0.76193357 0.28672512 -72.18123785
Axis 0.74996599 0.04611884 0.65986671
Axis point 0.00000000 125.96199032 26.58252675
Rotation angle (degrees) 105.27081321
Shift along axis 7.32387673
> select subtract #34.1
Nothing selected
> select add #34.2
2236 atoms, 2278 bonds, 4 pseudobonds, 351 residues, 2 models selected
> fitmap sel inMap #33
Fit molecule copy of 13. vvd+iberdo int1.pdb G (#34.2) to map combination of
22 and 23 (#33) using 2236 atoms
average map value = 5.896, steps = 76
shifted from previous position = 1.14
rotated from previous position = 2.85 degrees
atoms outside contour = 589, contour level = 2.7987
Position of copy of 13. vvd+iberdo int1.pdb G (#34.2) relative to combination
of 22 and 23 (#33) coordinates:
Matrix rotation and translation
0.44344600 -0.63389462 0.63366652 71.75468851
0.67511779 -0.22879669 -0.70133305 176.58897148
0.58955205 0.73880287 0.32649456 -74.75561140
Axis 0.73980171 0.02266172 0.67244321
Axis point 0.00000000 129.64772120 24.41606470
Rotation angle (degrees) 103.26340176
Shift along axis 6.81714860
> select subtract #34.2
Nothing selected
> select add #34.3
18 atoms, 20 bonds, 1 residue, 1 model selected
> select subtract #34.3
Nothing selected
> volume #33 level 4.263
> select add #34
8572 atoms, 8732 bonds, 4 pseudobonds, 1176 residues, 5 models selected
> combine sel
> rename #35 "vvd+iberdo intT.pdb"
> close #34
> color zone #33 near #35 distance 8
> hide #!35 models
> volume #33 level 5.801
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!13 models
> hide #!20 models
> hide #!33 models
> show #!33 models
> show #!20 models
> hide #!13 models
> show #!10 models
> show #!11 models
> show #!13 models
> hide #!20 models
> hide #!33 models
> volume #10 level 9.255
> hide #!10 models
> show #!10 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> hide #!11 models
> show #!11 models
> hide #!10 models
> hide #!11 models
> show #!20 models
> show #!35 models
> hide #!35 models
> show #!33 models
> show #!3 models
> hide #!20 models
> hide #!33 models
> show #!33 models
> hide #!33 models
> show #!20 models
> hide #!20 models
> volume #3 level 4.554
> show #!14 models
> hide #!3 models
> show #!35 models
> hide #!35 models
> show #!33 models
> hide #!14 models
> volume #33 level 4.52
> volume #33 level 4.007
> volume #33 level 4.373
> volume #33 level 4.666
> show #!15 models
> hide #!15 models
> volume copy #33 modelId #36
Opened combination of 22 and 23 copy as #36, grid size 438,438,438, pixel 0.5,
shown at step 1, values float32
> show #!35 models
> color zone #36 near #35 distance 8
> hide #!35 models
> show #!16 models
> hide #!36 models
> show #!14 models
> hide #!16 models
> show #!36 models
> select add #36
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #36,0.97911,-0.16791,0.11466,13.358,0.15621,0.26023,-0.95283,192.83,0.13015,0.95083,0.28103,-63.585
> select subtract #36
Nothing selected
> color #36 darkgrey models
> color #36 #a9a9a9b1 models
> color #36 #a9a9a9b0 models
> select add #36
2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #36,0.97911,-0.16791,0.11466,31.329,0.15621,0.26023,-0.95283,187.23,0.13015,0.95083,0.28103,-64.985
Must specify one map, got 8
> hide #!14 models
> show #!3 models
> fitmap #36 inMap #3
Fit map combination of 22 and 23 copy in map 6a. combination of 2526 and 2540
emready2 using 414467 points
correlation = 0.9261, correlation about mean = 0.6457, overlap = 2.816e+07
steps = 204, shift = 12.5, angle = 7.94 degrees
Position of combination of 22 and 23 copy (#36) relative to 6a. combination of
2526 and 2540 emready2 (#3) coordinates:
Matrix rotation and translation
0.99962918 0.02226516 -0.01567676 -0.49377100
-0.02233593 0.99974104 -0.00435423 4.75196594
0.01557575 0.00470277 0.99986763 -1.11245630
Axis 0.16405010 -0.56607901 -0.80786269
Axis point 165.16995213 11.13270144 0.00000000
Rotation angle (degrees) 1.58181509
Shift along axis -1.87227942
> select clear
> volume #3 level 3.39
> volume #3 level 4.252
> hide #!36 models
> volume #3 level 3.476
> show #!36 models
> volume #36 level 3.48
> hide #!36 models
> show #!36 models
> hide #!36 models
> show #!36 models
> hide #!3 models
> show #!35 models
> hide #!35 models
> show #!6 models
> hide #!6 models
> show #!3 models
> hide #!3 models
> close #36
> show #!33 models
> show #!35 models
> save "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN-
> inhibitor/Figures/Fig 2b final EMready fig maps/0. figure 2 making .cxs"
> includeMaps true
——— End of log from Thu Feb 26 14:52:15 2026 ———
> view name session-start
opened ChimeraX session
> hide #!35 models
> show #!35 models
> ui tool show "Color Zone"
> volume #33 level 3.679
> volume splitbyzone #33
Opened combination of 22 and 23 0 as #34.1, grid size 438,438,438, pixel 0.5,
shown at level 3.68, step 1, values float32
Opened combination of 22 and 23 1 as #34.2, grid size 438,438,438, pixel 0.5,
shown at level 3.68, step 1, values float32
Opened combination of 22 and 23 2 as #34.3, grid size 438,438,438, pixel 0.5,
shown at level 3.68, step 1, values float32
Opened combination of 22 and 23 3 as #34.4, grid size 438,438,438, pixel 0.5,
shown at level 3.68, step 1, values float32
Opened combination of 22 and 23 4 as #34.5, grid size 438,438,438, pixel 0.5,
shown at level 3.68, step 1, values float32
Opened combination of 22 and 23 5 as #34.6, grid size 438,438,438, pixel 0.5,
shown at level 3.68, step 1, values float32
Opened combination of 22 and 23 6 as #34.7, grid size 438,438,438, pixel 0.5,
shown at level 3.68, step 1, values float32
Opened combination of 22 and 23 7 as #34.8, grid size 438,438,438, pixel 0.5,
shown at level 3.68, step 1, values float32
> hide #!35 models
> volume #34.1 level 6.344
> volume #34.2 level 5.958
> volume #34.3 level 5.16
> volume #34.4 level 3.856
> volume #34.5 level 4.357
> volume #34.6 level 4.173
> volume #34.7 level 3.106
> volume #34.8 level 0.8963
> split #34.8
> hide #34.8.1 models
> show #34.8.1 models
> hide #!34.8 models
> show #!34.8 models
> volume #34.8 level 2.434
> volume #34.6 level 3.308
> ui mousemode right "map eraser"
Can only have one displayed volume when erasing
[Repeated 1 time(s)]
> hide #!34.7 models
> hide #!34.6 models
> hide #!34.5 models
> hide #!34.4 models
> hide #!34.3 models
> hide #!34.2 models
> hide #!34.1 models
> hide #!34 models
> show #!34 models
> volume erase #34.8 center 120.33,109.23,128.57 radius 1.8615
> show #!34.1 models
> hide #!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
Can only have one displayed volume when erasing
> hide #!34.7 models
> hide #!34.6 models
> hide #!34.5 models
> hide #!34.4 models
> hide #!34.3 models
> hide #!34.2 models
> volume erase #34.8 center 119.25,108.39,128.28 radius 1.2045
> show #!34.7 models
> show #!34.6 models
> show #!34.5 models
> show #!34.4 models
> hide #!34.4 models
> hide #!34.5 models
> show #!34.5 models
> hide #!34.7 models
> hide #!34.5 models
> hide #!34.6 models
> volume erase #34.8 center 121.8,109.59,127.84 radius 1.2045
> show #!34.7 models
> show #!34.6 models
> show #!34.5 models
> hide #!34.7 models
> hide #!34.6 models
> hide #!34.5 models
> volume erase #34.8 center 121.22,109.7,127.61 radius 1.2045
> hide #36 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 #36 models
> hide #!34.7 models
> hide #!34.6 models
> hide #!34.5 models
> hide #!34.4 models
> hide #!34.3 models
> hide #!34.2 models
> volume erase #34.8 center 115.77,109.2,129.16 radius 1.2045
> show #!34.5 models
> show #!34.4 models
> hide #!34.4 models
> show #!34.6 models
> hide #!34.5 models
Can only have one displayed volume when erasing
> hide #!34.6 models
> volume erase #34.8 center 114.83,108.58,128.85 radius 0.438
> hide #36 models
> show #!34.7 models
> show #!34.6 models
> show #!34.5 models
> show #!34.4 models
> show #!34.3 models
> show #!34.2 models
> volume #34.8 level 5.949
> volume #34.8 level 7.438
> show #!35 models
> hide #!35 models
> volume #34.6 level 2.123
> volume #34.6 level 2.716
> volume copy #34.8 modelId #37
Opened combination of 22 and 23 7 copy as #37, grid size 438,438,438, pixel
0.5, shown at step 1, values float32
> volume #34.6 level 3.531
> hide #!37 models
> show #!37 models
> show #!34.8 models
> hide #!34.8 models
> hide #34.8.1 models
> hide #!34.7 models
> hide #!34.6 models
> hide #!34.5 models
> show #!34.5 models
> show #!34.6 models
> show #!34.7 models
> volume #37 level 1.653
> hide #!34.6 models
> hide #!34.7 models
> hide #!34.5 models
> hide #!34.4 models
> hide #!34.3 models
> hide #!34.2 models
> show #36 models
> volume erase #37 center 118.25,112.1,126.67 radius 10.731
> show #!34.8 models
> show #34.8.1 models
> show #!34.7 models
> show #!34.6 models
> show #!34.5 models
> show #!34.4 models
> show #!34.3 models
> show #!34.2 models
> volume #34.4 level 4.063
> volume #34.2 level 6.366
> volume #34.2 level 6.706
> volume #34.3 level 5.881
> volume #34.5 level 5.067
> volume #34.6 level 3.333
> save "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN-
> inhibitor/Figures/Fig 2b final EMready fig maps/int 1/intT.png" width 1800
> height 1541 supersample 4 transparentBackground true
Cell requested for row 35 is out of bounds for table with 47 rows! Resizing
table model.
> close #36
> save "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN-
> inhibitor/Figures/Fig 2b final EMready fig maps/0. figure 2 making .cxs"
> includeMaps true
——— End of log from Thu Feb 26 15:13:55 2026 ———
> view name session-start
opened ChimeraX session
> hide #!34 models
> hide #!37 models
> show #!20 models
> open "/Users/zrizvi/Downloads/cryosparc_P341_J2527_map (3).mrc"
Opened cryosparc_P341_J2527_map (3).mrc as #36, grid size 300,300,300, pixel
0.74, shown at level 0.00925, step 2, values float32
> volume #36 step 1
> show #!22 models
> volume #36 level 0.003026
> color #36 #b2b2b2ab models
> hide #!22 models
> show #!21 models
> hide #!20 models
> show #!22 models
> hide #!21 models
> ui tool show "Color Zone"
Need to color zone map before it can be split
> color zone #36 near #22 distance 4.44
> color zone #36 near #22 distance 4.54
> color zone #36 near #22 distance 4.64
> color zone #36 near #22 distance 4.74
> color zone #36 near #22 distance 1
> color zone #36 near #22 distance 10
[Repeated 1 time(s)]
> color zone #36 near #22 distance 11
> color zone #36 near #22 distance 12
> color zone #36 near #22 distance 13
> color zone #36 near #22 distance 14
> color zone #36 near #22 distance 15
> color zone #36 near #22 distance 16
> color zone #36 near #22 distance 17
> color zone #36 near #22 distance 18
> color zone #36 near #22 distance 19
[Repeated 1 time(s)]
> volume splitbyzone #36
Opened cryosparc_P341_J2527_map (3).mrc 0 as #38.1, grid size 300,300,300,
pixel 0.74, shown at level 0.00303, step 1, values float32
Opened cryosparc_P341_J2527_map (3).mrc 1 as #38.2, grid size 300,300,300,
pixel 0.74, shown at level 0.00303, step 1, values float32
Opened cryosparc_P341_J2527_map (3).mrc 2 as #38.3, grid size 300,300,300,
pixel 0.74, shown at level 0.00303, step 1, values float32
Opened cryosparc_P341_J2527_map (3).mrc 3 as #38.4, grid size 300,300,300,
pixel 0.74, shown at level 0.00303, step 1, values float32
Opened cryosparc_P341_J2527_map (3).mrc 4 as #38.5, grid size 300,300,300,
pixel 0.74, shown at level 0.00303, step 1, values float32
Opened cryosparc_P341_J2527_map (3).mrc 5 as #38.6, grid size 300,300,300,
pixel 0.74, shown at level 0.00303, step 1, values float32
Opened cryosparc_P341_J2527_map (3).mrc 6 as #38.7, grid size 300,300,300,
pixel 0.74, shown at level 0.00303, step 1, values float32
Opened cryosparc_P341_J2527_map (3).mrc 7 as #38.8, grid size 300,300,300,
pixel 0.74, shown at level 0.00303, step 1, values float32
> hide #!22 models
> hide #!38.2 models
> hide #!38.3 models
> color #38.4 darkgrey models
> color #38.5 darkgrey models
> color #38.6 darkgrey models
> color #38.6 #a9a9a9ae models
> hide #!38.7 models
> color #38.6 #a9a9a9ad models
> color #38.5 #a9a9a9ad models
> color #38.4 #a9a9a9ad models
> show #!20 models
> volume #20 level 6.805
> show #!29 models
> hide #!29 models
> show #!29 models
> hide #!29 models
> show #!29 models
> hide #!29 models
> hide #!38.8 models
> show #!38.8 models
> hide #!38.8 models
> show #!38.8 models
> hide #!38.6 models
> show #!38.6 models
> hide #!38.5 models
> show #!38.5 models
> hide #!38.4 models
> show #!38.4 models
> volume #38.8 level 0.009034
> volume copy #38.8 modelId #39
Opened cryosparc_P341_J2527_map (3).mrc 7 copy as #39, grid size 300,300,300,
pixel 0.74, shown at step 1, values float32
> volume #39 level 0.009534
> volume #39 level 0.004671
> show #!38.8 models
> hide #!38 models
> hide #!20 models
> show #!20 models
> volume #39 level 0.003813
> hide #!20 models
> ui mousemode right "map eraser"
> volume erase #39 center 101.4,96.436,134.1 radius 9.6285
> volume erase #39 center 98.503,100.69,141.99 radius 9.6285
> volume erase #39 center 103.91,97.962,145.36 radius 9.6285
> show #!38 models
> show #!38.8 models
> show #!20 models
> volume #38.6 level 0.002838
> volume #38.5 level 0.001958
> volume #38.4 level 0.002883
> volume #38.5 level 0.002171
> save "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN-
> inhibitor/Figures/Fig 2b final EMready fig maps/int 1/int1withLOWRES.png"
> width 1800 height 1643 supersample 4 transparentBackground true
> hide #!38 models
> hide #!39 models
> hide #!20 models
> show #!24 models
> open "/Users/zrizvi/Downloads/cryosparc_P341_J2574_006_volume_map (4).mrc"
Opened cryosparc_P341_J2574_006_volume_map (4).mrc as #40, grid size
300,300,300, pixel 0.731, shown at level 0.0255, step 2, values float32
> select add #40
2 models selected
> show #!39 models
> show #!38 models
> select subtract #40
Nothing selected
> hide #!40 models
> hide #!24 models
> show #!20 models
> color #38.4 #d6d6d6ff models
> color #38.5 #d6d6d6ff models
> color #38.6 #d6d6d6ff models
> color #38.4 #d6d6d680 models
> color #38.5 #d6d6d680 models
> color #38.6 #d6d6d680 models
> select clear
> save "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN-
> inhibitor/Figures/Fig 2b final EMready fig maps/int 1/int1withLOWRES.png"
> width 1800 height 1643 supersample 4 transparentBackground true
> hide #!38 models
> hide #!39 models
> hide #!20 models
> show #!40 models
> show #!24 models
> volume #40 step 1
> volume #40 level 0.08603
> select add #40
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #40,1,0,0,0.29592,0,1,0,38.019,0,0,1,1.4105
> ui mousemode right translate
> fitmap #40 inMap #24
Fit map cryosparc_P341_J2574_006_volume_map (4).mrc in map 16. combination of
2612 and 2614 using 76567 points
correlation = 0.9704, correlation about mean = 0.6325, overlap = 1.003e+05
steps = 76, shift = 1.78, angle = 0.0636 degrees
Position of cryosparc_P341_J2574_006_volume_map (4).mrc (#40) relative to 16.
combination of 2612 and 2614 (#24) coordinates:
Matrix rotation and translation
0.99999997 -0.00011331 -0.00020616 0.84203922
0.00011353 0.99999940 0.00108507 36.29613778
0.00020603 -0.00108510 0.99999939 0.89143909
Axis -0.97729698 -0.18562141 0.10215333
Axis point 0.00000000 1542.77868389 -32171.78243850
Rotation angle (degrees) 0.06361512
Shift along axis -7.46919917
> select clear
> volume #40 level 0.03029
> show #!25 models
> hide #!24 models
> color zone #40 near #25 distance 20
> volume splitbyzone #40
Opened cryosparc_P341_J2574_006_volume_map (4).mrc 0 as #41.1, grid size
300,300,300, pixel 0.731, shown at level 0.0303, step 1, values float32
Opened cryosparc_P341_J2574_006_volume_map (4).mrc 1 as #41.2, grid size
300,300,300, pixel 0.731, shown at level 0.0303, step 1, values float32
Opened cryosparc_P341_J2574_006_volume_map (4).mrc 2 as #41.3, grid size
300,300,300, pixel 0.731, shown at level 0.0303, step 1, values float32
Opened cryosparc_P341_J2574_006_volume_map (4).mrc 3 as #41.4, grid size
300,300,300, pixel 0.731, shown at level 0.0303, step 1, values float32
Opened cryosparc_P341_J2574_006_volume_map (4).mrc 4 as #41.5, grid size
300,300,300, pixel 0.731, shown at level 0.0303, step 1, values float32
Opened cryosparc_P341_J2574_006_volume_map (4).mrc 5 as #41.6, grid size
300,300,300, pixel 0.731, shown at level 0.0303, step 1, values float32
Opened cryosparc_P341_J2574_006_volume_map (4).mrc 6 as #41.7, grid size
300,300,300, pixel 0.731, shown at level 0.0303, step 1, values float32
Opened cryosparc_P341_J2574_006_volume_map (4).mrc 7 as #41.8, grid size
300,300,300, pixel 0.731, shown at level 0.0303, step 1, values float32
Opened cryosparc_P341_J2574_006_volume_map (4).mrc 8 as #41.9, grid size
300,300,300, pixel 0.731, shown at level 0.0303, step 1, values float32
> hide #!41.2 models
> hide #!41.3 models
> hide #!25 models
> show #!24 models
> hide #!24 models
> show #!24 models
> hide #!41.7 models
> hide #!41.8 models
> hide #!41.9 models
> color #41.4 #d6d6d6ff models
> color #41.5 #d6d6d6ff models
> color #41.6 #d6d6d6ff models
> color #41.4 #d6d6d680 models
> color #41.5 #d6d6d680 models
> color #41.6 #d6d6d680 models
> volume #41.4 level 0.02525
> volume #41.5 level 0.03192
> volume #41.6 level 0.02225
> volume #41.6 level 0.01654
> volume #41.5 level 0.02215
> volume #41.4 level 0.0175
> volume #41.6 level 0.01676
> volume #41.5 level 0.03626
> save "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN-
> inhibitor/Figures/Fig 2b final EMready fig maps/int 2/int2withLOWRES.png"
> width 1800 height 2071 supersample 4 transparentBackground true
> hide #!41.4 models
> show #!41.4 models
> hide #!41.1 models
> show #!41.1 models
> hide #!41 models
> hide #!24 models
> open "/Users/zrizvi/Downloads/cryosparc_P341_J2526_map (3).mrc"
Opened cryosparc_P341_J2526_map (3).mrc as #42, grid size 300,300,300, pixel
0.74, shown at level 0.0102, step 2, values float32
> open "/Users/zrizvi/Downloads/cryosparc_P341_J2527_map (3).mrc"
Opened cryosparc_P341_J2527_map (3).mrc as #43, grid size 300,300,300, pixel
0.74, shown at level 0.00925, step 2, values float32
> rename #42 "OPEN cryosparc_P341_J2526_map (3).mrc"
> rename #43 "INT1 cryosparc_P341_J2527_map (3).mrc"
> volume #42 step 1
> volume #43 step 1
> volume #42 level 0.008174
> volume #43 level 0.003606
> volume #43 level 0.004475
> fitmap #42 inMap #43
Fit map OPEN cryosparc_P341_J2526_map (3).mrc in map INT1
cryosparc_P341_J2527_map (3).mrc using 302851 points
correlation = 0.9587, correlation about mean = 0.8943, overlap = 311.4
steps = 84, shift = 0.372, angle = 1.93 degrees
Position of OPEN cryosparc_P341_J2526_map (3).mrc (#42) relative to INT1
cryosparc_P341_J2527_map (3).mrc (#43) coordinates:
Matrix rotation and translation
0.99994514 -0.00782905 0.00695917 0.32141175
0.00804782 0.99945593 -0.03198565 2.52472465
-0.00670496 0.03203990 0.99946410 -3.99736918
Axis 0.95042634 0.20283696 0.23568399
Axis point 0.00000000 125.14400802 77.59405627
Rotation angle (degrees) 1.93023280
Shift along axis -0.12453025
> volume #42 level 0.009173
> ui tool show "Side View"
> volume #42 color #d6d6d6
> volume #43 color #797979
> color #43 khaki
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting soft
> volume #43 color #f0e68c68
> volume #43 color #f0e68c69
> volume #42 color #d6d6d6
> volume #42 color silver
> volume #42 color darkgrey
> volume #42 color #a9a9a980
> volume #43 color khaki
> volume #43 level 0.003606
> volume #43 color #f0e68c80
> volume #42 color #d6d6d6
> volume #42 level 0.007674
> show #!6 models
> hide #!6 models
> show #!3 models
> show #!43 models
> ui mousemode right "rotate selected models"
> hide #!43 models
> select add #42
4 models selected
> view matrix models
> #42,0.74119,-0.63871,-0.20662,142.23,0.12355,0.43232,-0.89322,164.37,0.65983,0.63651,0.39934,-98.741
> view matrix models
> #42,0.74119,-0.63871,-0.20662,144.66,0.12355,0.43232,-0.89322,143.85,0.65983,0.63651,0.39934,-102.15
> view matrix models
> #42,0.44408,-0.89568,0.023216,189.36,0.37521,0.16238,-0.91261,154.39,0.81364,0.41398,0.40818,-89.996
> ui mousemode right translate
> ui mousemode right "rotate selected models"
> view matrix models
> #42,0.91023,-0.37692,-0.17151,84.578,-0.039193,0.33389,-0.9418,181.92,0.41225,0.86397,0.28915,-92.763
> view matrix models
> #42,0.91023,-0.37692,-0.17151,95.55,-0.039193,0.33389,-0.9418,183.8,0.41225,0.86397,0.28915,-76.869
> ui mousemode right translate
> ui mousemode right "translate selected models"
> view matrix models
> #42,0.91023,-0.37692,-0.17151,99.112,-0.039193,0.33389,-0.9418,188.29,0.41225,0.86397,0.28915,-84.482
> fitmap #42 inMap #3
Fit map OPEN cryosparc_P341_J2526_map (3).mrc in map 6a. combination of 2526
and 2540 emready2 using 311826 points
correlation = 0.9154, correlation about mean = 0.7726, overlap = 5.891e+04
steps = 164, shift = 5.11, angle = 13 degrees
Position of OPEN cryosparc_P341_J2526_map (3).mrc (#42) relative to 6a.
combination of 2526 and 2540 emready2 (#3) coordinates:
Matrix rotation and translation
0.99999988 -0.00020781 -0.00043686 0.14986729
0.00020809 0.99999978 0.00063070 -0.27744247
0.00043673 -0.00063079 0.99999970 0.09652282
Axis -0.79348717 -0.54949254 0.26160285
Axis point 0.00000000 128.45846825 388.72679196
Rotation angle (degrees) 0.04554435
Shift along axis 0.05878544
> select clear
> hide #!3 models
> show #!6 models
> hide #!6 models
> show #!6 models
> close #42-43
> open "/Users/zrizvi/Downloads/cryosparc_P341_J2526_map (3).mrc"
Opened cryosparc_P341_J2526_map (3).mrc as #42, grid size 300,300,300, pixel
0.74, shown at level 0.0102, step 2, values float32
> select add #42
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #42,0.4114,-0.69485,0.58986,99.53,0.61004,-0.27092,-0.74462,189.76,0.6772,0.66618,0.31242,-94.907
> ui mousemode right "translate selected models"
> view matrix models
> #42,0.4114,-0.69485,0.58986,88.89,0.61004,-0.27092,-0.74462,181.52,0.6772,0.66618,0.31242,-80.942
> ui mousemode right translate
> ui mousemode right "translate selected models"
> view matrix models
> #42,0.4114,-0.69485,0.58986,94.879,0.61004,-0.27092,-0.74462,190.11,0.6772,0.66618,0.31242,-70.537
> ui mousemode right translate
> fitmap #6 inMap #42
Fit molecule 6c. vvd+iberdo open.pdb (#6) to map cryosparc_P341_J2526_map
(3).mrc (#42) using 8572 atoms
average map value = 0.03997, steps = 100
shifted from previous position = 5.84
rotated from previous position = 6.69 degrees
atoms outside contour = 769, contour level = 0.010172
Position of 6c. vvd+iberdo open.pdb (#6) relative to cryosparc_P341_J2526_map
(3).mrc (#42) coordinates:
Matrix rotation and translation
0.99998883 0.00472722 0.00003282 -0.62446445
-0.00472717 0.99998796 -0.00131983 0.56931961
-0.00003906 0.00131966 0.99999913 -0.56430308
Axis 0.26889250 0.00732175 -0.96314237
Axis point 119.45514153 153.98357738 0.00000000
Rotation angle (degrees) 0.28121410
Shift along axis 0.37975882
> select clear
> open "/Users/zrizvi/Downloads/cryosparc_P341_J2527_map (3).mrc"
Opened INT1 cryosparc_P341_J2527_map (3).mrc as #43, grid size 300,300,300,
pixel 0.74, shown at level 0.00925, step 2, values float32
> hide #!6 models
> select add #43
2 models selected
> ui mousemode right "rotate selected models"
> ui mousemode right translate
> ui mousemode right "rotate selected models"
> view matrix models
> #43,0.20325,-0.63332,0.74673,97.599,0.52292,-0.57456,-0.62963,229.83,0.8278,0.51845,0.2144,-80.796
> ui mousemode right "translate selected models"
> view matrix models
> #43,0.20325,-0.63332,0.74673,90.103,0.52292,-0.57456,-0.62963,217.46,0.8278,0.51845,0.2144,-64.405
> ui mousemode right translate
> fitmap #43 inMap #42
Fit map INT1 cryosparc_P341_J2527_map (3).mrc in map cryosparc_P341_J2526_map
(3).mrc using 33711 points
correlation = 0.9633, correlation about mean = 0.8938, overlap = 38.63
steps = 208, shift = 16.4, angle = 21.5 degrees
Position of INT1 cryosparc_P341_J2527_map (3).mrc (#43) relative to
cryosparc_P341_J2526_map (3).mrc (#42) coordinates:
Matrix rotation and translation
0.99994614 0.00789387 -0.00673806 -0.33316626
-0.00767360 0.99945480 0.03211278 -2.42129604
0.00698788 -0.03205935 0.99946154 4.08392857
Axis -0.95147544 -0.20351341 -0.23081764
Axis point 0.00000000 125.11362206 78.36602072
Rotation angle (degrees) 1.93251941
Shift along axis -0.13287701
> select clear
> volume #42 step 1
> volume #43 step 1
> show #!6 models
> color zone #42 near #6 distance 8
> color zone #42 near #6 distance 15
> hide #!6 models
> show #!43 models
> color #43 #d6d6d6ff models
> color #43 #d6d6d682 models
[Repeated 1 time(s)]
> color #43 #d6d6d6ff models
> volume #43 level 0.004475
> color #43 #d6d6d680 models
> ui tool show "Side View"
> save "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN-
> inhibitor/Figures/Fig 2b final EMready fig maps/openTOintVVDshift.png" width
> 1800 height 2071 supersample 4 transparentBackground true
> ui tool show "Side View"
> volume #43 level 0.002738
> volume #42 level 0.01417
> volume #42 level 0.009173
> save "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN-
> inhibitor/Figures/Fig 2b final EMready fig
> maps/openTOintVVDshiftFULLimage.png" width 1800 height 2071 supersample 4
> transparentBackground true
> save "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN-
> inhibitor/Figures/Fig 2b final EMready fig maps/0. figure 2 making .cxs"
> includeMaps true
[Repeated 1 time(s)]
——— End of log from Fri Feb 27 10:44:17 2026 ———
> view name session-start
opened ChimeraX session
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M4
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac16,1
Model Number: MW2V3LL/A
Chip: Apple M4
Total Number of Cores: 10 (4 performance and 6 efficiency)
Memory: 16 GB
System Firmware Version: 11881.140.96
OS Loader Version: 11881.140.96
Software:
System Software Overview:
System Version: macOS 15.6.1 (24G90)
Kernel Version: Darwin 24.6.0
Time since boot: 26 minutes, 8 seconds
Graphics/Displays:
Apple M4:
Chipset Model: Apple M4
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
DELL U3011:
Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array)
UI Looks like: 1920 x 1200 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.2.0
autocommand: 2.2.2
babel: 2.17.0
backports.tarfile: 1.2.0
beautifulsoup4: 4.13.3
blockdiag: 3.0.0
blosc2: 3.2.0
build: 1.2.2.post1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.1
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.19.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.1.1
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.5
ChimeraX-AtomicLibrary: 14.1.13
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-Clipper: 0.23.0
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.10.dev202503130118
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ISOLDE: 1.8.dev0
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.5.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.7
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.15
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14.1
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.7
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-ProfileGrids: 1.0.2
ChimeraX-PubChem: 2.2
ChimeraX-QScore: 1.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.3
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.44
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
coverage: 7.6.12
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.12
debugpy: 1.8.13
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.0
filelock: 3.17.0
fonttools: 4.56.0
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h5py: 3.13.0
html2text: 2024.2.26
idna: 3.10
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
importlib_metadata: 8.0.0
inflect: 7.3.1
iniconfig: 2.0.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jaraco.collections: 5.1.0
jaraco.context: 5.3.0
jaraco.functools: 4.0.1
jaraco.text: 3.12.1
jedi: 0.19.1
Jinja2: 3.1.6
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.8
line_profiler: 4.2.0
lxml: 5.3.1
lz4: 4.4.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
more-itertools: 10.3.0
msgpack: 1.1.0
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 24.2
packaging: 24.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.4.0
pip: 25.0.1
pkginfo: 1.11.1
platformdirs: 4.3.6
platformdirs: 4.2.2
pluggy: 1.5.0
prompt_toolkit: 3.0.50
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.32
Pygments: 2.18.0
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.9
PyOpenGL-accelerate: 3.1.9
pyopenxr: 1.1.4501
pyparsing: 3.2.1
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.8.1
PyQt6-Qt6: 6.8.2
PyQt6-WebEngine-commercial: 6.8.0
PyQt6-WebEngine-Qt6: 6.8.2
PyQt6_sip: 13.10.0
pytest: 8.3.5
pytest-cov: 6.0.0
python-dateutil: 2.9.0.post0
pytz: 2025.1
pyzmq: 26.3.0
qtconsole: 5.5.2
QtPy: 2.4.3
qtshim: 1.1
RandomWords: 0.4.0
requests: 2.32.3
roman-numerals-py: 3.1.0
scipy: 1.14.0
Send2Trash: 1.8.3
SEQCROW: 1.8.21
setuptools: 75.8.2
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.1.0
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.7.1
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4.2
traitlets: 5.14.3
typeguard: 4.3.0
typing_extensions: 4.12.2
typing_extensions: 4.12.2
tzdata: 2025.1
urllib3: 2.3.0
wcwidth: 0.2.13
webcolors: 24.11.1
wheel: 0.45.1
wheel: 0.43.0
wheel-filename: 1.4.2
widgetsnbextension: 4.0.13
zipp: 3.19.2
Change History (1)
comment:1 by , 3 weeks ago
| Component: | Unassigned → Graphics |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash destroying OpenGL context on exit |
Note:
See TracTickets
for help on using tickets.
Reported by Zeba Rizvi