![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 7 weeks ago
Closed 7 weeks ago
#18814 closed defect (duplicate)
Crash on Mac waking from sleep
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: macOS-15.6.1-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX.
Fatal Python error: Segmentation fault
Current thread 0x00000001fcfbe0c0 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.surface._surface, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, chimerax.pdb_lib._load_libs, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, PIL._imagingmath, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, psutil._psutil_osx, psutil._psutil_posix, chimerax.segment._segment, chimerax.pdb._pdbio, chimerax.graphics._graphics, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize (total: 65)
{"app_name":"ChimeraX","timestamp":"2025-09-17 17:36:06.00 -0400","app_version":"1.9.0","slice_uuid":"17982d98-65bc-3327-8526-577ec996453c","build_version":"1.9.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 15.6.1 (24G90)","roots_installed":0,"name":"ChimeraX","incident_id":"AD35C0FE-DAB9-479D-A87A-A89971198D7E"}
{
"uptime" : 36000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 1082597089,
"deployVersion" : 210,
"modelCode" : "Mac14,6",
"coalitionID" : 2975,
"osVersion" : {
"train" : "macOS 15.6.1",
"build" : "24G90",
"releaseType" : "User"
},
"captureTime" : "2025-09-17 17:35:49.6749 -0400",
"codeSigningMonitor" : 1,
"incident" : "AD35C0FE-DAB9-479D-A87A-A89971198D7E",
"pid" : 73888,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-09-16 16:53:41.9199 -0400",
"procStartAbsTime" : 138562020478,
"procExitAbsTime" : 880534076593,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.9.0","CFBundleVersion":"1.9.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"F541DF5C-4F27-5987-9189-CFB3290AADA0","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "B895510A-4EA2-10AE-16C3-1C2F7A272112",
"appleIntelligenceStatus" : {"state":"unavailable","reasons":["assetIsNotReady","notOptedIn"]},
"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" : "1997C954-CE38-46A9-A87B-2D68FDFAE0D6",
"wakeTime" : 15615,
"sleepWakeUUID" : "9905AD7C-C1D8-4C72-8A0D-85EB90D66713",
"sip" : "enabled",
"vmRegionInfo" : "0x37bf7782d8c8 is not in any region. Bytes after previous region: 60814447007945 Bytes before following region: 44257632921400\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL reserved VM address space (unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000001, 0x0000b7bf7782d8c8","rawCodes":[1,202032971700424],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000b7bf7782d8c8 -> 0x000037bf7782d8c8 (possible pointer authentication failure)"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":73888},
"vmregioninfo" : "0x37bf7782d8c8 is not in any region. Bytes after previous region: 60814447007945 Bytes before following region: 44257632921400\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL reserved VM address space (unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
"threads" : [{"threadState":{"x":[{"value":0},{"value":0},{"value":1},{"value":6131334216},{"value":99},{"value":95},{"value":3458870066971874272},{"value":0},{"value":49366366148793452},{"value":49366367838500012},{"value":14757395258967641293},{"value":4294967286},{"value":6131334146},{"value":0},{"value":54},{"value":4294967280},{"value":328},{"value":8556467544},{"value":0},{"value":11},{"value":259},{"value":8539333024,"symbolLocation":224,"symbol":"_main_thread"},{"value":0},{"value":1},{"value":4355999280,"symbolLocation":0,"symbol":"faulthandler_handlers"},{"value":8500498432,"symbolLocation":0,"symbol":"OBJC_IVAR_$_NSTouchBarInputMethodCandidateList._list"},{"value":8500498432,"symbolLocation":0,"symbol":"OBJC_IVAR_$_NSTouchBarInputMethodCandidateList._list"},{"value":5},{"value":1}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6694287500},"cpsr":{"value":1073745920},"fp":{"value":6131334288},"sp":{"value":6131334256},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6694052744,"matchesCrashFrame":1},"far":{"value":0}},"id":278742,"triggered":true,"name":"CrBrowserMain","queue":"com.apple.main-thread","frames":[{"imageOffset":37768,"symbol":"__pthread_kill","symbolLocation":8,"imageIndex":163},{"imageOffset":26764,"symbol":"pthread_kill","symbolLocation":296,"imageIndex":164},{"imageOffset":265476,"symbol":"raise","symbolLocation":32,"imageIndex":165},{"imageOffset":2417160,"symbol":"faulthandler_fatal_error","symbolLocation":392,"imageIndex":1},{"imageOffset":13988,"symbol":"_sigtramp","symbolLocation":56,"imageIndex":166},{"imageOffset":349344,"imageIndex":69},{"imageOffset":349160,"imageIndex":69},{"imageOffset":381256,"symbol":"_NSViewHierarchyDidChangeBackingProperties","symbolLocation":244,"imageIndex":167},{"imageOffset":12004300,"symbol":"-[NSWindow _postWindowDidChangeBackingPropertiesAndDisplayWindowForPreviousBackingScaleFactor:previousColorSpace:]","symbolLocation":192,"imageIndex":167},{"imageOffset":2071804,"symbol":"__67-[NSWindow _updateSettingsSendingScreenChangeNotificationToScreen:]_block_invoke","symbolLocation":432,"imageIndex":167},{"imageOffset":507904,"symbol":"NSPerformVisuallyAtomicChange","symbolLocation":108,"imageIndex":167},{"imageOffset":2071360,"symbol":"-[NSWindow _updateSettingsSendingScreenChangeNotificationToScreen:]","symbolLocation":96,"imageIndex":167},{"imageOffset":513356,"symbol":"-[NSWindow _setFrameCommon:display:fromServer:]","symbolLocation":2016,"imageIndex":167},{"imageOffset":11974628,"symbol":"-[NSWindow(NSScreenLayout) _setFrame:fromAdjustmentToScreen:anchorIfNeeded:animate:]","symbolLocation":616,"imageIndex":167},{"imageOffset":3236944,"symbol":"-[NSWindow _adjustWindowToScreen]","symbolLocation":1184,"imageIndex":167},{"imageOffset":3366572,"symbol":"-[NSWindow _displayChangedSoAdjustWindows:]","symbolLocation":100,"imageIndex":167},{"imageOffset":15453360,"symbol":"___NSApplicationPerformScreenInvalidationReactions_block_invoke","symbolLocation":84,"imageIndex":167},{"imageOffset":219016,"symbol":"-[NSApplication enumerateWindowsWithOptions:usingBlock:]","symbolLocation":236,"imageIndex":167},{"imageOffset":15451568,"symbol":"___NSApplicationReactToScreenInvalidation_block_invoke","symbolLocation":1012,"imageIndex":167},{"imageOffset":15449584,"symbol":"_NSApplicationReactToScreenInvalidation","symbolLocation":308,"imageIndex":167},{"imageOffset":15450172,"symbol":"-[NSApplication(ScreenHandling) _reactToDisplayChanges:]","symbolLocation":416,"imageIndex":167},{"imageOffset":9874348,"symbol":"_NSCGSDisplayConfigurationUpdateAndInvokeObservers","symbolLocation":436,"imageIndex":167},{"imageOffset":9875600,"symbol":"_NSCGSDisplayConfigurationDidReconfigureNotificationHandler","symbolLocation":316,"imageIndex":167},{"imageOffset":45104,"symbol":"(anonymous namespace)::notify_datagram_handler(unsigned int, CGSDatagramType, void*, unsigned long, void*)","symbolLocation":920,"imageIndex":168},{"imageOffset":4298612,"symbol":"CGSDatagramReadStream::dispatchMainQueueDatagrams()","symbolLocation":284,"imageIndex":168},{"imageOffset":4298296,"symbol":"invocation function for block in CGSDatagramReadStream::mainQueueWakeup()","symbolLocation":28,"imageIndex":168},{"imageOffset":6956,"symbol":"_dispatch_call_block_and_release","symbolLocation":32,"imageIndex":169},{"imageOffset":112732,"symbol":"_dispatch_client_callout","symbolLocation":16,"imageIndex":169},{"imageOffset":232320,"symbol":"_dispatch_main_queue_drain.cold.5","symbolLocation":812,"imageIndex":169},{"imageOffset":69040,"symbol":"_dispatch_main_queue_drain","symbolLocation":180,"imageIndex":169},{"imageOffset":68844,"symbol":"_dispatch_main_queue_callback_4CF","symbolLocation":44,"imageIndex":169},{"imageOffset":764896,"symbol":"__CFRUNLOOP_IS_SERVICING_THE_MAIN_DISPATCH_QUEUE__","symbolLocation":16,"imageIndex":170},{"imageOffset":506076,"symbol":"__CFRunLoopRun","symbolLocation":1980,"imageIndex":170},{"imageOffset":502424,"symbol":"CFRunLoopRunSpecific","symbolLocation":572,"imageIndex":170},{"imageOffset":799356,"symbol":"RunCurrentEventLoopInMode","symbolLocation":324,"imageIndex":171},{"imageOffset":812264,"symbol":"ReceiveNextEventCommon","symbolLocation":676,"imageIndex":171},{"imageOffset":2430084,"symbol":"_BlockUntilNextEventMatchingListInModeWithFilter","symbolLocation":76,"imageIndex":171},{"imageOffset":240180,"symbol":"_DPSNextEvent","symbolLocation":684,"imageIndex":167},{"imageOffset":10328384,"symbol":"-[NSApplication(NSEventRouting) _nextEventMatchingEventMask:untilDate:inMode:dequeue:]","symbolLocation":688,"imageIndex":167},{"imageOffset":187364,"symbol":"-[NSApplication run]","symbolLocation":480,"imageIndex":167},{"imageOffset":88376,"imageIndex":69},{"imageOffset":572692,"symbol":"QEventLoop::exec(QFlags)","symbolLocation":540,"imageIndex":45},{"imageOffset":534620,"symbol":"QCoreApplication::exec()","symbolLocation":112,"imageIndex":45},{"imageOffset":2477972,"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":15700,"symbol":"main","symbolLocation":128,"imageIndex":0},{"imageOffset":27544,"symbol":"start","symbolLocation":6076,"imageIndex":172}]},{"id":278910,"name":"ThreadPoolServiceThread","threadState":{"x":[{"value":4},{"value":0},{"value":0},{"value":105553137942720},{"value":4},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":3},{"value":61572651169794},{"value":6320806480},{"value":38147},{"value":1},{"value":1},{"value":369},{"value":6335442944},{"value":0},{"value":5941124736},{"value":5943436224},{"value":6335442256},{"value":0},{"value":12297829382473034411},{"value":1},{"value":0},{"value":0},{"value":0},{"value":0}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6210567080},"cpsr":{"value":2684358656},"fp":{"value":6335442240},"sp":{"value":6335442144},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6694066524},"far":{"value":0}},"frames":[{"imageOffset":51548,"symbol":"kevent64","symbolLocation":8,"imageIndex":163},{"imageOffset":71187368,"imageIndex":56},{"imageOffset":71186848,"imageIndex":56},{"imageOffset":70809656,"imageIndex":56},{"imageOffset":70544784,"imageIndex":56},{"imageOffset":70952276,"imageIndex":56},{"imageOffset":70856668,"imageIndex":56},{"imageOffset":70952656,"imageIndex":56},{"imageOffset":71057880,"imageIndex":56},{"imageOffset":27660,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":164},{"imageOffset":7040,"symbol":"thread_start","symbolLocation":8,"imageIndex":164}]},{"id":278911,"name":"ThreadPoolForegroundWorker","threadState":{"x":[{"value":268451845},{"value":17179869186},{"value":0},{"value":162740605812736},{"value":0},{"value":162740605812736},{"value":32},{"value":0},{"value":0},{"value":17179869184},{"value":32},{"value":0},{"value":0},{"value":0},{"value":37891},{"value":2043},{"value":18446744073709551569},{"value":8556476000},{"value":0},{"value":0},{"value":32},{"value":162740605812736},{"value":0},{"value":162740605812736},{"value":6343863600},{"value":0},{"value":17179869186},{"value":18446744073709550527},{"value":2}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6694093728},"cpsr":{"value":4096},"fp":{"value":6343862944},"sp":{"value":6343862864},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6694018100},"far":{"value":0}},"frames":[{"imageOffset":3124,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":163},{"imageOffset":78752,"symbol":"mach_msg2_internal","symbolLocation":76,"imageIndex":163},{"imageOffset":38756,"symbol":"mach_msg_overwrite","symbolLocation":484,"imageIndex":163},{"imageOffset":4008,"symbol":"mach_msg","symbolLocation":24,"imageIndex":163},{"imageOffset":71161832,"imageIndex":56},{"imageOffset":70677284,"imageIndex":56},{"imageOffset":70900888,"imageIndex":56},{"imageOffset":70904380,"imageIndex":56},{"imageOffset":70902644,"imageIndex":56},{"imageOffset":71057880,"imageIndex":56},{"imageOffset":27660,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":164},{"imageOffset":7040,"symbol":"thread_start","symbolLocation":8,"imageIndex":164}]},{"id":278912,"name":"ThreadPoolBackgroundWorker","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":8556476000},{"value":0},{"value":0},{"value":32},{"value":280388349984768},{"value":0},{"value":280388349984768},{"value":6352284976},{"value":0},{"value":17179869186},{"value":18446744073709550527},{"value":2}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6694093728},"cpsr":{"value":4096},"fp":{"value":6352284320},"sp":{"value":6352284240},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6694018100},"far":{"value":0}},"frames":[{"imageOffset":3124,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":163},{"imageOffset":78752,"symbol":"mach_msg2_internal","symbolLocation":76,"imageIndex":163},{"imageOffset":38756,"symbol":"mach_msg_overwrite","symbolLocation":484,"imageIndex":163},{"imageOffset":4008,"symbol":"mach_msg","symbolLocation":24,"imageIndex":163},{"imageOffset":71161832,"imageIndex":56},{"imageOffset":70677284,"imageIndex":56},{"imageOffset":70900888,"imageIndex":56},{"imageOffset":70904380,"imageIndex":56},{"imageOffset":70902696,"imageIndex":56},{"imageOffset":71057880,"imageIndex":56},{"imageOffset":27660,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":164},{"imageOffset":7040,"symbol":"thread_start","symbolLocation":8,"imageIndex":164}]},{"id":278913,"name":"Chrome_IOThread","threadState":{"x":[{"value":4},{"value":0},{"value":0},{"value":13840425616},{"value":5},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":9223372036854775810},{"value":6320806528},{"value":45315},{"value":1},{"value":1},{"value":369},{"value":6360707072},{"value":0},{"value":5941116160},{"value":5943437152},{"value":6360706368},{"value":0},{"value":12297829382473034411},{"value":1},{"value":0},{"value":0},{"value":0},{"value":0}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6210567080},"cpsr":{"value":1610616832},"fp":{"value":6360706352},"sp":{"value":6360706256},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6694066524},"far":{"value":0}},"frames":[{"imageOffset":51548,"symbol":"kevent64","symbolLocation":8,"imageIndex":163},{"imageOffset":71187368,"imageIndex":56},{"imageOffset":71186848,"imageIndex":56},{"imageOffset":70809656,"imageIndex":56},{"imageOffset":70544784,"imageIndex":56},{"imageOffset":70952276,"imageIndex":56},{"imageOffset":45328188,"imageIndex":56},{"imageOffset":70952656,"imageIndex":56},{"imageOffset":71057880,"imageIndex":56},{"imageOffset":27660,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":164},{"imageOffset":7040,"symbol":"thread_start","symbolLocation":8,"imageIndex":164}]},{"id":278914,"name":"NetworkConfigWatcher","threadState":{"x":[{"value":268451845},{"value":17179869186},{"value":0},{"value":268293722079232},{"value":0},{"value":268293722079232},{"value":32},{"value":0},{"value":0},{"value":17179869184},{"value":32},{"value":0},{"value":0},{"value":0},{"value":62467},{"value":1},{"value":18446744073709551569},{"value":6369128448},{"value":0},{"value":0},{"value":32},{"value":268293722079232},{"value":0},{"value":268293722079232},{"value":6369127488},{"value":0},{"value":17179869186},{"value":18446744073709550527},{"value":2}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6694093728},"cpsr":{"value":4096},"fp":{"value":6369126832},"sp":{"value":6369126752},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6694018100},"far":{"value":0}},"frames":[{"imageOffset":3124,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":163},{"imageOffset":78752,"symbol":"mach_msg2_internal","symbolLocation":76,"imageIndex":163},{"imageOffset":38756,"symbol":"mach_msg_overwrite","symbolLocation":484,"imageIndex":163},{"imageOffset":4008,"symbol":"mach_msg","symbolLocation":24,"imageIndex":163},{"imageOffset":71161832,"imageIndex":56},{"imageOffset":70677284,"imageIndex":56},{"imageOffset":70677152,"imageIndex":56},{"imageOffset":70343492,"imageIndex":56},{"imageOffset":70809656,"imageIndex":56},{"imageOffset":70544784,"imageIndex":56},{"imageOffset":70952276,"imageIndex":56},{"imageOffset":70952656,"imageIndex":56},{"imageOffset":71057880,"imageIndex":56},{"imageOffset":27660,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":164},{"imageOffset":7040,"symbol":"thread_start","symbolLocation":8,"imageIndex":164}]},{"id":278916,"name":"ThreadPoolForegroundWorker","threadState":{"x":[{"value":268451845},{"value":17179869186},{"value":0},{"value":266146238431232},{"value":0},{"value":266146238431232},{"value":32},{"value":0},{"value":0},{"value":17179869184},{"value":32},{"value":0},{"value":0},{"value":0},{"value":61967},{"value":2043},{"value":18446744073709551569},{"value":8556476000},{"value":0},{"value":0},{"value":32},{"value":266146238431232},{"value":0},{"value":266146238431232},{"value":6377549104},{"value":0},{"value":17179869186},{"value":18446744073709550527},{"value":2}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6694093728},"cpsr":{"value":4096},"fp":{"value":6377548448},"sp":{"value":6377548368},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6694018100},"far":{"value":0}},"frames":[{"imageOffset":3124,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":163},{"imageOffset":78752,"symbol":"mach_msg2_internal","symbolLocation":76,"imageIndex":163},{"imageOffset":38756,"symbol":"mach_msg_overwrite","symbolLocation":484,"imageIndex":163},{"imageOffset":4008,"symbol":"mach_msg","symbolLocation":24,"imageIndex":163},{"imageOffset":71161832,"imageIndex":56},{"imageOffset":70677284,"imageIndex":56},{"imageOffset":70900888,"imageIndex":56},{"imageOffset":70904380,"imageIndex":56},{"imageOffset":70902644,"imageIndex":56},{"imageOffset":71057880,"imageIndex":56},{"imageOffset":27660,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":164},{"imageOffset":7040,"symbol":"thread_start","symbolLocation":8,"imageIndex":164}]},{"id":278917,"name":"ThreadPoolForegroundWorker","threadState":{"x":[{"value":268451845},{"value":17179869186},{"value":0},{"value":197924977901568},{"value":0},{"value":197924977901568},{"value":32},{"value":0},{"value":0},{"value":17179869184},{"value":32},{"value":0},{"value":0},{"value":0},{"value":46083},{"value":3120713907},{"value":18446744073709551569},{"value":134},{"value":0},{"value":0},{"value":32},{"value":197924977901568},{"value":0},{"value":197924977901568},{"value":6385970480},{"value":0},{"value":17179869186},{"value":18446744073709550527},{"value":2}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6694093728},"cpsr":{"value":4096},"fp":{"value":6385969824},"sp":{"value":6385969744},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6694018100},"far":{"value":0}},"frames":[{"imageOffset":3124,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":163},{"imageOffset":78752,"symbol":"mach_msg2_internal","symbolLocation":76,"imageIndex":163},{"imageOffset":38756,"symbol":"mach_msg_overwrite","symbolLocation":484,"imageIndex":163},{"imageOffset":4008,"symbol":"mach_msg","symbolLocation":24,"imageIndex":163},{"imageOffset":71161832,"imageIndex":56},{"imageOffset":70677284,"imageIndex":56},{"imageOffset":70900888,"imageIndex":56},{"imageOffset":70904380,"imageIndex":56},{"imageOffset":70902644,"imageIndex":56},{"imageOffset":71057880,"imageIndex":56},{"imageOffset":27660,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":164},{"imageOffset":7040,"symbol":"thread_start","symbolLocation":8,"imageIndex":164}]},{"id":278918,"name":"Chrome_InProcGpuThread","threadState":{"x":[{"value":268451845},{"value":17179869186},{"value":0},{"value":203422536040448},{"value":0},{"value":203422536040448},{"value":32},{"value":0},{"value":0},{"value":17179869184},{"value":32},{"value":0},{"value":0},{"value":0},{"value":47363},{"value":1},{"value":18446744073709551569},{"value":6394392576},{"value":0},{"value":0},{"value":32},{"value":203422536040448},{"value":0},{"value":203422536040448},{"value":6394391616},{"value":0},{"value":17179869186},{"value":18446744073709550527},{"value":2}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6694093728},"cpsr":{"value":4096},"fp":{"value":6394390960},"sp":{"value":6394390880},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6694018100},"far":{"value":0}},"frames":[{"imageOffset":3124,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":163},{"imageOffset":78752,"symbol":"mach_msg2_internal","symbolLocation":76,"imageIndex":163},{"imageOffset":38756,"symbol":"mach_msg_overwrite","symbolLocation":484,"imageIndex":163},{"imageOffset":4008,"symbol":"mach_msg","symbolLocation":24,"imageIndex":163},{"imageOffset":71161832,"imageIndex":56},{"imageOffset":70677284,"imageIndex":56},{"imageOffset":70677152,"imageIndex":56},{"imageOffset":70343492,"imageIndex":56},{"imageOffset":70809656,"imageIndex":56},{"imageOffset":70544784,"imageIndex":56},{"imageOffset":70952276,"imageIndex":56},{"imageOffset":70952656,"imageIndex":56},{"imageOffset":71057880,"imageIndex":56},{"imageOffset":27660,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":164},{"imageOffset":7040,"symbol":"thread_start","symbolLocation":8,"imageIndex":164}]},{"id":278919,"name":"Chrome_ChildIOThread","threadState":{"x":[{"value":4},{"value":0},{"value":0},{"value":105553166231248},{"value":1},{"value":0},{"value":0},{"value":6402811616},{"value":0},{"value":0},{"value":1},{"value":61572651169794},{"value":6320806624},{"value":58883},{"value":1},{"value":1},{"value":369},{"value":6402813952},{"value":0},{"value":5929716688},{"value":5943445904},{"value":6402813248},{"value":0},{"value":12297829382473034411},{"value":1},{"value":0},{"value":0},{"value":0},{"value":0}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6210567080},"cpsr":{"value":2684358656},"fp":{"value":6402813232},"sp":{"value":6402813136},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6694066524},"far":{"value":0}},"frames":[{"imageOffset":51548,"symbol":"kevent64","symbolLocation":8,"imageIndex":163},{"imageOffset":71187368,"imageIndex":56},{"imageOffset":71186848,"imageIndex":56},{"imageOffset":70809656,"imageIndex":56},{"imageOffset":70544784,"imageIndex":56},{"imageOffset":70952276,"imageIndex":56},{"imageOffset":114048632,"imageIndex":56},{"imageOffset":70952656,"imageIndex":56},{"imageOffset":71057880,"imageIndex":56},{"imageOffset":27660,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":164},{"imageOffset":7040,"symbol":"thread_start","symbolLocation":8,"imageIndex":164}]},{"id":278920,"name":"CompositorTileWorker1","threadState":{"x":[{"value":260},{"value":0},{"value":1024},{"value":0},{"value":0},{"value":161},{"value":0},{"value":0},{"value":6411234888},{"value":0},{"value":0},{"value":2},{"value":2},{"value":0},{"value":0},{"value":0},{"value":305},{"value":8556467472},{"value":0},{"value":5557817704},{"value":5557817832},{"value":6411235552},{"value":0},{"value":0},{"value":1024},{"value":1025},{"value":1280},{"value":0},{"value":0}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6694289632},"cpsr":{"value":1610616832},"fp":{"value":6411235008},"sp":{"value":6411234864},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6694032332},"far":{"value":0}},"frames":[{"imageOffset":17356,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":163},{"imageOffset":28896,"symbol":"_pthread_cond_wait","symbolLocation":984,"imageIndex":164},{"imageOffset":71055056,"imageIndex":56},{"imageOffset":104344336,"imageIndex":56},{"imageOffset":71057880,"imageIndex":56},{"imageOffset":27660,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":164},{"imageOffset":7040,"symbol":"thread_start","symbolLocation":8,"imageIndex":164}]},{"id":278921,"name":"ThreadPoolSingleThreadSharedForeground0","threadState":{"x":[{"value":268451845},{"value":17179869186},{"value":0},{"value":210019605807104},{"value":0},{"value":210019605807104},{"value":32},{"value":0},{"value":0},{"value":17179869184},{"value":32},{"value":0},{"value":0},{"value":0},{"value":48899},{"value":3789844787},{"value":18446744073709551569},{"value":303},{"value":0},{"value":0},{"value":32},{"value":210019605807104},{"value":0},{"value":210019605807104},{"value":6419655984},{"value":0},{"value":17179869186},{"value":18446744073709550527},{"value":2}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6694093728},"cpsr":{"value":4096},"fp":{"value":6419655328},"sp":{"value":6419655248},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6694018100},"far":{"value":0}},"frames":[{"imageOffset":3124,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":163},{"imageOffset":78752,"symbol":"mach_msg2_internal","symbolLocation":76,"imageIndex":163},{"imageOffset":38756,"symbol":"mach_msg_overwrite","symbolLocation":484,"imageIndex":163},{"imageOffset":4008,"symbol":"mach_msg","symbolLocation":24,"imageIndex":163},{"imageOffset":71161832,"imageIndex":56},{"imageOffset":70677284,"imageIndex":56},{"imageOffset":70900888,"imageIndex":56},{"imageOffset":70903324,"imageIndex":56},{"imageOffset":70902728,"imageIndex":56},{"imageOffset":71057880,"imageIndex":56},{"imageOffset":27660,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":164},{"imageOffset":7040,"symbol":"thread_start","symbolLocation":8,"imageIndex":164}]},{"id":278925,"name":"VizCompositorThread","threadState":{"x":[{"value":268451845},{"value":17179869186},{"value":0},{"value":214417652318208},{"value":0},{"value":214417652318208},{"value":32},{"value":0},{"value":0},{"value":17179869184},{"value":32},{"value":0},{"value":0},{"value":0},{"value":49923},{"value":1},{"value":18446744073709551569},{"value":6428078080},{"value":0},{"value":0},{"value":32},{"value":214417652318208},{"value":0},{"value":214417652318208},{"value":6428077120},{"value":0},{"value":17179869186},{"value":18446744073709550527},{"value":2}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6694093728},"cpsr":{"value":4096},"fp":{"value":6428076464},"sp":{"value":6428076384},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6694018100},"far":{"value":0}},"frames":[{"imageOffset":3124,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":163},{"imageOffset":78752,"symbol":"mach_msg2_internal","symbolLocation":76,"imageIndex":163},{"imageOffset":38756,"symbol":"mach_msg_overwrite","symbolLocation":484,"imageIndex":163},{"imageOffset":4008,"symbol":"mach_msg","symbolLocation":24,"imageIndex":163},{"imageOffset":71161832,"imageIndex":56},{"imageOffset":70677284,"imageIndex":56},{"imageOffset":70677152,"imageIndex":56},{"imageOffset":70343492,"imageIndex":56},{"imageOffset":70809656,"imageIndex":56},{"imageOffset":70544784,"imageIndex":56},{"imageOffset":70952276,"imageIndex":56},{"imageOffset":70952656,"imageIndex":56},{"imageOffset":71057880,"imageIndex":56},{"imageOffset":27660,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":164},{"imageOffset":7040,"symbol":"thread_start","symbolLocation":8,"imageIndex":164}]},{"id":278926,"name":"NetworkConfigWatcher","threadState":{"x":[{"value":268451845},{"value":17179869186},{"value":0},{"value":235308373245952},{"value":0},{"value":235308373245952},{"value":32},{"value":0},{"value":0},{"value":17179869184},{"value":32},{"value":0},{"value":0},{"value":0},{"value":54787},{"value":1},{"value":18446744073709551569},{"value":6436499456},{"value":0},{"value":0},{"value":32},{"value":235308373245952},{"value":0},{"value":235308373245952},{"value":6436498496},{"value":0},{"value":17179869186},{"value":18446744073709550527},{"value":2}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6694093728},"cpsr":{"value":4096},"fp":{"value":6436497840},"sp":{"value":6436497760},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6694018100},"far":{"value":0}},"frames":[{"imageOffset":3124,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":163},{"imageOffset":78752,"symbol":"mach_msg2_internal","symbolLocation":76,"imageIndex":163},{"imageOffset":38756,"symbol":"mach_msg_overwrite","symbolLocation":484,"imageIndex":163},{"imageOffset":4008,"symbol":"mach_msg","symbolLocation":24,"imageIndex":163},{"imageOffset":71161832,"imageIndex":56},{"imageOffset":70677284,"imageIndex":56},{"imageOffset":70677152,"imageIndex":56},{"imageOffset":70343492,"imageIndex":56},{"imageOffset":70809656,"imageIndex":56},{"imageOffset":70544784,"imageIndex":56},{"imageOffset":70952276,"imageIndex":56},{"imageOffset":70952656,"imageIndex":56},{"imageOffset":71057880,"imageIndex":56},{"imageOffset":27660,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":164},{"imageOffset":7040,"symbol":"thread_start","symbolLocation":8,"imageIndex":164}]},{"id":278938,"name":"NetworkService","threadState":{"x":[{"value":4},{"value":0},{"value":0},{"value":13361710896},{"value":10},{"value":0},{"value":0},{"value":13295953680},{"value":0},{"value":0},{"value":2},{"value":61572651169794},{"value":6320806816},{"value":51459},{"value":1},{"value":1},{"value":369},{"value":13295955968},{"value":0},{"value":5557943808},{"value":5943637040},{"value":13295955312},{"value":0},{"value":12297829382473034411},{"value":1},{"value":0},{"value":0},{"value":0},{"value":0}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6210567080},"cpsr":{"value":2684358656},"fp":{"value":13295955296},"sp":{"value":13295955200},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6694066524},"far":{"value":0}},"frames":[{"imageOffset":51548,"symbol":"kevent64","symbolLocation":8,"imageIndex":163},{"imageOffset":71187368,"imageIndex":56},{"imageOffset":71186848,"imageIndex":56},{"imageOffset":70809656,"imageIndex":56},{"imageOffset":70544784,"imageIndex":56},{"imageOffset":70952276,"imageIndex":56},{"imageOffset":70952656,"imageIndex":56},{"imageOffset":71057880,"imageIndex":56},{"imageOffset":27660,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":164},{"imageOffset":7040,"symbol":"thread_start","symbolLocation":8,"imageIndex":164}]},{"id":278939,"name":"NetworkNotificationThreadMac","threadState":{"x":[{"value":268451845},{"value":21592279046},{"value":8589934592},{"value":229810815107072},{"value":0},{"value":229810815107072},{"value":2},{"value":4294967295},{"value":0},{"value":17179869184},{"value":0},{"value":2},{"value":0},{"value":0},{"value":53507},{"value":0},{"value":18446744073709551569},{"value":8556469352},{"value":0},{"value":4294967295},{"value":2},{"value":229810815107072},{"value":0},{"value":229810815107072},{"value":13304372712},{"value":8589934592},{"value":21592279046},{"value":18446744073709550527},{"value":4412409862}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6694093728},"cpsr":{"value":4096},"fp":{"value":13304372560},"sp":{"value":13304372480},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6694018100},"far":{"value":0}},"frames":[{"imageOffset":3124,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":163},{"imageOffset":78752,"symbol":"mach_msg2_internal","symbolLocation":76,"imageIndex":163},{"imageOffset":38756,"symbol":"mach_msg_overwrite","symbolLocation":484,"imageIndex":163},{"imageOffset":4008,"symbol":"mach_msg","symbolLocation":24,"imageIndex":163},{"imageOffset":511164,"symbol":"__CFRunLoopServiceMachPort","symbolLocation":160,"imageIndex":170},{"imageOffset":505304,"symbol":"__CFRunLoopRun","symbolLocation":1208,"imageIndex":170},{"imageOffset":502424,"symbol":"CFRunLoopRunSpecific","symbolLocation":572,"imageIndex":170},{"imageOffset":367736,"symbol":"-[NSRunLoop(NSRunLoop) runMode:beforeDate:]","symbolLocation":212,"imageIndex":174},{"imageOffset":71382916,"imageIndex":56},{"imageOffset":71377136,"imageIndex":56},{"imageOffset":70809656,"imageIndex":56},{"imageOffset":70544784,"imageIndex":56},{"imageOffset":70952276,"imageIndex":56},{"imageOffset":70952656,"imageIndex":56},{"imageOffset":71057880,"imageIndex":56},{"imageOffset":27660,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":164},{"imageOffset":7040,"symbol":"thread_start","symbolLocation":8,"imageIndex":164}]},{"id":278940,"name":"NetworkConfigWatcher","threadState":{"x":[{"value":268451845},{"value":17179869186},{"value":0},{"value":373846838345728},{"value":0},{"value":373846838345728},{"value":32},{"value":0},{"value":0},{"value":17179869184},{"value":32},{"value":0},{"value":0},{"value":0},{"value":87043},{"value":1},{"value":18446744073709551569},{"value":13312798720},{"value":0},{"value":0},{"value":32},{"value":373846838345728},{"value":0},{"value":373846838345728},{"value":13312797760},{"value":0},{"value":17179869186},{"value":18446744073709550527},{"value":2}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6694093728},"cpsr":{"value":4096},"fp":{"value":13312797104},"sp":{"value":13312797024},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6694018100},"far":{"value":0}},"frames":[{"imageOffset":3124,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":163},{"imageOffset":78752,"symbol":"mach_msg2_internal","symbolLocation":76,"imageIndex":163},{"imageOffset":38756,"symbol":"mach_msg_overwrite","symbolLocation":484,"imageIndex":163},{"imageOffset":4008,"symbol":"mach_msg","symbolLocation":24,"imageIndex":163},{"imageOffset":71161832,"imageIndex":56},{"imageOffset":70677284,"imageIndex":56},{"imageOffset":70677152,"imageIndex":56},{"imageOffset":70343492,"imageIndex":56},{"imageOffset":70809656,"imageIndex":56},{"imageOffset":70544784,"imageIndex":56},{"imageOffset":70952276,"imageIndex":56},{"imageOffset":70952656,"imageIndex":56},{"imageOffset":71057880,"imageIndex":56},{"imageOffset":27660,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":164},{"imageOffset":7040,"symbol":"thread_start","symbolLocation":8,"imageIndex":164}]},{"id":278944,"name":"ThreadPoolSingleThreadForegroundBlocking1","threadState":{"x":[{"value":268451845},{"value":17179869186},{"value":0},{"value":284786396495872},{"value":0},{"value":284786396495872},{"value":32},{"value":0},{"value":0},{"value":17179869184},{"value":32},{"value":0},{"value":0},{"value":0},{"value":66307},{"value":4255654115},{"value":18446744073709551569},{"value":4632583168},{"value":0},{"value":0},{"value":32},{"value":284786396495872},{"value":0},{"value":284786396495872},{"value":13321219376},{"value":0},{"value":17179869186},{"value":18446744073709550527},{"value":2}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6694093728},"cpsr":{"value":4096},"fp":{"value":13321218720},"sp":{"value":13321218640},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6694018100},"far":{"value":0}},"frames":[{"imageOffset":3124,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":163},{"imageOffset":78752,"symbol":"mach_msg2_internal","symbolLocation":76,"imageIndex":163},{"imageOffset":38756,"symbol":"mach_msg_overwrite","symbolLocation":484,"imageIndex":163},{"imageOffset":4008,"symbol":"mach_msg","symbolLocation":24,"imageIndex":163},{"imageOffset":71161832,"imageIndex":56},{"imageOffset":70677284,"imageIndex":56},{"imageOffset":70900888,"imageIndex":56},{"imageOffset":70904380,"imageIndex":56},{"imageOffset":70902712,"imageIndex":56},{"imageOffset":71057880,"imageIndex":56},{"imageOffset":27660,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":164},{"imageOffset":7040,"symbol":"thread_start","symbolLocation":8,"imageIndex":164}]},{"id":278972,"name":"NetworkConfigWatcher","threadState":{"x":[{"value":268451845},{"value":17179869186},{"value":0},{"value":344160024395776},{"value":0},{"value":344160024395776},{"value":32},{"value":0},{"value":0},{"value":17179869184},{"value":32},{"value":0},{"value":0},{"value":0},{"value":80131},{"value":1},{"value":18446744073709551569},{"value":13398126592},{"value":0},{"value":0},{"value":32},{"value":344160024395776},{"value":0},{"value":344160024395776},{"value":13398125632},{"value":0},{"value":17179869186},{"value":18446744073709550527},{"value":2}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6694093728},"cpsr":{"value":4096},"fp":{"value":13398124976},"sp":{"value":13398124896},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6694018100},"far":{"value":0}},"frames":[{"imageOffset":3124,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":163},{"imageOffset":78752,"symbol":"mach_msg2_internal","symbolLocation":76,"imageIndex":163},{"imageOffset":38756,"symbol":"mach_msg_overwrite","symbolLocation":484,"imageIndex":163},{"imageOffset":4008,"symbol":"mach_msg","symbolLocation":24,"imageIndex":163},{"imageOffset":71161832,"imageIndex":56},{"imageOffset":70677284,"imageIndex":56},{"imageOffset":70677152,"imageIndex":56},{"imageOffset":70343492,"imageIndex":56},{"imageOffset":70809656,"imageIndex":56},{"imageOffset":70544784,"imageIndex":56},{"imageOffset":70952276,"imageIndex":56},{"imageOffset":70952656,"imageIndex":56},{"imageOffset":71057880,"imageIndex":56},{"imageOffset":27660,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":164},{"imageOffset":7040,"symbol":"thread_start","symbolLocation":8,"imageIndex":164}]},{"id":278987,"name":"ThreadPoolBackgroundWorker","threadState":{"x":[{"value":268451845},{"value":17179869186},{"value":0},{"value":568460396462080},{"value":0},{"value":568460396462080},{"value":32},{"value":0},{"value":0},{"value":17179869184},{"value":32},{"value":0},{"value":0},{"value":0},{"value":132355},{"value":2190104571},{"value":18446744073709551569},{"value":4901291008},{"value":0},{"value":0},{"value":32},{"value":568460396462080},{"value":0},{"value":568460396462080},{"value":13593668912},{"value":0},{"value":17179869186},{"value":18446744073709550527},{"value":2}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6694093728},"cpsr":{"value":4096},"fp":{"value":13593668256},"sp":{"value":13593668176},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6694018100},"far":{"value":0}},"frames":[{"imageOffset":3124,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":163},{"imageOffset":78752,"symbol":"mach_msg2_internal","symbolLocation":76,"imageIndex":163},{"imageOffset":38756,"symbol":"mach_msg_overwrite","symbolLocation":484,"imageIndex":163},{"imageOffset":4008,"symbol":"mach_msg","symbolLocation":24,"imageIndex":163},{"imageOffset":71161832,"imageIndex":56},{"imageOffset":70677284,"imageIndex":56},{"imageOffset":70900888,"imageIndex":56},{"imageOffset":70903324,"imageIndex":56},{"imageOffset":70902696,"imageIndex":56},{"imageOffset":71057880,"imageIndex":56},{"imageOffset":27660,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":164},{"imageOffset":7040,"symbol":"thread_start","symbolLocation":8,"imageIndex":164}]},{"id":279000,"name":"com.apple.NSEventThread","threadState":{"x":[{"value":0},{"value":21592279046},{"value":8589934592},{"value":738919058505728},{"value":0},{"value":738919058505728},{"value":2},{"value":4294967295},{"value":0},{"value":17179869184},{"value":0},{"value":2},{"value":0},{"value":0},{"value":172043},{"value":0},{"value":18446744073709551569},{"value":8556469352},{"value":0},{"value":4294967295},{"value":2},{"value":738919058505728},{"value":0},{"value":738919058505728},{"value":13529997448},{"value":8589934592},{"value":21592279046},{"value":18446744073709550527},{"value":4412409862}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6694093728},"cpsr":{"value":4096},"fp":{"value":13529997296},"sp":{"value":13529997216},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6694018100},"far":{"value":0}},"frames":[{"imageOffset":3124,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":163},{"imageOffset":78752,"symbol":"mach_msg2_internal","symbolLocation":76,"imageIndex":163},{"imageOffset":38756,"symbol":"mach_msg_overwrite","symbolLocation":484,"imageIndex":163},{"imageOffset":4008,"symbol":"mach_msg","symbolLocation":24,"imageIndex":163},{"imageOffset":511164,"symbol":"__CFRunLoopServiceMachPort","symbolLocation":160,"imageIndex":170},{"imageOffset":505304,"symbol":"__CFRunLoopRun","symbolLocation":1208,"imageIndex":170},{"imageOffset":502424,"symbol":"CFRunLoopRunSpecific","symbolLocation":572,"imageIndex":170},{"imageOffset":1435532,"symbol":"_NSEventThread","symbolLocation":140,"imageIndex":167},{"imageOffset":27660,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":164},{"imageOffset":7040,"symbol":"thread_start","symbolLocation":8,"imageIndex":164}]},{"id":279001,"name":"ThreadPoolForegroundWorker","threadState":{"x":[{"value":268451845},{"value":17179869186},{"value":0},{"value":581654535995392},{"value":0},{"value":581654535995392},{"value":32},{"value":0},{"value":0},{"value":17179869184},{"value":32},{"value":0},{"value":0},{"value":0},{"value":135427},{"value":768},{"value":18446744073709551569},{"value":8556467480},{"value":0},{"value":0},{"value":32},{"value":581654535995392},{"value":0},{"value":581654535995392},{"value":13538422064},{"value":0},{"value":17179869186},{"value":18446744073709550527},{"value":2}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6694093728},"cpsr":{"value":4096},"fp":{"value":13538421408},"sp":{"value":13538421328},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6694018100},"far":{"value":0}},"frames":[{"imageOffset":3124,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":163},{"imageOffset":78752,"symbol":"mach_msg2_internal","symbolLocation":76,"imageIndex":163},{"imageOffset":38756,"symbol":"mach_msg_overwrite","symbolLocation":484,"imageIndex":163},{"imageOffset":4008,"symbol":"mach_msg","symbolLocation":24,"imageIndex":163},{"imageOffset":71161832,"imageIndex":56},{"imageOffset":70677284,"imageIndex":56},{"imageOffset":70900888,"imageIndex":56},{"imageOffset":70904380,"imageIndex":56},{"imageOffset":70902644,"imageIndex":56},{"imageOffset":71057880,"imageIndex":56},{"imageOffset":27660,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":164},{"imageOffset":7040,"symbol":"thread_start","symbolLocation":8,"imageIndex":164}]},{"id":279002,"name":"MemoryInfra","threadState":{"x":[{"value":268451845},{"value":17179869186},{"value":0},{"value":710297396445184},{"value":0},{"value":710297396445184},{"value":32},{"value":0},{"value":0},{"value":17179869184},{"value":32},{"value":0},{"value":0},{"value":0},{"value":165379},{"value":1},{"value":18446744073709551569},{"value":13548662784},{"value":0},{"value":0},{"value":32},{"value":710297396445184},{"value":0},{"value":710297396445184},{"value":13548661824},{"value":0},{"value":17179869186},{"value":18446744073709550527},{"value":2}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6694093728},"cpsr":{"value":4096},"fp":{"value":13548661168},"sp":{"value":13548661088},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6694018100},"far":{"value":0}},"frames":[{"imageOffset":3124,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":163},{"imageOffset":78752,"symbol":"mach_msg2_internal","symbolLocation":76,"imageIndex":163},{"imageOffset":38756,"symbol":"mach_msg_overwrite","symbolLocation":484,"imageIndex":163},{"imageOffset":4008,"symbol":"mach_msg","symbolLocation":24,"imageIndex":163},{"imageOffset":71161832,"imageIndex":56},{"imageOffset":70677284,"imageIndex":56},{"imageOffset":70677152,"imageIndex":56},{"imageOffset":70343492,"imageIndex":56},{"imageOffset":70809656,"imageIndex":56},{"imageOffset":70544784,"imageIndex":56},{"imageOffset":70952276,"imageIndex":56},{"imageOffset":70952656,"imageIndex":56},{"imageOffset":71057880,"imageIndex":56},{"imageOffset":27660,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":164},{"imageOffset":7040,"symbol":"thread_start","symbolLocation":8,"imageIndex":164}]},{"id":279003,"name":"ThreadPoolSingleThreadSharedBackgroundBlocking2","threadState":{"x":[{"value":268451845},{"value":17179869186},{"value":0},{"value":589351117389824},{"value":0},{"value":589351117389824},{"value":32},{"value":0},{"value":0},{"value":17179869184},{"value":32},{"value":0},{"value":0},{"value":0},{"value":137219},{"value":2936662011},{"value":18446744073709551569},{"value":24},{"value":0},{"value":0},{"value":32},{"value":589351117389824},{"value":0},{"value":589351117389824},{"value":13668281648},{"value":0},{"value":17179869186},{"value":18446744073709550527},{"value":2}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6694093728},"cpsr":{"value":4096},"fp":{"value":13668280992},"sp":{"value":13668280912},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6694018100},"far":{"value":0}},"frames":[{"imageOffset":3124,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":163},{"imageOffset":78752,"symbol":"mach_msg2_internal","symbolLocation":76,"imageIndex":163},{"imageOffset":38756,"symbol":"mach_msg_overwrite","symbolLocation":484,"imageIndex":163},{"imageOffset":4008,"symbol":"mach_msg","symbolLocation":24,"imageIndex":163},{"imageOffset":71161832,"imageIndex":56},{"imageOffset":70677284,"imageIndex":56},{"imageOffset":70900888,"imageIndex":56},{"imageOffset":70903324,"imageIndex":56},{"imageOffset":70902760,"imageIndex":56},{"imageOffset":71057880,"imageIndex":56},{"imageOffset":27660,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":164},{"imageOffset":7040,"symbol":"thread_start","symbolLocation":8,"imageIndex":164}]},{"id":279010,"name":"ThreadPoolForegroundWorker","threadState":{"x":[{"value":268451845},{"value":17179869186},{"value":0},{"value":601445745295360},{"value":0},{"value":601445745295360},{"value":32},{"value":0},{"value":0},{"value":17179869184},{"value":32},{"value":0},{"value":0},{"value":0},{"value":140035},{"value":3374317564},{"value":18446744073709551569},{"value":4900467200},{"value":0},{"value":0},{"value":32},{"value":601445745295360},{"value":0},{"value":601445745295360},{"value":13677751600},{"value":0},{"value":17179869186},{"value":18446744073709550527},{"value":2}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6694093728},"cpsr":{"value":4096},"fp":{"value":13677750944},"sp":{"value":13677750864},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6694018100},"far":{"value":0}},"frames":[{"imageOffset":3124,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":163},{"imageOffset":78752,"symbol":"mach_msg2_internal","symbolLocation":76,"imageIndex":163},{"imageOffset":38756,"symbol":"mach_msg_overwrite","symbolLocation":484,"imageIndex":163},{"imageOffset":4008,"symbol":"mach_msg","symbolLocation":24,"imageIndex":163},{"imageOffset":71161832,"imageIndex":56},{"imageOffset":70677284,"imageIndex":56},{"imageOffset":70900888,"imageIndex":56},{"imageOffset":70903324,"imageIndex":56},{"imageOffset":70902644,"imageIndex":56},{"imageOffset":71057880,"imageIndex":56},{"imageOffset":27660,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":164},{"imageOffset":7040,"symbol":"thread_start","symbolLocation":8,"imageIndex":164}]},{"id":838812,"name":"QFileInfoGatherer","threadState":{"x":[{"value":260},{"value":0},{"value":6656},{"value":0},{"value":0},{"value":160},{"value":0},{"value":0},{"value":13583101320},{"value":0},{"value":0},{"value":2},{"value":2},{"value":0},{"value":0},{"value":0},{"value":305},{"value":8556467472},{"value":0},{"value":105553130881152},{"value":105553130881216},{"value":13583102176},{"value":0},{"value":0},{"value":6656},{"value":6657},{"value":6912},{"value":0},{"value":0}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6694289632},"cpsr":{"value":1610616832},"fp":{"value":13583101440},"sp":{"value":13583101296},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6694032332},"far":{"value":0}},"frames":[{"imageOffset":17356,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":163},{"imageOffset":28896,"symbol":"_pthread_cond_wait","symbolLocation":984,"imageIndex":164},{"imageOffset":2118012,"imageIndex":45},{"imageOffset":2117824,"symbol":"QWaitCondition::wait(QMutex*, QDeadlineTimer)","symbolLocation":108,"imageIndex":45},{"imageOffset":4264588,"symbol":"QFileInfoGatherer::run()","symbolLocation":136,"imageIndex":50},{"imageOffset":2063036,"imageIndex":45},{"imageOffset":27660,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":164},{"imageOffset":7040,"symbol":"thread_start","symbolLocation":8,"imageIndex":164}]},{"id":841249,"frames":[{"imageOffset":17356,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":163},{"imageOffset":28896,"symbol":"_pthread_cond_wait","symbolLocation":984,"imageIndex":164},{"imageOffset":1502040,"symbol":"blas_thread_server","symbolLocation":360,"imageIndex":19},{"imageOffset":27660,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":164},{"imageOffset":7040,"symbol":"thread_start","symbolLocation":8,"imageIndex":164}],"threadState":{"x":[{"value":260},{"value":0},{"value":23296},{"value":0},{"value":0},{"value":160},{"value":0},{"value":0},{"value":13698592456},{"value":0},{"value":0},{"value":2},{"value":2},{"value":0},{"value":0},{"value":0},{"value":305},{"value":8556467472},{"value":0},{"value":4380483600,"symbolLocation":16,"symbol":"thread_status"},{"value":4380483664,"symbolLocation":80,"symbol":"thread_status"},{"value":13698592992},{"value":0},{"value":0},{"value":23296},{"value":23297},{"value":23552},{"value":4380397568,"symbolLocation":16,"symbol":"gemm_driver.level3_lock"},{"value":1}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6694289632},"cpsr":{"value":1610616832},"fp":{"value":13698592576},"sp":{"value":13698592432},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6694032332},"far":{"value":0}}},{"id":841250,"frames":[{"imageOffset":17356,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":163},{"imageOffset":28896,"symbol":"_pthread_cond_wait","symbolLocation":984,"imageIndex":164},{"imageOffset":1502040,"symbol":"blas_thread_server","symbolLocation":360,"imageIndex":19},{"imageOffset":27660,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":164},{"imageOffset":7040,"symbol":"thread_start","symbolLocation":8,"imageIndex":164}],"threadState":{"x":[{"value":260},{"value":0},{"value":23296},{"value":0},{"value":0},{"value":160},{"value":0},{"value":0},{"value":13701525192},{"value":0},{"value":0},{"value":2},{"value":2},{"value":0},{"value":0},{"value":0},{"value":305},{"value":8556467472},{"value":0},{"value":4380483728,"symbolLocation":144,"symbol":"thread_status"},{"value":4380483792,"symbolLocation":208,"symbol":"thread_status"},{"value":13701525728},{"value":0},{"value":0},{"value":23296},{"value":23297},{"value":23552},{"value":4380397568,"symbolLocation":16,"symbol":"gemm_driver.level3_lock"},{"value":1}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6694289632},"cpsr":{"value":1610616832},"fp":{"value":13701525312},"sp":{"value":13701525168},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6694032332},"far":{"value":0}}},{"id":841251,"frames":[{"imageOffset":17356,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":163},{"imageOffset":28896,"symbol":"_pthread_cond_wait","symbolLocation":984,"imageIndex":164},{"imageOffset":1502040,"symbol":"blas_thread_server","symbolLocation":360,"imageIndex":19},{"imageOffset":27660,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":164},{"imageOffset":7040,"symbol":"thread_start","symbolLocation":8,"imageIndex":164}],"threadState":{"x":[{"value":260},{"value":0},{"value":0},{"value":0},{"value":0},{"value":160},{"value":0},{"value":0},{"value":13715304136},{"value":0},{"value":0},{"value":2},{"value":2},{"value":0},{"value":0},{"value":0},{"value":305},{"value":8556467472},{"value":0},{"value":4380483856,"symbolLocation":272,"symbol":"thread_status"},{"value":4380483920,"symbolLocation":336,"symbol":"thread_status"},{"value":13715304672},{"value":0},{"value":0},{"value":0},{"value":1},{"value":256},{"value":4380397568,"symbolLocation":16,"symbol":"gemm_driver.level3_lock"},{"value":1}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6694289632},"cpsr":{"value":1610616832},"fp":{"value":13715304256},"sp":{"value":13715304112},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6694032332},"far":{"value":0}}},{"id":841252,"frames":[{"imageOffset":17356,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":163},{"imageOffset":28896,"symbol":"_pthread_cond_wait","symbolLocation":984,"imageIndex":164},{"imageOffset":1502040,"symbol":"blas_thread_server","symbolLocation":360,"imageIndex":19},{"imageOffset":27660,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":164},{"imageOffset":7040,"symbol":"thread_start","symbolLocation":8,"imageIndex":164}],"threadState":{"x":[{"value":260},{"value":0},{"value":0},{"value":0},{"value":0},{"value":160},{"value":0},{"value":0},{"value":13794045640},{"value":0},{"value":0},{"value":2},{"value":2},{"value":0},{"value":0},{"value":0},{"value":305},{"value":8556467472},{"value":0},{"value":4380483984,"symbolLocation":400,"symbol":"thread_status"},{"value":4380484048,"symbolLocation":464,"symbol":"thread_status"},{"value":13794046176},{"value":0},{"value":0},{"value":0},{"value":1},{"value":256},{"value":4380397568,"symbolLocation":16,"symbol":"gemm_driver.level3_lock"},{"value":1}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6694289632},"cpsr":{"value":1610616832},"fp":{"value":13794045760},"sp":{"value":13794045616},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6694032332},"far":{"value":0}}},{"id":841253,"frames":[{"imageOffset":17356,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":163},{"imageOffset":28896,"symbol":"_pthread_cond_wait","symbolLocation":984,"imageIndex":164},{"imageOffset":1502040,"symbol":"blas_thread_server","symbolLocation":360,"imageIndex":19},{"imageOffset":27660,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":164},{"imageOffset":7040,"symbol":"thread_start","symbolLocation":8,"imageIndex":164}],"threadState":{"x":[{"value":260},{"value":0},{"value":0},{"value":0},{"value":0},{"value":160},{"value":0},{"value":0},{"value":13797076680},{"value":0},{"value":0},{"value":2},{"value":2},{"value":0},{"value":0},{"value":0},{"value":305},{"value":8556467472},{"value":0},{"value":4380484112,"symbolLocation":528,"symbol":"thread_status"},{"value":4380484176,"symbolLocation":592,"symbol":"thread_status"},{"value":13797077216},{"value":0},{"value":0},{"value":0},{"value":1},{"value":256},{"value":4380397568,"symbolLocation":16,"symbol":"gemm_driver.level3_lock"},{"value":1}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6694289632},"cpsr":{"value":1610616832},"fp":{"value":13797076800},"sp":{"value":13797076656},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6694032332},"far":{"value":0}}},{"id":841254,"frames":[{"imageOffset":17356,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":163},{"imageOffset":28896,"symbol":"_pthread_cond_wait","symbolLocation":984,"imageIndex":164},{"imageOffset":1502040,"symbol":"blas_thread_server","symbolLocation":360,"imageIndex":19},{"imageOffset":27660,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":164},{"imageOffset":7040,"symbol":"thread_start","symbolLocation":8,"imageIndex":164}],"threadState":{"x":[{"value":260},{"value":0},{"value":0},{"value":0},{"value":0},{"value":160},{"value":0},{"value":0},{"value":13800861384},{"value":0},{"value":0},{"value":2},{"value":2},{"value":0},{"value":0},{"value":0},{"value":305},{"value":8556467472},{"value":0},{"value":4380484240,"symbolLocation":656,"symbol":"thread_status"},{"value":4380484304,"symbolLocation":720,"symbol":"thread_status"},{"value":13800861920},{"value":0},{"value":0},{"value":0},{"value":1},{"value":256},{"value":4380397568,"symbolLocation":16,"symbol":"gemm_driver.level3_lock"},{"value":1}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6694289632},"cpsr":{"value":1610616832},"fp":{"value":13800861504},"sp":{"value":13800861360},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6694032332},"far":{"value":0}}},{"id":841255,"frames":[{"imageOffset":17356,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":163},{"imageOffset":28896,"symbol":"_pthread_cond_wait","symbolLocation":984,"imageIndex":164},{"imageOffset":1502040,"symbol":"blas_thread_server","symbolLocation":360,"imageIndex":19},{"imageOffset":27660,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":164},{"imageOffset":7040,"symbol":"thread_start","symbolLocation":8,"imageIndex":164}],"threadState":{"x":[{"value":260},{"value":0},{"value":0},{"value":0},{"value":0},{"value":160},{"value":0},{"value":0},{"value":13819932360},{"value":0},{"value":0},{"value":2},{"value":2},{"value":0},{"value":0},{"value":0},{"value":305},{"value":8556467472},{"value":0},{"value":4380484368,"symbolLocation":784,"symbol":"thread_status"},{"value":4380484432,"symbolLocation":848,"symbol":"thread_status"},{"value":13819932896},{"value":0},{"value":0},{"value":0},{"value":1},{"value":256},{"value":4380397568,"symbolLocation":16,"symbol":"gemm_driver.level3_lock"},{"value":1}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6694289632},"cpsr":{"value":1610616832},"fp":{"value":13819932480},"sp":{"value":13819932336},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6694032332},"far":{"value":0}}},{"id":841256,"frames":[{"imageOffset":17356,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":163},{"imageOffset":28896,"symbol":"_pthread_cond_wait","symbolLocation":984,"imageIndex":164},{"imageOffset":1502040,"symbol":"blas_thread_server","symbolLocation":360,"imageIndex":19},{"imageOffset":27660,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":164},{"imageOffset":7040,"symbol":"thread_start","symbolLocation":8,"imageIndex":164}],"threadState":{"x":[{"value":260},{"value":0},{"value":0},{"value":0},{"value":0},{"value":160},{"value":0},{"value":0},{"value":13820505800},{"value":0},{"value":0},{"value":2},{"value":2},{"value":0},{"value":0},{"value":0},{"value":305},{"value":8556467472},{"value":0},{"value":4380484496,"symbolLocation":912,"symbol":"thread_status"},{"value":4380484560,"symbolLocation":976,"symbol":"thread_status"},{"value":13820506336},{"value":0},{"value":0},{"value":0},{"value":1},{"value":256},{"value":4380397568,"symbolLocation":16,"symbol":"gemm_driver.level3_lock"},{"value":1}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6694289632},"cpsr":{"value":1610616832},"fp":{"value":13820505920},"sp":{"value":13820505776},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6694032332},"far":{"value":0}}},{"id":841257,"frames":[{"imageOffset":17356,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":163},{"imageOffset":28896,"symbol":"_pthread_cond_wait","symbolLocation":984,"imageIndex":164},{"imageOffset":1502040,"symbol":"blas_thread_server","symbolLocation":360,"imageIndex":19},{"imageOffset":27660,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":164},{"imageOffset":7040,"symbol":"thread_start","symbolLocation":8,"imageIndex":164}],"threadState":{"x":[{"value":260},{"value":0},{"value":0},{"value":0},{"value":0},{"value":160},{"value":0},{"value":0},{"value":13821079240},{"value":0},{"value":0},{"value":2},{"value":2},{"value":0},{"value":0},{"value":0},{"value":305},{"value":8556467472},{"value":0},{"value":4380484624,"symbolLocation":1040,"symbol":"thread_status"},{"value":4380484688,"symbolLocation":1104,"symbol":"thread_status"},{"value":13821079776},{"value":0},{"value":0},{"value":0},{"value":1},{"value":256},{"value":4380397568,"symbolLocation":16,"symbol":"gemm_driver.level3_lock"},{"value":1}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6694289632},"cpsr":{"value":1610616832},"fp":{"value":13821079360},"sp":{"value":13821079216},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6694032332},"far":{"value":0}}},{"id":841258,"frames":[{"imageOffset":17356,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":163},{"imageOffset":28896,"symbol":"_pthread_cond_wait","symbolLocation":984,"imageIndex":164},{"imageOffset":1502040,"symbol":"blas_thread_server","symbolLocation":360,"imageIndex":19},{"imageOffset":27660,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":164},{"imageOffset":7040,"symbol":"thread_start","symbolLocation":8,"imageIndex":164}],"threadState":{"x":[{"value":260},{"value":0},{"value":0},{"value":0},{"value":0},{"value":160},{"value":0},{"value":0},{"value":13826502344},{"value":0},{"value":0},{"value":2},{"value":2},{"value":0},{"value":0},{"value":0},{"value":305},{"value":8556467472},{"value":0},{"value":4380484752,"symbolLocation":1168,"symbol":"thread_status"},{"value":4380484816,"symbolLocation":1232,"symbol":"thread_status"},{"value":13826502880},{"value":0},{"value":0},{"value":0},{"value":1},{"value":256},{"value":4380397568,"symbolLocation":16,"symbol":"gemm_driver.level3_lock"},{"value":1}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6694289632},"cpsr":{"value":1610616832},"fp":{"value":13826502464},"sp":{"value":13826502320},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6694032332},"far":{"value":0}}},{"id":841259,"frames":[{"imageOffset":17356,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":163},{"imageOffset":28896,"symbol":"_pthread_cond_wait","symbolLocation":984,"imageIndex":164},{"imageOffset":1502040,"symbol":"blas_thread_server","symbolLocation":360,"imageIndex":19},{"imageOffset":27660,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":164},{"imageOffset":7040,"symbol":"thread_start","symbolLocation":8,"imageIndex":164}],"threadState":{"x":[{"value":260},{"value":0},{"value":0},{"value":0},{"value":0},{"value":160},{"value":0},{"value":0},{"value":13829697224},{"value":0},{"value":0},{"value":2},{"value":2},{"value":0},{"value":0},{"value":0},{"value":305},{"value":8556467472},{"value":0},{"value":4380484880,"symbolLocation":1296,"symbol":"thread_status"},{"value":4380484944,"symbolLocation":1360,"symbol":"thread_status"},{"value":13829697760},{"value":0},{"value":0},{"value":0},{"value":1},{"value":256},{"value":4380397568,"symbolLocation":16,"symbol":"gemm_driver.level3_lock"},{"value":1}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6694289632},"cpsr":{"value":1610616832},"fp":{"value":13829697344},"sp":{"value":13829697200},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6694032332},"far":{"value":0}}},{"id":927439,"frames":[{"imageOffset":7020,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":164}],"threadState":{"x":[{"value":13749481472},{"value":95803},{"value":13748944896},{"value":13749480320},{"value":5128196},{"value":1},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0}],"flavor":"ARM_THREAD_STATE64","lr":{"value":0},"cpsr":{"value":4096},"fp":{"value":0},"sp":{"value":13749480304},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6694267756},"far":{"value":0}}},{"id":927557,"frames":[{"imageOffset":7020,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":164}],"threadState":{"x":[{"value":16853118976},{"value":123819},{"value":16852582400},{"value":0},{"value":409604},{"value":18446744073709551615},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0}],"flavor":"ARM_THREAD_STATE64","lr":{"value":0},"cpsr":{"value":4096},"fp":{"value":0},"sp":{"value":16853118976},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6694267756},"far":{"value":0}}},{"id":929773,"frames":[{"imageOffset":7020,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":164}],"threadState":{"x":[{"value":13507129344},{"value":257299},{"value":13506592768},{"value":13507128192},{"value":5193733},{"value":1},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0}],"flavor":"ARM_THREAD_STATE64","lr":{"value":0},"cpsr":{"value":4096},"fp":{"value":0},"sp":{"value":13507128176},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6694267756},"far":{"value":0}}},{"id":929774,"frames":[{"imageOffset":7020,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":164}],"threadState":{"x":[{"value":13515075584},{"value":111179},{"value":13514539008},{"value":0},{"value":409604},{"value":18446744073709551615},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0}],"flavor":"ARM_THREAD_STATE64","lr":{"value":0},"cpsr":{"value":4096},"fp":{"value":0},"sp":{"value":13515075584},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6694267756},"far":{"value":0}}},{"id":930230,"frames":[{"imageOffset":7020,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":164}],"threadState":{"x":[{"value":13631025152},{"value":116195},{"value":13630488576},{"value":0},{"value":409604},{"value":18446744073709551615},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0}],"flavor":"ARM_THREAD_STATE64","lr":{"value":0},"cpsr":{"value":4096},"fp":{"value":0},"sp":{"value":13631025152},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6694267756},"far":{"value":0}}},{"id":930231,"frames":[{"imageOffset":7020,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":164}],"threadState":{"x":[{"value":13682470912},{"value":191439},{"value":13681934336},{"value":0},{"value":409604},{"value":18446744073709551615},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0}],"flavor":"ARM_THREAD_STATE64","lr":{"value":0},"cpsr":{"value":4096},"fp":{"value":0},"sp":{"value":13682470912},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6694267756},"far":{"value":0}}},{"id":930386,"name":"Thread (pooled)","threadState":{"x":[{"value":260},{"value":0},{"value":144384},{"value":0},{"value":0},{"value":160},{"value":29},{"value":999999000},{"value":13520563592},{"value":0},{"value":512},{"value":2199023256066},{"value":2199023256066},{"value":512},{"value":0},{"value":2199023256064},{"value":305},{"value":8556467472},{"value":0},{"value":105553131758336},{"value":105553131758400},{"value":13520564448},{"value":999999000},{"value":29},{"value":144384},{"value":144385},{"value":144640},{"value":18446744072709551616},{"value":105553131963376}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6694289632},"cpsr":{"value":1610616832},"fp":{"value":13520563712},"sp":{"value":13520563568},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6694032332},"far":{"value":0}},"frames":[{"imageOffset":17356,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":163},{"imageOffset":28896,"symbol":"_pthread_cond_wait","symbolLocation":984,"imageIndex":164},{"imageOffset":2118156,"imageIndex":45},{"imageOffset":2117824,"symbol":"QWaitCondition::wait(QMutex*, QDeadlineTimer)","symbolLocation":108,"imageIndex":45},{"imageOffset":2094896,"imageIndex":45},{"imageOffset":2063036,"imageIndex":45},{"imageOffset":27660,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":164},{"imageOffset":7040,"symbol":"thread_start","symbolLocation":8,"imageIndex":164}]},{"id":930387,"name":"Thread (pooled)","threadState":{"x":[{"value":260},{"value":0},{"value":192256},{"value":0},{"value":0},{"value":160},{"value":29},{"value":999998000},{"value":13750054280},{"value":0},{"value":512},{"value":2199023256066},{"value":2199023256066},{"value":512},{"value":0},{"value":2199023256064},{"value":305},{"value":8556467472},{"value":0},{"value":105553132250880},{"value":105553132250944},{"value":13750055136},{"value":999998000},{"value":29},{"value":192256},{"value":192257},{"value":192512},{"value":18446744072709551616},{"value":5943679504}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6694289632},"cpsr":{"value":1610616832},"fp":{"value":13750054400},"sp":{"value":13750054256},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6694032332},"far":{"value":0}},"frames":[{"imageOffset":17356,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":163},{"imageOffset":28896,"symbol":"_pthread_cond_wait","symbolLocation":984,"imageIndex":164},{"imageOffset":2118156,"imageIndex":45},{"imageOffset":2117824,"symbol":"QWaitCondition::wait(QMutex*, QDeadlineTimer)","symbolLocation":108,"imageIndex":45},{"imageOffset":2094896,"imageIndex":45},{"imageOffset":2063036,"imageIndex":45},{"imageOffset":27660,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":164},{"imageOffset":7040,"symbol":"thread_start","symbolLocation":8,"imageIndex":164}]},{"id":930388,"name":"Thread (pooled)","threadState":{"x":[{"value":260},{"value":0},{"value":204032},{"value":0},{"value":0},{"value":160},{"value":29},{"value":999999000},{"value":13830892936},{"value":0},{"value":0},{"value":2},{"value":2},{"value":0},{"value":0},{"value":0},{"value":305},{"value":8556467472},{"value":0},{"value":105553132250496},{"value":105553132250560},{"value":13830893792},{"value":999999000},{"value":29},{"value":204032},{"value":204033},{"value":204288},{"value":18446744072709551616},{"value":105553131963376}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6694289632},"cpsr":{"value":1610616832},"fp":{"value":13830893056},"sp":{"value":13830892912},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6694032332},"far":{"value":0}},"frames":[{"imageOffset":17356,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":163},{"imageOffset":28896,"symbol":"_pthread_cond_wait","symbolLocation":984,"imageIndex":164},{"imageOffset":2118156,"imageIndex":45},{"imageOffset":2117824,"symbol":"QWaitCondition::wait(QMutex*, QDeadlineTimer)","symbolLocation":108,"imageIndex":45},{"imageOffset":2094896,"imageIndex":45},{"imageOffset":2063036,"imageIndex":45},{"imageOffset":27660,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":164},{"imageOffset":7040,"symbol":"thread_start","symbolLocation":8,"imageIndex":164}]},{"id":930714,"name":"QFileInfoGatherer","threadState":{"x":[{"value":260},{"value":0},{"value":1024},{"value":0},{"value":0},{"value":160},{"value":0},{"value":0},{"value":13517417864},{"value":0},{"value":0},{"value":2},{"value":2},{"value":0},{"value":0},{"value":0},{"value":305},{"value":8556467472},{"value":0},{"value":105553130120064},{"value":105553130120128},{"value":13517418720},{"value":0},{"value":0},{"value":1024},{"value":1025},{"value":1280},{"value":0},{"value":0}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6694289632},"cpsr":{"value":1610616832},"fp":{"value":13517417984},"sp":{"value":13517417840},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6694032332},"far":{"value":0}},"frames":[{"imageOffset":17356,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":163},{"imageOffset":28896,"symbol":"_pthread_cond_wait","symbolLocation":984,"imageIndex":164},{"imageOffset":2118012,"imageIndex":45},{"imageOffset":2117824,"symbol":"QWaitCondition::wait(QMutex*, QDeadlineTimer)","symbolLocation":108,"imageIndex":45},{"imageOffset":4264588,"symbol":"QFileInfoGatherer::run()","symbolLocation":136,"imageIndex":50},{"imageOffset":2063036,"imageIndex":45},{"imageOffset":27660,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":164},{"imageOffset":7040,"symbol":"thread_start","symbolLocation":8,"imageIndex":164}]},{"id":930783,"frames":[{"imageOffset":7020,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":164}],"threadState":{"x":[{"value":16480169984},{"value":0},{"value":16479633408},{"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":4096},"fp":{"value":0},"sp":{"value":16480169984},"esr":{"value":0,"description":" Address size fault"},"pc":{"value":6694267756},"far":{"value":0}}}],
"usedImages" : [
[deleted to fit within ticket limits]
],
"sharedCache" : {
"base" : 6689619968,
"size" : 5040898048,
"uuid" : "4c1223e5-cace-3982-a003-6110a7a8a25c"
},
"vmSummary" : "ReadOnly portion of Libraries: Total=1.9G resident=0K(0%) swapped_out_or_unallocated=1.9G(100%)\nWritable regions: Total=18.2G written=9.8M(0%) resident=9.8M(0%) swapped_out=0K(0%) unallocated=18.2G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 256K 2 \nActivity Tracing 256K 1 \nCG image 4368K 80 \nCG raster data 384K 8 \nColorSync 704K 38 \nCoreAnimation 11.3M 594 \nCoreGraphics 176K 11 \nCoreImage 288K 9 \nCoreServices 624K 2 \nCoreUI image data 5552K 41 \nFoundation 48K 2 \nKernel Alloc Once 32K 1 \nMALLOC 16.6G 219 \nMALLOC guard page 288K 18 \nMach message 64K 3 \nOpenGL GLSL 384K 4 \nSTACK GUARD 56.8M 48 \nStack 205.1M 48 \nVM_ALLOCATE 1.2G 2703 \nVM_ALLOCATE (reserved) 224.0M 2 reserved VM address space (unallocated)\n__AUTH 5520K 696 \n__AUTH_CONST 77.4M 943 \n__CTF 824 1 \n__DATA 34.3M 1094 \n__DATA_CONST 37.1M 1113 \n__DATA_DIRTY 2777K 342 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 648.7M 164 \n__OBJC_RO 61.4M 1 \n__OBJC_RW 2396K 1 \n__TEXT 1.3G 1133 \n__TPRO_CONST 128K 2 \ndyld private memory 4256K 35 \nmapped file 370.1M 88 \npage table in kernel 9.8M 1 \nshared memory 3712K 25 \n=========== ======= ======= \nTOTAL 20.8G 9476 \nTOTAL, minus reserved VM space 20.5G 9476 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"logWritingSignature" : "1df040d3026c31c32a32d1b43bdb250b448109b0",
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "670e9bd77a111748a97092a1",
"factorPackIds" : {
"SIRI_TTS_DEVICE_TRAINING" : "67d07fb744f1a3655d87002b"
},
"deploymentId" : 240000016
},
{
"rolloutId" : "686eddef0a353675271ea2b8",
"factorPackIds" : {
},
"deploymentId" : 240000006
}
],
"experiments" : [
]
}
}
===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3985_00049_volume_series/J3985_class_01_00049_volume.mrc
Opened J3985_class_01_00049_volume.mrc as #1, grid size 128,128,128, pixel
2.74, shown at level 0.0714, step 1, values float32
> open
> /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3985_00049_volume_series/J3985_class_00_00049_volume.mrc
Opened J3985_class_00_00049_volume.mrc as #2, grid size 128,128,128, pixel
2.74, shown at level 0.0704, step 1, values float32
> volume #2 level 0.1464
> volume #2 level 0.1878
> volume #1 level 0.1749
> volume #1 level 0.2362
> volume #2 level 0.2672
> volume #1 level 0.2324
> volume #1 level 0.2937
> volume #1 level 0.1634
> volume #1 level 0.1979
> volume #2 level 0.2879
> volume #1 level 0.2247
> volume #1 level 0.2055
> volume #2 level 0.3432
> volume #1 level 0.3014
> volume #1 level 0.1557
> ui tool show "Segment Map"
Select a density map in the Segment map field
Segmenting J3985_class_01_00049_volume.mrc, density threshold 0.155709
Showing 1 region surfaces
187 watershed regions, grouped to 1 regions
Showing J3985_class_01_00049_volume.seg - 1 regions, 1 surfaces
Ungrouped to 3 regions
> select #3.3
1 model selected
Ungrouped to 8 regions
> select #3.6
1 model selected
Ungrouped to 5 regions
> select #3.3
1 model selected
> select add #3.14
2 models selected
> select add #3.9
3 models selected
Grouped 3 regions
Ungrouped to 3 regions
> select #3.6
1 model selected
Ungrouped to 3 regions
> select #3.3
1 model selected
Ungrouped to 15 regions
> select #3.31
1 model selected
> select add #3.9
2 models selected
> select add #3.14
3 models selected
Grouped 3 regions
Saving 1 regions to mrc file...
Opened J3985_class_01_00049_volume_region_234.mrc as #4, grid size 21,17,18,
pixel 2.74, shown at step 1, values float32
Wrote J3985_class_01_00049_volume_region_234.mrc
> volume resample #4 onGrid 1
Invalid "onGrid" argument: invalid density maps specifier
> volume resample #4 onGrid #1
Opened J3985_class_01_00049_volume_region_234.mrc resampled as #5, grid size
128,128,128, pixel 2.74, shown at step 1, values float32
> hide #!3 models
> volume #5 level 0.2124
> volume #5 level 0.1251
> save
> /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3985_00049_volume_series/J3985_class_01_00049_volume_region_p.mrc
> models #5
> open /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3986_006_volume_map.mrc
Opened cryosparc_P9_J3986_006_volume_map.mrc as #6, grid size 480,480,480,
pixel 0.732, shown at level 0.0101, step 2, values float32
> volume #6 level 0.0249
> volume #6 level 0.01868
> volume #6 level 0.03345
> volume #!5-6 hide
> volume #1 level 0.2702
> volume #2 level 0.1264
> volume #1 level 0.1478
> volume #1 level 0.1123
> volume #2 level 0.1797
> volume #1 level 0.2623
> volume #2 level 0.3574
> volume #1 level 0.3294
> open /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3984_007_volume_map.mrc
Opened cryosparc_P9_J3984_007_volume_map.mrc as #7, grid size 480,480,480,
pixel 0.732, shown at level 0.0104, step 2, values float32
> volume #!1,7 hide
> volume #7 level 0.02771
> volume #7 level 0.04405
> volume #7 level 0.03924
> volume #7 level 0.04789
> volume #7 level 0.0575
> open /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3983_007_volume_map.mrc
Opened cryosparc_P9_J3983_007_volume_map.mrc as #8, grid size 480,480,480,
pixel 0.732, shown at level 0.0105, step 2, values float32
> volume #8 level 0.0575
> volume #8 level 0.04195
> volume #7 level 0.03636
> select add #7
3 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #3.3,0.99455,-0.074938,-0.072552,27.272,0.072407,0.99669,-0.036905,-6.1312,0.075078,0.03145,0.99668,-18.795,#7,0.99455,-0.074938,-0.072552,27.272,0.072407,0.99669,-0.036905,-6.1312,0.075078,0.03145,0.99668,-18.795
> view matrix models
> #3.3,-0.95397,0.23474,0.18664,285.38,-0.25208,-0.2905,-0.92307,440.11,-0.16246,-0.92764,0.3363,312.93,#7,-0.95397,0.23474,0.18664,285.38,-0.25208,-0.2905,-0.92307,440.11,-0.16246,-0.92764,0.3363,312.93
> fitmap #7 inMap #8
Fit map cryosparc_P9_J3984_007_volume_map.mrc in map
cryosparc_P9_J3983_007_volume_map.mrc using 49963 points
correlation = 0.9959, correlation about mean = 0.984, overlap = 500.7
steps = 380, shift = 16.1, angle = 34.3 degrees
Position of cryosparc_P9_J3984_007_volume_map.mrc (#7) relative to
cryosparc_P9_J3983_007_volume_map.mrc (#8) coordinates:
Matrix rotation and translation
-0.72583440 0.68279829 -0.08337219 201.41842056
-0.29586248 -0.41930957 -0.85828018 446.74544623
-0.62099100 -0.59830258 0.50636370 306.03816839
Axis 0.22676305 0.46893301 -0.85362776
Axis point 224.32984314 270.00684921 0.00000000
Rotation angle (degrees) 145.02379031
Shift along axis -6.07473264
> fitmap #7 inMap #8
Fit map cryosparc_P9_J3984_007_volume_map.mrc in map
cryosparc_P9_J3983_007_volume_map.mrc using 49963 points
correlation = 0.9959, correlation about mean = 0.984, overlap = 500.7
steps = 64, shift = 0.012, angle = 0.00824 degrees
Position of cryosparc_P9_J3984_007_volume_map.mrc (#7) relative to
cryosparc_P9_J3983_007_volume_map.mrc (#8) coordinates:
Matrix rotation and translation
-0.72583244 0.68280184 -0.08336017 201.41856784
-0.29596038 -0.41938679 -0.85820870 446.76271306
-0.62094664 -0.59824441 0.50648682 306.00978970
Axis 0.22673791 0.46887682 -0.85366530
Axis point 224.32617617 269.99245085 0.00000000
Rotation angle (degrees) 145.02139829
Shift along axis -6.08403693
> fitmap #7 inMap #8
Fit map cryosparc_P9_J3984_007_volume_map.mrc in map
cryosparc_P9_J3983_007_volume_map.mrc using 49963 points
correlation = 0.9959, correlation about mean = 0.984, overlap = 500.7
steps = 44, shift = 0.0118, angle = 0.00629 degrees
Position of cryosparc_P9_J3984_007_volume_map.mrc (#7) relative to
cryosparc_P9_J3983_007_volume_map.mrc (#8) coordinates:
Matrix rotation and translation
-0.72584163 0.68278694 -0.08340211 201.42434440
-0.29586571 -0.41935773 -0.85825554 446.75301724
-0.62098100 -0.59828178 0.50640054 306.02837341
Axis 0.22676494 0.46890903 -0.85364043
Axis point 224.32912008 270.00287478 0.00000000
Rotation angle (degrees) 145.02471726
Shift along axis -6.07568669
> fitmap #7 inMap #8
Fit map cryosparc_P9_J3984_007_volume_map.mrc in map
cryosparc_P9_J3983_007_volume_map.mrc using 49963 points
correlation = 0.9959, correlation about mean = 0.984, overlap = 500.7
steps = 100, shift = 0.0117, angle = 0.00919 degrees
Position of cryosparc_P9_J3984_007_volume_map.mrc (#7) relative to
cryosparc_P9_J3983_007_volume_map.mrc (#8) coordinates:
Matrix rotation and translation
-0.72585579 0.68276216 -0.08348176 201.44447216
-0.29589017 -0.41949591 -0.85817958 446.76049346
-0.62095280 -0.59821318 0.50651615 305.99878042
Axis 0.22676890 0.46883644 -0.85367925
Axis point 224.32788267 269.98130269 0.00000000
Rotation angle (degrees) 145.02655337
Shift along axis -6.08586737
> volume #8 level 0.0364
> select subtract #7
1 model selected
> view matrix models
> #3.3,-0.95397,0.23474,0.18664,285.38,-0.25208,-0.2905,-0.92307,440.11,-0.16246,-0.92764,0.3363,312.93
> volume #7 level 0.06423
> view matrix models
> #3.3,-0.95397,0.23474,0.18664,285.38,-0.25208,-0.2905,-0.92307,440.11,-0.16246,-0.92764,0.3363,312.93
> volume #7 level 0.02003
> volume #8 level 0.02571
> volume #8 level 0.04417
> open /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3969_006_volume_map.mrc
Opened cryosparc_P9_J3969_006_volume_map.mrc as #9, grid size 480,480,480,
pixel 0.732, shown at level 0.0103, step 2, values float32
> volume #9 level 0.03176
> volume #9 level 0.01519
> open /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3951_008_volume_map.mrc
Opened cryosparc_P9_J3951_008_volume_map.mrc as #10, grid size 480,480,480,
pixel 0.732, shown at level 0.0114, step 2, values float32
> volume #!8,10 hide
> volume #10 level 0.03828
> volume #10 level 0.02869
> volume #10 level 0.04979
> fitmap #1 inMap #10
Fit map J3985_class_01_00049_volume.mrc in map
cryosparc_P9_J3951_008_volume_map.mrc using 6629 points
correlation = 0.8689, correlation about mean = 0.602, overlap = 377
steps = 96, shift = 1.6, angle = 4.19 degrees
Position of J3985_class_01_00049_volume.mrc (#1) relative to
cryosparc_P9_J3951_008_volume_map.mrc (#10) coordinates:
Matrix rotation and translation
0.99743315 -0.00176327 -0.07158214 11.61334330
0.00282388 0.99988770 0.01471808 -3.39292521
0.07154815 -0.01488244 0.99732611 -10.23271671
Axis -0.20242295 -0.97879565 0.03136921
Axis point 149.23497483 0.00000000 158.72238428
Rotation angle (degrees) 4.19295196
Shift along axis 0.64918094
> fitmap #1 inMap #10
Fit map J3985_class_01_00049_volume.mrc in map
cryosparc_P9_J3951_008_volume_map.mrc using 6629 points
correlation = 0.8688, correlation about mean = 0.6019, overlap = 377
steps = 40, shift = 0.0111, angle = 0.00583 degrees
Position of J3985_class_01_00049_volume.mrc (#1) relative to
cryosparc_P9_J3951_008_volume_map.mrc (#10) coordinates:
Matrix rotation and translation
0.99743292 -0.00175838 -0.07158540 11.60987325
0.00281177 0.99988921 0.01461711 -3.38346500
0.07155176 -0.01478087 0.99732736 -10.24684374
Axis -0.20108561 -0.97907475 0.03126035
Axis point 149.42296601 0.00000000 158.67147531
Rotation angle (degrees) 4.19195597
Shift along axis 0.65776684
> fitmap #1 inMap #10
Fit map J3985_class_01_00049_volume.mrc in map
cryosparc_P9_J3951_008_volume_map.mrc using 6629 points
correlation = 0.8688, correlation about mean = 0.6019, overlap = 377
steps = 60, shift = 0.00202, angle = 0.00304 degrees
Position of J3985_class_01_00049_volume.mrc (#1) relative to
cryosparc_P9_J3951_008_volume_map.mrc (#10) coordinates:
Matrix rotation and translation
0.99743293 -0.00175093 -0.07158545 11.60870841
0.00280811 0.99988844 0.01467011 -3.38985788
0.07155178 -0.01483347 0.99732658 -10.23757914
Axis -0.20177899 -0.97893465 0.03117985
Axis point 149.29375605 0.00000000 158.66352892
Rotation angle (degrees) 4.19255884
Shift along axis 0.65684980
> fitmap #1 inMap #10
Fit map J3985_class_01_00049_volume.mrc in map
cryosparc_P9_J3951_008_volume_map.mrc using 6629 points
correlation = 0.8688, correlation about mean = 0.6019, overlap = 377
steps = 96, shift = 0.002, angle = 0.00324 degrees
Position of J3985_class_01_00049_volume.mrc (#1) relative to
cryosparc_P9_J3951_008_volume_map.mrc (#10) coordinates:
Matrix rotation and translation
0.99743159 -0.00171901 -0.07160488 11.60617014
0.00277352 0.99988913 0.01463001 -3.37850973
0.07157180 -0.01479103 0.99732578 -10.24880751
Axis -0.20118700 -0.97907100 0.03072081
Axis point 149.40364660 0.00000000 158.57590880
Rotation angle (degrees) 4.19313151
Shift along axis 0.65793867
> open
> /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3989_00048_volume_series/J3989_class_01_00048_volume.mrc
Opened J3989_class_01_00048_volume.mrc as #11, grid size 128,128,128, pixel
2.74, shown at level 0.0696, step 1, values float32
> open
> /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3989_00048_volume_series/J3989_class_00_00048_volume.mrc
Opened J3989_class_00_00048_volume.mrc as #12, grid size 128,128,128, pixel
2.74, shown at level 0.0695, step 1, values float32
> volume #!1,10-12 hide
> volume #12 level 0.1515
> volume #11 level 0.1326
> volume #11 level 0.1548
> volume #1 level 0.211
> volume #2 level 0.1832
> volume #!2 hide
> open
> /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3968_00116_volume_series/J3968_class_01_00116_volume.mrc
Opened J3968_class_01_00116_volume.mrc as #13, grid size 144,144,144, pixel
2.75, shown at level 0.0545, step 1, values float32
> open
> /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3968_00116_volume_series/J3968_class_00_00116_volume.mrc
Opened J3968_class_00_00116_volume.mrc as #14, grid size 144,144,144, pixel
2.75, shown at level 0.0495, step 1, values float32
> volume #14 level 0.115
> volume #13 level 0.1179
> select add #13
3 models selected
> hide #!14 models
> fitmap #13 inMap #11
Fit map J3968_class_01_00116_volume.mrc in map J3989_class_01_00048_volume.mrc
using 15819 points
correlation = 0.8706, correlation about mean = 0.722, overlap = 2919
steps = 140, shift = 37.7, angle = 1.37 degrees
Position of J3968_class_01_00116_volume.mrc (#13) relative to
J3989_class_01_00048_volume.mrc (#11) coordinates:
Matrix rotation and translation
0.99971437 0.01959626 0.01368115 -28.66197852
-0.01958627 0.99980780 -0.00086396 -16.84931847
-0.01369545 0.00059576 0.99990604 -19.58306288
Axis 0.03052447 0.57247681 -0.81935252
Axis point -1036.02962297 1456.12966984 0.00000000
Rotation angle (degrees) 1.37011058
Shift along axis 5.52469615
> fitmap #13 inMap #11
Fit map J3968_class_01_00116_volume.mrc in map J3989_class_01_00048_volume.mrc
using 15819 points
correlation = 0.8705, correlation about mean = 0.7217, overlap = 2919
steps = 56, shift = 0.023, angle = 0.0138 degrees
Position of J3968_class_01_00116_volume.mrc (#13) relative to
J3989_class_01_00048_volume.mrc (#11) coordinates:
Matrix rotation and translation
0.99971346 0.01976263 0.01350659 -28.68065746
-0.01975270 0.99980452 -0.00086839 -16.82188386
-0.01352112 0.00060135 0.99990840 -19.61515682
Axis 0.03068551 0.56428859 -0.82500714
Axis point -1031.91078715 1445.31671200 0.00000000
Rotation angle (degrees) 1.37227811
Shift along axis 5.81016679
> fitmap #11 inMap #14
Fit map J3989_class_01_00048_volume.mrc in map J3968_class_00_00116_volume.mrc
using 11649 points
correlation = 0.8966, correlation about mean = 0.7157, overlap = 2894
steps = 124, shift = 38, angle = 1.45 degrees
Position of J3989_class_01_00048_volume.mrc (#11) relative to
J3968_class_00_00116_volume.mrc (#14) coordinates:
Matrix rotation and translation
0.99969266 -0.02253533 -0.01033133 28.08037343
0.02259070 0.99973088 0.00527456 16.14208619
0.01020969 -0.00550634 0.99993272 21.38876177
Axis -0.21247458 -0.40483111 0.88936287
Axis point -815.69812369 1318.66977759 0.00000000
Rotation angle (degrees) 1.45374188
Shift along axis 6.52118636
> fitmap #11 inMap #14
Fit map J3989_class_01_00048_volume.mrc in map J3968_class_00_00116_volume.mrc
using 11649 points
correlation = 0.8967, correlation about mean = 0.7151, overlap = 2889
steps = 80, shift = 0.042, angle = 0.00904 degrees
Position of J3989_class_01_00048_volume.mrc (#11) relative to
J3968_class_00_00116_volume.mrc (#14) coordinates:
Matrix rotation and translation
0.99969400 -0.02251644 -0.01024267 28.07371662
0.02257002 0.99973202 0.00514573 16.13692320
0.01012406 -0.00537533 0.99993430 21.40764237
Axis -0.20801043 -0.40266782 0.89139794
Axis point -819.63745883 1320.26275326 0.00000000
Rotation angle (degrees) 1.44915013
Shift along axis 6.74528284
> fitmap #11 inMap #14
Fit map J3989_class_01_00048_volume.mrc in map J3968_class_00_00116_volume.mrc
using 11649 points
correlation = 0.8965, correlation about mean = 0.7152, overlap = 2893
steps = 80, shift = 0.0478, angle = 0.0308 degrees
Position of J3989_class_01_00048_volume.mrc (#11) relative to
J3968_class_00_00116_volume.mrc (#14) coordinates:
Matrix rotation and translation
0.99968804 -0.02285456 -0.01007459 28.12280975
0.02291102 0.99972224 0.00552539 16.05278061
0.00994551 -0.00575449 0.99993398 21.48943495
Axis -0.22026445 -0.39093637 0.89367350
Axis point -799.73209073 1306.33286302 0.00000000
Rotation angle (degrees) 1.46723678
Shift along axis 6.73446774
> fitmap #11 inMap #14
Fit map J3989_class_01_00048_volume.mrc in map J3968_class_00_00116_volume.mrc
using 11649 points
correlation = 0.8965, correlation about mean = 0.7151, overlap = 2893
steps = 64, shift = 0.00592, angle = 0.0116 degrees
Position of J3989_class_01_00048_volume.mrc (#11) relative to
J3968_class_00_00116_volume.mrc (#14) coordinates:
Matrix rotation and translation
0.99969172 -0.02267013 -0.01012540 28.09508155
0.02272756 0.99972605 0.00559283 16.07389740
0.00999584 -0.00582123 0.99993310 21.49281283
Axis -0.22401656 -0.39490657 0.89099123
Axis point -804.48634434 1314.55289352 0.00000000
Rotation angle (degrees) 1.45982216
Shift along axis 6.50845650
> hide #!11 models
> select subtract #13
1 model selected
> volume #14 level 0.2241
> volume #14 level 0.06262
> volume #14 level 0.2241
> volume #14 level 0.4248
> volume #14 level 0.115
> volume #14 level 0.1717
> volume #14 level 0.211
> volume #14 level 0.1237
> volume #14 level 0.06698
> volume #14 level 0.2764
> volume #14 level 0.2241
> volume #14 level 0.2197
> volume #14 level 0.2808
> view matrix models
> #3.3,-0.95397,0.23474,0.18664,285.38,-0.25208,-0.2905,-0.92307,440.11,-0.16246,-0.92764,0.3363,312.93
> volume #14 level 0.1673
> volume #14 level 0.211
> view matrix models
> #3.3,-0.95397,0.23474,0.18664,285.38,-0.25208,-0.2905,-0.92307,440.11,-0.16246,-0.92764,0.3363,312.93
> volume #14 level 0.09752
> volume #14 level 0.1804
> volume #14 level 0.307
> volume #14 level 0.08007
> volume #14 level 0.1062
> view matrix models
> #3.3,-0.95397,0.23474,0.18664,285.38,-0.25208,-0.2905,-0.92307,440.11,-0.16246,-0.92764,0.3363,312.93
> volume #14 level 0.1542
> volume #14 level 0.1979
> view matrix models
> #3.3,-0.95397,0.23474,0.18664,285.38,-0.25208,-0.2905,-0.92307,440.11,-0.16246,-0.92764,0.3363,312.93
> volume #14 level 0.1499
> volume #14 level 0.2066
> volume #14 level 0.1019
> volume #14 level 0.1542
> volume #14 level 0.2022
> view matrix models
> #3.3,-0.95397,0.23474,0.18664,285.38,-0.25208,-0.2905,-0.92307,440.11,-0.16246,-0.92764,0.3363,312.93
> volume #14 level 0.115
> volume #14 level 0.403
> volume #14 level 0.1019
> open /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3967_007_volume_map.mrc
Opened cryosparc_P9_J3967_007_volume_map.mrc as #15, grid size 324,324,324,
pixel 1.22, shown at level 0.0302, step 2, values float32
> volume #15 level 0.08332
> volume #15 level 0.101
> volume #15 level 0.08996
> volume #15 level 0.07669
> volume #15 level 0.09438
> volume #15 level 0.163
> volume #15 level 0.1696
Segmenting cryosparc_P9_J3967_007_volume_map.mrc, density threshold 0.169599
Showing 17 region surfaces
1009 watershed regions, grouped to 17 regions
Showing cryosparc_P9_J3967_007_volume_map.seg - 17 regions, 17 surfaces
Segmenting cryosparc_P9_J3967_007_volume_map.mrc, density threshold 0.169599
Showing 17 region surfaces
1009 watershed regions, grouped to 17 regions
Showing cryosparc_P9_J3967_007_volume_map.seg - 17 regions, 17 surfaces
> select #3.17
1 model selected
Deleted 1 regions
> select #3.3
1 model selected
> select clear
> select #3.1
1 model selected
> select add #3.7
2 models selected
> select add #3.8
3 models selected
> select add #3.12
4 models selected
> select add #3.10
5 models selected
> select add #3.16
6 models selected
> select add #3.2
7 models selected
> select add #3.3
8 models selected
> select add #3.11
9 models selected
> select add #3.6
10 models selected
> select add #3.4
11 models selected
> select add #3.5
12 models selected
> select subtract #3.2
11 models selected
> select add #3.9
12 models selected
> select clear
Drag select of 1359, 48002 of 48056 triangles, 1356, 1362, 1341, 1360, 1345,
1335, 1339, 1350, 1357, 1358, 1344, 1347, 1281, 1361, 1338, 15
cryosparc_P9_J3967_007_volume_map.mrc
> view matrix models
> #15,0.99872,0.022913,-0.045133,5.562,-0.023142,0.99972,-0.0045577,5.6738,0.045016,0.0055963,0.99897,-9.8796,#3.1,0.99872,0.022913,-0.045133,5.562,-0.023142,0.99972,-0.0045577,5.6738,0.045016,0.0055963,0.99897,-9.8796,#3.2,0.99872,0.022913,-0.045133,5.562,-0.023142,0.99972,-0.0045577,5.6738,0.045016,0.0055963,0.99897,-9.8796,#3.3,0.99872,0.022913,-0.045133,5.562,-0.023142,0.99972,-0.0045577,5.6738,0.045016,0.0055963,0.99897,-9.8796,#3.4,0.99872,0.022913,-0.045133,5.562,-0.023142,0.99972,-0.0045577,5.6738,0.045016,0.0055963,0.99897,-9.8796,#3.5,0.99872,0.022913,-0.045133,5.562,-0.023142,0.99972,-0.0045577,5.6738,0.045016,0.0055963,0.99897,-9.8796,#3.6,0.99872,0.022913,-0.045133,5.562,-0.023142,0.99972,-0.0045577,5.6738,0.045016,0.0055963,0.99897,-9.8796,#3.7,0.99872,0.022913,-0.045133,5.562,-0.023142,0.99972,-0.0045577,5.6738,0.045016,0.0055963,0.99897,-9.8796,#3.8,0.99872,0.022913,-0.045133,5.562,-0.023142,0.99972,-0.0045577,5.6738,0.045016,0.0055963,0.99897,-9.8796,#3.9,0.99872,0.022913,-0.045133,5.562,-0.023142,0.99972,-0.0045577,5.6738,0.045016,0.0055963,0.99897,-9.8796,#3.10,0.99872,0.022913,-0.045133,5.562,-0.023142,0.99972,-0.0045577,5.6738,0.045016,0.0055963,0.99897,-9.8796,#3.11,0.99872,0.022913,-0.045133,5.562,-0.023142,0.99972,-0.0045577,5.6738,0.045016,0.0055963,0.99897,-9.8796,#3.12,0.99872,0.022913,-0.045133,5.562,-0.023142,0.99972,-0.0045577,5.6738,0.045016,0.0055963,0.99897,-9.8796,#3.13,0.99872,0.022913,-0.045133,5.562,-0.023142,0.99972,-0.0045577,5.6738,0.045016,0.0055963,0.99897,-9.8796,#3.14,0.99872,0.022913,-0.045133,5.562,-0.023142,0.99972,-0.0045577,5.6738,0.045016,0.0055963,0.99897,-9.8796,#3.15,0.99872,0.022913,-0.045133,5.562,-0.023142,0.99972,-0.0045577,5.6738,0.045016,0.0055963,0.99897,-9.8796,#3.16,0.99872,0.022913,-0.045133,5.562,-0.023142,0.99972,-0.0045577,5.6738,0.045016,0.0055963,0.99897,-9.8796
Saving 16 regions to mrc file...
Opened cryosparc_P9_J3967_007_volume_map_16_regions.mrc as #16, grid size
73,125,114, pixel 1.22, shown at step 1, values float32
Wrote cryosparc_P9_J3967_007_volume_map_16_regions.mrc
> volume resample #16 onGrid #15
Opened cryosparc_P9_J3967_007_volume_map_16_regions.mrc resampled as #17, grid
size 324,324,324, pixel 1.22, shown at step 1, values float32
> hide #!3 models
> volume #17 level 0.09743
> save
> /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3967_007_volume_map_16_regions.mrc
> models #17
> volume #16 level 0.296
> volume #16 level 0.2176
> volume #16 level 0.2393
> close #16
> close #17
> volume #15 level 0.06784
> volume #15 level 0.03687
> volume #15 level 0.0966
> volume #15 level 0.08111
> volume #15 level 0.1254
> view matrix models
> #15,0.72018,0.3333,-0.60848,124.77,-0.59513,0.74757,-0.29489,225.67,0.3566,0.5745,0.73674,-117.69,#3.1,0.72018,0.3333,-0.60848,124.77,-0.59513,0.74757,-0.29489,225.67,0.3566,0.5745,0.73674,-117.69,#3.2,0.72018,0.3333,-0.60848,124.77,-0.59513,0.74757,-0.29489,225.67,0.3566,0.5745,0.73674,-117.69,#3.3,0.72018,0.3333,-0.60848,124.77,-0.59513,0.74757,-0.29489,225.67,0.3566,0.5745,0.73674,-117.69,#3.4,0.72018,0.3333,-0.60848,124.77,-0.59513,0.74757,-0.29489,225.67,0.3566,0.5745,0.73674,-117.69,#3.5,0.72018,0.3333,-0.60848,124.77,-0.59513,0.74757,-0.29489,225.67,0.3566,0.5745,0.73674,-117.69,#3.6,0.72018,0.3333,-0.60848,124.77,-0.59513,0.74757,-0.29489,225.67,0.3566,0.5745,0.73674,-117.69,#3.7,0.72018,0.3333,-0.60848,124.77,-0.59513,0.74757,-0.29489,225.67,0.3566,0.5745,0.73674,-117.69,#3.8,0.72018,0.3333,-0.60848,124.77,-0.59513,0.74757,-0.29489,225.67,0.3566,0.5745,0.73674,-117.69,#3.9,0.72018,0.3333,-0.60848,124.77,-0.59513,0.74757,-0.29489,225.67,0.3566,0.5745,0.73674,-117.69,#3.10,0.72018,0.3333,-0.60848,124.77,-0.59513,0.74757,-0.29489,225.67,0.3566,0.5745,0.73674,-117.69,#3.11,0.72018,0.3333,-0.60848,124.77,-0.59513,0.74757,-0.29489,225.67,0.3566,0.5745,0.73674,-117.69,#3.12,0.72018,0.3333,-0.60848,124.77,-0.59513,0.74757,-0.29489,225.67,0.3566,0.5745,0.73674,-117.69,#3.13,0.72018,0.3333,-0.60848,124.77,-0.59513,0.74757,-0.29489,225.67,0.3566,0.5745,0.73674,-117.69,#3.14,0.72018,0.3333,-0.60848,124.77,-0.59513,0.74757,-0.29489,225.67,0.3566,0.5745,0.73674,-117.69,#3.15,0.72018,0.3333,-0.60848,124.77,-0.59513,0.74757,-0.29489,225.67,0.3566,0.5745,0.73674,-117.69,#3.16,0.72018,0.3333,-0.60848,124.77,-0.59513,0.74757,-0.29489,225.67,0.3566,0.5745,0.73674,-117.69
> close session
> open
> /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3977_00142_volumes/J3977_class_03_00142_volume.mrc
Opened J3977_class_03_00142_volume.mrc as #1, grid size 128,128,128, pixel
3.09, shown at level 0.0569, step 1, values float32
> open
> /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3977_00142_volumes/J3977_class_02_00142_volume.mrc
Opened J3977_class_02_00142_volume.mrc as #2, grid size 128,128,128, pixel
3.09, shown at level 0.0652, step 1, values float32
> open
> /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3977_00142_volumes/J3977_class_01_00142_volume.mrc
Opened J3977_class_01_00142_volume.mrc as #3, grid size 128,128,128, pixel
3.09, shown at level 0.0644, step 1, values float32
> open
> /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3977_00142_volumes/J3977_class_00_00142_volume.mrc
Opened J3977_class_00_00142_volume.mrc as #4, grid size 128,128,128, pixel
3.09, shown at level 0.0511, step 1, values float32
> surface dust #1 size 30.9
> surface dust #2 size 30.9
> surface dust #3 size 30.9
> surface dust #4 size 30.9
> volume #!1-2,4 hide
> select add #4
2 models selected
> view matrix models
> #4,0.94781,0.16804,0.27096,-68.241,-0.31283,0.32602,0.8921,34.283,0.061569,-0.93031,0.36157,273.55
> view matrix models
> #4,0.95967,0.13122,0.24861,-59.846,-0.27903,0.33713,0.89916,24.083,0.034174,-0.93227,0.36015,279.75
> view matrix models
> #4,0.81403,-0.58022,0.026318,142.13,0.23948,0.37658,0.89489,-88.181,-0.52915,-0.72217,0.4455,340.15
> volume #3 level 0.08997
> volume #3 level 0.1412
> volume #4 level 0.1357
> view matrix models
> #4,-0.98182,-0.15393,0.11102,400.77,-0.16014,0.98586,-0.049341,48.503,-0.10186,-0.066224,-0.99259,395.11
> view matrix models
> #4,-0.88503,0.34552,0.312,251.01,0.33497,0.93805,-0.088657,-33.002,-0.3233,0.026046,-0.94594,412.92
> volume #4 level 0.3894
> volume #4 z flip
Expected a keyword
> volume #4 zflip
Expected a keyword
> volume #4 flipNormals
Missing "flipNormals" keyword's argument
> volume flip #4
Opened J3977_class_00_00142_volume.mrc z flip as #5, grid size 128,128,128,
pixel 3.09, shown at step 1, values float32
> select #5
2 models selected
> view matrix models
> #5,-0.85933,0.30635,0.40953,234.55,-0.2375,0.47014,-0.85004,313.88,-0.45294,-0.82772,-0.33125,480.43
> fitmap #5 inMap #3
Fit map J3977_class_00_00142_volume.mrc z flip in map
J3977_class_01_00142_volume.mrc using 4563 points
correlation = 0.9699, correlation about mean = 0.7826, overlap = 2457
steps = 132, shift = 31.6, angle = 38.4 degrees
Position of J3977_class_00_00142_volume.mrc z flip (#5) relative to
J3977_class_01_00142_volume.mrc (#3) coordinates:
Matrix rotation and translation
-0.99116610 0.00155516 -0.13261718 420.28508914
0.12896783 0.24454249 -0.96102354 304.65893499
0.03093599 -0.96963731 -0.24258280 429.65932782
Axis -0.04151142 -0.78819365 0.61402571
Axis point 188.06887356 0.00000000 347.37550767
Rotation angle (degrees) 174.04473730
Shift along axis 6.24500964
> fitmap #5 inMap #3
Fit map J3977_class_00_00142_volume.mrc z flip in map
J3977_class_01_00142_volume.mrc using 4563 points
correlation = 0.9699, correlation about mean = 0.7826, overlap = 2457
steps = 48, shift = 0.0213, angle = 0.0281 degrees
Position of J3977_class_00_00142_volume.mrc z flip (#5) relative to
J3977_class_01_00142_volume.mrc (#3) coordinates:
Matrix rotation and translation
-0.99117083 0.00165958 -0.13258052 420.24478315
0.12894289 0.24500496 -0.96090909 304.53529817
0.03088818 -0.96952039 -0.24305576 429.72894017
Axis -0.04152874 -0.78834163 0.61383453
Axis point 188.06053369 0.00000000 347.28922017
Rotation angle (degrees) 174.04894559
Shift along axis 6.25237502
> volume #3 level 0.6852
> volume #5 level 0.188
> volume #3 level 0.1028
> volume #3 level 0.138
> volume #5 level 0.1598
> volume #5 level 0.1679
> volume #3 level 0.07077
> volume #3 level 0.1988
> volume #5 level 0.2806
> volume #1 level 0.2265
> fitmap #5 inMap #1
Fit map J3977_class_00_00142_volume.mrc z flip in map
J3977_class_03_00142_volume.mrc using 6115 points
correlation = 0.9725, correlation about mean = 0.8601, overlap = 2909
steps = 84, shift = 2.02, angle = 4.3 degrees
Position of J3977_class_00_00142_volume.mrc z flip (#5) relative to
J3977_class_03_00142_volume.mrc (#1) coordinates:
Matrix rotation and translation
-0.99754203 0.02498920 -0.06546303 405.36740821
0.06977180 0.26807185 -0.96086906 311.85792420
-0.00646256 -0.96307476 -0.26915648 438.89272991
Axis -0.02976493 -0.79618479 0.60432096
Axis point 191.78070263 0.00000000 342.51916349
Rotation angle (degrees) 177.87659093
Shift along axis 4.86980674
> fitmap #5 inMap #1
Fit map J3977_class_00_00142_volume.mrc z flip in map
J3977_class_03_00142_volume.mrc using 6115 points
correlation = 0.9725, correlation about mean = 0.8601, overlap = 2909
steps = 44, shift = 0.0143, angle = 0.0162 degrees
Position of J3977_class_00_00142_volume.mrc z flip (#5) relative to
J3977_class_03_00142_volume.mrc (#1) coordinates:
Matrix rotation and translation
-0.99754942 0.02519611 -0.06527087 405.29719322
0.06964248 0.26808225 -0.96087554 311.87541512
-0.00671237 -0.96306647 -0.26918001 438.93275976
Axis -0.02978898 -0.79618924 0.60431392
Axis point 191.77820368 0.00000000 342.50753611
Rotation angle (degrees) 177.89251633
Shift along axis 4.86793646
> volume #1 level 0.3043
> volume #1 level 0.2513
> volume sel hide
> volume #1 level 0.1453
> volume #4 level 0.1961
> close #4
> volume #5 level 0.2122
> volume #1 level 0.2053
> fitmap #5 inMap #1
Fit map J3977_class_00_00142_volume.mrc z flip in map
J3977_class_03_00142_volume.mrc using 7583 points
correlation = 0.9685, correlation about mean = 0.8754, overlap = 2994
steps = 48, shift = 0.038, angle = 0.0347 degrees
Position of J3977_class_00_00142_volume.mrc z flip (#5) relative to
J3977_class_03_00142_volume.mrc (#1) coordinates:
Matrix rotation and translation
-0.99750974 0.02523858 -0.06585823 405.37295159
0.07022047 0.26819842 -0.96080105 311.75529366
-0.00658618 -0.96303302 -0.26930280 438.93804803
Axis -0.02998281 -0.79622383 0.60425876
Axis point 191.71948602 0.00000000 342.50624022
Rotation angle (degrees) 177.86691692
Shift along axis 4.85094606
> fitmap #5 inMap #1
Fit map J3977_class_00_00142_volume.mrc z flip in map
J3977_class_03_00142_volume.mrc using 7583 points
correlation = 0.9684, correlation about mean = 0.8752, overlap = 2994
steps = 44, shift = 0.0584, angle = 0.026 degrees
Position of J3977_class_00_00142_volume.mrc z flip (#5) relative to
J3977_class_03_00142_volume.mrc (#1) coordinates:
Matrix rotation and translation
-0.99752439 0.02490787 -0.06576214 405.45522347
0.07003701 0.26791788 -0.96089271 311.91208460
-0.00631494 -0.96311971 -0.26899910 438.84730228
Axis -0.02982470 -0.79613522 0.60438332
Axis point 191.77259653 0.00000000 342.57395662
Rotation angle (degrees) 177.86037271
Shift along axis 4.81521528
> select subtract #5
Nothing selected
> show #!5 models
> volume #5 level 0.2525
> hide #!5 models
> show #!1 models
> volume #1 level 0.2795
> volume #1 level 0.276
> volume #1 level 0.08519
> volume #1 level 0.1665
> volume #2 level 0.1703
> volume #2 level 0.1327
> volume #2 level 0.1928
> volume #1 level 0.223
> fitmap #1 inMap #2
Fit map J3977_class_03_00142_volume.mrc in map J3977_class_02_00142_volume.mrc
using 7452 points
correlation = 0.9571, correlation about mean = 0.8286, overlap = 2948
steps = 84, shift = 1.2, angle = 2.65 degrees
Position of J3977_class_03_00142_volume.mrc (#1) relative to
J3977_class_02_00142_volume.mrc (#2) coordinates:
Matrix rotation and translation
0.99892948 -0.04344038 -0.01590040 11.73510950
0.04345212 0.99905543 0.00039400 -9.71668965
0.01586826 -0.00108448 0.99987350 -3.49169470
Axis -0.01597843 -0.34333482 0.93907715
Axis point 230.39658326 264.41720009 0.00000000
Rotation angle (degrees) 2.65172634
Shift along axis -0.13040143
> hide #!1 models
> volume #2 level 0.08769
> volume #2 level 0.0539
> volume #2 level 0.03889
> volume #3 level 0.03877
> volume #3 level 0.08037
> volume #2 level 0.0539
> volume #2 level 0.06517
> volume #2 level 0.07267
> volume #2 level 0.07643
> volume #2 level 0.08018
> volume #!2 hide
> volume #5 level 0.06724
> volume #5 level 0.1156
> volume #5 level 0.5102
> volume #5 level 0.3088
> volume #5 level 0.2364
> volume #5 level 0.2202
> volume #5 level 0.2162
> volume #5 level 0.2122
> volume #5 level 0.2082
> volume #5 level 0.2041
> volume #5 level 0.2001
> volume #5 level 0.1961
> volume #5 level 0.1921
> volume #5 level 0.188
> volume #5 level 0.184
> volume #5 level 0.18
> volume #5 level 0.176
> volume #5 level 0.1719
> volume #5 level 0.1679
> volume #5 level 0.1639
> volume #5 level 0.1598
> volume #5 level 0.1558
> volume #5 level 0.1518
> volume #5 level 0.1478
> volume #5 level 0.1437
> volume #5 level 0.1397
> open /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3954_006_volume_map.mrc
Opened cryosparc_P9_J3954_006_volume_map.mrc as #4, grid size 324,324,324,
pixel 1.22, shown at level 0.0183, step 2, values float32
> volume #!4-5 hide
> volume #4 level 0.06737
> volume #4 level 0.08168
> volume #4 level 0.03262
> volume #4 level 0.0551
> volume #4 level 0.0735
> ui tool show Segmentations
> ui view fourup
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1580, in
_surfaceChosen
self._update_position_label_text()
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
_update_position_label_text
dicom_data = self.view.drawing.parent.data.dicom_data
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'MRCGrid' object has no attribute 'dicom_data'
AttributeError: 'MRCGrid' object has no attribute 'dicom_data'
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
_update_position_label_text
dicom_data = self.view.drawing.parent.data.dicom_data
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1580, in
_surfaceChosen
self._update_position_label_text()
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
_update_position_label_text
dicom_data = self.view.drawing.parent.data.dicom_data
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'MRCGrid' object has no attribute 'dicom_data'
AttributeError: 'MRCGrid' object has no attribute 'dicom_data'
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
_update_position_label_text
dicom_data = self.view.drawing.parent.data.dicom_data
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1580, in
_surfaceChosen
self._update_position_label_text()
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
_update_position_label_text
dicom_data = self.view.drawing.parent.data.dicom_data
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'MRCGrid' object has no attribute 'dicom_data'
AttributeError: 'MRCGrid' object has no attribute 'dicom_data'
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
_update_position_label_text
dicom_data = self.view.drawing.parent.data.dicom_data
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> close session
> open /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3954_006_volume_map.mrc
Opened cryosparc_P9_J3954_006_volume_map.mrc as #1, grid size 324,324,324,
pixel 1.22, shown at level 0.0183, step 2, values float32
> volume #1 level 0.03022
> ui tool show "Segment Map"
> volume #1 level 0.06089
Segmenting cryosparc_P9_J3954_006_volume_map.mrc, density threshold 0.060885
Showing 17 region surfaces
1782 watershed regions, grouped to 17 regions
Showing cryosparc_P9_J3954_006_volume_map.seg - 17 regions, 17 surfaces
> select #2.4
1 model selected
Saving 1 regions to mrc file...
Opened cryosparc_P9_J3954_006_volume_map_region_2128.mrc as #3, grid size
42,45,72, pixel 1.22, shown at step 1, values float32
Wrote cryosparc_P9_J3954_006_volume_map_region_2128.mrc
> volume resample #3 onGrid #1
Opened cryosparc_P9_J3954_006_volume_map_region_2128.mrc resampled as #4, grid
size 324,324,324, pixel 1.22, shown at step 1, values float32
> save
> /Users/frazaodesouzam2/Downloads/cryosparc_P9_J3954_006_volume_map_region_2128.mrc
> models #4
> volume #1 level 0.07315
> close session
> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V2_holo-
> coot-2.pdb
Summary of feedback from opening
/Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V2_holo-
coot-2.pdb
---
warnings | Duplicate atom serial number found: 8964
Duplicate atom serial number found: 8965
Duplicate atom serial number found: 8966
Duplicate atom serial number found: 8967
Duplicate atom serial number found: 8968
26 messages similar to the above omitted
Chain information for V2_holo-coot-2.pdb #1
---
Chain | Description
A | No description available
B | No description available
> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V3_holo-
> coot-2.pdb
Summary of feedback from opening
/Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V3_holo-
coot-2.pdb
---
warnings | Duplicate atom serial number found: 8964
Duplicate atom serial number found: 8965
Duplicate atom serial number found: 8966
Duplicate atom serial number found: 8967
Duplicate atom serial number found: 8968
26 messages similar to the above omitted
Chain information for V3_holo-coot-2.pdb #2
---
Chain | Description
A | No description available
B | No description available
> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V4_holo-
> coot-3.pdb
Summary of feedback from opening
/Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V4_holo-
coot-3.pdb
---
warnings | Duplicate atom serial number found: 8965
Duplicate atom serial number found: 8966
Duplicate atom serial number found: 8967
Duplicate atom serial number found: 8968
Duplicate atom serial number found: 8969
30 messages similar to the above omitted
Chain information for V4_holo-coot-3.pdb #3
---
Chain | Description
A | No description available
B | No description available
> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V5_holo-
> coot-1.pdb
Summary of feedback from opening
/Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V5_holo-
coot-1.pdb
---
warnings | Duplicate atom serial number found: 8965
Duplicate atom serial number found: 8966
Duplicate atom serial number found: 8967
Duplicate atom serial number found: 8968
Duplicate atom serial number found: 8969
17 messages similar to the above omitted
Chain information for V5_holo-coot-1.pdb #4
---
Chain | Description
A | No description available
B | No description available
> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V6_holo-
> coot-1.pdb
Summary of feedback from opening
/Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V6_holo-
coot-1.pdb
---
warnings | Duplicate atom serial number found: 8965
Duplicate atom serial number found: 8966
Duplicate atom serial number found: 8967
Duplicate atom serial number found: 8968
Duplicate atom serial number found: 8969
20 messages similar to the above omitted
Chain information for V6_holo-coot-1.pdb #5
---
Chain | Description
A | No description available
B | No description available
> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V7_holo-
> coot-2.pdb
Chain information for V7_holo-coot-2.pdb #6
---
Chain | Description
A | No description available
B | No description available
> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V9_holo-
> coot-0.pdb
Summary of feedback from opening
/Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V9_holo-
coot-0.pdb
---
warnings | Duplicate atom serial number found: 8965
Duplicate atom serial number found: 8966
Duplicate atom serial number found: 8967
Duplicate atom serial number found: 8968
Duplicate atom serial number found: 8969
24 messages similar to the above omitted
Chain information for V9_holo-coot-0.pdb #7
---
Chain | Description
A | No description available
B | No description available
> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V10_holo-
> coot-1.pdb
Chain information for V10_holo-coot-1.pdb #8
---
Chain | Description
A | No description available
B | No description available
> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V11_holo-
> coot-1.pdb
Summary of feedback from opening
/Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V11_holo-
coot-1.pdb
---
warnings | Duplicate atom serial number found: 8965
Duplicate atom serial number found: 8966
Duplicate atom serial number found: 8967
Duplicate atom serial number found: 8968
Duplicate atom serial number found: 8969
29 messages similar to the above omitted
Chain information for V11_holo-coot-1.pdb #9
---
Chain | Description
A | No description available
B | No description available
> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V12_holo-
> coot-3.pdb
Chain information for V12_holo-coot-3.pdb #10
---
Chain | Description
A | No description available
B | No description available
> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V14_holo-
> coot-1.pdb
Summary of feedback from opening
/Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V14_holo-
coot-1.pdb
---
warnings | Duplicate atom serial number found: 8964
Duplicate atom serial number found: 8965
Duplicate atom serial number found: 8966
Duplicate atom serial number found: 8967
Duplicate atom serial number found: 8968
28 messages similar to the above omitted
Chain information for V14_holo-coot-1.pdb #11
---
Chain | Description
A | No description available
B | No description available
> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V15_holo-
> coot-1.pdb
Summary of feedback from opening
/Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V15_holo-
coot-1.pdb
---
warnings | Duplicate atom serial number found: 8965
Duplicate atom serial number found: 8966
Duplicate atom serial number found: 8968
Duplicate atom serial number found: 8969
Duplicate atom serial number found: 8970
20 messages similar to the above omitted
Chain information for V15_holo-coot-1.pdb #12
---
Chain | Description
A | No description available
B | No description available
> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V17_holo-
> coot-3.pdb
Summary of feedback from opening
/Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V17_holo-
coot-3.pdb
---
warnings | Duplicate atom serial number found: 8965
Duplicate atom serial number found: 8966
Duplicate atom serial number found: 8967
Duplicate atom serial number found: 8968
Duplicate atom serial number found: 8969
22 messages similar to the above omitted
Chain information for V17_holo-coot-3.pdb #13
---
Chain | Description
A | No description available
B | No description available
> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V18_holo-
> coot-1.pdb
Summary of feedback from opening
/Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V18_holo-
coot-1.pdb
---
warnings | Duplicate atom serial number found: 8965
Duplicate atom serial number found: 8966
Duplicate atom serial number found: 8967
Duplicate atom serial number found: 8968
Duplicate atom serial number found: 8969
24 messages similar to the above omitted
Chain information for V18_holo-coot-1.pdb #14
---
Chain | Description
A | No description available
B | No description available
> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V19_holo-
> coot-6.pdb
Summary of feedback from opening
/Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V19_holo-
coot-6.pdb
---
warnings | Duplicate atom serial number found: 8965
Duplicate atom serial number found: 8966
Duplicate atom serial number found: 8967
Duplicate atom serial number found: 8968
Duplicate atom serial number found: 8969
26 messages similar to the above omitted
Chain information for V19_holo-coot-6.pdb #15
---
Chain | Description
A | No description available
B | No description available
> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V21_holo-
> coot-2.pdb
Summary of feedback from opening
/Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V21_holo-
coot-2.pdb
---
warnings | Duplicate atom serial number found: 8964
Duplicate atom serial number found: 8965
Duplicate atom serial number found: 8966
Duplicate atom serial number found: 8967
Duplicate atom serial number found: 8968
23 messages similar to the above omitted
Chain information for V21_holo-coot-2.pdb #16
---
Chain | Description
A | No description available
B | No description available
> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V23_holo-
> coot-2.pdb
Chain information for V23_holo-coot-2.pdb #17
---
Chain | Description
A | No description available
B | No description available
> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V25_holo-
> coot-2.pdb
Summary of feedback from opening
/Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/holo_only/V25_holo-
coot-2.pdb
---
warnings | Duplicate atom serial number found: 8964
Duplicate atom serial number found: 8965
Duplicate atom serial number found: 8966
Duplicate atom serial number found: 8967
Duplicate atom serial number found: 8968
30 messages similar to the above omitted
Chain information for V25_holo-coot-2.pdb #18
---
Chain | Description
A | No description available
B | No description available
Computing secondary structure
> select #1/A:59, 60, 78, 79,49, 51, 394, 395,49, 394, 395,272, 273, 274,
> 275,113, 114, 136,277, 278, 329, 330, 331,274, 275, 276, 277, 301,256, 257,
> 258,100, 101, 102, 103, 104,100, 101, 102, 103,285, 298, 299,291, 292, 293,
> 294,299, 300, 301, 302,49, 50, 51, 388, 389, 390,59, 60, 78, 79,80, 81
983 atoms, 1091 bonds, 45 residues, 1 model selected
> hide #2-18 target m
> select #1/A:59, 60, 78, 79,49, 51, 394, 395,49, 394, 395,272, 273, 274,
> 275,113, 114, 136,277, 278, 329, 330, 331,274, 275, 276, 277, 301,256, 257,
> 258,100, 101, 102, 103, 104,100, 101, 102, 103,285, 298, 299,291, 292, 293,
> 294,299, 300, 301, 302,49, 50, 51, 388, 389, 390,59, 60, 78, 79,80, 81
983 atoms, 1091 bonds, 45 residues, 1 model selected
> select #8/A:100, 101, 102, 103,256, 257, 258,261, 271, 272, 273,26, 27, 28,
> 41,275, 276, 332, 333,275, 276, 333,49, 50, 51, 388, 389, 390,48, 50, 386,
> 387, 399,385, 386, 387,291, 292, 293, 294,277, 278, 329, 330, 331,275, 276,
> 333,113, 114, 136,15, 16, 17,25, 26, 274, 332,25, 26, 332,26, 274, 332,272,
> 273, 274,272, 273, 274, 275,273, 333,337, 338, 388,337, 388,382, 383,
> 384,49, 389, 390, 392, 393,49, 394, 395,49, 51, 394, 395,56, 57, 254,59, 60,
> 78, 79,61, 81, 250,80, 81
1459 atoms, 1618 bonds, 67 residues, 1 model selected
> show #8 models
> hide #1 models
> select
> #1/A:15,21-29,39-67,69-84,96-101,105-112,249-261,272-293,295-312,327-340,386-400
3255 atoms, 3639 bonds, 151 residues, 1 model selected
> hide #8 models
> show #1 models
> show #2-18 target m
> ui tool show Matchmaker
> matchmaker #2-18 to #1 & sel matrix Nucleic
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V3_holo-coot-2.pdb, chain A
(#2), sequence alignment score = 604
RMSD between 150 pruned atom pairs is 0.380 angstroms; (across all 151 pairs:
0.413)
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V4_holo-coot-3.pdb, chain A
(#3), sequence alignment score = 604
RMSD between 151 pruned atom pairs is 0.322 angstroms; (across all 151 pairs:
0.322)
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V5_holo-coot-1.pdb, chain A
(#4), sequence alignment score = 604
RMSD between 151 pruned atom pairs is 0.445 angstroms; (across all 151 pairs:
0.445)
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V6_holo-coot-1.pdb, chain A
(#5), sequence alignment score = 604
RMSD between 151 pruned atom pairs is 0.365 angstroms; (across all 151 pairs:
0.365)
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V7_holo-coot-2.pdb, chain A
(#6), sequence alignment score = 604
RMSD between 151 pruned atom pairs is 0.323 angstroms; (across all 151 pairs:
0.323)
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V9_holo-coot-0.pdb, chain A
(#7), sequence alignment score = 604
RMSD between 151 pruned atom pairs is 0.325 angstroms; (across all 151 pairs:
0.325)
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V10_holo-coot-1.pdb, chain A
(#8), sequence alignment score = 604
RMSD between 151 pruned atom pairs is 0.364 angstroms; (across all 151 pairs:
0.364)
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V11_holo-coot-1.pdb, chain A
(#9), sequence alignment score = 604
RMSD between 151 pruned atom pairs is 0.374 angstroms; (across all 151 pairs:
0.374)
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V12_holo-coot-3.pdb, chain A
(#10), sequence alignment score = 604
RMSD between 151 pruned atom pairs is 0.367 angstroms; (across all 151 pairs:
0.367)
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V14_holo-coot-1.pdb, chain A
(#11), sequence alignment score = 604
RMSD between 149 pruned atom pairs is 0.402 angstroms; (across all 151 pairs:
0.464)
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V15_holo-coot-1.pdb, chain A
(#12), sequence alignment score = 604
RMSD between 151 pruned atom pairs is 0.359 angstroms; (across all 151 pairs:
0.359)
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V17_holo-coot-3.pdb, chain A
(#13), sequence alignment score = 604
RMSD between 149 pruned atom pairs is 0.351 angstroms; (across all 151 pairs:
0.441)
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V18_holo-coot-1.pdb, chain A
(#14), sequence alignment score = 604
RMSD between 151 pruned atom pairs is 0.367 angstroms; (across all 151 pairs:
0.367)
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V19_holo-coot-6.pdb, chain A
(#15), sequence alignment score = 604
RMSD between 151 pruned atom pairs is 0.488 angstroms; (across all 151 pairs:
0.488)
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V21_holo-coot-2.pdb, chain A
(#16), sequence alignment score = 604
RMSD between 151 pruned atom pairs is 0.445 angstroms; (across all 151 pairs:
0.445)
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V23_holo-coot-2.pdb, chain A
(#17), sequence alignment score = 604
RMSD between 151 pruned atom pairs is 0.368 angstroms; (across all 151 pairs:
0.368)
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V25_holo-coot-2.pdb, chain A
(#18), sequence alignment score = 604
RMSD between 151 pruned atom pairs is 0.430 angstroms; (across all 151 pairs:
0.430)
> select
178904 atoms, 198000 bonds, 10136 residues, 18 models selected
> hide sel target a
> select #1/C
31 atoms, 31 residues, 1 model selected
> select #1-18/C
542 atoms, 542 residues, 18 models selected
> show sel target ab
> style sel sphere
Changed 542 atom styles
> hide #2-18 target m
> hide #1 models
> show #1 models
> show #2 models
> hide #1 models
> show #1 models
> hide #1 models
> show #3 models
> hide #3 models
> show #4 models
> hide #4 models
> show #5 models
> hide #5 models
> show #6 models
> hide #6 models
> show #7 models
> hide #7 models
> show #8 models
> hide #8 models
> show #9 models
> hide #9 models
> show #10 models
> hide #10 models
> show #11 models
> show #12 models
> show #13 models
> hide #13 models
> show #13 models
> hide #13 models
> show #14 models
> hide #14 models
> show #15 models
> show #16 models
> show #17 models
> hide #17 models
> show #18 models
> select #1-18/C/7
542 atoms, 542 residues, 18 models selected
> select #1-18/C:7
18 atoms, 18 residues, 18 models selected
> select #1-18/C:4
18 atoms, 18 residues, 18 models selected
> select #1-18/C:24
12 atoms, 12 residues, 12 models selected
> select clear
> hide #2 models
> hide #11 models
> hide #12 models
> hide #15 models
> hide #16 models
> hide #18 models
> show #1 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #3 models
> show #2 models
> show #4 models
> show #5 models
> hide #5 models
> show #5 models
> show #6 models
> show #7 models
> show #8 models
> show #9 models
> show #10 models
> show #11 models
> show #12 models
> show #13 models
> show #14 models
> show #15 models
> show #16 models
> show #17 models
> show #18 models
> set bgColor white
> select #1-18/A
161316 atoms, 180684 bonds, 7506 residues, 18 models selected
> ui tool show "Color Actions"
> color sel light slate gray
> select #1-18/B
17046 atoms, 17316 bonds, 2088 residues, 18 models selected
> ui tool show "Color Actions"
> color sel plum
> surface sel
> surface hidePatches (#!1-18 & sel)
> select #1/B
947 atoms, 962 bonds, 116 residues, 1 model selected
> surface (#!1 & sel)
> surface hidePatches (#!1 & sel)
> surface (#!1 & sel)
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for V2_holo-coot-2.pdb_B SES surface #1.1: minimum, -9.82,
mean 5.09, maximum 22.28
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> surface hidePatches (#!1 & sel)
> select #1-18/C:1
7 atoms, 7 residues, 7 models selected
> select #1-18/A:50,389,390
1188 atoms, 1314 bonds, 54 residues, 18 models selected
> cartoon hide sel
> show sel target ab
> hide (sel-residues & (protein|nucleic)) target a
> cartoon hide sel-residues
> show (sel-residues & backbone) target ab
> hide sel target a
> hide (sel-residues & (protein|nucleic)) target a
> cartoon hide sel-residues
> show (sel-residues & backbone) target ab
> hide (sel-residues & (protein|nucleic)) target a
> cartoon hide sel-residues
> show (sel-residues & ((protein&@ca)|(nucleic&@p))) target ab
> show (sel-residues & sidechain) target ab
> hide (sel-residues & (protein|nucleic)) target a
> cartoon hide sel-residues
> show (sel-residues & backbone) target ab
> hide sel target a
> hide (sel-residues & (protein|nucleic)) target a
> cartoon hide sel-residues
> show (sel-residues & backbone) target ab
> nucleotides sel atoms
> style nucleic & sel stick
Changed 1188 atom styles
> select #1-18/A:7
360 atoms, 378 bonds, 18 residues, 18 models selected
> select #1-18/A:50,389,390
1188 atoms, 1314 bonds, 54 residues, 18 models selected
> color sel red
> select #6/A:392
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #15/A:393
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #3/C:68@MG
1 atom, 1 residue, 1 model selected
> select up
35 atoms, 35 residues, 1 model selected
> select #1-18/C:7
18 atoms, 18 residues, 18 models selected
> ui tool show "Selection Inspector"
> size sel atomRadius 0.7
Changed 18 atom radii
> color sel red
> select #1-18/A:50,389,390
1188 atoms, 1314 bonds, 54 residues, 18 models selected
> ui tool show "Color Actions"
> color sel brown
> color sel coral
> color sel orange
> color sel coral
> color sel tomato
> color sel coral
> select #14/C:80@MG
1 atom, 1 residue, 1 model selected
> select add #13/C:7@MG
2 atoms, 2 residues, 2 models selected
> ui tool show Distances
> distance #14/C:80@MG #13/C:7@MG
Distance between V18_holo-coot-1.pdb #14/C MG 80 MG and V17_holo-coot-3.pdb
#13/C MG 7 MG: 14.313Å
> select #10/C:80@MG
1 atom, 1 residue, 1 model selected
> select add #12/C:7@MG
2 atoms, 2 residues, 2 models selected
> distance #10/C:80@MG #12/C:7@MG
Distance between V12_holo-coot-3.pdb #10/C MG 80 MG and V15_holo-coot-1.pdb
#12/C MG 7 MG: 12.866Å
> hide #!1-18 target m
> show #!1 models
> show #!2 models
> show #!3 models
> show #!4 models
> show #!5 models
> show #!6 models
> hide #!6 models
> show #!6 models
> show #!7 models
> show #!8 models
> show #!9 models
> show #!10 models
> hide #!10 models
> show #!10 models
> show #!11 models
> show #!12 models
> hide #!12 models
> show #!12 models
> show #!13 models
> show #!14 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> select #6/C:24@MG
1 atom, 1 residue, 1 model selected
> select add #6/C:75@MG
2 atoms, 2 residues, 1 model selected
> distance #6/C:24@MG #6/C:75@MG
Distance between V7_holo-coot-2.pdb #6/C MG 24 MG and MG 75 MG: 6.929Å
> select #10/C:84@MG
1 atom, 1 residue, 1 model selected
> select add #6/C:24@MG
2 atoms, 2 residues, 2 models selected
> distance #10/C:84@MG #6/C:24@MG
Distance between V12_holo-coot-3.pdb #10/C MG 84 MG and V7_holo-coot-2.pdb
#6/C MG 24 MG: 3.368Å
> select #6/C:24@MG
1 atom, 1 residue, 1 model selected
> select add #5/C:7@MG
2 atoms, 2 residues, 2 models selected
> distance #6/C:24@MG #5/C:7@MG
Distance between V7_holo-coot-2.pdb #6/C MG 24 MG and V6_holo-coot-1.pdb #5/C
MG 7 MG: 7.527Å
> select #9/C:4@MG
1 atom, 1 residue, 1 model selected
> select add #12/C:7@MG
2 atoms, 2 residues, 2 models selected
> distance #9/C:4@MG #12/C:7@MG
Distance between V11_holo-coot-1.pdb #9/C MG 4 MG and V15_holo-coot-1.pdb
#12/C MG 7 MG: 9.036Å
> ~distance #6/C:24@MG #6/C:75@MG
> ~distance #9/C:4@MG #12/C:7@MG
> ~distance #14/C:80@MG #13/C:7@MG
> ~distance #10/C:84@MG #6/C:24@MG
> ~distance #6/C:24@MG #5/C:7@MG
> ~distance #10/C:80@MG #12/C:7@MG
> select #1-18/A:50,389,390
1188 atoms, 1314 bonds, 54 residues, 18 models selected
> ui tool show "Color Actions"
> color sel tomato
> color sel chocolate
> color sel fire brick
> color sel coral
> color sel goldenrod
> color (#!1-14 & sel) #ff2600ff
> color sel sienna
> color sel cyan
> color sel medium blue
> color sel cornflower blue
> select #1-18/C:7
18 atoms, 18 residues, 18 models selected
> color (#!1-14 & sel) blue
> color sel red
> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/pdb_models_YTZ/holoES-
> pretRNA-5mM-Ca/Ternary_pretRNA_5mM_Ca-coot-7_real_space_refined_018.pdb
Chain information for Ternary_pretRNA_5mM_Ca-coot-7_real_space_refined_018.pdb
#19
---
Chain | Description
A | No description available
B | No description available
C | No description available
E | No description available
Computing secondary structure
> select up
542 atoms, 542 residues, 18 models selected
> select up
178904 atoms, 198000 bonds, 10136 residues, 18 models selected
> select
> #1/A:15,21-29,39-67,69-84,96-101,105-112,249-261,272-293,295-312,327-340,386-400
3255 atoms, 3639 bonds, 151 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #19 to #1 & sel matrix Nucleic
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with Ternary_pretRNA_5mM_Ca-
coot-7_real_space_refined_018.pdb, chain A (#19), sequence alignment score =
604
RMSD between 150 pruned atom pairs is 0.728 angstroms; (across all 151 pairs:
0.766)
> select #19
12016 atoms, 13315 bonds, 661 residues, 1 model selected
> hide sel target a
> select #19/C
1889 atoms, 2107 bonds, 89 residues, 1 model selected
> hide #19 models
> show #19 models
> hide #19 models
> show #19 models
> color sel yellow
> select #19/D
30 atoms, 30 residues, 1 model selected
> show sel target ab
> hide #19 models
> show #19 models
> hide #19 models
> show #19 models
> select #10/C:84@MG
1 atom, 1 residue, 1 model selected
> select clear
> select #10/C:84@MG
1 atom, 1 residue, 1 model selected
> select add #11/A:390@OP2
2 atoms, 2 residues, 2 models selected
> distance #10/C:84@MG #11/A:390@OP2
Distance between V12_holo-coot-3.pdb #10/C MG 84 MG and V14_holo-coot-1.pdb
#11/A A 390 OP2: 3.278Å
> select #10/C:84@MG
1 atom, 1 residue, 1 model selected
> select #19/D:5@CA
1 atom, 1 residue, 1 model selected
> select add #10/C:84@MG
2 atoms, 2 residues, 2 models selected
> distance #19/D:5@CA #10/C:84@MG
Distance between Ternary_pretRNA_5mM_Ca-coot-7_real_space_refined_018.pdb
#19/D CA 5 CA and V12_holo-coot-3.pdb #10/C MG 84 MG: 6.302Å
> select #10/C:84@MG
1 atom, 1 residue, 1 model selected
> select add #19/D:30@CA
2 atoms, 2 residues, 2 models selected
> distance #10/C:84@MG #19/D:30@CA
Distance between V12_holo-coot-3.pdb #10/C MG 84 MG and
Ternary_pretRNA_5mM_Ca-coot-7_real_space_refined_018.pdb #19/D CA 30 CA:
7.802Å
> hide #19 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> select #13/C:24@MG
1 atom, 1 residue, 1 model selected
> select #9/C:24@MG
1 atom, 1 residue, 1 model selected
> select add #10/C:84@MG
2 atoms, 2 residues, 2 models selected
> distance #9/C:24@MG #10/C:84@MG
Distance between V11_holo-coot-1.pdb #9/C MG 24 MG and V12_holo-coot-3.pdb
#10/C MG 84 MG: 3.570Å
> select #10/C:84@MG
1 atom, 1 residue, 1 model selected
> hide #!1-14 target m
> show #!12 models
> show #19 models
> hide #19 models
> show #19 models
> hide #19 models
> hide #!12 models
> show #!10 models
> show #19 models
> select #19/C:0
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #19/C:1
23 atoms, 25 bonds, 1 residue, 1 model selected
> select add #19/C:0
43 atoms, 46 bonds, 2 residues, 1 model selected
> hide #19 models
> show #!1-18 target m
> select #10/C:80@MG
1 atom, 1 residue, 1 model selected
> select clear
> show #19 models
> hide #19 models
> show #19 models
> hide #19 models
> show #19 models
> hide #19 models
> select #1-18/
Expected an objects specifier or a keyword
> select #1-18
178904 atoms, 198000 bonds, 2 pseudobonds, 10136 residues, 19 models selected
> select #1-18/C
542 atoms, 1 pseudobond, 542 residues, 19 models selected
> ui tool show "Color Actions"
> color sel forest green
> select #1-18/C:7
18 atoms, 18 residues, 18 models selected
> ui tool show "Color Actions"
> color sel dark red
> color sel maroon
> color sel dark red
> ui tool show "Selection Inspector"
> ~distance #10/C:84@MG #11/A:390@OP2
> ~distance #19/D:5@CA #10/C:84@MG
> ~distance #9/C:24@MG #10/C:84@MG
> ~distance #10/C:84@MG #19/D:30@CA
> select #10/C:84@MG
1 atom, 1 residue, 1 model selected
> select add #17/C:87@MG
2 atoms, 2 residues, 2 models selected
> select #1-18/C
542 atoms, 542 residues, 18 models selected
> ui tool show "Selection Inspector"
> size sel atomRadius 0.7
Changed 542 atom radii
> select #13/C:22@MG
1 atom, 1 residue, 1 model selected
> select #1-18/C:9
16 atoms, 16 residues, 16 models selected
[deleted to fit within ticket limits]
> color sel #5e5e5e9f
> color sel #5e5e5e9d
> color sel #5e5e5e9b
> color sel #5e5e5e99
> color sel #5e5e5e97
> color sel #5e5e5e93
> color sel #5e5e5e91
> color sel #5e5e5e8f
> color sel #5e5e5e8d
> color sel #5e5e5e8a
> color sel #5e5e5e87
> color sel #5e5e5e85
> color sel #5e5e5e82
> color sel #5e5e5e80
> color sel #5e5e5e7f
> color sel #5e5e5e7d
> color sel #5e5e5e7c
> color sel #5e5e5e7b
[Repeated 1 time(s)]
> color sel #5e5e5e7a
[Repeated 1 time(s)]
> color sel #5e5e5e78
> color sel #5e5e5e77
> color sel #5e5e5e76
> color sel #5e5e5e75
> color sel #5e5e5e74
[Repeated 1 time(s)]
> color sel #5e5e5e73
[Repeated 2 time(s)]
> color sel #5e5e5e72
[Repeated 3 time(s)]
> color sel #5e5e5e71
> color sel #5e5e5e70
[Repeated 1 time(s)]
> color sel #5e5e5e6f
[Repeated 1 time(s)]
> color sel #5e5e5e6e
> color sel #5e5e5e6d
[Repeated 1 time(s)]
> color sel #5e5e5e6c
[Repeated 2 time(s)]
> color sel #5e5e5e6b
[Repeated 2 time(s)]
> color sel #5e5e5e6a
[Repeated 1 time(s)]
> color sel #5e5e5e69
[Repeated 4 time(s)]
> color sel #5e5e5e68
[Repeated 2 time(s)]
> color sel #5e5e5e67
[Repeated 2 time(s)]
> color sel #5e5e5e66
[Repeated 2 time(s)]
> color sel #5e5e5e65
[Repeated 4 time(s)]
> color sel #5e5e5e64
[Repeated 2 time(s)]
> color sel #5e5e5e63
[Repeated 1 time(s)]
> color sel #5e5e5e64
> color sel #5e5e5e65
> color sel #5e5e5e67
> color sel #5e5e5e68
> color sel #5e5e5e6a
> color sel #5e5e5e6c
> color sel #5e5e5e6d
> color sel #5e5e5e6e
> color sel #5e5e5e70
> color sel #5e5e5e71
> color sel #5e5e5e72
> color sel #5e5e5e74
> color sel #5e5e5e75
> color sel #5e5e5e77
> color sel #5e5e5e79
> color sel #5e5e5e7a
> color sel #5e5e5e7b
> color sel #5e5e5e7c
> color sel #5e5e5e7d
> color sel #5e5e5e7e
[Repeated 1 time(s)]
> color sel #5e5e5e7f
[Repeated 1 time(s)]
> color sel #5e5e5e80
> color sel #5e5e5e84
[Repeated 1 time(s)]
> color sel #5e5e5e86
> color sel #5e5e5e87
> color sel #5e5e5e89
> color sel #5e5e5e8a
> color sel #5e5e5e8b
[Repeated 1 time(s)]
> color sel #5e5e5e8c
> color sel #5e5e5e8d
> color sel #5e5e5e8e
> color sel #5e5e5e8f
> color sel #5e5e5e90
> color sel #5e5e5e91
> color sel #5e5e5e93
> color sel #5e5e5e95
> color sel #5e5e5e96
> color sel #5e5e5e99
> color sel #5e5e5e9c
> color sel #5e5e5e9f
> color sel #5e5e5ea2
> color sel #5e5e5ea4
> color sel #5e5e5ea5
> color sel #5e5e5ea6
> color sel #5e5e5ea7
> color sel #5e5e5ea8
> color sel #5e5e5eaa
> color sel #5e5e5eae
> color sel #5e5e5eb1
> color sel #5e5e5eb5
> color sel #5e5e5ebc
> color sel #5e5e5ec2
> color sel #5e5e5ec4
> color sel #5e5e5ec6
[Repeated 1 time(s)]
> color sel #5e5e5ec7
> color sel #5e5e5ec8
[Repeated 1 time(s)]
> color sel #5e5e5ec9
> color sel #5e5e5ecd
> color sel #5e5e5ecf
> color sel #5e5e5ed6
> color sel #5e5e5edd
> color sel #5e5e5ee2
> color sel #5e5e5ee4
> color sel #5e5e5ee5
> color sel #5e5e5ee6
[Repeated 1 time(s)]
> color sel #5e5e5ee7
> color sel #5e5e5ee8
> color sel #5e5e5ee9
> color sel #5e5e5eeb
> color sel #5e5e5eed
> color sel #5e5e5ef0
> color sel #5e5e5ef4
> color sel #5e5e5ef8
> color sel #5e5e5efb
> color sel #5e5e5efd
> color sel #5e5e5eff
[Repeated 1 time(s)]
> color sel #4c4c4cff
[Repeated 1 time(s)]
> color sel #4d4d4dff
> color sel #4e4e4eff
[Repeated 1 time(s)]
> color sel #4f4f4fff
> color sel #505050ff
> color sel #515151ff
[Repeated 1 time(s)]
> color sel #525252ff
[Repeated 1 time(s)]
> color sel #535353ff
> color sel #545454ff
[Repeated 2 time(s)]
> color sel #555555ff
> color sel #565656ff
[Repeated 1 time(s)]
> color sel #575757ff
> color sel #595959ff
> color sel #5a5a5aff
> color sel #5b5b5bff
> color sel #5c5c5cff
> color sel #5d5d5dff
> color sel #5e5e5eff
> color sel #5f5f5fff
> color sel #616161ff
> color sel #636363ff
> color sel #656565ff
> color sel #696969ff
> color sel #6b6b6bff
> color sel #717171ff
> color sel #767676ff
> color sel #7a7a7aff
> color sel #7d7d7dff
> color sel #808080ff
> color sel #848484ff
> color sel #868686ff
> color sel #878787ff
> color sel #898989ff
> color sel #8b8b8bff
> color sel #8c8c8cff
> color sel #8f8f8fff
> color sel #909090ff
> color sel #929292ff
> color sel #939393ff
> color sel #949494ff
[Repeated 1 time(s)]
> color sel #959595ff
[Repeated 3 time(s)]
> color sel #969696ff
> color sel #979797ff
> color sel #989898ff
[Repeated 1 time(s)]
> color sel #999999ff
[Repeated 1 time(s)]
> color sel #9a9a9aff
[Repeated 1 time(s)]
> color sel #9b9b9bff
> color sel #9c9c9cff
[Repeated 1 time(s)]
> color sel #9d9d9dff
[Repeated 1 time(s)]
> color sel #9e9e9eff
> color sel #9f9f9fff
> color sel #a0a0a0ff
> color sel #a1a1a1ff
> color sel #a3a3a3ff
> color sel #a4a4a4ff
> color sel #a6a6a6ff
> color sel #a7a7a7ff
> color sel #a8a8a8ff
> color sel #aaaaaaff
> color sel #abababff
> color sel #acacacff
> color sel #aeaeaeff
> color sel #b0b0b0ff
> color sel #b1b1b1ff
> color sel #b2b2b2ff
> color sel #b3b3b3ff
> color sel #b4b4b4ff
[Repeated 1 time(s)]
> color sel #b5b5b5ff
> color sel #b6b6b6ff
[Repeated 1 time(s)]
> color sel #b7b7b7ff
[Repeated 5 time(s)]
> color sel #b8b8b8ff
[Repeated 4 time(s)]
> color sel #b7b7b7ff
[Repeated 1 time(s)]
> color sel #b6b6b6ff
> color sel #b5b5b5ff
> color sel #b3b3b3ff
> color sel #afafafff
> color sel #a4a4a4ff
> color sel #989898ff
> color sel #8f8f8fff
> color sel #878787ff
> color sel #828282ff
> color sel #7c7c7cff
> color sel #767676ff
> color sel #727272ff
> color sel #6d6d6dff
> color sel #686868ff
> color sel #646464ff
> color sel #606060ff
> color sel #5b5b5bff
> color sel #585858ff
> color sel #535353ff
> color sel #4f4f4fff
> color sel #4c4c4cff
> color sel #4a4a4aff
> color sel #474747ff
> color sel #454545ff
> color sel #444444ff
> color sel #424242ff
> color sel #404040ff
> color sel #3f3f3fff
> color sel #3d3d3dff
> color sel #3b3b3bff
> color sel #3a3a3aff
> color sel #383838ff
> color sel #373737ff
[Repeated 1 time(s)]
> color sel #363636ff
> color sel #353535ff
> color sel #343434ff
> color sel #333333ff
> color sel #313131ff
[Repeated 1 time(s)]
> color sel #303030ff
> color sel #2f2f2fff
[Repeated 3 time(s)]
> color sel #2e2e2eff
[Repeated 2 time(s)]
> color sel #2d2d2dff
[Repeated 2 time(s)]
> color sel #2e2e2eff
> color sel #303030ff
> color sel #343434ff
> color sel #393939ff
> color sel #3d3d3dff
> color sel #434343ff
> color sel #4a4a4aff
> color sel #4d4d4dff
> color sel #515151ff
> color sel #525252ff
> color sel #535353ff
> color sel #545454ff
> color sel #555555ff
> color sel #565656ff
> color sel #575757ff
> color sel #585858ff
[Repeated 1 time(s)]
> color sel #595959ff
> color sel #5a5a5aff
> color sel #5c5c5cff
> color sel #5e5e5eff
> color sel #5f5f5fff
> color sel #606060ff
> color sel #616161ff
[Repeated 1 time(s)]
> color sel #626262ff
[Repeated 3 time(s)]
> color sel #636363ff
[Repeated 1 time(s)]
> color sel #646464ff
[Repeated 2 time(s)]
> color sel #656565ff
[Repeated 1 time(s)]
> color sel #666666ff
[Repeated 2 time(s)]
> color sel #676767ff
[Repeated 1 time(s)]
> color sel #686868ff
[Repeated 1 time(s)]
> color sel #696969ff
> color sel #6a6a6aff
> color sel #6b6b6bff
[Repeated 1 time(s)]
> color sel #6a6a6aff
> color sel #686868ff
> color sel #676767ff
> color sel #666666ff
> color sel #646464ff
[Repeated 1 time(s)]
> color sel #626262ff
> color sel #616161ff
> color sel #5f5f5fff
[Repeated 1 time(s)]
> color sel #5e5e5eff
> color sel #5d5d5dff
[Repeated 1 time(s)]
> color sel #5c5c5cff
[Repeated 1 time(s)]
> color sel #5b5b5bff
[Repeated 2 time(s)]
> color sel #5a5a5aff
[Repeated 1 time(s)]
> color sel #595959ff
[Repeated 2 time(s)]
> color sel #585858ff
[Repeated 2 time(s)]
> color sel #575757ff
[Repeated 1 time(s)]
> color sel #565656ff
[Repeated 1 time(s)]
> color sel #555555ff
[Repeated 1 time(s)]
> color sel #545454ff
[Repeated 2 time(s)]
> color sel #535353ff
[Repeated 1 time(s)]
> color sel #525252ff
[Repeated 1 time(s)]
> color sel #515151ff
> color sel #505050ff
[Repeated 1 time(s)]
> color sel #4f4f4fff
[Repeated 2 time(s)]
> color sel #4e4e4eff
> color sel #4d4d4dff
[Repeated 2 time(s)]
> color sel #4c4c4cff
[Repeated 1 time(s)]
> color sel #4b4b4bff
[Repeated 2 time(s)]
> color sel #4a4a4aff
[Repeated 2 time(s)]
> color sel #494949ff
[Repeated 2 time(s)]
> color sel #484848ff
[Repeated 3 time(s)]
> color sel #474747ff
[Repeated 3 time(s)]
> color sel #464646ff
[Repeated 2 time(s)]
> color sel #454545ff
[Repeated 5 time(s)]
> color sel #464646ff
> color sel #474747ff
> color sel #494949ff
> color sel #4b4b4bff
> color sel #4c4c4cff
> color sel #4d4d4dff
> color sel #4e4e4eff
> color sel #505050ff
> color sel #515151ff
[Repeated 1 time(s)]
> color sel #525252ff
[Repeated 2 time(s)]
> color sel #535353ff
[Repeated 1 time(s)]
> color sel #545454ff
[Repeated 2 time(s)]
> color sel #555555ff
[Repeated 1 time(s)]
> color sel #565656ff
> color sel #575757ff
> color sel #585858ff
[Repeated 1 time(s)]
> color sel #595959ff
[Repeated 2 time(s)]
> color sel #5a5a5aff
[Repeated 2 time(s)]
> color sel #5b5b5bff
> color sel #5c5c5cff
> color sel #5f5f5fff
> color sel #606060ff
> color sel #626262ff
> color sel #646464ff
> color sel #656565ff
> color sel #676767ff
> color sel #696969ff
> color sel #6a6a6aff
> color sel #6c6c6cff
> color sel #6e6e6eff
> color sel #6f6f6fff
> color sel #717171ff
> color sel #737373ff
> color sel #757575ff
> color sel #767676ff
> color sel #787878ff
> color sel #797979ff
> color sel #7a7a7aff
> color sel #7b7b7bff
> color sel #7c7c7cff
> color sel #7d7d7dff
> color sel #7f7f7fff
> color sel #808080ff
> color sel #848484ff
> color sel #858585ff
> color sel #878787ff
> color sel #898989ff
> color sel #8a8a8aff
> color sel #8c8c8cff
> color sel #8e8e8eff
> color sel #8f8f8fff
> color sel #919191ff
> color sel #929292ff
> color sel #949494ff
> color sel #969696ff
> color sel #979797ff
> color sel #989898ff
> color sel #999999ff
[Repeated 2 time(s)]
> color sel #989898ff
> color sel #949494ff
> color sel #8a8a8aff
> color sel #838383ff
> color sel #7d7d7dff
> color sel #7a7a7aff
> color sel #777777ff
> color sel #747474ff
> color sel #717171ff
> color sel #6f6f6fff
> color sel #6d6d6dff
> color sel #6b6b6bff
> color sel #696969ff
> color sel #676767ff
> color sel #666666ff
> color sel #646464ff
> color sel #636363ff
> color sel #616161ff
> color sel #606060ff
> color sel #5f5f5fff
> color sel #5e5e5eff
[Repeated 2 time(s)]
> color sel #5d5d5dff
[Repeated 4 time(s)]
> color sel #5c5c5cff
[Repeated 1 time(s)]
> color sel #5b5b5bff
[Repeated 1 time(s)]
> color sel #5a5a5aff
[Repeated 2 time(s)]
> color sel #595959ff
[Repeated 1 time(s)]
> color sel #585858ff
[Repeated 3 time(s)]
> color sel #575757ff
[Repeated 3 time(s)]
> color sel #565656ff
[Repeated 3 time(s)]
> color sel #555555ff
[Repeated 2 time(s)]
> color sel #565656ff
> color sel #575757ff
> color sel #585858ff
> color sel #5a5a5aff
> color sel #5b5b5bff
> color sel #5c5c5cff
> color sel #5d5d5dff
> color sel #5e5e5eff
[Repeated 2 time(s)]
> color sel #5f5f5fff
> select #10/C:84@MG
1 atom, 1 residue, 1 model selected
> select add #17/C:87@MG
2 atoms, 2 residues, 2 models selected
> distance #10/C:84@MG #17/C:87@MG
Distance between V12_holo-coot-3.pdb #10/C MG 84 MG and V23_holo-coot-2.pdb
#17/C MG 87 MG: 3.390Å
> select #10/C:84@MG
1 atom, 1 residue, 1 model selected
> select add #19/C:1@O3'
2 atoms, 2 residues, 2 models selected
> distance #10/C:84@MG #19/C:1@O3'
Distance between V12_holo-coot-3.pdb #10/C MG 84 MG and
Ternary_pretRNA_5mM_Ca-coot-7_real_space_refined_018.pdb #19/C G 1 O3': 7.687Å
> select #10/C:84@MG
1 atom, 1 residue, 1 model selected
> select add #19/D:5@CA
2 atoms, 2 residues, 2 models selected
> select #19/D:5@CA
1 atom, 1 residue, 1 model selected
> select add #10/C:84@MG
2 atoms, 2 residues, 2 models selected
> distance #19/D:5@CA #10/C:84@MG
Distance between Ternary_pretRNA_5mM_Ca-coot-7_real_space_refined_018.pdb
#19/D CA 5 CA and V12_holo-coot-3.pdb #10/C MG 84 MG: 6.681Å
> select #10/C:84@MG
1 atom, 1 residue, 1 model selected
> select add #19/D:6@CA
2 atoms, 2 residues, 2 models selected
> distance #10/C:84@MG #19/D:6@CA
Distance between V12_holo-coot-3.pdb #10/C MG 84 MG and
Ternary_pretRNA_5mM_Ca-coot-7_real_space_refined_018.pdb #19/D CA 6 CA: 2.783Å
> select #10/C:84@MG
1 atom, 1 residue, 1 model selected
> select add #3/C:24@MG
2 atoms, 2 residues, 2 models selected
> distance #10/C:84@MG #3/C:24@MG
Distance between V12_holo-coot-3.pdb #10/C MG 84 MG and V4_holo-coot-3.pdb
#3/C MG 24 MG: 3.250Å
> select #17/C:87@MG
1 atom, 1 residue, 1 model selected
> select add #19/D:6@CA
2 atoms, 2 residues, 2 models selected
> distance #17/C:87@MG #19/D:6@CA
Distance between V23_holo-coot-2.pdb #17/C MG 87 MG and
Ternary_pretRNA_5mM_Ca-coot-7_real_space_refined_018.pdb #19/D CA 6 CA: 5.916Å
> select #17/C:87@MG
1 atom, 1 residue, 1 model selected
> select add #19/C:1@O3'
2 atoms, 2 residues, 2 models selected
> distance #17/C:87@MG #19/C:1@O3'
Distance between V23_holo-coot-2.pdb #17/C MG 87 MG and
Ternary_pretRNA_5mM_Ca-coot-7_real_space_refined_018.pdb #19/C G 1 O3': 4.880Å
> select #17/C:87@MG
1 atom, 1 residue, 1 model selected
> select add #19/D:5@CA
2 atoms, 2 residues, 2 models selected
> distance #17/C:87@MG #19/D:5@CA
Distance between V23_holo-coot-2.pdb #17/C MG 87 MG and
Ternary_pretRNA_5mM_Ca-coot-7_real_space_refined_018.pdb #19/D CA 5 CA: 6.174Å
> select #17/C:87@MG
1 atom, 1 residue, 1 model selected
> select add #19/C:1@OP1
2 atoms, 2 residues, 2 models selected
> distance #17/C:87@MG #19/C:1@OP1
Distance between V23_holo-coot-2.pdb #17/C MG 87 MG and
Ternary_pretRNA_5mM_Ca-coot-7_real_space_refined_018.pdb #19/C G 1 OP1: 6.874Å
> select #19/D:5@CA
1 atom, 1 residue, 1 model selected
> select add #19/C:1@OP1
2 atoms, 2 residues, 1 model selected
> distance #19/D:5@CA #19/C:1@OP1
Distance between Ternary_pretRNA_5mM_Ca-coot-7_real_space_refined_018.pdb
#19/D CA 5 CA and /C G 1 OP1: 2.234Å
> select #19/D:7@CA
1 atom, 1 residue, 1 model selected
> select add #19/C:1@OP2
2 atoms, 2 residues, 1 model selected
> distance #19/D:7@CA #19/C:1@OP2
Distance between Ternary_pretRNA_5mM_Ca-coot-7_real_space_refined_018.pdb
#19/D CA 7 CA and /C G 1 OP2: 2.625Å
> ~distance #10/C:84@MG #17/C:87@MG
> ~distance #19/D:5@CA #10/C:84@MG
> ~distance #10/C:84@MG #19/C:1@O3'
> ~distance #19/D:7@CA #19/C:1@OP2
> ~distance #17/C:87@MG #19/C:1@O3'
> ~distance #19/D:5@CA #19/C:1@OP1
> ~distance #17/C:87@MG #19/C:1@OP1
> ~distance #10/C:84@MG #19/D:6@CA
> ~distance #17/C:87@MG #19/D:5@CA
> ~distance #10/C:84@MG #3/C:24@MG
> ~distance #17/C:87@MG #19/D:6@CA
> color sel #5f5f5fff
> color sel #5f5f5ffe
> color sel #5f5f5ffd
[Repeated 3 time(s)]
> color sel #5f5f5ffc
[Repeated 1 time(s)]
> color sel #5f5f5ffb
[Repeated 1 time(s)]
> color sel #5f5f5ffa
[Repeated 1 time(s)]
> color sel #5f5f5ff9
[Repeated 1 time(s)]
> color sel #5f5f5ff8
> color sel #5f5f5ff7
> color sel #5f5f5ff6
> color sel #5f5f5ff5
> color sel #5f5f5ff3
> color sel #5f5f5ff2
> color sel #5f5f5ff1
> color sel #5f5f5ff0
> color sel #5f5f5fee
> color sel #5f5f5fec
> color sel #5f5f5feb
> color sel #5f5f5fea
> color sel #5f5f5fe9
[Repeated 3 time(s)]
> color sel #5f5f5fe8
[Repeated 2 time(s)]
> color sel #5f5f5fe7
[Repeated 6 time(s)]
> select #19/C
1889 atoms, 2107 bonds, 89 residues, 1 model selected
> lighting simple
> lighting soft
> lighting full
> lighting soft
> lighting simple
> lighting soft
> lighting simple
> color sel #5f5f5fe7
> color sel #5f5f5fe6
> color sel #5f5f5fe3
> color sel #5f5f5fe2
> color sel #5f5f5fe1
[Repeated 1 time(s)]
> color sel #5f5f5fe0
> color sel #5f5f5fdf
[Repeated 2 time(s)]
> color sel #5f5f5fde
[Repeated 1 time(s)]
> color sel #5f5f5fdd
> color sel #5f5f5fdc
> color sel #5f5f5fda
> color sel #5f5f5fd8
> color sel #5f5f5fd6
> color sel #5f5f5fd4
> color sel #5f5f5fd2
> color sel #5f5f5fd1
> color sel #5f5f5fd0
> color sel #5f5f5fcf
> color sel #5f5f5fcd
> color sel #5f5f5fcc
> color sel #5f5f5fca
> color sel #5f5f5fc9
> color sel #5f5f5fc7
> color sel #5f5f5fc5
> color sel #5f5f5fc1
> color sel #5f5f5fbf
> color sel #5f5f5fbd
> color sel #5f5f5fbb
> color sel #5f5f5fba
> color sel #5f5f5fb8
> color sel #5f5f5fb5
> color sel #5f5f5fb4
> color sel #5f5f5fb1
> color sel #5f5f5fb0
> color sel #5f5f5fae
[Repeated 2 time(s)]
> color sel #5f5f5fad
> color sel #5f5f5fac
> color sel #5f5f5fab
> color sel #5f5f5fa9
> color sel #5f5f5fa7
> color sel #5f5f5fa3
> color sel #5f5f5f9f
> color sel #5f5f5f9b
> color sel #5f5f5f99
> color sel #5f5f5f96
[Repeated 3 time(s)]
> color sel #5f5f5f95
> color sel #5f5f5f94
> color sel #5f5f5f93
> color sel #5f5f5f92
> color sel #5f5f5f90
> color sel #5f5f5f8f
> color sel #5f5f5f8e
> color sel #5f5f5f8d
> color sel #5f5f5f8c
[Repeated 1 time(s)]
> color sel #5f5f5f8b
> color sel #5f5f5f89
> color sel #5f5f5f88
[Repeated 1 time(s)]
> color sel #5f5f5f87
> color sel #5f5f5f85
> color sel #5f5f5f84
[Repeated 1 time(s)]
> color sel #5f5f5f83
[Repeated 2 time(s)]
> color sel #5f5f5f84
> color sel #5f5f5f87
> color sel #5f5f5f8d
> color sel #5f5f5f95
> color sel #5f5f5f99
> color sel #5f5f5f9d
> color sel #5f5f5f9f
> color sel #5f5f5fa1
> color sel #5f5f5fa3
> color sel #5f5f5fa4
> color sel #5f5f5fa5
[Repeated 2 time(s)]
> color sel #5f5f5fa6
> color sel #5f5f5fa8
> color sel #5f5f5fab
> color sel #5f5f5fad
> color sel #5f5f5fae
> color sel #5f5f5faf
[Repeated 2 time(s)]
> color sel #5f5f5fb1
> color sel #5f5f5fb2
> color sel #5f5f5fb5
> color sel #5f5f5fb6
> color sel #5f5f5fb7
[Repeated 1 time(s)]
> color sel #5f5f5fb8
[Repeated 2 time(s)]
> color sel #5f5f5fb9
[Repeated 1 time(s)]
> color sel #5f5f5fbb
> color sel #5f5f5fbd
> color sel #5f5f5fc1
> color sel #5f5f5fc7
> color sel #5f5f5fcc
> color sel #5f5f5fcf
> color sel #5f5f5fd0
> color sel #5f5f5fce
> color sel #5f5f5fc2
> color sel #5f5f5fb8
> color sel #5f5f5fb2
> color sel #5f5f5fb1
[Repeated 1 time(s)]
> color sel #5f5f5fb0
> color sel #5f5f5fad
> color sel #5f5f5fab
> color sel #5f5f5fa9
> color sel #5f5f5fa5
> color sel #5f5f5fa3
> select #19/D:30@CA
1 atom, 1 residue, 1 model selected
> select add #19/D:5@CA
2 atoms, 2 residues, 1 model selected
> color sel #404040ff
> select #19/D:7@CA
1 atom, 1 residue, 1 model selected
> select #19/D:7@CA
1 atom, 1 residue, 1 model selected
> color sel #404040ff
> color sel #3f3f3fff
> color sel #3e3e3eff
> color sel #3d3d3dff
[Repeated 4 time(s)]
> color sel #3c3c3cff
[Repeated 2 time(s)]
> color sel #3d3d3dff
[Repeated 1 time(s)]
> select #19/D:6@CA
1 atom, 1 residue, 1 model selected
> select add #19/D:1@CA
2 atoms, 2 residues, 1 model selected
> select add #19/D:3@CA
3 atoms, 3 residues, 1 model selected
> color sel #4f8f00ff
> color sel #005493ff
> select clear
> save
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/apo_holo_analysis/ions/ions_holo_new_core_aa_models_ternary_comp.cxs
> hide #19 models
> save ions_core_holo.png supersample 3 transparentBackground true
> lighting simple
> lighting soft
> lighting simple
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> ui tool show "Side View"
> lighting soft
> lighting simple
> lighting soft
> save ions_core_holo_2.png supersample 3 transparentBackground true
> select #10/C:84@MG
1 atom, 1 residue, 1 model selected
> select add #11/A:390@OP2
2 atoms, 2 residues, 2 models selected
> distance #10/C:84@MG #11/A:390@OP2
Distance between V12_holo-coot-3.pdb #10/C MG 84 MG and V14_holo-coot-1.pdb
#11/A A 390 OP2: 3.278Å
> select #6/C:24@MG
1 atom, 1 residue, 1 model selected
> select add #6/A:390@OP2
2 atoms, 2 residues, 1 model selected
> distance #6/C:24@MG #6/A:390@OP2
Distance between V7_holo-coot-2.pdb #6/C MG 24 MG and /A A 390 OP2: 4.213Å
> select #6/C:24@MG
1 atom, 1 residue, 1 model selected
> select #10/C:84@MG
1 atom, 1 residue, 1 model selected
> select clear
> select #17/C:87@MG
1 atom, 1 residue, 1 model selected
> select add #11/A:390@OP2
2 atoms, 2 residues, 2 models selected
> distance #17/C:87@MG #11/A:390@OP2
Distance between V23_holo-coot-2.pdb #17/C MG 87 MG and V14_holo-coot-1.pdb
#11/A A 390 OP2: 4.350Å
> ~distance #6/C:24@MG #6/A:390@OP2
> ~distance #10/C:84@MG #11/A:390@OP2
> ~distance #17/C:87@MG #11/A:390@OP2
> select clear
> lighting simple
> toolshed show
> select #18/C:24@MG
1 atom, 1 residue, 1 model selected
> select add #11/A:390@OP2
2 atoms, 2 residues, 2 models selected
> distance #18/C:24@MG #11/A:390@OP2
Distance between V25_holo-coot-2.pdb #18/C MG 24 MG and V14_holo-coot-1.pdb
#11/A A 390 OP2: 4.140Å
> select #17/A:50@OP2
1 atom, 1 residue, 1 model selected
> select add #9/C:4@MG
2 atoms, 2 residues, 2 models selected
> distance #17/A:50@OP2 #9/C:4@MG
Distance between V23_holo-coot-2.pdb #17/A A 50 OP2 and V11_holo-coot-1.pdb
#9/C MG 4 MG: 5.979Å
> select #11/A:390@OP2
1 atom, 1 residue, 1 model selected
> select add #10/C:84@MG
2 atoms, 2 residues, 2 models selected
> distance #11/A:390@OP2 #10/C:84@MG
Distance between V14_holo-coot-1.pdb #11/A A 390 OP2 and V12_holo-coot-3.pdb
#10/C MG 84 MG: 3.278Å
> select #17/C:87@MG
1 atom, 1 residue, 1 model selected
> select add #10/C:84@MG
2 atoms, 2 residues, 2 models selected
> distance #17/C:87@MG #10/C:84@MG
Distance between V23_holo-coot-2.pdb #17/C MG 87 MG and V12_holo-coot-3.pdb
#10/C MG 84 MG: 3.390Å
> select #10/C:84@MG
1 atom, 1 residue, 1 model selected
> select add #17/C:87@MG
2 atoms, 2 residues, 2 models selected
> select #10/C:84@MG
1 atom, 1 residue, 1 model selected
> select #10/C:84@MG
1 atom, 1 residue, 1 model selected
> color sel lime
> color sel purple
> ~distance #11/A:390@OP2 #10/C:84@MG
> ~distance #17/A:50@OP2 #9/C:4@MG
> ~distance #17/C:87@MG #10/C:84@MG
> ~distance #18/C:24@MG #11/A:390@OP2
> select clear
> select #7/C:24@MG
1 atom, 1 residue, 1 model selected
> select add #7/A:390@C5'
2 atoms, 2 residues, 1 model selected
> distance #7/C:24@MG #7/A:390@C5'
Distance between V9_holo-coot-0.pdb #7/C MG 24 MG and /A A 390 C5': 5.156Å
> select clear
> select #7/C:24@MG
1 atom, 1 residue, 1 model selected
> select add #11/A:390@OP2
2 atoms, 2 residues, 2 models selected
> distance #7/C:24@MG #11/A:390@OP2
Distance between V9_holo-coot-0.pdb #7/C MG 24 MG and V14_holo-coot-1.pdb
#11/A A 390 OP2: 4.308Å
> select #3/C:24@MG
1 atom, 1 residue, 1 model selected
> select add #11/A:390@OP2
2 atoms, 2 residues, 2 models selected
> distance #3/C:24@MG #11/A:390@OP2
Distance between V4_holo-coot-3.pdb #3/C MG 24 MG and V14_holo-coot-1.pdb
#11/A A 390 OP2: 4.180Å
> select #13/C:24@MG
1 atom, 1 residue, 1 model selected
> select #11/A:390@OP2
1 atom, 1 residue, 1 model selected
> select add #13/C:24@MG
2 atoms, 2 residues, 2 models selected
> distance #11/A:390@OP2 #13/C:24@MG
Distance between V14_holo-coot-1.pdb #11/A A 390 OP2 and V17_holo-coot-3.pdb
#13/C MG 24 MG: 4.168Å
> select #4/C:24@MG
1 atom, 1 residue, 1 model selected
> select add #11/A:390@OP2
2 atoms, 2 residues, 2 models selected
> distance #4/C:24@MG #11/A:390@OP2
Distance between V5_holo-coot-1.pdb #4/C MG 24 MG and V14_holo-coot-1.pdb
#11/A A 390 OP2: 4.683Å
> ~distance #7/C:24@MG #7/A:390@C5'
> ~distance #4/C:24@MG #11/A:390@OP2
> ~distance #3/C:24@MG #11/A:390@OP2
> ~distance #7/C:24@MG #11/A:390@OP2
> ~distance #11/A:390@OP2 #13/C:24@MG
> select clear
> save ions_core_holo_2.png supersample 3 transparentBackground true
> save
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/apo_holo_analysis/ions/ions_holo_new_core_aa_models.cxs
> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V1_Mg-
> coot-1.pdb
Chain information for V1_Mg-coot-1.pdb #20
---
Chain | Description
A | No description available
> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V2_Mg-
> coot-1.pdb
Chain information for V2_Mg-coot-1.pdb #21
---
Chain | Description
A | No description available
> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V3_Mg-
> coot-2.pdb
Chain information for V3_Mg-coot-2.pdb #22
---
Chain | Description
A | No description available
> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V4_Mg-
> coot-2.pdb
Chain information for V4_Mg-coot-2.pdb #23
---
Chain | Description
A | No description available
> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V5_Mg-
> coot-1.pdb
Chain information for V5_Mg-coot-1.pdb #24
---
Chain | Description
A | No description available
> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V6_Mg-
> coot-1.pdb
Chain information for V6_Mg-coot-1.pdb #25
---
Chain | Description
A | No description available
> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V7_Mg-
> coot-2.pdb
Chain information for V7_Mg-coot-2.pdb #26
---
Chain | Description
A | No description available
> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V8_Mg-
> coot-2.pdb
Chain information for V8_Mg-coot-2.pdb #27
---
Chain | Description
A | No description available
> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V9_Mg-
> coot-3.pdb
Chain information for V9_Mg-coot-3.pdb #28
---
Chain | Description
A | No description available
> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V10_Mg-
> coot-3.pdb
Chain information for V10_Mg-coot-3.pdb #29
---
Chain | Description
A | No description available
> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V11_Mg-
> coot-2.pdb
Chain information for V11_Mg-coot-2.pdb #30
---
Chain | Description
A | No description available
> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V12_real_space_refined_011-coot-0.pdb
Chain information for V12_real_space_refined_011-coot-0.pdb #31
---
Chain | Description
A | No description available
> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V13_Mg-
> coot-2.pdb
Chain information for V13_Mg-coot-2.pdb #32
---
Chain | Description
A | No description available
> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V13_Mg-
> coot-3_6.pdb
Chain information for V13_Mg-coot-3_6.pdb #33
---
Chain | Description
A | No description available
> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V14_Mg-
> coot-1.pdb
Chain information for V14_Mg-coot-1.pdb #34
---
Chain | Description
A | No description available
> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V15_Mg-
> coot-2.pdb
Chain information for V15_Mg-coot-2.pdb #35
---
Chain | Description
A | No description available
> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V16_Mg-
> coot-1.pdb
Chain information for V16_Mg-coot-1.pdb #36
---
Chain | Description
A | No description available
> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V17_Mg-
> coot-2.pdb
Chain information for V17_Mg-coot-2.pdb #37
---
Chain | Description
A | No description available
> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V18_Mg-
> coot-1.pdb
Chain information for V18_Mg-coot-1.pdb #38
---
Chain | Description
A | No description available
> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V19_Mg-
> coot-3.pdb
Chain information for V19_Mg-coot-3.pdb #39
---
Chain | Description
A | No description available
> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V20_Mg-
> coot-2.pdb
Chain information for V20_Mg-coot-2.pdb #40
---
Chain | Description
A | No description available
> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V21_Mg_real_space_refined_002-coot-1.pdb
Chain information for V21_Mg_real_space_refined_002-coot-1.pdb #41
---
Chain | Description
A | No description available
> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V22_Mg_6sig.pdb
Chain information for V22_Mg_6sig.pdb #42
---
Chain | Description
A | No description available
> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V22_Mg_real_space_refined_002-coot-1.pdb
Chain information for V22_Mg_real_space_refined_002-coot-1.pdb #43
---
Chain | Description
A | No description available
> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V23_Mg_6sig.pdb
Chain information for V23_Mg_6sig.pdb #44
---
Chain | Description
A | No description available
> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V23_Mg-
> coot-1.pdb
Chain information for V23_Mg-coot-1.pdb #45
---
Chain | Description
A | No description available
> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V24_6sig.pdb
Chain information for V24_6sig.pdb #46
---
Chain | Description
A | No description available
> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V24_Mg-
> coot-6.pdb
Chain information for V24_Mg-coot-6.pdb #47
---
Chain | Description
A | No description available
> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V25_Mg-
> coot-1.pdb
Chain information for V25_Mg-coot-1.pdb #48
---
Chain | Description
A | No description available
> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V26_Mg-
> coot-1.pdb
Chain information for V26_Mg-coot-1.pdb #49
---
Chain | Description
A | No description available
> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V27_Mg-
> coot-2.pdb
Chain information for V27_Mg-coot-2.pdb #50
---
Chain | Description
A | No description available
> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V28_Mg-
> coot-1.pdb
Chain information for V28_Mg-coot-1.pdb #51
---
Chain | Description
A | No description available
> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V29_Mg-
> coot-2.pdb
Chain information for V29_Mg-coot-2.pdb #52
---
Chain | Description
A | No description available
> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V30_Mg-
> coot-3.pdb
Chain information for V30_Mg-coot-3.pdb #53
---
Chain | Description
A | No description available
> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V31_Mg-
> coot-3.pdb
Chain information for V31_Mg-coot-3.pdb #54
---
Chain | Description
A | No description available
> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V32_Mg-
> coot-2.pdb
Chain information for V32_Mg-coot-2.pdb #55
---
Chain | Description
A | No description available
> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V33_Mg-
> coot-2.pdb
Chain information for V33_Mg-coot-2.pdb #56
---
Chain | Description
A | No description available
> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V34_Mg-
> coot-3.pdb
Chain information for V34_Mg-coot-3.pdb #57
---
Chain | Description
A | No description available
> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V35_Mg-
> coot-2.pdb
Chain information for V35_Mg-coot-2.pdb #58
---
Chain | Description
A | No description available
> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V36_Mg-
> coot-1.pdb
Chain information for V36_Mg-coot-1.pdb #59
---
Chain | Description
A | No description available
> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V37_Mg-
> coot-1.pdb
Chain information for V37_Mg-coot-1.pdb #60
---
Chain | Description
A | No description available
> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V38_Mg-
> coot-1.pdb
Chain information for V38_Mg-coot-1.pdb #61
---
Chain | Description
A | No description available
> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V39_Mg_real_space_refined_002-coot-0.pdb
Chain information for V39_Mg_real_space_refined_002-coot-0.pdb #62
---
Chain | Description
A | No description available
> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V40_Mg_real_space_refined_003-coot-0_aligned.pdb
Chain information for V40_Mg_real_space_refined_003-coot-0_aligned.pdb #63
---
Chain | Description
A | No description available
> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V40_Mg_real_space_refined_003-coot-0.pdb
Chain information for V40_Mg_real_space_refined_003-coot-0.pdb #64
---
Chain | Description
A | No description available
> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V41_Mg_real_space_refined_003-coot-0.pdb
Chain information for V41_Mg_real_space_refined_003-coot-0.pdb #65
---
Chain | Description
A | No description available
> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V42_Mg_real_space_refined_003-coot-0.pdb
Chain information for V42_Mg_real_space_refined_003-coot-0.pdb #66
---
Chain | Description
A | No description available
> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V43_Mg_real_space_refined_001-coot-0.pdb
Chain information for V43_Mg_real_space_refined_001-coot-0.pdb #67
---
Chain | Description
A | No description available
> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V44_Mg_real_space_refined_003-coot-0.pdb
Chain information for V44_Mg_real_space_refined_003-coot-0.pdb #68
---
Chain | Description
A | No description available
> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V45_Mg-
> coot-3.pdb
Chain information for V45_Mg-coot-3.pdb #69
---
Chain | Description
A | No description available
> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V46_Mg-
> coot-2.pdb
Chain information for V46_Mg-coot-2.pdb #70
---
Chain | Description
A | No description available
> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V47_Mg-
> coot-4.pdb
Chain information for V47_Mg-coot-4.pdb #71
---
Chain | Description
A | No description available
> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V48_Mg-
> coot-1.pdb
Chain information for V48_Mg-coot-1.pdb #72
---
Chain | Description
A | No description available
> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/Apo_1mM_Mg/QScore/pdb_new_ions_ref/aligned_pdbs_apo/V49_Mg-
> coot-2.pdb
Chain information for V49_Mg-coot-2.pdb #73
---
Chain | Description
A | No description available
Computing secondary structure
[Repeated 53 time(s)]
> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/apo_conf/V1_holo_set_noprot-
> coot-2.pdb
Chain information for V1_holo_set_noprot-coot-2.pdb #74
---
Chain | Description
A | No description available
> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/apo_conf/V8_holo_no_prot_a-
> coot-4.pdb
Summary of feedback from opening
/Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/apo_conf/V8_holo_no_prot_a-
coot-4.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ASN B 10 GLN B 19 1 10
Start residue of secondary structure not found: HELIX 2 2 ALA B 54 GLU B 70 1
17
Start residue of secondary structure not found: HELIX 3 3 GLN B 87 ALA B 89 1
3
Start residue of secondary structure not found: HELIX 4 4 TYR B 94 LYS B 107 1
14
Start residue of secondary structure not found: SHEET 1 1 1 PHE B 28 ASP B 34
0
2 messages similar to the above omitted
Chain information for V8_holo_no_prot_a-coot-4.pdb #75
---
Chain | Description
A | No description available
> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/apo_conf/V13_holo_set_noapo-
> coot-3.pdb
Summary of feedback from opening
/Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/apo_conf/V13_holo_set_noapo-
coot-3.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ASN B 10 GLN B 19 1 10
Start residue of secondary structure not found: HELIX 2 2 ALA B 54 GLU B 70 1
17
Start residue of secondary structure not found: HELIX 3 3 GLN B 87 ALA B 89 1
3
Start residue of secondary structure not found: HELIX 4 4 TYR B 94 LYS B 107 1
14
Start residue of secondary structure not found: SHEET 1 1 1 PHE B 28 ASP B 34
0
2 messages similar to the above omitted
Chain information for V13_holo_set_noapo-coot-3.pdb #76
---
Chain | Description
A | No description available
> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/apo_conf/V20_holo_no_prot-
> coot-1.pdb
Chain information for V20_holo_no_prot-coot-1.pdb #77
---
Chain | Description
A | No description available
> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/apo_conf/V22_holo_no_prot-
> coot-1.pdb
Chain information for V22_holo_no_prot-coot-1.pdb #78
---
Chain | Description
A | No description available
> open
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/holo_Enzyme/Final_Volumes/apo_conf/V24_holo_no_prot-
> coot-3.pdb
Chain information for V24_holo_no_prot-coot-3.pdb #79
---
Chain | Description
A | No description available
Computing secondary structure
[Repeated 5 time(s)]
> select
> #1/A:15,21-29,39-67,69-84,96-101,105-112,249-261,272-293,295-312,327-340,386-400
3255 atoms, 3639 bonds, 151 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #20-49,51-79#!50 to #1 & sel matrix Nucleic
Computing secondary structure
[Repeated 60 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V1_Mg-coot-1.pdb, chain A
(#20), sequence alignment score = 604
RMSD between 150 pruned atom pairs is 0.460 angstroms; (across all 151 pairs:
0.510)
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V2_Mg-coot-1.pdb, chain A
(#21), sequence alignment score = 604
RMSD between 150 pruned atom pairs is 0.443 angstroms; (across all 151 pairs:
0.490)
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V3_Mg-coot-2.pdb, chain A
(#22), sequence alignment score = 604
RMSD between 150 pruned atom pairs is 0.478 angstroms; (across all 151 pairs:
0.530)
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V4_Mg-coot-2.pdb, chain A
(#23), sequence alignment score = 604
RMSD between 150 pruned atom pairs is 0.470 angstroms; (across all 151 pairs:
0.515)
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V5_Mg-coot-1.pdb, chain A
(#24), sequence alignment score = 604
RMSD between 150 pruned atom pairs is 0.472 angstroms; (across all 151 pairs:
0.521)
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V6_Mg-coot-1.pdb, chain A
(#25), sequence alignment score = 604
RMSD between 150 pruned atom pairs is 0.469 angstroms; (across all 151 pairs:
0.519)
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V7_Mg-coot-2.pdb, chain A
(#26), sequence alignment score = 604
RMSD between 148 pruned atom pairs is 0.517 angstroms; (across all 151 pairs:
0.622)
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V8_Mg-coot-2.pdb, chain A
(#27), sequence alignment score = 604
RMSD between 150 pruned atom pairs is 0.465 angstroms; (across all 151 pairs:
0.504)
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V9_Mg-coot-3.pdb, chain A
(#28), sequence alignment score = 604
RMSD between 150 pruned atom pairs is 0.490 angstroms; (across all 151 pairs:
0.523)
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V10_Mg-coot-3.pdb, chain A
(#29), sequence alignment score = 604
RMSD between 150 pruned atom pairs is 0.491 angstroms; (across all 151 pairs:
0.532)
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V11_Mg-coot-2.pdb, chain A
(#30), sequence alignment score = 604
RMSD between 150 pruned atom pairs is 0.480 angstroms; (across all 151 pairs:
0.536)
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with
V12_real_space_refined_011-coot-0.pdb, chain A (#31), sequence alignment score
= 604
RMSD between 150 pruned atom pairs is 0.523 angstroms; (across all 151 pairs:
0.559)
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V13_Mg-coot-2.pdb, chain A
(#32), sequence alignment score = 604
RMSD between 150 pruned atom pairs is 0.504 angstroms; (across all 151 pairs:
0.540)
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V13_Mg-coot-3_6.pdb, chain A
(#33), sequence alignment score = 604
RMSD between 150 pruned atom pairs is 0.504 angstroms; (across all 151 pairs:
0.540)
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V14_Mg-coot-1.pdb, chain A
(#34), sequence alignment score = 604
RMSD between 150 pruned atom pairs is 0.477 angstroms; (across all 151 pairs:
0.534)
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V15_Mg-coot-2.pdb, chain A
(#35), sequence alignment score = 604
RMSD between 150 pruned atom pairs is 0.461 angstroms; (across all 151 pairs:
0.518)
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V16_Mg-coot-1.pdb, chain A
(#36), sequence alignment score = 604
RMSD between 150 pruned atom pairs is 0.452 angstroms; (across all 151 pairs:
0.506)
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V17_Mg-coot-2.pdb, chain A
(#37), sequence alignment score = 604
RMSD between 150 pruned atom pairs is 0.439 angstroms; (across all 151 pairs:
0.502)
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V18_Mg-coot-1.pdb, chain A
(#38), sequence alignment score = 604
RMSD between 150 pruned atom pairs is 0.461 angstroms; (across all 151 pairs:
0.498)
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V19_Mg-coot-3.pdb, chain A
(#39), sequence alignment score = 604
RMSD between 150 pruned atom pairs is 0.458 angstroms; (across all 151 pairs:
0.496)
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V20_Mg-coot-2.pdb, chain A
(#40), sequence alignment score = 604
RMSD between 150 pruned atom pairs is 0.458 angstroms; (across all 151 pairs:
0.520)
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with
V21_Mg_real_space_refined_002-coot-1.pdb, chain A (#41), sequence alignment
score = 604
RMSD between 150 pruned atom pairs is 0.480 angstroms; (across all 151 pairs:
0.525)
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V22_Mg_6sig.pdb, chain A
(#42), sequence alignment score = 604
RMSD between 150 pruned atom pairs is 0.449 angstroms; (across all 151 pairs:
0.508)
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with
V22_Mg_real_space_refined_002-coot-1.pdb, chain A (#43), sequence alignment
score = 604
RMSD between 150 pruned atom pairs is 0.449 angstroms; (across all 151 pairs:
0.508)
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V23_Mg_6sig.pdb, chain A
(#44), sequence alignment score = 604
RMSD between 150 pruned atom pairs is 0.495 angstroms; (across all 151 pairs:
0.534)
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V23_Mg-coot-1.pdb, chain A
(#45), sequence alignment score = 604
RMSD between 150 pruned atom pairs is 0.495 angstroms; (across all 151 pairs:
0.534)
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V24_6sig.pdb, chain A (#46),
sequence alignment score = 604
RMSD between 150 pruned atom pairs is 0.487 angstroms; (across all 151 pairs:
0.552)
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V24_Mg-coot-6.pdb, chain A
(#47), sequence alignment score = 604
RMSD between 150 pruned atom pairs is 0.487 angstroms; (across all 151 pairs:
0.552)
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V25_Mg-coot-1.pdb, chain A
(#48), sequence alignment score = 604
RMSD between 150 pruned atom pairs is 0.465 angstroms; (across all 151 pairs:
0.518)
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V26_Mg-coot-1.pdb, chain A
(#49), sequence alignment score = 604
RMSD between 150 pruned atom pairs is 0.491 angstroms; (across all 151 pairs:
0.546)
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V28_Mg-coot-1.pdb, chain A
(#51), sequence alignment score = 604
RMSD between 150 pruned atom pairs is 0.514 angstroms; (across all 151 pairs:
0.557)
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V29_Mg-coot-2.pdb, chain A
(#52), sequence alignment score = 604
RMSD between 150 pruned atom pairs is 0.486 angstroms; (across all 151 pairs:
0.512)
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V30_Mg-coot-3.pdb, chain A
(#53), sequence alignment score = 604
RMSD between 150 pruned atom pairs is 0.427 angstroms; (across all 151 pairs:
0.470)
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V31_Mg-coot-3.pdb, chain A
(#54), sequence alignment score = 604
RMSD between 150 pruned atom pairs is 0.462 angstroms; (across all 151 pairs:
0.524)
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V32_Mg-coot-2.pdb, chain A
(#55), sequence alignment score = 604
RMSD between 149 pruned atom pairs is 0.454 angstroms; (across all 151 pairs:
0.624)
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V33_Mg-coot-2.pdb, chain A
(#56), sequence alignment score = 604
RMSD between 150 pruned atom pairs is 0.472 angstroms; (across all 151 pairs:
0.515)
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V34_Mg-coot-3.pdb, chain A
(#57), sequence alignment score = 604
RMSD between 149 pruned atom pairs is 0.539 angstroms; (across all 151 pairs:
0.609)
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V35_Mg-coot-2.pdb, chain A
(#58), sequence alignment score = 604
RMSD between 150 pruned atom pairs is 0.538 angstroms; (across all 151 pairs:
0.577)
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V36_Mg-coot-1.pdb, chain A
(#59), sequence alignment score = 604
RMSD between 149 pruned atom pairs is 0.505 angstroms; (across all 151 pairs:
0.589)
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V37_Mg-coot-1.pdb, chain A
(#60), sequence alignment score = 604
RMSD between 150 pruned atom pairs is 0.476 angstroms; (across all 151 pairs:
0.520)
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V38_Mg-coot-1.pdb, chain A
(#61), sequence alignment score = 604
RMSD between 150 pruned atom pairs is 0.462 angstroms; (across all 151 pairs:
0.509)
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with
V39_Mg_real_space_refined_002-coot-0.pdb, chain A (#62), sequence alignment
score = 604
RMSD between 150 pruned atom pairs is 0.495 angstroms; (across all 151 pairs:
0.539)
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with
V40_Mg_real_space_refined_003-coot-0_aligned.pdb, chain A (#63), sequence
alignment score = 604
RMSD between 149 pruned atom pairs is 0.522 angstroms; (across all 151 pairs:
0.591)
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with
V40_Mg_real_space_refined_003-coot-0.pdb, chain A (#64), sequence alignment
score = 604
RMSD between 149 pruned atom pairs is 0.526 angstroms; (across all 151 pairs:
0.595)
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with
V41_Mg_real_space_refined_003-coot-0.pdb, chain A (#65), sequence alignment
score = 604
RMSD between 150 pruned atom pairs is 0.484 angstroms; (across all 151 pairs:
0.540)
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with
V42_Mg_real_space_refined_003-coot-0.pdb, chain A (#66), sequence alignment
score = 604
RMSD between 150 pruned atom pairs is 0.482 angstroms; (across all 151 pairs:
0.526)
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with
V43_Mg_real_space_refined_001-coot-0.pdb, chain A (#67), sequence alignment
score = 604
RMSD between 149 pruned atom pairs is 0.513 angstroms; (across all 151 pairs:
0.602)
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with
V44_Mg_real_space_refined_003-coot-0.pdb, chain A (#68), sequence alignment
score = 604
RMSD between 150 pruned atom pairs is 0.507 angstroms; (across all 151 pairs:
0.549)
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V45_Mg-coot-3.pdb, chain A
(#69), sequence alignment score = 604
RMSD between 150 pruned atom pairs is 0.494 angstroms; (across all 151 pairs:
0.546)
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V46_Mg-coot-2.pdb, chain A
(#70), sequence alignment score = 604
RMSD between 150 pruned atom pairs is 0.436 angstroms; (across all 151 pairs:
0.490)
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V47_Mg-coot-4.pdb, chain A
(#71), sequence alignment score = 604
RMSD between 150 pruned atom pairs is 0.564 angstroms; (across all 151 pairs:
0.596)
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V48_Mg-coot-1.pdb, chain A
(#72), sequence alignment score = 604
RMSD between 150 pruned atom pairs is 0.468 angstroms; (across all 151 pairs:
0.523)
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V49_Mg-coot-2.pdb, chain A
(#73), sequence alignment score = 604
RMSD between 150 pruned atom pairs is 0.461 angstroms; (across all 151 pairs:
0.529)
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V1_holo_set_noprot-
coot-2.pdb, chain A (#74), sequence alignment score = 604
RMSD between 149 pruned atom pairs is 0.402 angstroms; (across all 151 pairs:
0.464)
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V8_holo_no_prot_a-coot-4.pdb,
chain A (#75), sequence alignment score = 604
RMSD between 149 pruned atom pairs is 0.486 angstroms; (across all 151 pairs:
0.562)
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V13_holo_set_noapo-
coot-3.pdb, chain A (#76), sequence alignment score = 604
RMSD between 151 pruned atom pairs is 0.491 angstroms; (across all 151 pairs:
0.491)
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V20_holo_no_prot-coot-1.pdb,
chain A (#77), sequence alignment score = 604
RMSD between 151 pruned atom pairs is 0.442 angstroms; (across all 151 pairs:
0.442)
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V22_holo_no_prot-coot-1.pdb,
chain A (#78), sequence alignment score = 604
RMSD between 149 pruned atom pairs is 0.357 angstroms; (across all 151 pairs:
0.438)
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V24_holo_no_prot-coot-3.pdb,
chain A (#79), sequence alignment score = 604
RMSD between 150 pruned atom pairs is 0.494 angstroms; (across all 151 pairs:
0.557)
Matchmaker V2_holo-coot-2.pdb, chain A (#1) with V27_Mg-coot-2.pdb, chain A
(#50), sequence alignment score = 604
RMSD between 150 pruned atom pairs is 0.544 angstroms; (across all 151 pairs:
0.594)
> select #20-79/A
537720 atoms, 602280 bonds, 25020 residues, 60 models selected
> color sel dim gray
> hide sel target a
> select #20-79/A:50,389,390
3960 atoms, 4380 bonds, 180 residues, 60 models selected
> cartoon hide sel
> show sel target ab
> nucleotides sel atoms
> style nucleic & sel stick
Changed 3960 atom styles
> hide (sel-residues & (protein|nucleic)) target a
> cartoon hide sel-residues
> show (sel-residues & backbone) target ab
> ui tool show "Color Actions"
> color sel cornflower blue
> hide #19#!1-18 target m
> select #20/C:1@O
1 atom, 1 residue, 1 model selected
> select add #42/B:67@MG
2 atoms, 2 residues, 2 models selected
> select add #61/B:65@MG
3 atoms, 3 residues, 3 models selected
> select add #65/B:44@MG
4 atoms, 4 residues, 4 models selected
> hide sel target a
> select #30/B:61@MG
1 atom, 1 residue, 1 model selected
> select add #69/B:62@MG
2 atoms, 2 residues, 2 models selected
> hide sel target a
> select #20-79/B
2199 atoms, 1 pseudobond, 2199 residues, 56 models selected
> ui tool show "Selection Inspector"
> size sel atomRadius 0.7
Changed 2199 atom radii
> select clear
> select #46/B:66@MG
1 atom, 1 residue, 1 model selected
> select add #75/A:390@O3'
2 atoms, 2 residues, 2 models selected
> distance #46/B:66@MG #75/A:390@O3'
Distance between V24_6sig.pdb #46/B MG 66 MG and V8_holo_no_prot_a-coot-4.pdb
#75/A A 390 O3': 5.502Å
> close #42
> close #44
> close #46
> select #20-79/B
2062 atoms, 1 pseudobond, 2062 residues, 53 models selected
> close #33
> close #63
> select #20-79/B:7
50 atoms, 50 residues, 50 models selected
> select #75/C:7@MG
1 atom, 1 residue, 1 model selected
> select add #69/B:7@MG
2 atoms, 2 residues, 2 models selected
> select add #68/B:7@MG
3 atoms, 3 residues, 3 models selected
> select add #55/B:7@MG
4 atoms, 4 residues, 4 models selected
> select #20-79/B
1987 atoms, 1 pseudobond, 1987 residues, 51 models selected
> select #20-79/C
187 atoms, 187 residues, 6 models selected
> ui tool show "Selection Inspector"
> size sel atomRadius 0.7
Changed 187 atom radii
> select #20-79/B:7
50 atoms, 50 residues, 50 models selected
> ui tool show "Color Actions"
> color sel #941100ff
> select #20-79/C:7
5 atoms, 5 residues, 5 models selected
> ui tool show "Color Actions"
> select #20-79/C:7
5 atoms, 5 residues, 5 models selected
> ui tool show "Color Actions"
> color sel #4f8f00ff
> color sel #941100ff
> select #20-79/B
1987 atoms, 1 pseudobond, 1987 residues, 51 models selected
> ui tool show "Color Actions"
> color sel forest green
> select #20-79/C
187 atoms, 187 residues, 6 models selected
> ui tool show "Color Actions"
> color sel forest green
> select #20-79/C:7
5 atoms, 5 residues, 5 models selected
> ui tool show "Color Actions"
> select #20-79/B:7
50 atoms, 50 residues, 50 models selected
> ui tool show "Color Actions"
> color sel #945200ff
> color sel #941100ff
> select #20-79/C:7
5 atoms, 5 residues, 5 models selected
> ui tool show "Color Actions"
> color sel #945200ff
> color sel #941100ff
> select clear
> select #20-79/B:57
21 atoms, 21 residues, 21 models selected
> select #20-79/B:57,66
35 atoms, 35 residues, 25 models selected
> select clear
> select #65/B:41@MG
1 atom, 1 residue, 1 model selected
> select add #39/B:64@MG
2 atoms, 2 residues, 2 models selected
> select add #41/B:62@MG
3 atoms, 3 residues, 3 models selected
> select add #43/B:63@MG
4 atoms, 4 residues, 4 models selected
> select subtract #43/B:63@MG
3 atoms, 3 residues, 3 models selected
> select add #43/B:63@MG
4 atoms, 4 residues, 4 models selected
> select subtract #41/B:62@MG
3 atoms, 3 residues, 3 models selected
> select add #31/B:58@MG
4 atoms, 4 residues, 4 models selected
> select add #30/B:57@MG
5 atoms, 5 residues, 5 models selected
> select subtract #31/B:58@MG
4 atoms, 4 residues, 4 models selected
> select subtract #65/B:41@MG
3 atoms, 3 residues, 3 models selected
> select add #65/B:41@MG
4 atoms, 4 residues, 4 models selected
> select add #31/B:58@MG
5 atoms, 5 residues, 5 models selected
> select subtract #31/B:58@MG
4 atoms, 4 residues, 4 models selected
> select subtract #39/B:64@MG
3 atoms, 3 residues, 3 models selected
> select add #39/B:64@MG
4 atoms, 4 residues, 4 models selected
> select add #38/B:61@MG
5 atoms, 5 residues, 5 models selected
> select add #36/B:60@MG
6 atoms, 6 residues, 6 models selected
> select subtract #43/B:63@MG
5 atoms, 5 residues, 5 models selected
> select add #43/B:63@MG
6 atoms, 6 residues, 6 models selected
> hide sel target a
> select #26/B:49@MG
1 atom, 1 residue, 1 model selected
> select add #31/B:58@MG
2 atoms, 2 residues, 2 models selected
> select add #41/B:62@MG
3 atoms, 3 residues, 3 models selected
> select add #34/B:59@MG
4 atoms, 4 residues, 4 models selected
> hide sel target a
> select #43/B:65@MG
1 atom, 1 residue, 1 model selected
> select add #30/B:60@MG
2 atoms, 2 residues, 2 models selected
> show #19 models
> hide #19 models
> show #19 models
> hide #19 models
> show #19 models
> hide #19 models
> show #19 models
> hide #19 models
> show #19 models
> hide #19 models
> show #19 models
> hide #19 models
> show #19 models
> hide #19 models
> show #19 models
> hide #19 models
> select #50/B:64@MG
1 atom, 1 residue, 1 model selected
> select add #35/B:62@MG
2 atoms, 2 residues, 2 models selected
> select add #51/B:68@MG
3 atoms, 3 residues, 3 models selected
> select add #69/B:57@MG
4 atoms, 4 residues, 4 models selected
> select add #62/B:45@MG
5 atoms, 5 residues, 5 models selected
> select add #64/B:42@MG
6 atoms, 6 residues, 6 models selected
> select add #27/B:54@MG
7 atoms, 7 residues, 7 models selected
> select add #59/B:66@MG
8 atoms, 8 residues, 8 models selected
> hide sel target a
> show sel target ab
> show #19 models
> hide #19 models
> show #19 models
> hide #19 models
> show #19 models
> hide #19 models
> show #19 models
> hide #19 models
> show #19 models
> hide #19 models
> show #19 models
> hide #19 models
> select #21/B:38@MG
1 atom, 1 residue, 1 model selected
> select add #30/B:38@MG
2 atoms, 2 residues, 2 models selected
> select add #26/B:38@MG
3 atoms, 3 residues, 3 models selected
> select #26/B:38@MG
1 atom, 1 residue, 1 model selected
> select add #59/B:64@MG
2 atoms, 2 residues, 2 models selected
> distance #26/B:38@MG #59/B:64@MG
Distance between V7_Mg-coot-2.pdb #26/B MG 38 MG and V36_Mg-coot-1.pdb #59/B
MG 64 MG: 9.452Å
> select #26/B:38@MG
1 atom, 1 residue, 1 model selected
> select add #23/B:7@MG
2 atoms, 2 residues, 2 models selected
> distance #26/B:38@MG #23/B:7@MG
Distance between V7_Mg-coot-2.pdb #26/B MG 38 MG and V4_Mg-coot-2.pdb #23/B MG
7 MG: 8.150Å
> select #26/B:38@MG
1 atom, 1 residue, 1 model selected
> select add #21/B:38@MG
2 atoms, 2 residues, 2 models selected
> select add #30/B:38@MG
3 atoms, 3 residues, 3 models selected
> hide sel target a
> select #36/B:38@MG
1 atom, 1 residue, 1 model selected
> select add #59/B:38@MG
2 atoms, 2 residues, 2 models selected
> hide sel target a
> select add #62/B:30@MG
3 atoms, 3 residues, 3 models selected
> select #53/B:65@MG
1 atom, 1 residue, 1 model selected
> select #75/A:390@O3'
1 atom, 1 residue, 1 model selected
> select add #24/B:50@MG
2 atoms, 2 residues, 2 models selected
> distance #75/A:390@O3' #24/B:50@MG
Distance between V8_holo_no_prot_a-coot-4.pdb #75/A A 390 O3' and V5_Mg-
coot-1.pdb #24/B MG 50 MG: 5.771Å
> select #24/B:50@MG
1 atom, 1 residue, 1 model selected
> select #47/B:66@MG
1 atom, 1 residue, 1 model selected
> select add #34/B:61@MG
2 atoms, 2 residues, 2 models selected
> select add #32/B:60@MG
3 atoms, 3 residues, 3 models selected
> select add #24/B:50@MG
4 atoms, 4 residues, 4 models selected
> select add #53/B:65@MG
5 atoms, 5 residues, 5 models selected
> select add #48/B:69@MG
6 atoms, 6 residues, 6 models selected
> select add #36/B:61@MG
7 atoms, 7 residues, 7 models selected
> select #47/B:66@MG
1 atom, 1 residue, 1 model selected
> select add #55/B:62@MG
2 atoms, 2 residues, 2 models selected
> distance #47/B:66@MG #55/B:62@MG
Distance between V24_Mg-coot-6.pdb #47/B MG 66 MG and V32_Mg-coot-2.pdb #55/B
MG 62 MG: 5.257Å
> save
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/apo_holo_analysis/ions/ions_apo_holo_new_core_aa_models.cxs
> select #43/B:65@MG
1 atom, 1 residue, 1 model selected
> select add #58/B:4@MG
2 atoms, 2 residues, 2 models selected
> distance #43/B:65@MG #58/B:4@MG
Distance between V22_Mg_real_space_refined_002-coot-1.pdb #43/B MG 65 MG and
V35_Mg-coot-2.pdb #58/B MG 4 MG: 9.512Å
> select #43/B:65@MG
1 atom, 1 residue, 1 model selected
> select add #30/B:60@MG
2 atoms, 2 residues, 2 models selected
> hide sel target a
> save
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/apo_holo_analysis/ions/ions_apo_holo_new_core_aa_models.cxs
> select #59/B:64@MG
1 atom, 1 residue, 1 model selected
> select clear
> select #48/B:30@MG
1 atom, 1 residue, 1 model selected
> select add #75/C:7@MG
2 atoms, 2 residues, 2 models selected
> distance #48/B:30@MG #75/C:7@MG
Distance between V25_Mg-coot-1.pdb #48/B MG 30 MG and V8_holo_no_prot_a-
coot-4.pdb #75/C MG 7 MG: 7.041Å
> select #48/B:30@MG
1 atom, 1 residue, 1 model selected
> select add #58/A:389@OP1
2 atoms, 2 residues, 2 models selected
> distance #48/B:30@MG #58/A:389@OP1
Distance between V25_Mg-coot-1.pdb #48/B MG 30 MG and V35_Mg-coot-2.pdb #58/A
A 389 OP1: 2.362Å
> select #69/B:30@MG
1 atom, 1 residue, 1 model selected
> select add #65/B:30@MG
2 atoms, 2 residues, 2 models selected
> select add #48/B:30@MG
3 atoms, 3 residues, 3 models selected
> select add #41/B:30@MG
4 atoms, 4 residues, 4 models selected
> select add #55/B:66@MG
5 atoms, 5 residues, 5 models selected
> select add #50/B:30@MG
6 atoms, 6 residues, 6 models selected
> color sel blue
> select clear
> select #39/B:65@MG
1 atom, 1 residue, 1 model selected
> select add #75/A:390@O3'
2 atoms, 2 residues, 2 models selected
> distance #39/B:65@MG #75/A:390@O3'
Distance between V19_Mg-coot-3.pdb #39/B MG 65 MG and V8_holo_no_prot_a-
coot-4.pdb #75/A A 390 O3': 4.560Å
> select #28/B:40@MG
1 atom, 1 residue, 1 model selected
> select #75/A:390@O3'
1 atom, 1 residue, 1 model selected
> select add #72/B:40@MG
2 atoms, 2 residues, 2 models selected
> distance #75/A:390@O3' #72/B:40@MG
Distance between V8_holo_no_prot_a-coot-4.pdb #75/A A 390 O3' and V48_Mg-
coot-1.pdb #72/B MG 40 MG: 5.512Å
> select #20-79/B:40
33 atoms, 33 residues, 33 models selected
> save
> /Users/frazaodesouzam2/Documents/Project/FL_RnaseP/Conf_Space_CryoEM/apo_holo_analysis/ions/ions_apo_holo_new_core_aa_models.cxs
——— End of log from Wed Sep 17 17:35:30 2025 ———
opened ChimeraX session
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M2 Max
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac14,6
Model Number: Z1760005VLL/A
Chip: Apple M2 Max
Total Number of Cores: 12 (8 performance and 4 efficiency)
Memory: 64 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: 1 day, 18 hours, 31 minutes
Graphics/Displays:
Apple M2 Max:
Chipset Model: Apple M2 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 38
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3456 x 2234 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
DELL P2715Q:
Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
DELL P2715Q:
Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMalign: 0.1.3
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
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: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-QScore: 1.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
finufft: 2.4.1
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
Change History (2)
comment:1 by , 7 weeks ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash on Mac waking from sleep |
comment:2 by , 7 weeks ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
Note:
See TracTickets
for help on using tickets.
