![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 8 months ago
Closed 8 months ago
#17005 closed defect (duplicate)
Crash moving window between screens
| 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-15.3.1-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
Thread 0x000000036c32f000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 324 in wait
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 622 in wait
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1392 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x00000001ff30c840 (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.pdb_lib._load_libs, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, PIL._imagingmath, PIL._webp, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.morph._morph (total: 65)
{"app_name":"ChimeraX","timestamp":"2025-03-03 13:35:08.00 +0100","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 15.3.1 (24D70)","roots_installed":0,"name":"ChimeraX","incident_id":"9782CA2D-5A89-4C19-9B3E-ECD3B6B484B0"}
{
"uptime" : 180000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac16,7",
"coalitionID" : 14336,
"osVersion" : {
"train" : "macOS 15.3.1",
"build" : "24D70",
"releaseType" : "User"
},
"captureTime" : "2025-03-03 13:34:46.9367 +0100",
"codeSigningMonitor" : 2,
"incident" : "9782CA2D-5A89-4C19-9B3E-ECD3B6B484B0",
"pid" : 17000,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-02-27 12:40:56.3368 +0100",
"procStartAbsTime" : 3351816961773,
"procExitAbsTime" : 4415856305383,
"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":"F389F855-0584-56F7-848A-B2585D35F3B4","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "511A271C-020F-4A16-9735-C09A474EDA11",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRcuD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkWfg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"bootSessionUUID" : "2A44346E-7630-42B6-8E78-A23A5B6C092C",
"wakeTime" : 13830,
"sleepWakeUUID" : "9AA0E56F-688B-4719-944F-5433D7DD36FD",
"sip" : "enabled",
"vmRegionInfo" : "0xffffb09930000000 is not in any region. Bytes after previous region: 18446550847550849025 \n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n owned unmapped memory unmapped-unmapped [ 2.1G] rw-\/rw- SM=PRV owned physical footprint (unmapped)\n---> \n UNUSED SPACE AT END",
"exception" : {"codes":"0x0000000000000001, 0x01ff309930000000","rawCodes":[1,143887147592581120],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x01ff309930000000 -> 0xffffb09930000000 (possible pointer authentication failure)"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":17000},
"vmregioninfo" : "0xffffb09930000000 is not in any region. Bytes after previous region: 18446550847550849025 \n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n owned unmapped memory unmapped-unmapped [ 2.1G] rw-\/rw- SM=PRV owned physical footprint (unmapped)\n---> \n UNUSED SPACE AT END",
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
"threads" : [{"threadState":{"x":[{"value":0},{"value":0},{"value":1},{"value":6093299368},{"value":99},{"value":122},{"value":2305948562361062944},{"value":4789395770},{"value":7114413129772265387},{"value":7114413136429688811},{"value":14757395258967641293},{"value":4294967286},{"value":6093299298},{"value":0},{"value":54},{"value":4294967280},{"value":328},{"value":8717132480},{"value":0},{"value":11},{"value":259},{"value":8576354592,"symbolLocation":224,"symbol":"_main_thread"},{"value":0},{"value":1},{"value":4394075696,"symbolLocation":0,"symbol":"faulthandler_handlers"},{"value":8539344896,"symbolLocation":0,"symbol":"OBJC_IVAR_$_NSTableView._rowSizeStyle"},{"value":8539344896,"symbolLocation":0,"symbol":"OBJC_IVAR_$_NSTableView._rowSizeStyle"},{"value":5},{"value":1}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6804848496},"cpsr":{"value":1073741824},"fp":{"value":6093299440},"sp":{"value":6093299408},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6804616992,"matchesCrashFrame":1},"far":{"value":0}},"id":2018229,"triggered":true,"name":"CrBrowserMain","queue":"com.apple.main-thread","frames":[{"imageOffset":38688,"symbol":"__pthread_kill","symbolLocation":8,"imageIndex":169},{"imageOffset":28528,"symbol":"pthread_kill","symbolLocation":288,"imageIndex":170},{"imageOffset":269336,"symbol":"raise","symbolLocation":32,"imageIndex":171},{"imageOffset":2417160,"symbol":"faulthandler_fatal_error","symbolLocation":392,"imageIndex":1},{"imageOffset":15844,"symbol":"_sigtramp","symbolLocation":56,"imageIndex":172},{"imageOffset":349380,"imageIndex":69},{"imageOffset":349160,"imageIndex":69},{"imageOffset":386264,"symbol":"_NSViewHierarchyDidChangeBackingProperties","symbolLocation":244,"imageIndex":173},{"imageOffset":11754200,"symbol":"-[NSWindow _postWindowDidChangeBackingPropertiesAndDisplayWindowForPreviousBackingScaleFactor:previousColorSpace:]","symbolLocation":192,"imageIndex":173},{"imageOffset":2081172,"symbol":"__67-[NSWindow _updateSettingsSendingScreenChangeNotificationToScreen:]_block_invoke","symbolLocation":440,"imageIndex":173},{"imageOffset":513240,"symbol":"NSPerformVisuallyAtomicChange","symbolLocation":108,"imageIndex":173},{"imageOffset":2080720,"symbol":"-[NSWindow _updateSettingsSendingScreenChangeNotificationToScreen:]","symbolLocation":96,"imageIndex":173},{"imageOffset":518736,"symbol":"-[NSWindow _setFrameCommon:display:fromServer:]","symbolLocation":2060,"imageIndex":173},{"imageOffset":11762456,"symbol":"-[NSWindow _windowMovedToRect:dueToMoveEvent:]","symbolLocation":184,"imageIndex":173},{"imageOffset":1453488,"symbol":"-[NSWindow _windowMoved:]","symbolLocation":924,"imageIndex":173},{"imageOffset":1452488,"symbol":"-[NSWindow _internalHandleAppKitDefinedEvent:]","symbolLocation":152,"imageIndex":173},{"imageOffset":1451884,"symbol":"-[NSWindow(NSEventRouting) _reallySendEvent:isDelayedEvent:]","symbolLocation":500,"imageIndex":173},{"imageOffset":1450920,"symbol":"-[NSWindow(NSEventRouting) sendEvent:]","symbolLocation":284,"imageIndex":173},{"imageOffset":423528,"imageIndex":69},{"imageOffset":10095308,"symbol":"-[NSApplication(NSEventRouting) sendEvent:]","symbolLocation":1852,"imageIndex":173},{"imageOffset":38456,"imageIndex":69},{"imageOffset":5929732,"symbol":"-[NSApplication _handleEvent:]","symbolLocation":60,"imageIndex":173},{"imageOffset":190620,"symbol":"-[NSApplication run]","symbolLocation":520,"imageIndex":173},{"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":25204,"symbol":"start","symbolLocation":2840,"imageIndex":174}]},{"id":2018383,"name":"ThreadPoolServiceThread","threadState":{"x":[{"value":4},{"value":0},{"value":0},{"value":105553158652288},{"value":4},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":3},{"value":239693534910978},{"value":13454334544},{"value":43779},{"value":1},{"value":1},{"value":369},{"value":6437810176},{"value":0},{"value":6388522976},{"value":6381666544},{"value":6437809488},{"value":0},{"value":12297829382473034411},{"value":1},{"value":0},{"value":0},{"value":0},{"value":0}],"flavor":"ARM_THREAD_STATE64","lr":{"value":13344095144},"cpsr":{"value":2684354560},"fp":{"value":6437809472},"sp":{"value":6437809376},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6804630780},"far":{"value":0}},"frames":[{"imageOffset":52476,"symbol":"kevent64","symbolLocation":8,"imageIndex":169},{"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":29412,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":170},{"imageOffset":8444,"symbol":"thread_start","symbolLocation":8,"imageIndex":170}]},{"id":2018384,"name":"ThreadPoolForegroundWorker","threadState":{"x":[{"value":268451845},{"value":17179869186},{"value":0},{"value":280388349984768},{"value":0},{"value":280388349984768},{"value":32},{"value":0},{"value":18446744073709550527},{"value":32},{"value":0},{"value":0},{"value":0},{"value":65283},{"value":2095104},{"value":2043},{"value":18446744073709551569},{"value":8717135552},{"value":0},{"value":0},{"value":32},{"value":280388349984768},{"value":0},{"value":280388349984768},{"value":13030681904},{"value":0},{"value":17179869186},{"value":17179869186},{"value":2}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6804657668},"cpsr":{"value":0},"fp":{"value":13030681248},"sp":{"value":13030681168},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6804582228},"far":{"value":0}},"frames":[{"imageOffset":3924,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":169},{"imageOffset":79364,"symbol":"mach_msg2_internal","symbolLocation":80,"imageIndex":169},{"imageOffset":39672,"symbol":"mach_msg_overwrite","symbolLocation":480,"imageIndex":169},{"imageOffset":4764,"symbol":"mach_msg","symbolLocation":24,"imageIndex":169},{"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":29412,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":170},{"imageOffset":8444,"symbol":"thread_start","symbolLocation":8,"imageIndex":170}]},{"id":2018385,"name":"ThreadPoolBackgroundWorker","threadState":{"x":[{"value":268451845},{"value":17179869186},{"value":0},{"value":190228396507136},{"value":0},{"value":190228396507136},{"value":32},{"value":0},{"value":18446744073709550527},{"value":32},{"value":0},{"value":0},{"value":0},{"value":44291},{"value":2095104},{"value":2043},{"value":18446744073709551569},{"value":8717135552},{"value":0},{"value":0},{"value":32},{"value":190228396507136},{"value":0},{"value":190228396507136},{"value":13039103280},{"value":0},{"value":17179869186},{"value":17179869186},{"value":2}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6804657668},"cpsr":{"value":0},"fp":{"value":13039102624},"sp":{"value":13039102544},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6804582228},"far":{"value":0}},"frames":[{"imageOffset":3924,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":169},{"imageOffset":79364,"symbol":"mach_msg2_internal","symbolLocation":80,"imageIndex":169},{"imageOffset":39672,"symbol":"mach_msg_overwrite","symbolLocation":480,"imageIndex":169},{"imageOffset":4764,"symbol":"mach_msg","symbolLocation":24,"imageIndex":169},{"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":29412,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":170},{"imageOffset":8444,"symbol":"thread_start","symbolLocation":8,"imageIndex":170}]},{"id":2018386,"name":"Chrome_IOThread","threadState":{"x":[{"value":4},{"value":0},{"value":0},{"value":105553158366400},{"value":3},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":9223372036854775809},{"value":13454334592},{"value":64003},{"value":1},{"value":1},{"value":369},{"value":13047525376},{"value":0},{"value":6388514400},{"value":4806342736},{"value":13047524672},{"value":0},{"value":12297829382473034411},{"value":1},{"value":0},{"value":0},{"value":0},{"value":0}],"flavor":"ARM_THREAD_STATE64","lr":{"value":13344095144},"cpsr":{"value":1610612736},"fp":{"value":13047524656},"sp":{"value":13047524560},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6804630780},"far":{"value":0}},"frames":[{"imageOffset":52476,"symbol":"kevent64","symbolLocation":8,"imageIndex":169},{"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":29412,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":170},{"imageOffset":8444,"symbol":"thread_start","symbolLocation":8,"imageIndex":170}]},{"id":2018387,"name":"NetworkConfigWatcher","threadState":{"x":[{"value":268451845},{"value":17179869186},{"value":0},{"value":270492745334784},{"value":0},{"value":270492745334784},{"value":32},{"value":0},{"value":18446744073709550527},{"value":32},{"value":0},{"value":0},{"value":0},{"value":62979},{"value":1},{"value":1},{"value":18446744073709551569},{"value":13055946752},{"value":0},{"value":0},{"value":32},{"value":270492745334784},{"value":0},{"value":270492745334784},{"value":13055945792},{"value":0},{"value":17179869186},{"value":17179869186},{"value":2}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6804657668},"cpsr":{"value":0},"fp":{"value":13055945136},"sp":{"value":13055945056},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6804582228},"far":{"value":0}},"frames":[{"imageOffset":3924,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":169},{"imageOffset":79364,"symbol":"mach_msg2_internal","symbolLocation":80,"imageIndex":169},{"imageOffset":39672,"symbol":"mach_msg_overwrite","symbolLocation":480,"imageIndex":169},{"imageOffset":4764,"symbol":"mach_msg","symbolLocation":24,"imageIndex":169},{"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":29412,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":170},{"imageOffset":8444,"symbol":"thread_start","symbolLocation":8,"imageIndex":170}]},{"id":2018388,"name":"ThreadPoolForegroundWorker","threadState":{"x":[{"value":268451845},{"value":17179869186},{"value":0},{"value":204539227537408},{"value":0},{"value":204539227537408},{"value":32},{"value":0},{"value":18446744073709550527},{"value":32},{"value":0},{"value":0},{"value":0},{"value":47623},{"value":2095104},{"value":2043},{"value":18446744073709551569},{"value":8717135552},{"value":0},{"value":0},{"value":32},{"value":204539227537408},{"value":0},{"value":204539227537408},{"value":13064367408},{"value":0},{"value":17179869186},{"value":17179869186},{"value":2}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6804657668},"cpsr":{"value":0},"fp":{"value":13064366752},"sp":{"value":13064366672},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6804582228},"far":{"value":0}},"frames":[{"imageOffset":3924,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":169},{"imageOffset":79364,"symbol":"mach_msg2_internal","symbolLocation":80,"imageIndex":169},{"imageOffset":39672,"symbol":"mach_msg_overwrite","symbolLocation":480,"imageIndex":169},{"imageOffset":4764,"symbol":"mach_msg","symbolLocation":24,"imageIndex":169},{"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":29412,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":170},{"imageOffset":8444,"symbol":"thread_start","symbolLocation":8,"imageIndex":170}]},{"id":2018389,"name":"ThreadPoolForegroundWorker","threadState":{"x":[{"value":268451845},{"value":17179869186},{"value":0},{"value":268293722079232},{"value":0},{"value":268293722079232},{"value":32},{"value":0},{"value":18446744073709550527},{"value":32},{"value":0},{"value":0},{"value":0},{"value":62467},{"value":2095104},{"value":2043},{"value":18446744073709551569},{"value":8717135552},{"value":0},{"value":0},{"value":32},{"value":268293722079232},{"value":0},{"value":268293722079232},{"value":13072788784},{"value":0},{"value":17179869186},{"value":17179869186},{"value":2}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6804657668},"cpsr":{"value":0},"fp":{"value":13072788128},"sp":{"value":13072788048},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6804582228},"far":{"value":0}},"frames":[{"imageOffset":3924,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":169},{"imageOffset":79364,"symbol":"mach_msg2_internal","symbolLocation":80,"imageIndex":169},{"imageOffset":39672,"symbol":"mach_msg_overwrite","symbolLocation":480,"imageIndex":169},{"imageOffset":4764,"symbol":"mach_msg","symbolLocation":24,"imageIndex":169},{"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":29412,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":170},{"imageOffset":8444,"symbol":"thread_start","symbolLocation":8,"imageIndex":170}]},{"id":2018390,"name":"Chrome_InProcGpuThread","threadState":{"x":[{"value":268451845},{"value":17179869442},{"value":0},{"value":260597140684800},{"value":0},{"value":260597140684800},{"value":32},{"value":118},{"value":18446744073709550527},{"value":32},{"value":0},{"value":0},{"value":0},{"value":60675},{"value":1},{"value":1},{"value":18446744073709551569},{"value":13081210880},{"value":0},{"value":118},{"value":32},{"value":260597140684800},{"value":0},{"value":260597140684800},{"value":13081209936},{"value":0},{"value":17179870466},{"value":17179869442},{"value":1282}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6804657668},"cpsr":{"value":0},"fp":{"value":13081209280},"sp":{"value":13081209200},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6804582228},"far":{"value":0}},"frames":[{"imageOffset":3924,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":169},{"imageOffset":79364,"symbol":"mach_msg2_internal","symbolLocation":80,"imageIndex":169},{"imageOffset":39672,"symbol":"mach_msg_overwrite","symbolLocation":480,"imageIndex":169},{"imageOffset":4764,"symbol":"mach_msg","symbolLocation":24,"imageIndex":169},{"imageOffset":71161832,"imageIndex":56},{"imageOffset":70677284,"imageIndex":56},{"imageOffset":70343392,"imageIndex":56},{"imageOffset":70809656,"imageIndex":56},{"imageOffset":70544784,"imageIndex":56},{"imageOffset":70952276,"imageIndex":56},{"imageOffset":70952656,"imageIndex":56},{"imageOffset":71057880,"imageIndex":56},{"imageOffset":29412,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":170},{"imageOffset":8444,"symbol":"thread_start","symbolLocation":8,"imageIndex":170}]},{"id":2018391,"name":"Chrome_ChildIOThread","threadState":{"x":[{"value":4},{"value":0},{"value":0},{"value":105553136264336},{"value":1},{"value":0},{"value":0},{"value":13089629920},{"value":0},{"value":0},{"value":1},{"value":288072046544386},{"value":13454334688},{"value":49411},{"value":1},{"value":1},{"value":369},{"value":13089632256},{"value":0},{"value":6388525472},{"value":6382241872},{"value":13089631552},{"value":0},{"value":12297829382473034411},{"value":1},{"value":0},{"value":0},{"value":0},{"value":0}],"flavor":"ARM_THREAD_STATE64","lr":{"value":13344095144},"cpsr":{"value":2684354560},"fp":{"value":13089631536},"sp":{"value":13089631440},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6804630780},"far":{"value":0}},"frames":[{"imageOffset":52476,"symbol":"kevent64","symbolLocation":8,"imageIndex":169},{"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":29412,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":170},{"imageOffset":8444,"symbol":"thread_start","symbolLocation":8,"imageIndex":170}]},{"id":2018392,"name":"CompositorTileWorker1","threadState":{"x":[{"value":260},{"value":0},{"value":512},{"value":0},{"value":0},{"value":161},{"value":0},{"value":0},{"value":13098053192},{"value":0},{"value":0},{"value":2},{"value":2},{"value":0},{"value":0},{"value":0},{"value":305},{"value":8717132408},{"value":0},{"value":4415664888},{"value":4415665016},{"value":13098053856},{"value":0},{"value":0},{"value":512},{"value":513},{"value":768},{"value":0},{"value":0}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6804850836},"cpsr":{"value":1610612736},"fp":{"value":13098053312},"sp":{"value":13098053168},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6804596460},"far":{"value":0}},"frames":[{"imageOffset":18156,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":169},{"imageOffset":30868,"symbol":"_pthread_cond_wait","symbolLocation":1204,"imageIndex":170},{"imageOffset":71055056,"imageIndex":56},{"imageOffset":104344336,"imageIndex":56},{"imageOffset":71057880,"imageIndex":56},{"imageOffset":29412,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":170},{"imageOffset":8444,"symbol":"thread_start","symbolLocation":8,"imageIndex":170}]},{"id":2018393,"name":"ThreadPoolSingleThreadSharedForeground0","threadState":{"x":[{"value":268451845},{"value":17179869186},{"value":0},{"value":214452012056576},{"value":0},{"value":214452012056576},{"value":32},{"value":0},{"value":18446744073709550527},{"value":32},{"value":0},{"value":0},{"value":0},{"value":49931},{"value":3854844109},{"value":3852746747},{"value":18446744073709551569},{"value":205},{"value":0},{"value":0},{"value":32},{"value":214452012056576},{"value":0},{"value":214452012056576},{"value":13106474288},{"value":0},{"value":17179869186},{"value":17179869186},{"value":2}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6804657668},"cpsr":{"value":0},"fp":{"value":13106473632},"sp":{"value":13106473552},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6804582228},"far":{"value":0}},"frames":[{"imageOffset":3924,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":169},{"imageOffset":79364,"symbol":"mach_msg2_internal","symbolLocation":80,"imageIndex":169},{"imageOffset":39672,"symbol":"mach_msg_overwrite","symbolLocation":480,"imageIndex":169},{"imageOffset":4764,"symbol":"mach_msg","symbolLocation":24,"imageIndex":169},{"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":29412,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":170},{"imageOffset":8444,"symbol":"thread_start","symbolLocation":8,"imageIndex":170}]},{"id":2018394,"name":"NetworkConfigWatcher","threadState":{"x":[{"value":268451845},{"value":17179869186},{"value":0},{"value":247403001151488},{"value":0},{"value":247403001151488},{"value":32},{"value":0},{"value":18446744073709550527},{"value":32},{"value":0},{"value":0},{"value":0},{"value":57603},{"value":1},{"value":1},{"value":18446744073709551569},{"value":13114896384},{"value":0},{"value":0},{"value":32},{"value":247403001151488},{"value":0},{"value":247403001151488},{"value":13114895424},{"value":0},{"value":17179869186},{"value":17179869186},{"value":2}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6804657668},"cpsr":{"value":0},"fp":{"value":13114894768},"sp":{"value":13114894688},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6804582228},"far":{"value":0}},"frames":[{"imageOffset":3924,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":169},{"imageOffset":79364,"symbol":"mach_msg2_internal","symbolLocation":80,"imageIndex":169},{"imageOffset":39672,"symbol":"mach_msg_overwrite","symbolLocation":480,"imageIndex":169},{"imageOffset":4764,"symbol":"mach_msg","symbolLocation":24,"imageIndex":169},{"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":29412,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":170},{"imageOffset":8444,"symbol":"thread_start","symbolLocation":8,"imageIndex":170}]},{"id":2018395,"name":"VizCompositorThread","threadState":{"x":[{"value":268451845},{"value":17179869442},{"value":0},{"value":227611791851520},{"value":0},{"value":227611791851520},{"value":32},{"value":16},{"value":18446744073709550527},{"value":32},{"value":0},{"value":0},{"value":0},{"value":52995},{"value":1},{"value":1},{"value":18446744073709551569},{"value":13123317760},{"value":0},{"value":16},{"value":32},{"value":227611791851520},{"value":0},{"value":227611791851520},{"value":13123316816},{"value":0},{"value":17179870466},{"value":17179869442},{"value":1282}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6804657668},"cpsr":{"value":0},"fp":{"value":13123316160},"sp":{"value":13123316080},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6804582228},"far":{"value":0}},"frames":[{"imageOffset":3924,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":169},{"imageOffset":79364,"symbol":"mach_msg2_internal","symbolLocation":80,"imageIndex":169},{"imageOffset":39672,"symbol":"mach_msg_overwrite","symbolLocation":480,"imageIndex":169},{"imageOffset":4764,"symbol":"mach_msg","symbolLocation":24,"imageIndex":169},{"imageOffset":71161832,"imageIndex":56},{"imageOffset":70677284,"imageIndex":56},{"imageOffset":70343392,"imageIndex":56},{"imageOffset":70809656,"imageIndex":56},{"imageOffset":70544784,"imageIndex":56},{"imageOffset":70952276,"imageIndex":56},{"imageOffset":70952656,"imageIndex":56},{"imageOffset":71057880,"imageIndex":56},{"imageOffset":29412,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":170},{"imageOffset":8444,"symbol":"thread_start","symbolLocation":8,"imageIndex":170}]},{"id":2018397,"name":"ThreadPoolForegroundWorker","threadState":{"x":[{"value":268451845},{"value":17179869186},{"value":0},{"value":228728483348480},{"value":0},{"value":228728483348480},{"value":32},{"value":0},{"value":18446744073709550527},{"value":32},{"value":0},{"value":0},{"value":0},{"value":53255},{"value":2095104},{"value":2043},{"value":18446744073709551569},{"value":8717135552},{"value":0},{"value":0},{"value":32},{"value":228728483348480},{"value":0},{"value":228728483348480},{"value":13134114096},{"value":0},{"value":17179869186},{"value":17179869186},{"value":2}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6804657668},"cpsr":{"value":0},"fp":{"value":13134113440},"sp":{"value":13134113360},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6804582228},"far":{"value":0}},"frames":[{"imageOffset":3924,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":169},{"imageOffset":79364,"symbol":"mach_msg2_internal","symbolLocation":80,"imageIndex":169},{"imageOffset":39672,"symbol":"mach_msg_overwrite","symbolLocation":480,"imageIndex":169},{"imageOffset":4764,"symbol":"mach_msg","symbolLocation":24,"imageIndex":169},{"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":29412,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":170},{"imageOffset":8444,"symbol":"thread_start","symbolLocation":8,"imageIndex":170}]},{"id":2018398,"name":"NetworkService","threadState":{"x":[{"value":4},{"value":0},{"value":0},{"value":105553176270080},{"value":2},{"value":0},{"value":0},{"value":13142533904},{"value":0},{"value":0},{"value":2},{"value":288072046544386},{"value":13454334880},{"value":54019},{"value":1},{"value":1},{"value":369},{"value":13142536192},{"value":0},{"value":6403911040},{"value":6381975040},{"value":13142535536},{"value":0},{"value":12297829382473034411},{"value":1},{"value":0},{"value":0},{"value":0},{"value":0}],"flavor":"ARM_THREAD_STATE64","lr":{"value":13344095144},"cpsr":{"value":2684354560},"fp":{"value":13142535520},"sp":{"value":13142535424},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6804630780},"far":{"value":0}},"frames":[{"imageOffset":52476,"symbol":"kevent64","symbolLocation":8,"imageIndex":169},{"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":29412,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":170},{"imageOffset":8444,"symbol":"thread_start","symbolLocation":8,"imageIndex":170}]},{"id":2018399,"name":"NetworkNotificationThreadMac","threadState":{"x":[{"value":268451845},{"value":21592279046},{"value":8589934592},{"value":235308373245952},{"value":0},{"value":235308373245952},{"value":2},{"value":4294967295},{"value":18446744073709550527},{"value":2},{"value":0},{"value":0},{"value":0},{"value":54787},{"value":12032},{"value":0},{"value":18446744073709551569},{"value":8717114872},{"value":0},{"value":4294967295},{"value":2},{"value":235308373245952},{"value":0},{"value":235308373245952},{"value":13150952920},{"value":8589934592},{"value":21592279046},{"value":21592279046},{"value":4412409862}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6804657668},"cpsr":{"value":0},"fp":{"value":13150952768},"sp":{"value":13150952688},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6804582228},"far":{"value":0}},"frames":[{"imageOffset":3924,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":169},{"imageOffset":79364,"symbol":"mach_msg2_internal","symbolLocation":80,"imageIndex":169},{"imageOffset":39672,"symbol":"mach_msg_overwrite","symbolLocation":480,"imageIndex":169},{"imageOffset":4764,"symbol":"mach_msg","symbolLocation":24,"imageIndex":169},{"imageOffset":514636,"symbol":"__CFRunLoopServiceMachPort","symbolLocation":160,"imageIndex":176},{"imageOffset":508588,"symbol":"__CFRunLoopRun","symbolLocation":1212,"imageIndex":176},{"imageOffset":505652,"symbol":"CFRunLoopRunSpecific","symbolLocation":588,"imageIndex":176},{"imageOffset":369944,"symbol":"-[NSRunLoop(NSRunLoop) runMode:beforeDate:]","symbolLocation":212,"imageIndex":177},{"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":29412,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":170},{"imageOffset":8444,"symbol":"thread_start","symbolLocation":8,"imageIndex":170}]},{"id":2018400,"name":"NetworkConfigWatcher","threadState":{"x":[{"value":268451845},{"value":17179869186},{"value":0},{"value":282587373240320},{"value":0},{"value":282587373240320},{"value":32},{"value":0},{"value":18446744073709550527},{"value":32},{"value":0},{"value":0},{"value":0},{"value":65795},{"value":1},{"value":1},{"value":18446744073709551569},{"value":13159378944},{"value":0},{"value":0},{"value":32},{"value":282587373240320},{"value":0},{"value":282587373240320},{"value":13159377984},{"value":0},{"value":17179869186},{"value":17179869186},{"value":2}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6804657668},"cpsr":{"value":0},"fp":{"value":13159377328},"sp":{"value":13159377248},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6804582228},"far":{"value":0}},"frames":[{"imageOffset":3924,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":169},{"imageOffset":79364,"symbol":"mach_msg2_internal","symbolLocation":80,"imageIndex":169},{"imageOffset":39672,"symbol":"mach_msg_overwrite","symbolLocation":480,"imageIndex":169},{"imageOffset":4764,"symbol":"mach_msg","symbolLocation":24,"imageIndex":169},{"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":29412,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":170},{"imageOffset":8444,"symbol":"thread_start","symbolLocation":8,"imageIndex":170}]},{"id":2018401,"name":"ThreadPoolSingleThreadForegroundBlocking1","threadState":{"x":[{"value":268451845},{"value":17179869186},{"value":0},{"value":363951233695744},{"value":0},{"value":363951233695744},{"value":32},{"value":0},{"value":18446744073709550527},{"value":32},{"value":0},{"value":0},{"value":0},{"value":84739},{"value":1845495850},{"value":1843396723},{"value":18446744073709551569},{"value":4986168320},{"value":0},{"value":0},{"value":32},{"value":363951233695744},{"value":0},{"value":363951233695744},{"value":13167799600},{"value":0},{"value":17179869186},{"value":17179869186},{"value":2}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6804657668},"cpsr":{"value":0},"fp":{"value":13167798944},"sp":{"value":13167798864},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6804582228},"far":{"value":0}},"frames":[{"imageOffset":3924,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":169},{"imageOffset":79364,"symbol":"mach_msg2_internal","symbolLocation":80,"imageIndex":169},{"imageOffset":39672,"symbol":"mach_msg_overwrite","symbolLocation":480,"imageIndex":169},{"imageOffset":4764,"symbol":"mach_msg","symbolLocation":24,"imageIndex":169},{"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":29412,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":170},{"imageOffset":8444,"symbol":"thread_start","symbolLocation":8,"imageIndex":170}]},{"id":2018424,"name":"NetworkConfigWatcher","threadState":{"x":[{"value":268451845},{"value":17179869186},{"value":0},{"value":307876140679168},{"value":0},{"value":307876140679168},{"value":32},{"value":0},{"value":18446744073709550527},{"value":32},{"value":0},{"value":0},{"value":0},{"value":71683},{"value":1},{"value":1},{"value":18446744073709551569},{"value":13740109824},{"value":0},{"value":0},{"value":32},{"value":307876140679168},{"value":0},{"value":307876140679168},{"value":13740108864},{"value":0},{"value":17179869186},{"value":17179869186},{"value":2}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6804657668},"cpsr":{"value":0},"fp":{"value":13740108208},"sp":{"value":13740108128},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6804582228},"far":{"value":0}},"frames":[{"imageOffset":3924,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":169},{"imageOffset":79364,"symbol":"mach_msg2_internal","symbolLocation":80,"imageIndex":169},{"imageOffset":39672,"symbol":"mach_msg_overwrite","symbolLocation":480,"imageIndex":169},{"imageOffset":4764,"symbol":"mach_msg","symbolLocation":24,"imageIndex":169},{"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":29412,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":170},{"imageOffset":8444,"symbol":"thread_start","symbolLocation":8,"imageIndex":170}]},{"id":2018429,"name":"ThreadPoolBackgroundWorker","threadState":{"x":[{"value":268451845},{"value":17179869186},{"value":0},{"value":510203460059136},{"value":0},{"value":510203460059136},{"value":32},{"value":0},{"value":18446744073709550527},{"value":32},{"value":0},{"value":0},{"value":0},{"value":118791},{"value":2657755198},{"value":2655656016},{"value":18446744073709551569},{"value":4711109120},{"value":0},{"value":0},{"value":32},{"value":510203460059136},{"value":0},{"value":510203460059136},{"value":14062038320},{"value":0},{"value":17179869186},{"value":17179869186},{"value":2}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6804657668},"cpsr":{"value":0},"fp":{"value":14062037664},"sp":{"value":14062037584},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6804582228},"far":{"value":0}},"frames":[{"imageOffset":3924,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":169},{"imageOffset":79364,"symbol":"mach_msg2_internal","symbolLocation":80,"imageIndex":169},{"imageOffset":39672,"symbol":"mach_msg_overwrite","symbolLocation":480,"imageIndex":169},{"imageOffset":4764,"symbol":"mach_msg","symbolLocation":24,"imageIndex":169},{"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":29412,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":170},{"imageOffset":8444,"symbol":"thread_start","symbolLocation":8,"imageIndex":170}]},{"id":2018476,"name":"com.apple.NSEventThread","threadState":{"x":[{"value":268451845},{"value":21592279046},{"value":8589934592},{"value":423324861595648},{"value":0},{"value":423324861595648},{"value":2},{"value":4294967295},{"value":18446744073709550527},{"value":2},{"value":0},{"value":0},{"value":0},{"value":98563},{"value":512},{"value":0},{"value":18446744073709551569},{"value":8717114872},{"value":0},{"value":4294967295},{"value":2},{"value":423324861595648},{"value":0},{"value":423324861595648},{"value":13895245928},{"value":8589934592},{"value":21592279046},{"value":21592279046},{"value":4412409862}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6804657668},"cpsr":{"value":0},"fp":{"value":13895245776},"sp":{"value":13895245696},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6804582228},"far":{"value":0}},"frames":[{"imageOffset":3924,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":169},{"imageOffset":79364,"symbol":"mach_msg2_internal","symbolLocation":80,"imageIndex":169},{"imageOffset":39672,"symbol":"mach_msg_overwrite","symbolLocation":480,"imageIndex":169},{"imageOffset":4764,"symbol":"mach_msg","symbolLocation":24,"imageIndex":169},{"imageOffset":514636,"symbol":"__CFRunLoopServiceMachPort","symbolLocation":160,"imageIndex":176},{"imageOffset":508588,"symbol":"__CFRunLoopRun","symbolLocation":1212,"imageIndex":176},{"imageOffset":505652,"symbol":"CFRunLoopRunSpecific","symbolLocation":588,"imageIndex":176},{"imageOffset":1442424,"symbol":"_NSEventThread","symbolLocation":148,"imageIndex":173},{"imageOffset":29412,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":170},{"imageOffset":8444,"symbol":"thread_start","symbolLocation":8,"imageIndex":170}]},{"id":2018477,"name":"MemoryInfra","threadState":{"x":[{"value":268451845},{"value":17179869186},{"value":0},{"value":475001908101120},{"value":0},{"value":475001908101120},{"value":32},{"value":0},{"value":18446744073709550527},{"value":32},{"value":0},{"value":0},{"value":0},{"value":110595},{"value":1},{"value":1},{"value":18446744073709551569},{"value":13903720448},{"value":0},{"value":0},{"value":32},{"value":475001908101120},{"value":0},{"value":475001908101120},{"value":13903719488},{"value":0},{"value":17179869186},{"value":17179869186},{"value":2}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6804657668},"cpsr":{"value":0},"fp":{"value":13903718832},"sp":{"value":13903718752},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6804582228},"far":{"value":0}},"frames":[{"imageOffset":3924,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":169},{"imageOffset":79364,"symbol":"mach_msg2_internal","symbolLocation":80,"imageIndex":169},{"imageOffset":39672,"symbol":"mach_msg_overwrite","symbolLocation":480,"imageIndex":169},{"imageOffset":4764,"symbol":"mach_msg","symbolLocation":24,"imageIndex":169},{"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":29412,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":170},{"imageOffset":8444,"symbol":"thread_start","symbolLocation":8,"imageIndex":170}]},{"id":2018478,"name":"ThreadPoolSingleThreadSharedBackgroundBlocking2","threadState":{"x":[{"value":268451845},{"value":17179869186},{"value":0},{"value":480499466240000},{"value":0},{"value":480499466240000},{"value":32},{"value":0},{"value":18446744073709550527},{"value":32},{"value":0},{"value":0},{"value":0},{"value":111875},{"value":2699690062},{"value":2697590870},{"value":18446744073709551569},{"value":78},{"value":0},{"value":0},{"value":32},{"value":480499466240000},{"value":0},{"value":480499466240000},{"value":13912141104},{"value":0},{"value":17179869186},{"value":17179869186},{"value":2}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6804657668},"cpsr":{"value":0},"fp":{"value":13912140448},"sp":{"value":13912140368},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6804582228},"far":{"value":0}},"frames":[{"imageOffset":3924,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":169},{"imageOffset":79364,"symbol":"mach_msg2_internal","symbolLocation":80,"imageIndex":169},{"imageOffset":39672,"symbol":"mach_msg_overwrite","symbolLocation":480,"imageIndex":169},{"imageOffset":4764,"symbol":"mach_msg","symbolLocation":24,"imageIndex":169},{"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":29412,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":170},{"imageOffset":8444,"symbol":"thread_start","symbolLocation":8,"imageIndex":170}]},{"id":2018481,"name":"ThreadPoolForegroundWorker","threadState":{"x":[{"value":268451845},{"value":17179869186},{"value":0},{"value":206875689746432},{"value":0},{"value":206875689746432},{"value":32},{"value":0},{"value":18446744073709550527},{"value":32},{"value":0},{"value":0},{"value":0},{"value":48167},{"value":3139573823},{"value":3137474625},{"value":18446744073709551569},{"value":6157273088},{"value":0},{"value":0},{"value":32},{"value":206875689746432},{"value":0},{"value":206875689746432},{"value":15321345328},{"value":0},{"value":17179869186},{"value":17179869186},{"value":2}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6804657668},"cpsr":{"value":0},"fp":{"value":15321344672},"sp":{"value":15321344592},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6804582228},"far":{"value":0}},"frames":[{"imageOffset":3924,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":169},{"imageOffset":79364,"symbol":"mach_msg2_internal","symbolLocation":80,"imageIndex":169},{"imageOffset":39672,"symbol":"mach_msg_overwrite","symbolLocation":480,"imageIndex":169},{"imageOffset":4764,"symbol":"mach_msg","symbolLocation":24,"imageIndex":169},{"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":29412,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":170},{"imageOffset":8444,"symbol":"thread_start","symbolLocation":8,"imageIndex":170}]},{"id":2606593,"frames":[{"imageOffset":18156,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":169},{"imageOffset":30868,"symbol":"_pthread_cond_wait","symbolLocation":1204,"imageIndex":170},{"imageOffset":1502040,"symbol":"blas_thread_server","symbolLocation":360,"imageIndex":19},{"imageOffset":29412,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":170},{"imageOffset":8444,"symbol":"thread_start","symbolLocation":8,"imageIndex":170}],"threadState":{"x":[{"value":260},{"value":0},{"value":39168},{"value":0},{"value":0},{"value":160},{"value":0},{"value":0},{"value":6098235080},{"value":0},{"value":0},{"value":2},{"value":2},{"value":0},{"value":0},{"value":0},{"value":305},{"value":8717132408},{"value":0},{"value":4828504080,"symbolLocation":16,"symbol":"thread_status"},{"value":4828504144,"symbolLocation":80,"symbol":"thread_status"},{"value":6098235616},{"value":0},{"value":0},{"value":39168},{"value":39169},{"value":39424},{"value":4828418048,"symbolLocation":16,"symbol":"gemm_driver.level3_lock"},{"value":1}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6804850836},"cpsr":{"value":1610612736},"fp":{"value":6098235200},"sp":{"value":6098235056},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6804596460},"far":{"value":0}}},{"id":2606594,"frames":[{"imageOffset":18156,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":169},{"imageOffset":30868,"symbol":"_pthread_cond_wait","symbolLocation":1204,"imageIndex":170},{"imageOffset":1502040,"symbol":"blas_thread_server","symbolLocation":360,"imageIndex":19},{"imageOffset":29412,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":170},{"imageOffset":8444,"symbol":"thread_start","symbolLocation":8,"imageIndex":170}],"threadState":{"x":[{"value":260},{"value":0},{"value":39168},{"value":0},{"value":0},{"value":160},{"value":0},{"value":0},{"value":6098808520},{"value":0},{"value":0},{"value":2},{"value":2},{"value":0},{"value":0},{"value":0},{"value":305},{"value":8717132408},{"value":0},{"value":4828504208,"symbolLocation":144,"symbol":"thread_status"},{"value":4828504272,"symbolLocation":208,"symbol":"thread_status"},{"value":6098809056},{"value":0},{"value":0},{"value":39168},{"value":39169},{"value":39424},{"value":4828418048,"symbolLocation":16,"symbol":"gemm_driver.level3_lock"},{"value":1}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6804850836},"cpsr":{"value":1610612736},"fp":{"value":6098808640},"sp":{"value":6098808496},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6804596460},"far":{"value":0}}},{"id":2606595,"frames":[{"imageOffset":18156,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":169},{"imageOffset":30868,"symbol":"_pthread_cond_wait","symbolLocation":1204,"imageIndex":170},{"imageOffset":1502040,"symbol":"blas_thread_server","symbolLocation":360,"imageIndex":19},{"imageOffset":29412,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":170},{"imageOffset":8444,"symbol":"thread_start","symbolLocation":8,"imageIndex":170}],"threadState":{"x":[{"value":260},{"value":0},{"value":0},{"value":0},{"value":0},{"value":160},{"value":0},{"value":0},{"value":6100365000},{"value":0},{"value":0},{"value":2},{"value":2},{"value":0},{"value":0},{"value":0},{"value":305},{"value":8717132408},{"value":0},{"value":4828504336,"symbolLocation":272,"symbol":"thread_status"},{"value":4828504400,"symbolLocation":336,"symbol":"thread_status"},{"value":6100365536},{"value":0},{"value":0},{"value":0},{"value":1},{"value":256},{"value":4828418048,"symbolLocation":16,"symbol":"gemm_driver.level3_lock"},{"value":1}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6804850836},"cpsr":{"value":1610612736},"fp":{"value":6100365120},"sp":{"value":6100364976},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6804596460},"far":{"value":0}}},{"id":2606596,"frames":[{"imageOffset":18156,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":169},{"imageOffset":30868,"symbol":"_pthread_cond_wait","symbolLocation":1204,"imageIndex":170},{"imageOffset":1502040,"symbol":"blas_thread_server","symbolLocation":360,"imageIndex":19},{"imageOffset":29412,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":170},{"imageOffset":8444,"symbol":"thread_start","symbolLocation":8,"imageIndex":170}],"threadState":{"x":[{"value":260},{"value":0},{"value":0},{"value":0},{"value":0},{"value":160},{"value":0},{"value":0},{"value":13229125320},{"value":0},{"value":0},{"value":2},{"value":2},{"value":0},{"value":0},{"value":0},{"value":305},{"value":8717132408},{"value":0},{"value":4828504464,"symbolLocation":400,"symbol":"thread_status"},{"value":4828504528,"symbolLocation":464,"symbol":"thread_status"},{"value":13229125856},{"value":0},{"value":0},{"value":0},{"value":1},{"value":256},{"value":4828418048,"symbolLocation":16,"symbol":"gemm_driver.level3_lock"},{"value":1}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6804850836},"cpsr":{"value":1610612736},"fp":{"value":13229125440},"sp":{"value":13229125296},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6804596460},"far":{"value":0}}},{"id":2606597,"frames":[{"imageOffset":18156,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":169},{"imageOffset":30868,"symbol":"_pthread_cond_wait","symbolLocation":1204,"imageIndex":170},{"imageOffset":1502040,"symbol":"blas_thread_server","symbolLocation":360,"imageIndex":19},{"imageOffset":29412,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":170},{"imageOffset":8444,"symbol":"thread_start","symbolLocation":8,"imageIndex":170}],"threadState":{"x":[{"value":260},{"value":0},{"value":0},{"value":0},{"value":0},{"value":160},{"value":0},{"value":0},{"value":13230370504},{"value":0},{"value":0},{"value":2},{"value":2},{"value":0},{"value":0},{"value":0},{"value":305},{"value":8717132408},{"value":0},{"value":4828504592,"symbolLocation":528,"symbol":"thread_status"},{"value":4828504656,"symbolLocation":592,"symbol":"thread_status"},{"value":13230371040},{"value":0},{"value":0},{"value":0},{"value":1},{"value":256},{"value":4828418048,"symbolLocation":16,"symbol":"gemm_driver.level3_lock"},{"value":1}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6804850836},"cpsr":{"value":1610612736},"fp":{"value":13230370624},"sp":{"value":13230370480},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6804596460},"far":{"value":0}}},{"id":2606598,"frames":[{"imageOffset":18156,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":169},{"imageOffset":30868,"symbol":"_pthread_cond_wait","symbolLocation":1204,"imageIndex":170},{"imageOffset":1502040,"symbol":"blas_thread_server","symbolLocation":360,"imageIndex":19},{"imageOffset":29412,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":170},{"imageOffset":8444,"symbol":"thread_start","symbolLocation":8,"imageIndex":170}],"threadState":{"x":[{"value":260},{"value":0},{"value":0},{"value":0},{"value":0},{"value":160},{"value":0},{"value":0},{"value":13234613960},{"value":0},{"value":0},{"value":2},{"value":2},{"value":0},{"value":0},{"value":0},{"value":305},{"value":8717132408},{"value":0},{"value":4828504720,"symbolLocation":656,"symbol":"thread_status"},{"value":4828504784,"symbolLocation":720,"symbol":"thread_status"},{"value":13234614496},{"value":0},{"value":0},{"value":0},{"value":1},{"value":256},{"value":4828418048,"symbolLocation":16,"symbol":"gemm_driver.level3_lock"},{"value":1}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6804850836},"cpsr":{"value":1610612736},"fp":{"value":13234614080},"sp":{"value":13234613936},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6804596460},"far":{"value":0}}},{"id":2606599,"frames":[{"imageOffset":18156,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":169},{"imageOffset":30868,"symbol":"_pthread_cond_wait","symbolLocation":1204,"imageIndex":170},{"imageOffset":1502040,"symbol":"blas_thread_server","symbolLocation":360,"imageIndex":19},{"imageOffset":29412,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":170},{"imageOffset":8444,"symbol":"thread_start","symbolLocation":8,"imageIndex":170}],"threadState":{"x":[{"value":260},{"value":0},{"value":0},{"value":0},{"value":0},{"value":160},{"value":0},{"value":0},{"value":13235744456},{"value":0},{"value":0},{"value":2},{"value":2},{"value":0},{"value":0},{"value":0},{"value":305},{"value":8717132408},{"value":0},{"value":4828504848,"symbolLocation":784,"symbol":"thread_status"},{"value":4828504912,"symbolLocation":848,"symbol":"thread_status"},{"value":13235744992},{"value":0},{"value":0},{"value":0},{"value":1},{"value":256},{"value":4828418048,"symbolLocation":16,"symbol":"gemm_driver.level3_lock"},{"value":1}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6804850836},"cpsr":{"value":1610612736},"fp":{"value":13235744576},"sp":{"value":13235744432},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6804596460},"far":{"value":0}}},{"id":2606600,"frames":[{"imageOffset":18156,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":169},{"imageOffset":30868,"symbol":"_pthread_cond_wait","symbolLocation":1204,"imageIndex":170},{"imageOffset":1502040,"symbol":"blas_thread_server","symbolLocation":360,"imageIndex":19},{"imageOffset":29412,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":170},{"imageOffset":8444,"symbol":"thread_start","symbolLocation":8,"imageIndex":170}],"threadState":{"x":[{"value":260},{"value":0},{"value":0},{"value":0},{"value":0},{"value":160},{"value":0},{"value":0},{"value":13237661384},{"value":0},{"value":0},{"value":2},{"value":2},{"value":0},{"value":0},{"value":0},{"value":305},{"value":8717132408},{"value":0},{"value":4828504976,"symbolLocation":912,"symbol":"thread_status"},{"value":4828505040,"symbolLocation":976,"symbol":"thread_status"},{"value":13237661920},{"value":0},{"value":0},{"value":0},{"value":1},{"value":256},{"value":4828418048,"symbolLocation":16,"symbol":"gemm_driver.level3_lock"},{"value":1}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6804850836},"cpsr":{"value":1610612736},"fp":{"value":13237661504},"sp":{"value":13237661360},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6804596460},"far":{"value":0}}},{"id":2606601,"frames":[{"imageOffset":18156,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":169},{"imageOffset":30868,"symbol":"_pthread_cond_wait","symbolLocation":1204,"imageIndex":170},{"imageOffset":1502040,"symbol":"blas_thread_server","symbolLocation":360,"imageIndex":19},{"imageOffset":29412,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":170},{"imageOffset":8444,"symbol":"thread_start","symbolLocation":8,"imageIndex":170}],"threadState":{"x":[{"value":260},{"value":0},{"value":0},{"value":0},{"value":0},{"value":160},{"value":0},{"value":0},{"value":13460549320},{"value":0},{"value":0},{"value":2},{"value":2},{"value":0},{"value":0},{"value":0},{"value":305},{"value":8717132408},{"value":0},{"value":4828505104,"symbolLocation":1040,"symbol":"thread_status"},{"value":4828505168,"symbolLocation":1104,"symbol":"thread_status"},{"value":13460549856},{"value":0},{"value":0},{"value":0},{"value":1},{"value":256},{"value":4828418048,"symbolLocation":16,"symbol":"gemm_driver.level3_lock"},{"value":1}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6804850836},"cpsr":{"value":1610612736},"fp":{"value":13460549440},"sp":{"value":13460549296},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6804596460},"far":{"value":0}}},{"id":2606602,"frames":[{"imageOffset":18156,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":169},{"imageOffset":30868,"symbol":"_pthread_cond_wait","symbolLocation":1204,"imageIndex":170},{"imageOffset":1502040,"symbol":"blas_thread_server","symbolLocation":360,"imageIndex":19},{"imageOffset":29412,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":170},{"imageOffset":8444,"symbol":"thread_start","symbolLocation":8,"imageIndex":170}],"threadState":{"x":[{"value":260},{"value":0},{"value":0},{"value":0},{"value":0},{"value":160},{"value":0},{"value":0},{"value":13461122760},{"value":0},{"value":0},{"value":2},{"value":2},{"value":0},{"value":0},{"value":0},{"value":305},{"value":8717132408},{"value":0},{"value":4828505232,"symbolLocation":1168,"symbol":"thread_status"},{"value":4828505296,"symbolLocation":1232,"symbol":"thread_status"},{"value":13461123296},{"value":0},{"value":0},{"value":0},{"value":1},{"value":256},{"value":4828418048,"symbolLocation":16,"symbol":"gemm_driver.level3_lock"},{"value":1}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6804850836},"cpsr":{"value":1610612736},"fp":{"value":13461122880},"sp":{"value":13461122736},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6804596460},"far":{"value":0}}},{"id":2606603,"frames":[{"imageOffset":18156,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":169},{"imageOffset":30868,"symbol":"_pthread_cond_wait","symbolLocation":1204,"imageIndex":170},{"imageOffset":1502040,"symbol":"blas_thread_server","symbolLocation":360,"imageIndex":19},{"imageOffset":29412,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":170},{"imageOffset":8444,"symbol":"thread_start","symbolLocation":8,"imageIndex":170}],"threadState":{"x":[{"value":260},{"value":0},{"value":0},{"value":0},{"value":0},{"value":160},{"value":0},{"value":0},{"value":13466283720},{"value":0},{"value":0},{"value":2},{"value":2},{"value":0},{"value":0},{"value":0},{"value":305},{"value":8717132408},{"value":0},{"value":4828505360,"symbolLocation":1296,"symbol":"thread_status"},{"value":4828505424,"symbolLocation":1360,"symbol":"thread_status"},{"value":13466284256},{"value":0},{"value":0},{"value":0},{"value":1},{"value":256},{"value":4828418048,"symbolLocation":16,"symbol":"gemm_driver.level3_lock"},{"value":1}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6804850836},"cpsr":{"value":1610612736},"fp":{"value":13466283840},"sp":{"value":13466283696},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6804596460},"far":{"value":0}}},{"id":2606604,"frames":[{"imageOffset":18156,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":169},{"imageOffset":30868,"symbol":"_pthread_cond_wait","symbolLocation":1204,"imageIndex":170},{"imageOffset":1502040,"symbol":"blas_thread_server","symbolLocation":360,"imageIndex":19},{"imageOffset":29412,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":170},{"imageOffset":8444,"symbol":"thread_start","symbolLocation":8,"imageIndex":170}],"threadState":{"x":[{"value":260},{"value":0},{"value":0},{"value":0},{"value":0},{"value":160},{"value":0},{"value":0},{"value":13466857160},{"value":0},{"value":0},{"value":2},{"value":2},{"value":0},{"value":0},{"value":0},{"value":305},{"value":8717132408},{"value":0},{"value":4828505488,"symbolLocation":1424,"symbol":"thread_status"},{"value":4828505552,"symbolLocation":1488,"symbol":"thread_status"},{"value":13466857696},{"value":0},{"value":0},{"value":0},{"value":1},{"value":256},{"value":4828418048,"symbolLocation":16,"symbol":"gemm_driver.level3_lock"},{"value":1}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6804850836},"cpsr":{"value":1610612736},"fp":{"value":13466857280},"sp":{"value":13466857136},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6804596460},"far":{"value":0}}},{"id":2606605,"frames":[{"imageOffset":18156,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":169},{"imageOffset":30868,"symbol":"_pthread_cond_wait","symbolLocation":1204,"imageIndex":170},{"imageOffset":1502040,"symbol":"blas_thread_server","symbolLocation":360,"imageIndex":19},{"imageOffset":29412,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":170},{"imageOffset":8444,"symbol":"thread_start","symbolLocation":8,"imageIndex":170}],"threadState":{"x":[{"value":260},{"value":0},{"value":0},{"value":0},{"value":0},{"value":160},{"value":0},{"value":0},{"value":13540241096},{"value":0},{"value":0},{"value":2},{"value":2},{"value":0},{"value":0},{"value":0},{"value":305},{"value":8717132408},{"value":0},{"value":4828505616,"symbolLocation":1552,"symbol":"thread_status"},{"value":4828505680,"symbolLocation":1616,"symbol":"thread_status"},{"value":13540241632},{"value":0},{"value":0},{"value":0},{"value":1},{"value":256},{"value":4828418048,"symbolLocation":16,"symbol":"gemm_driver.level3_lock"},{"value":1}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6804850836},"cpsr":{"value":1610612736},"fp":{"value":13540241216},"sp":{"value":13540241072},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6804596460},"far":{"value":0}}},{"id":2783045,"frames":[{"imageOffset":8424,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":170}],"threadState":{"x":[{"value":13577515008},{"value":175487},{"value":13576978432},{"value":0},{"value":409604},{"value":18446744073709551615},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0}],"flavor":"ARM_THREAD_STATE64","lr":{"value":0},"cpsr":{"value":0},"fp":{"value":0},"sp":{"value":13577515008},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6804828392},"far":{"value":0}}},{"id":2785313,"frames":[{"imageOffset":8424,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":170}],"threadState":{"x":[{"value":13564030976},{"value":210831},{"value":13563494400},{"value":0},{"value":409604},{"value":18446744073709551615},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0}],"flavor":"ARM_THREAD_STATE64","lr":{"value":0},"cpsr":{"value":0},"fp":{"value":0},"sp":{"value":13564030976},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6804828392},"far":{"value":0}}},{"id":2787642,"frames":[{"imageOffset":8424,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":170}],"threadState":{"x":[{"value":6099742720},{"value":191635},{"value":6099206144},{"value":0},{"value":409604},{"value":18446744073709551615},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0}],"flavor":"ARM_THREAD_STATE64","lr":{"value":0},"cpsr":{"value":0},"fp":{"value":0},"sp":{"value":6099742720},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6804828392},"far":{"value":0}}},{"id":2787644,"frames":[{"imageOffset":8424,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":170}],"threadState":{"x":[{"value":13240594432},{"value":204591},{"value":13240057856},{"value":0},{"value":409604},{"value":18446744073709551615},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0}],"flavor":"ARM_THREAD_STATE64","lr":{"value":0},"cpsr":{"value":0},"fp":{"value":0},"sp":{"value":13240594432},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6804828392},"far":{"value":0}}},{"id":2787645,"frames":[{"imageOffset":8424,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":170}],"threadState":{"x":[{"value":13543534592},{"value":186959},{"value":13542998016},{"value":0},{"value":409604},{"value":18446744073709551615},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0}],"flavor":"ARM_THREAD_STATE64","lr":{"value":0},"cpsr":{"value":0},"fp":{"value":0},"sp":{"value":13543534592},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6804828392},"far":{"value":0}}},{"id":2787993,"frames":[{"imageOffset":18156,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":169},{"imageOffset":30868,"symbol":"_pthread_cond_wait","symbolLocation":1204,"imageIndex":170},{"imageOffset":2309180,"symbol":"PyThread_acquire_lock_timed","symbolLocation":336,"imageIndex":1},{"imageOffset":2844860,"symbol":"acquire_timed","symbolLocation":308,"imageIndex":1},{"imageOffset":2845440,"symbol":"lock_PyThread_acquire_lock","symbolLocation":56,"imageIndex":1},{"imageOffset":664632,"symbol":"method_vectorcall_VARARGS_KEYWORDS","symbolLocation":148,"imageIndex":1},{"imageOffset":1788292,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":54032,"imageIndex":1},{"imageOffset":1811404,"symbol":"_PyEval_Vector","symbolLocation":156,"imageIndex":1},{"imageOffset":611492,"symbol":"method_vectorcall","symbolLocation":388,"imageIndex":1},{"imageOffset":2848544,"symbol":"thread_run","symbolLocation":200,"imageIndex":1},{"imageOffset":2308224,"symbol":"pythread_wrapper","symbolLocation":48,"imageIndex":1},{"imageOffset":29412,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":170},{"imageOffset":8444,"symbol":"thread_start","symbolLocation":8,"imageIndex":170}],"threadState":{"x":[{"value":260},{"value":0},{"value":0},{"value":0},{"value":0},{"value":160},{"value":15},{"value":0},{"value":14700178200},{"value":0},{"value":0},{"value":2},{"value":2},{"value":0},{"value":0},{"value":0},{"value":305},{"value":8717132408},{"value":0},{"value":105700740579896},{"value":105700740579848},{"value":14700179680},{"value":0},{"value":15},{"value":0},{"value":1},{"value":256},{"value":2361183241434822607},{"value":18428297329650842065}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6804850836},"cpsr":{"value":1610612736},"fp":{"value":14700178320},"sp":{"value":14700178176},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6804596460},"far":{"value":0}}},{"id":2788014,"name":"Thread (pooled)","threadState":{"x":[{"value":260},{"value":0},{"value":64256},{"value":0},{"value":0},{"value":160},{"value":29},{"value":999999000},{"value":13237087624},{"value":0},{"value":0},{"value":2},{"value":2},{"value":0},{"value":0},{"value":0},{"value":305},{"value":8717132408},{"value":0},{"value":105601286076288},{"value":105601286076352},{"value":13237088480},{"value":999999000},{"value":29},{"value":64256},{"value":64257},{"value":64512},{"value":18446744072709551616},{"value":105601219120560}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6804850836},"cpsr":{"value":1610612736},"fp":{"value":13237087744},"sp":{"value":13237087600},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6804596460},"far":{"value":0}},"frames":[{"imageOffset":18156,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":169},{"imageOffset":30868,"symbol":"_pthread_cond_wait","symbolLocation":1204,"imageIndex":170},{"imageOffset":2118156,"imageIndex":45},{"imageOffset":2117824,"symbol":"QWaitCondition::wait(QMutex*, QDeadlineTimer)","symbolLocation":108,"imageIndex":45},{"imageOffset":2094896,"imageIndex":45},{"imageOffset":2063036,"imageIndex":45},{"imageOffset":29412,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":170},{"imageOffset":8444,"symbol":"thread_start","symbolLocation":8,"imageIndex":170}]},{"id":2788015,"name":"Thread (pooled)","threadState":{"x":[{"value":260},{"value":0},{"value":60672},{"value":0},{"value":0},{"value":160},{"value":29},{"value":999996000},{"value":13601992072},{"value":0},{"value":0},{"value":2},{"value":2},{"value":0},{"value":0},{"value":0},{"value":305},{"value":8717132408},{"value":0},{"value":105601286075904},{"value":105601286075968},{"value":13601992928},{"value":999996000},{"value":29},{"value":60672},{"value":60673},{"value":60928},{"value":18446744072709551616},{"value":105601219120584}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6804850836},"cpsr":{"value":1610612736},"fp":{"value":13601992192},"sp":{"value":13601992048},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6804596460},"far":{"value":0}},"frames":[{"imageOffset":18156,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":169},{"imageOffset":30868,"symbol":"_pthread_cond_wait","symbolLocation":1204,"imageIndex":170},{"imageOffset":2118156,"imageIndex":45},{"imageOffset":2117824,"symbol":"QWaitCondition::wait(QMutex*, QDeadlineTimer)","symbolLocation":108,"imageIndex":45},{"imageOffset":2094896,"imageIndex":45},{"imageOffset":2063036,"imageIndex":45},{"imageOffset":29412,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":170},{"imageOffset":8444,"symbol":"thread_start","symbolLocation":8,"imageIndex":170}]},{"id":2788016,"name":"Thread (pooled)","threadState":{"x":[{"value":260},{"value":0},{"value":127232},{"value":0},{"value":0},{"value":160},{"value":29},{"value":999999000},{"value":13697527176},{"value":0},{"value":0},{"value":2},{"value":2},{"value":0},{"value":0},{"value":0},{"value":305},{"value":8717132408},{"value":0},{"value":105553170775040},{"value":105553170775104},{"value":13697528032},{"value":999999000},{"value":29},{"value":127232},{"value":127233},{"value":127488},{"value":18446744072709551616},{"value":4383638640}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6804850836},"cpsr":{"value":1610612736},"fp":{"value":13697527296},"sp":{"value":13697527152},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6804596460},"far":{"value":0}},"frames":[{"imageOffset":18156,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":169},{"imageOffset":30868,"symbol":"_pthread_cond_wait","symbolLocation":1204,"imageIndex":170},{"imageOffset":2118156,"imageIndex":45},{"imageOffset":2117824,"symbol":"QWaitCondition::wait(QMutex*, QDeadlineTimer)","symbolLocation":108,"imageIndex":45},{"imageOffset":2094896,"imageIndex":45},{"imageOffset":2063036,"imageIndex":45},{"imageOffset":29412,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":170},{"imageOffset":8444,"symbol":"thread_start","symbolLocation":8,"imageIndex":170}]},{"id":2788017,"name":"Thread (pooled)","threadState":{"x":[{"value":260},{"value":0},{"value":125184},{"value":0},{"value":0},{"value":160},{"value":29},{"value":999999000},{"value":13701606792},{"value":0},{"value":0},{"value":2},{"value":2},{"value":0},{"value":0},{"value":0},{"value":305},{"value":8717132408},{"value":0},{"value":105553170775808},{"value":105553170775872},{"value":13701607648},{"value":999999000},{"value":29},{"value":125184},{"value":125185},{"value":125440},{"value":18446744072709551616},{"value":4383638640}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6804850836},"cpsr":{"value":1610612736},"fp":{"value":13701606912},"sp":{"value":13701606768},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6804596460},"far":{"value":0}},"frames":[{"imageOffset":18156,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":169},{"imageOffset":30868,"symbol":"_pthread_cond_wait","symbolLocation":1204,"imageIndex":170},{"imageOffset":2118156,"imageIndex":45},{"imageOffset":2117824,"symbol":"QWaitCondition::wait(QMutex*, QDeadlineTimer)","symbolLocation":108,"imageIndex":45},{"imageOffset":2094896,"imageIndex":45},{"imageOffset":2063036,"imageIndex":45},{"imageOffset":29412,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":170},{"imageOffset":8444,"symbol":"thread_start","symbolLocation":8,"imageIndex":170}]},{"id":2788045,"frames":[{"imageOffset":8424,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":170}],"threadState":{"x":[{"value":13726691328},{"value":0},{"value":13726154752},{"value":0},{"value":278532},{"value":18446744073709551615},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0}],"flavor":"ARM_THREAD_STATE64","lr":{"value":0},"cpsr":{"value":0},"fp":{"value":0},"sp":{"value":13726691328},"esr":{"value":0,"description":" Address size fault"},"pc":{"value":6804828392},"far":{"value":0}}}],
"usedImages" : [
[deleted to fit within ticket limits]
],
"sharedCache" : {
"base" : 6800343040,
"size" : 4865835008,
"uuid" : "d272b91e-f9f0-3854-b5b9-508b21c25dcc"
},
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"logWritingSignature" : "bf40fcc68ad205c4596c22a625bba319fe723fcb",
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "642da32dea3b2418c750f848",
"factorPackIds" : {
"VISUAL_INTELLIGENCE_VICTORIA" : "66d8b2f77cd4b62688efd2cf"
},
"deploymentId" : 240000004
},
{
"rolloutId" : "644114de41e7236e6177f9bd",
"factorPackIds" : {
},
"deploymentId" : 240000013
}
],
"experiments" : [
]
}
}
===== Log before crash start =====
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/jojudernatz/Desktop/mMIP_Model/250225_mMIP_J325.cxs
Opened cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc as #1.1, grid size
400,400,400, pixel 1.32, shown at level 0.0332, step 1, values float32
Log from Tue Feb 25 11:58:40 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/tzviya/Documents/projects/mMIP/J325_spaca9_sh3_modeling.cxs
Opened cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc as #1.1, grid size
400,400,400, pixel 1.32, shown at level 0.0332, step 1, values float32
Log from Mon Feb 24 14:02:57 2025 Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/tzviya/Documents/projects/mMIP/J325_SPACA9_SH3.py
Failed opening file /Users/tzviya/Documents/projects/mMIP/J325_SPACA9_SH3.py:
ChimeraX cannot open a regular Chimera session. An exporter from Chimera to
ChimeraX is available in the latest Chimera release. Use its File->Export
Scene
menu item, and change the resulting dialog's "File Type" to ChimeraX.
> open /Volumes/nonshib-webdav/shared/mMIP/J325_SPACA9_SH3.py
Failed opening file /Volumes/nonshib-webdav/shared/mMIP/J325_SPACA9_SH3.py:
ChimeraX cannot open a regular Chimera session. An exporter from Chimera to
ChimeraX is available in the latest Chimera release. Use its File->Export
Scene
menu item, and change the resulting dialog's "File Type" to ChimeraX.
> cd /Users/tzviya/Documents/projects/mMIP
Current working directory is: /Users/tzviya/Documents/projects/mMIP
> open
> /Users/tzviya/Documents/projects/mMIP/maps/cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc
> /Users/tzviya/Documents/projects/mMIP/maps/J325_007_volume_map_deepem_highRes_erase0.1_crop64.mrc
Opened cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc as #1.1, grid size
400,400,400, pixel 1.32, shown at level 0.0785, step 2, values float32
Opened J325_007_volume_map_deepem_highRes_erase0.1_crop64.mrc as #1.2, grid
size 64,64,64, pixel 1.32, shown at level 0.000336, step 1, values float32
> volume #1.2 level 0.005917
> close #1.2
> volume #1.1 step 1
> open /Users/tzviya/Documents/projects/mMIP/models/spaca9_q4v8p4_fitJ325.pdb
spaca9_q4v8p4_fitJ325.pdb title:
Alphafold monomer V2.0 prediction for sperm acrosome-associated protein 9
(Q4V8P4) [more info...]
Chain information for spaca9_q4v8p4_fitJ325.pdb #2
---
Chain | Description | UniProt
A | sperm acrosome-associated protein 9 | SACA9_RAT 1-168
> volume #1.1 color #b2b2b280
> open /Users/tzviya/Documents/projects/mMIP/models/f6pus4_fitJ325.pdb
f6pus4_fitJ325.pdb title:
Alphafold monomer V2.0 prediction for SH3 domain-containing 21 (F6PUS4) [more
info...]
Chain information for f6pus4_fitJ325.pdb #3
---
Chain | Description | UniProt
A | SH3 domain-containing 21 | F6PUS4_RAT 1-544
> open
> /Users/tzviya/Documents/projects/mMIP/models/GDP_kin_MT_MancMT_A1_fitJ325.pdb
Chain information for GDP_kin_MT_MancMT_A1_fitJ325.pdb #4
---
Chain | Description
A C D J K L M P | No description available
B E F G H I N O | No description available
> open
> /Users/tzviya/Documents/projects/mMIP/models/GDP_kin_MT_MancMT_A13_fitJ325.pdb
Chain information for GDP_kin_MT_MancMT_A13_fitJ325.pdb #5
---
Chain | Description
A C D J K L M P | No description available
B E F G H I N O | No description available
> show cartoons
> hide atoms
> save /Users/tzviya/Documents/projects/mMIP/J325_spaca9_sh3.cxs
> volume #1.1 level 0.03316
> ui tool show "Show Sequence Viewer"
> sequence chain #2/A
Alignment identifier is 2/A
> ui tool show "Show Sequence Viewer"
> sequence chain #3/A
Alignment identifier is 3/A
> ui mousemode right clip
> select #3/A:69-71,91-96,104-109,112-117
181 atoms, 183 bonds, 21 residues, 1 model selected
> select #3/A:118-120
27 atoms, 27 bonds, 3 residues, 1 model selected
> select clear
> select #3/A:124
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:124-126
21 atoms, 23 bonds, 3 residues, 1 model selected
> select #2/A:110-111
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #2/A:110-114
41 atoms, 40 bonds, 5 residues, 1 model selected
> select #2/A:2-35,46-55,60-86,91-104,121-124,127-133,137-157
965 atoms, 975 bonds, 117 residues, 1 model selected
> select #2/A:58
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:58
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:57-58
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #2/A:2-35,46-55,60-86,91-104,121-124,127-133,137-157
965 atoms, 975 bonds, 117 residues, 1 model selected
> select #2/A:38
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:38-40
25 atoms, 24 bonds, 3 residues, 1 model selected
> select #2/A:2-35,46-55,60-86,91-104,121-124,127-133,137-157
965 atoms, 975 bonds, 117 residues, 1 model selected
> open 8OU0
8ou0 title:
bovine sperm endpiece singlet microtubules (one tubulin dimer and associated
microtubule inner proteins) [more info...]
Chain information for 8ou0 #6
---
Chain | Description | UniProt
A | Tubulin alpha-3 chain | TBA3_BOVIN 1-450
B | Tubulin beta-4B chain | TBB4B_BOVIN 1-455
C | Sperm acrosome associated 9 | A0A3Q1MYU9_BOVIN 1-224
D | Stabilizer of axonemal microtubules 1 | A0A3S5ZPV0_BOVIN 38-514
Non-standard residues in 8ou0 #6
---
GDP — guanosine-5'-diphosphate
GTP — guanosine-5'-triphosphate
MG — magnesium ion
> ui mousemode right rotate
> mmaker #6 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker spaca9_q4v8p4_fitJ325.pdb, chain A (#2) with 8ou0, chain C (#6),
sequence alignment score = 777.8
RMSD between 148 pruned atom pairs is 0.761 angstroms; (across all 153 pairs:
0.903)
> hide #!1 models
> hide #!6 models
> show #!6 models
> color #6 #011993ff
Drag select of 3 residues
> select up
132 atoms, 132 bonds, 18 residues, 1 model selected
> select up
3337 atoms, 3412 bonds, 426 residues, 1 model selected
> select up
3365 atoms, 3442 bonds, 427 residues, 1 model selected
> select up
8139 atoms, 8322 bonds, 1030 residues, 1 model selected
> select down
3365 atoms, 3442 bonds, 427 residues, 1 model selected
> hide sel cartoons
Drag select of 2 residues
> select up
78 atoms, 82 bonds, 9 residues, 1 model selected
> select up
3062 atoms, 3132 bonds, 391 residues, 1 model selected
> select up
3122 atoms, 3193 bonds, 399 residues, 1 model selected
> select up
3341 atoms, 3417 bonds, 428 residues, 1 model selected
> select up
3374 atoms, 3451 bonds, 430 residues, 1 model selected
> select up
8139 atoms, 8322 bonds, 1030 residues, 1 model selected
> select down
3374 atoms, 3451 bonds, 430 residues, 1 model selected
> hide sel cartoons
> select clear
[Repeated 1 time(s)]Drag select of 2 residues
> select up
164 atoms, 168 bonds, 20 residues, 1 model selected
> select up
8139 atoms, 8322 bonds, 1030 residues, 1 model selected
> select down
164 atoms, 168 bonds, 20 residues, 1 model selected
> hide sel cartoons
> show #!1 models
> hide #!1 models
> ui tool show "Show Sequence Viewer"
> sequence chain #6/C
Alignment identifier is 6/C
Drag select of 2 residues
> select up
63 atoms, 63 bonds, 8 residues, 1 model selected
> select up
1236 atoms, 1261 bonds, 153 residues, 1 model selected
> select up
8139 atoms, 8322 bonds, 1030 residues, 1 model selected
> select down
1236 atoms, 1261 bonds, 153 residues, 1 model selected
> save /Users/tzviya/Documents/projects/mMIP/models/spaca9_bovine.pdb models
> #6 selectedOnly true relModel #1
> select #2/56
Nothing selected
> select #2/C:56
Nothing selected
> select #2 /C:56
Nothing selected
> select #2/C
Nothing selected
> select #2
1363 atoms, 1389 bonds, 168 residues, 1 model selected
> select #2 /C
Nothing selected
> select #2:56
12 atoms, 12 bonds, 1 residue, 1 model selected
> hide #!6 models
> ui tool show "Show Sequence Viewer"
> sequence chain #4/A
Alignment identifier is 4/A
> select #4/A:437
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #4/A:1-437
3350 atoms, 3427 bonds, 1 pseudobond, 428 residues, 2 models selected
> save /Users/tzviya/Documents/projects/mMIP/GDP_kin_MT_MancMT_A1 format fasta
> alignment 4/A
> ui tool show "Show Sequence Viewer"
> sequence chain #4/H
Alignment identifier is 4/H
> select #4/H:1-2
16 atoms, 15 bonds, 2 residues, 1 model selected
> select #4/H:1-436
3340 atoms, 3415 bonds, 426 residues, 1 model selected
> save /Users/tzviya/Documents/projects/mMIP/MTalpha1a format fasta alignment
> 4/H
> select #4/A:153
8 atoms, 7 bonds, 1 residue, 1 model selected
Drag select of 72 residues
> select up
1072 atoms, 1083 bonds, 138 residues, 1 model selected
> select up
3340 atoms, 3415 bonds, 426 residues, 1 model selected
> select up
3368 atoms, 3445 bonds, 427 residues, 1 model selected
> select up
54008 atoms, 55248 bonds, 6856 residues, 1 model selected
> select down
3368 atoms, 3445 bonds, 427 residues, 1 model selected
Drag select of 6 residues
> select up
3518 atoms, 3594 bonds, 445 residues, 1 model selected
> select up
6439 atoms, 6587 bonds, 818 residues, 1 model selected
> select up
6503 atoms, 6652 bonds, 827 residues, 1 model selected
> select up
6718 atoms, 6872 bonds, 855 residues, 1 model selected
> select up
6751 atoms, 6906 bonds, 857 residues, 1 model selected
> select up
54008 atoms, 55248 bonds, 6856 residues, 1 model selected
> select down
6751 atoms, 6906 bonds, 857 residues, 1 model selected
> save /Users/tzviya/Documents/projects/mMIP/models/tubAB.pdb models #4-5
> selectedOnly true relModel #1.1
> open /Users/tzviya/Documents/projects/mMIP/models/tubAB.pdb
Summary of feedback from opening
/Users/tzviya/Documents/projects/mMIP/models/tubAB.pdb
---
warnings | Start residue of secondary structure not found: HELIX 21 21 GLY B 10 GLU B 27 1 18
Start residue of secondary structure not found: HELIX 22 22 ASP B 41 GLU B 47
1 5
Start residue of secondary structure not found: HELIX 23 23 ILE B 49 VAL B 51
1 3
Start residue of secondary structure not found: HELIX 24 24 PRO B 72 SER B 80
1 9
Start residue of secondary structure not found: HELIX 25 25 PRO B 89 ASN B 91
1 3
443 messages similar to the above omitted
Chain information for tubAB.pdb #7
---
Chain | Description
A | No description available
H | No description available
> select clear
> hide #!4 models
> hide #!5 models
> ui tool show "Show Sequence Viewer"
> sequence chain #7/A
Alignment identifier is 7/A
> sequence chain #7/H
Alignment identifier is 7/H
> open /Users/tzviya/Downloads/AF-P68370-F1-model_v4.pdb
AF-P68370-F1-model_v4.pdb title:
Alphafold monomer V2.0 prediction for tubulin α-1A chain (P68370) [more
info...]
Chain information for AF-P68370-F1-model_v4.pdb #8
---
Chain | Description | UniProt
A | tubulin α-1A chain | TBA1A_RAT 1-451
> mmaker #8 to #7/A
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker tubAB.pdb, chain A (#7) with AF-P68370-F1-model_v4.pdb, chain A
(#8), sequence alignment score = 2202.6
RMSD between 403 pruned atom pairs is 0.876 angstroms; (across all 428 pairs:
1.266)
> show #!1 models
> hide #!1 models
> show #!1 models
> save /Users/tzviya/Documents/projects/mMIP/J325_spaca9_sh3_modeling.cxs
——— End of log from Mon Feb 24 14:02:57 2025 ———
opened ChimeraX session
> open /Users/tzviya/Documents/projects/mMIP/models/mMIP.pdb
Chain information for mMIP.pdb #9
---
Chain | Description
A B | No description available
C | No description available
D | No description available
H I | No description available
> hide #2-3,8#!7,9 atoms
> show #2-3,8#!7,9 cartoons
> close #2
> hide #!1 models
> hide #!9 models
> show #!9 models
> hide #3 models
> show #3 models
> close #3
> hide #!7 models
> show #!7 models
> close #7
> close #8
> close #6
> close #4
> close #5
> hide #!1.1 models
> show #!1.1 models
> save /Users/tzviya/Documents/projects/mMIP/250225_mMIP_J325.cxs includeMaps
> true
——— End of log from Tue Feb 25 11:58:40 2025 ———
opened ChimeraX session
> set bgColor gray
> set bgColor white
> lighting soft
> graphics silhouettes true
> hide #!1 models
> select ::name="GTP"
64 atoms, 68 bonds, 2 residues, 1 model selected
> show sel atoms
> select ::name="GDP"
56 atoms, 60 bonds, 2 residues, 1 model selected
> show sel atoms
> combine #9
> show #!1 models
> ui mousemode right translate
> select add #9
15396 atoms, 15748 bonds, 2 pseudobonds, 1944 residues, 2 models selected
> select subtract #9
Nothing selected
> select add #2
15396 atoms, 15748 bonds, 2 pseudobonds, 1944 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models #2,1,0,0,3.9338,0,1,0,-4.6426,0,0,1,-65.158
> view matrix models #2,1,0,0,5.698,0,1,0,-2.2369,0,0,1,-80.89
> select add #3
30792 atoms, 31496 bonds, 4 pseudobonds, 3888 residues, 4 models selected
> view matrix models
> #2,1,0,0,5.0696,0,1,0,-8.1136,0,0,1,-13.182,#3,1,0,0,-0.62849,0,1,0,-5.8767,0,0,1,67.708
> undo
> select subtract #2
15396 atoms, 15748 bonds, 2 pseudobonds, 1944 residues, 2 models selected
> view matrix models #3,1,0,0,-21.284,0,1,0,2.7018,0,0,1,79.961
> view matrix models #3,1,0,0,-20.559,0,1,0,1.1889,0,0,1,83.09
> ui tool show "Fit in Map"
> fitmap #2 inMap #1.1
Fit molecule copy of mMIP.pdb (#2) to map
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) using 15396 atoms
average map value = 0.3073, steps = 84
shifted from previous position = 6.43
rotated from previous position = 0.148 degrees
atoms outside contour = 2429, contour level = 0.033162
Position of copy of mMIP.pdb (#2) relative to
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) coordinates:
Matrix rotation and translation
0.99999721 -0.00128678 -0.00198245 1.01235758
0.00128888 0.99999861 0.00105916 0.00170375
0.00198108 -0.00106172 0.99999747 -80.49863569
Axis -0.40936473 -0.76502812 0.49714434
Axis point 30476.54375940 0.00000000 -7881.90973263
Rotation angle (degrees) 0.14842204
Shift along axis -40.43516816
> fitmap #3 inMap #1.1
Fit molecule copy of mMIP.pdb (#3) to map
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) using 15396 atoms
average map value = 0.116, steps = 196
shifted from previous position = 20.4
rotated from previous position = 1.36 degrees
atoms outside contour = 7964, contour level = 0.033162
Position of copy of mMIP.pdb (#3) relative to
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) coordinates:
Matrix rotation and translation
0.99972609 -0.02313589 -0.00353325 6.98382522
0.02312368 0.99972663 -0.00345891 -6.91791981
0.00361231 0.00337626 0.99998778 82.42336252
Axis 0.14449265 -0.15105400 0.97790826
Axis point -243.27873956 -211.48115483 0.00000000
Rotation angle (degrees) 1.35530384
Shift along axis 82.65657778
> view matrix models
> #3,0.99973,-0.023136,-0.0035332,7.0028,0.023124,0.99973,-0.0034589,-7.1344,0.0036123,0.0033763,0.99999,78.472
> fitmap #3 inMap #1.1
Fit molecule copy of mMIP.pdb (#3) to map
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) using 15396 atoms
average map value = 0.2768, steps = 80
shifted from previous position = 1.28
rotated from previous position = 1.72 degrees
atoms outside contour = 2613, contour level = 0.033162
Position of copy of mMIP.pdb (#3) relative to
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) coordinates:
Matrix rotation and translation
0.99997859 0.00644474 0.00113719 -2.22031144
-0.00644424 0.99997914 -0.00044339 1.76633518
-0.00114003 0.00043606 0.99999926 80.29757244
Axis 0.06704098 0.17359332 -0.98253288
Axis point 2396.61000487 -466.58030398 0.00000000
Rotation angle (degrees) 0.37580898
Shift along axis -78.73723315
> select subtract #3
Nothing selected
> select add #4
15396 atoms, 15748 bonds, 2 pseudobonds, 1944 residues, 2 models selected
> view matrix models #4,1,0,0,-38.631,0,1,0,3.7278,0,0,1,-106.8
> view matrix models #4,1,0,0,-38.427,0,1,0,5.7775,0,0,1,-138.91
> view matrix models #4,1,0,0,-38.282,0,1,0,7.1271,0,0,1,-155.79
> view matrix models #4,1,0,0,-0.74921,0,1,0,5.7378,0,0,1,-153.85
> view matrix models #4,1,0,0,-0.066444,0,1,0,5.4112,0,0,1,-151.76
> view matrix models #4,1,0,0,-4.6042,0,1,0,4.9323,0,0,1,-164.92
> ui mousemode right translate
> ui mousemode right "translate selected models"
> view matrix models #4,1,0,0,-4.3706,0,1,0,4.6142,0,0,1,-160.4
> fitmap #4 inMap #1.1
Fit molecule copy of mMIP.pdb (#4) to map
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) using 15396 atoms
average map value = 0.1853, steps = 80
shifted from previous position = 5.58
rotated from previous position = 0.274 degrees
atoms outside contour = 3971, contour level = 0.033162
Position of copy of mMIP.pdb (#4) relative to
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) coordinates:
Matrix rotation and translation
0.99998872 -0.00398943 -0.00257922 2.09099398
0.00399068 0.99999192 0.00047929 -0.06625752
0.00257729 -0.00048958 0.99999656 -160.90385628
Axis -0.10144871 -0.53992501 0.83557713
Axis point 18224.79317796 -2950.81942119 0.00000000
Rotation angle (degrees) 0.27360012
Shift along axis -134.62393736
> select add #9
30792 atoms, 31496 bonds, 4 pseudobonds, 3888 residues, 4 models selected
> select subtract #4
15396 atoms, 15748 bonds, 2 pseudobonds, 1944 residues, 2 models selected
> select subtract #9
Nothing selected
> combine #9
> select add #5
15396 atoms, 15748 bonds, 2 pseudobonds, 1944 residues, 2 models selected
> select #5/A
3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected
> select #5/C
1363 atoms, 1391 bonds, 168 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #5/D
521 atoms, 535 bonds, 64 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select add #5
13512 atoms, 13822 bonds, 2 pseudobonds, 1712 residues, 2 models selected
> view matrix models #5,1,0,0,-38.857,0,1,0,-93.428,0,0,1,142.04
> hide #!1 models
> show #!1 models
> view matrix models
> #5,0.99426,0.10615,0.013394,-68.018,-0.10621,0.99433,0.0042454,-53.514,-0.012867,-0.0056436,0.9999,148.34
> view matrix models
> #5,0.96161,0.26505,0.07114,-113.9,-0.26439,0.96424,-0.018669,20.211,-0.073544,-0.00085621,0.99729,170.57
> ui mousemode right clip
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.84722,0.52498,0.081333,-141.06,-0.52137,0.85105,-0.062368,158.46,-0.10196,0.010435,0.99473,179.05
> view matrix models
> #5,0.69401,0.71552,0.079928,-132.38,-0.7085,0.69847,-0.10089,279.18,-0.12802,0.013391,0.99168,188.95
> view matrix models
> #5,0.69401,0.71552,0.079928,-148.18,-0.7085,0.69847,-0.10089,293.92,-0.12802,0.013391,0.99168,188.81
> view matrix models
> #5,0.62205,0.77117,0.13547,-152.2,-0.77018,0.6338,-0.071475,324.86,-0.14098,-0.059874,0.9882,213.5
> select #5/H
3374 atoms, 3451 bonds, 427 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #5/I
3374 atoms, 3451 bonds, 427 residues, 1 model selected
> select #5/B
3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected
> select #5/A
3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected
> delete atoms (#!5 & sel)
> delete bonds (#!5 & sel)
> select add #5
6756 atoms, 6911 bonds, 1 pseudobond, 856 residues, 2 models selected
> ui mousemode right translate
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.62205,0.77117,0.13547,-120.33,-0.77018,0.6338,-0.071475,324.67,-0.14098,-0.059874,0.9882,157.83
> view matrix models
> #5,0.66535,0.74535,-0.04192,-73.236,-0.74106,0.66622,0.083552,256.25,0.090204,-0.024526,0.99562,60.986
> view matrix models
> #5,0.66535,0.74535,-0.04192,-60.997,-0.74106,0.66622,0.083552,278.03,0.090204,-0.024526,0.99562,68.893
> view matrix models
> #5,0.95573,0.24827,-0.15793,-15.839,-0.23442,0.96685,0.10125,13.251,0.17784,-0.059746,0.98224,48.752
> view matrix models
> #5,0.95573,0.24827,-0.15793,-16.865,-0.23442,0.96685,0.10125,17.715,0.17784,-0.059746,0.98224,37.101
> view matrix models
> #5,0.95573,0.24827,-0.15793,-18.36,-0.23442,0.96685,0.10125,16.724,0.17784,-0.059746,0.98224,38.06
> fitmap #5 inMap #1.1
Fit molecule copy of mMIP.pdb (#5) to map
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) using 6756 atoms
average map value = 0.131, steps = 96
shifted from previous position = 5.08
rotated from previous position = 14.4 degrees
atoms outside contour = 1961, contour level = 0.033162
Position of copy of mMIP.pdb (#5) relative to
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) coordinates:
Matrix rotation and translation
0.91834743 0.39575015 0.00445134 -92.66320147
-0.39574163 0.91835794 -0.00269341 124.27123419
-0.00515384 0.00071191 0.99998647 90.56129759
Axis 0.00430204 0.01213454 -0.99991712
Axis point 257.69116462 286.34114864 0.00000000
Rotation angle (degrees) 23.31454797
Shift along axis -89.44445883
> combine #5
> select subtract #5
Nothing selected
> select add #6
6756 atoms, 6911 bonds, 1 pseudobond, 856 residues, 2 models selected
> view matrix models
> #6,0.91835,0.39575,0.0044513,-107.04,-0.39574,0.91836,-0.0026934,143.78,-0.0051538,0.00071191,0.99999,17.562
> fitmap #6 inMap #1.1
Fit molecule copy of copy of mMIP.pdb (#6) to map
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) using 6756 atoms
average map value = 0.06972, steps = 120
shifted from previous position = 21
rotated from previous position = 18 degrees
atoms outside contour = 4139, contour level = 0.033162
Position of copy of copy of mMIP.pdb (#6) relative to
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) coordinates:
Matrix rotation and translation
0.98989843 0.12239790 0.07155313 -76.09738890
-0.11440270 0.98767612 -0.10680778 43.04729272
-0.08374436 0.09754298 0.99170169 29.11932259
Axis 0.58517189 0.44470462 -0.67809414
Axis point 503.50989628 447.50309023 0.00000000
Rotation angle (degrees) 10.05581573
Shift along axis -45.13236471
> view matrix models
> #6,0.9899,0.1224,0.071553,-79.166,-0.1144,0.98768,-0.10681,44.1,-0.083744,0.097543,0.9917,17.998
> view matrix models
> #6,0.82543,0.56033,0.068499,-119.06,-0.56239,0.82675,0.014023,209.73,-0.048775,-0.050099,0.99755,37.529
> view matrix models
> #6,0.82543,0.56033,0.068499,-121.94,-0.56239,0.82675,0.014023,207.1,-0.048775,-0.050099,0.99755,39.628
> fitmap #6 inMap #1.1
Fit molecule copy of copy of mMIP.pdb (#6) to map
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) using 6756 atoms
average map value = 0.1742, steps = 80
shifted from previous position = 7
rotated from previous position = 11.9 degrees
atoms outside contour = 1538, contour level = 0.033162
Position of copy of copy of mMIP.pdb (#6) relative to
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) coordinates:
Matrix rotation and translation
0.92091360 0.38974558 0.00406478 -91.72390206
-0.38973614 0.92092189 -0.00293383 122.21373240
-0.00488679 0.00111762 0.99998744 10.35738873
Axis 0.00519721 0.01148308 -0.99992056
Axis point 255.60854812 287.08485186 0.00000000
Rotation angle (degrees) 22.94030251
Shift along axis -9.42988334
> combine #5
> select add #7
13512 atoms, 13822 bonds, 2 pseudobonds, 1712 residues, 4 models selected
> select subtract #6
6756 atoms, 6911 bonds, 1 pseudobond, 856 residues, 2 models selected
> view matrix models
> #7,0.91835,0.39575,0.0044513,-128.57,-0.39574,0.91836,-0.0026934,113.24,-0.0051538,0.00071191,0.99999,-66.615
> view matrix models
> #7,0.91835,0.39575,0.0044513,-128.66,-0.39574,0.91836,-0.0026934,110.3,-0.0051538,0.00071191,0.99999,-70.579
> view matrix models
> #7,0.91835,0.39575,0.0044513,-97.594,-0.39574,0.91836,-0.0026934,131.94,-0.0051538,0.00071191,0.99999,-76.842
> fitmap #7 inMap #1.1
Fit molecule copy of copy of mMIP.pdb (#7) to map
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) using 6756 atoms
average map value = 0.07479, steps = 112
shifted from previous position = 6.48
rotated from previous position = 14 degrees
atoms outside contour = 3994, contour level = 0.033162
Position of copy of copy of mMIP.pdb (#7) relative to
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) coordinates:
Matrix rotation and translation
0.79592567 0.60438871 0.03488002 -106.08919174
-0.60466952 0.79647069 -0.00303608 233.31119526
-0.02961589 -0.01867439 0.99938690 -64.82063147
Axis -0.01291485 0.05326375 -0.99849696
Axis point 287.71445014 271.00149999 0.00000000
Rotation angle (degrees) 37.26044669
Shift along axis 78.52035761
> ui mousemode right translate
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.79593,0.60439,0.03488,-105.63,-0.60467,0.79647,-0.0030361,233.33,-0.029616,-0.018674,0.99939,-56.277
> fitmap #7 inMap #1.1
Fit molecule copy of copy of mMIP.pdb (#7) to map
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) using 6756 atoms
average map value = 0.1795, steps = 92
shifted from previous position = 2.2
rotated from previous position = 14.7 degrees
atoms outside contour = 1459, contour level = 0.033162
Position of copy of copy of mMIP.pdb (#7) relative to
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) coordinates:
Matrix rotation and translation
0.92308918 0.38456910 0.00360195 -90.71929907
-0.38456771 0.92309613 -0.00109779 119.75381467
-0.00374712 -0.00037183 0.99999291 -69.75287743
Axis 0.00094382 0.00955452 -0.99995391
Axis point 252.33887914 286.53815501 0.00000000
Rotation angle (degrees) 22.61804896
Shift along axis 70.80822957
> combine #5,6,7
Remapping chain ID 'B' in copy of copy of mMIP.pdb #6 to 'C'
Remapping chain ID 'I' in copy of copy of mMIP.pdb #6 to 'J'
Remapping chain ID 'B' in copy of copy of mMIP.pdb #7 to 'D'
Remapping chain ID 'I' in copy of copy of mMIP.pdb #7 to 'K'
> select add #8
27024 atoms, 27644 bonds, 4 pseudobonds, 3424 residues, 4 models selected
> select subtract #7
20268 atoms, 20733 bonds, 3 pseudobonds, 2568 residues, 2 models selected
> close #8
> combine #7
> select add #8
6756 atoms, 6911 bonds, 1 pseudobond, 856 residues, 2 models selected
> view matrix models
> #8,0.92309,0.38457,0.0036019,-100.98,-0.38457,0.9231,-0.0010978,124.92,-0.0037471,-0.00037183,0.99999,-148.42
> fitmap #8 inMap #1.1
Fit molecule copy of copy of copy of mMIP.pdb (#8) to map
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) using 6756 atoms
average map value = 0.154, steps = 104
shifted from previous position = 11.7
rotated from previous position = 0.148 degrees
atoms outside contour = 1660, contour level = 0.033162
Position of copy of copy of copy of mMIP.pdb (#8) relative to
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) coordinates:
Matrix rotation and translation
0.92398309 0.38240908 0.00430702 -90.39185690
-0.38241174 0.92399200 -0.00022055 119.07355107
-0.00406399 -0.00144327 0.99999070 -149.39511898
Axis -0.00159861 0.01094440 -0.99993883
Axis point 250.31215151 285.50234805 0.00000000
Rotation angle (degrees) 22.48451962
Shift along axis 150.83366987
> combine #5,6,7,8
Remapping chain ID 'B' in copy of copy of mMIP.pdb #6 to 'C'
Remapping chain ID 'I' in copy of copy of mMIP.pdb #6 to 'J'
Remapping chain ID 'B' in copy of copy of mMIP.pdb #7 to 'D'
Remapping chain ID 'I' in copy of copy of mMIP.pdb #7 to 'K'
Remapping chain ID 'B' in copy of copy of copy of mMIP.pdb #8 to 'E'
Remapping chain ID 'I' in copy of copy of copy of mMIP.pdb #8 to 'L'
> select subtract #8
Nothing selected
> select add #10
27024 atoms, 27644 bonds, 4 pseudobonds, 3424 residues, 2 models selected
> view matrix models
> #10,0.91835,0.39575,0.0044513,-134.3,-0.39574,0.91836,-0.0026934,92.516,-0.0051538,0.00071191,0.99999,100.1
> fitmap #10 inMap #1.1
Fit molecule combination (#10) to map
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) using 27024 atoms
average map value = 0.09391, steps = 220
shifted from previous position = 5.13
rotated from previous position = 24 degrees
atoms outside contour = 10006, contour level = 0.033162
Position of combination (#10) relative to
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) coordinates:
Matrix rotation and translation
0.67734782 0.73564842 0.00461946 -126.09717895
-0.73562348 0.67736317 -0.00610098 280.45778731
-0.00761723 0.00073430 0.99997072 100.52087226
Axis 0.00464562 0.00831670 -0.99995462
Axis point 257.86060481 283.88237518 0.00000000
Rotation angle (degrees) 47.36380401
Shift along axis -98.76962602
> combine #10
> select subtract #10
Nothing selected
> select add #11
27024 atoms, 27644 bonds, 4 pseudobonds, 3424 residues, 2 models selected
> view matrix models
> #11,0.67735,0.73565,0.0046195,-175.92,-0.73562,0.67736,-0.006101,264.11,-0.0076172,0.0007343,0.99997,107.7
> view matrix models
> #11,0.67735,0.73565,0.0046195,-174.86,-0.73562,0.67736,-0.006101,267.51,-0.0076172,0.0007343,0.99997,107.76
> fitmap #11 inMap #1.1
Fit molecule copy of combination (#11) to map
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) using 27024 atoms
average map value = 0.05089, steps = 260
shifted from previous position = 8.09
rotated from previous position = 25.8 degrees
atoms outside contour = 15205, contour level = 0.033162
Position of copy of combination (#11) relative to
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) coordinates:
Matrix rotation and translation
0.28988911 0.95704848 0.00474406 -84.80672105
-0.95701087 0.28992094 -0.00872055 447.93528473
-0.00972140 -0.00201213 0.99995072 111.07403012
Axis 0.00350470 0.00755721 -0.99996530
Axis point 260.20382069 281.28339161 0.00000000
Rotation angle (degrees) 73.14920495
Shift along axis -107.98225509
> combine #10
> select subtract #11
Nothing selected
> select add #12
27024 atoms, 27644 bonds, 4 pseudobonds, 3424 residues, 2 models selected
> view matrix models
> #12,0.67735,0.73565,0.0046195,-110.27,-0.73562,0.67736,-0.006101,470.99,-0.0076172,0.0007343,0.99997,54.513
> view matrix models
> #12,0.99867,0.00086147,0.051551,-67.695,0.0069006,0.98863,-0.1502,149.75,-0.051095,0.15036,0.98731,38.268
> view matrix models
> #12,0.95499,-0.29001,0.062338,14.596,0.29203,0.95606,-0.025987,25.668,-0.052062,0.043022,0.99772,61.671
> view matrix models
> #12,0.95499,-0.29001,0.062338,42.695,0.29203,0.95606,-0.025987,40.061,-0.052062,0.043022,0.99772,58.514
> view matrix models
> #12,0.95431,-0.28981,0.07286,40.772,0.29267,0.95568,-0.032048,41.139,-0.060343,0.051907,0.99683,59.706
> view matrix models
> #12,0.95677,-0.28994,0.022956,49.99,0.29009,0.95699,-0.0032607,35.965,-0.021023,0.0097791,0.99973,54.295
> view matrix models
> #12,0.95677,-0.28994,0.022956,67.597,0.29009,0.95699,-0.0032607,19.101,-0.021023,0.0097791,0.99973,25.92
> fitmap #12 inMap #1.1
Fit molecule copy of combination (#12) to map
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) using 27024 atoms
average map value = 0.07201, steps = 128
shifted from previous position = 21.7
rotated from previous position = 1.37 degrees
atoms outside contour = 16334, contour level = 0.033162
Position of copy of combination (#12) relative to
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) coordinates:
Matrix rotation and translation
0.95142820 -0.30774064 0.00894910 63.26891588
0.30772849 0.95147027 0.00273846 -4.44752520
-0.00935754 0.00014845 0.99995621 25.57250537
Axis -0.00420629 0.02973079 0.99954909
Axis point 48.16170512 198.33407674 0.00000000
Rotation angle (degrees) 17.93111780
Shift along axis 25.16261854
> combine #5
> select subtract #12
Nothing selected
> select add #13
6756 atoms, 6911 bonds, 1 pseudobond, 856 residues, 2 models selected
> view matrix models
> #13,0.91835,0.39575,0.0044513,-68.592,-0.39574,0.91836,-0.0026934,222.95,-0.0051538,0.00071191,0.99999,118.59
> view matrix models
> #13,0.7398,0.02313,-0.67243,303.25,-0.34513,0.87095,-0.34975,327.08,0.57757,0.49082,0.65231,-100.93
> view matrix models
> #13,0.8937,0.44749,0.032428,-80.5,-0.4318,0.87749,-0.20873,312.38,-0.12186,0.17254,0.97744,129.28
> fitmap #13 inMap #1.1
Fit molecule copy of copy of mMIP.pdb (#13) to map
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) using 6756 atoms
average map value = 0.07907, steps = 96
shifted from previous position = 5.21
rotated from previous position = 7.79 degrees
atoms outside contour = 4040, contour level = 0.033162
Position of copy of copy of mMIP.pdb (#13) relative to
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) coordinates:
Matrix rotation and translation
0.85267637 0.50100712 0.14810426 -111.64102628
-0.46179706 0.85534842 -0.23478196 335.89371419
-0.24430818 0.13179892 0.96069900 185.86327437
Axis 0.33251954 0.35595092 -0.87334397
Axis point 673.69137305 367.91650398 0.00000000
Rotation angle (degrees) 33.45054758
Shift along axis -79.88371484
> ui mousemode right translate
> ui mousemode right "translate selected models"
> view matrix models
> #13,0.7894,0.59326,0.15776,-112.69,-0.54776,0.79674,-0.25527,388.23,-0.27713,0.1151,0.95391,204.19
> view matrix models
> #13,0.7894,0.59326,0.15776,-112.78,-0.54776,0.79674,-0.25527,389.55,-0.27713,0.1151,0.95391,204.7
> view matrix models
> #13,0.93252,-0.35174,0.081761,78.918,0.35045,0.9361,0.030152,-69.937,-0.087142,0.00053538,0.9962,146.96
> view matrix models
> #13,0.93252,-0.35174,0.081761,79.105,0.35045,0.9361,0.030152,-72.026,-0.087142,0.00053538,0.9962,145.5
> fitmap #13 inMap #1.1
Fit molecule copy of copy of mMIP.pdb (#13) to map
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) using 6756 atoms
average map value = 0.1847, steps = 128
shifted from previous position = 4.18
rotated from previous position = 22.3 degrees
atoms outside contour = 1726, contour level = 0.033162
Position of copy of copy of mMIP.pdb (#13) relative to
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) coordinates:
Matrix rotation and translation
0.73944390 -0.67320479 -0.00424649 257.24330528
0.67321493 0.73944524 0.00155136 -137.61078825
0.00209567 -0.00400594 0.99998978 111.02021230
Axis -0.00412738 -0.00471030 0.99998039
Axis point 305.95707423 264.37843466 0.00000000
Rotation angle (degrees) 42.31631220
Shift along axis 110.60448113
> combine #13
> select subtract #13
Nothing selected
> select add #14
6756 atoms, 6911 bonds, 1 pseudobond, 856 residues, 2 models selected
> view matrix models
> #14,0.73944,-0.6732,-0.0042465,242,0.67321,0.73945,0.0015514,-87.886,0.0020957,-0.0040059,0.99999,108.26
> fitmap #14 inMap #1.1
Fit molecule copy of copy of copy of mMIP.pdb (#14) to map
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) using 6756 atoms
average map value = 0.1435, steps = 112
shifted from previous position = 14.7
rotated from previous position = 24.5 degrees
atoms outside contour = 1834, contour level = 0.033162
Position of copy of copy of copy of mMIP.pdb (#14) relative to
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) coordinates:
Matrix rotation and translation
0.39312960 -0.91946420 -0.00589211 416.41983098
0.91947507 0.39314485 -0.00165376 -104.02927569
0.00383702 -0.00476751 0.99998128 101.75491661
Axis -0.00169321 -0.00529054 0.99998457
Axis point 286.69846749 263.85262924 0.00000000
Rotation angle (degrees) 66.85073548
Shift along axis 101.59863340
> ui mousemode right translate
> ui mousemode right "translate selected models"
> ui mousemode right select
> select clear
> combine #13
> select add #15
6756 atoms, 6911 bonds, 1 pseudobond, 856 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #15,0.73944,-0.6732,-0.0042465,208.82,0.67321,0.73945,0.0015514,-177.12,0.0020957,-0.0040059,0.99999,-93.853
> view matrix models
> #15,0.73944,-0.6732,-0.0042465,179.44,0.67321,0.73945,0.0015514,-175.86,0.0020957,-0.0040059,0.99999,-233.35
> view matrix models
> #15,0.73944,-0.6732,-0.0042465,245.49,0.67321,0.73945,0.0015514,-185.01,0.0020957,-0.0040059,0.99999,-255.79
> hide sel atoms
> view matrix models
> #15,0.73944,-0.6732,-0.0042465,249.56,0.67321,0.73945,0.0015514,-191.77,0.0020957,-0.0040059,0.99999,-241.83
> view matrix models
> #15,0.93909,-0.34083,0.044165,81.942,0.32849,0.92791,0.1763,-163.58,-0.10107,-0.15105,0.98335,-163.68
> view matrix models
> #15,0.92009,-0.38816,0.052597,97.35,0.37608,0.91294,0.15843,-172.07,-0.10951,-0.12599,0.98597,-167.22
> view matrix models
> #15,0.94006,-0.34041,0.020452,89.128,0.3391,0.93943,0.04981,-129.43,-0.036169,-0.039889,0.99855,-218.72
> view matrix models
> #15,0.93777,-0.33619,-0.086985,123.65,0.34328,0.93528,0.086034,-141.71,0.052432,-0.11054,0.99249,-233.31
> fitmap #15 inMap #1.1
Fit molecule copy of copy of copy of mMIP.pdb (#15) to map
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) using 6756 atoms
average map value = 0.08735, steps = 172
shifted from previous position = 6.88
rotated from previous position = 20.7 degrees
atoms outside contour = 3144, contour level = 0.033162
Position of copy of copy of copy of mMIP.pdb (#15) relative to
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) coordinates:
Matrix rotation and translation
0.99996178 -0.00873777 -0.00031230 2.63630829
0.00873778 0.99996183 0.00003151 -0.95549519
0.00031201 -0.00003424 0.99999995 -240.15619250
Axis -0.00375993 -0.03570192 0.99935541
Axis point 1090.72787957 193.67875602 0.00000000
Rotation angle (degrees) 0.50096669
Shift along axis -239.97718956
> combine #15
> view matrix models
> #15,0.99996,-0.0087378,-0.0003123,-28.199,0.0087378,0.99996,3.1511e-05,-39.322,0.00031201,-3.4238e-05,1,-233.42
> fitmap #15 inMap #1.1
Fit molecule copy of copy of copy of mMIP.pdb (#15) to map
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) using 6756 atoms
average map value = 0.07215, steps = 108
shifted from previous position = 5.31
rotated from previous position = 22.4 degrees
atoms outside contour = 3140, contour level = 0.033162
Position of copy of copy of copy of mMIP.pdb (#15) relative to
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) coordinates:
Matrix rotation and translation
0.92800351 0.37257140 0.00021964 -87.83331787
-0.37256919 0.92799972 -0.00295282 116.00908582
-0.00130397 0.00265839 0.99999562 -231.35294610
Axis 0.00753018 0.00204467 -0.99996956
Axis point 254.15601289 289.52985069 0.00000000
Rotation angle (degrees) 21.87492174
Shift along axis 230.92170241
> ui mousemode right translate
> ui mousemode right select
> select clear
> hide atoms
> select clear
> hide #!1 models
> combine #12
> select add #17
27024 atoms, 27644 bonds, 4 pseudobonds, 3424 residues, 2 models selected
> close #17
> select add #11
27024 atoms, 27644 bonds, 4 pseudobonds, 3424 residues, 2 models selected
> select add #12
54048 atoms, 55288 bonds, 8 pseudobonds, 6848 residues, 4 models selected
> select subtract #12
27024 atoms, 27644 bonds, 4 pseudobonds, 3424 residues, 2 models selected
> select subtract #11
Nothing selected
> select add #10
27024 atoms, 27644 bonds, 4 pseudobonds, 3424 residues, 2 models selected
> select subtract #10
Nothing selected
> select add #12
27024 atoms, 27644 bonds, 4 pseudobonds, 3424 residues, 2 models selected
> select subtract #12
Nothing selected
> combine #12,14
Remapping chain ID 'B' in copy of copy of copy of mMIP.pdb #14 to 'F'
Remapping chain ID 'I' in copy of copy of copy of mMIP.pdb #14 to 'M'
> select add #17
33780 atoms, 34555 bonds, 5 pseudobonds, 4280 residues, 2 models selected
> show #!1 models
> ui mousemode right "translate selected models"
> view matrix models
> #17,0.95143,-0.30774,0.0089491,-72.445,0.30773,0.95147,0.0027385,-142.66,-0.0093575,0.00014845,0.99996,3.319
> view matrix models
> #17,0.95143,-0.30774,0.0089491,-73.257,0.30773,0.95147,0.0027385,-142.2,-0.0093575,0.00014845,0.99996,3.3405
> view matrix models
> #17,0.95143,-0.30774,0.0089491,-78.177,0.30773,0.95147,0.0027385,-143.48,-0.0093575,0.00014845,0.99996,4.266
> ui mousemode right "rotate selected models"
> view matrix models
> #17,0.9508,-0.30972,0.0073568,-77.101,0.30971,0.95083,0.002236,-143.94,-0.0076876,0.00015244,0.99997,3.6428
> view matrix models
> #17,-0.89418,0.44103,0.077017,415.87,-0.41745,-0.88349,0.21254,499.13,0.16178,0.1579,0.97411,-89.398
> view matrix models
> #17,-0.89523,0.44561,6.7934e-05,433.85,-0.44517,-0.89433,-0.044681,574.28,-0.019849,-0.04003,0.999,17.686
> ui mousemode right "translate selected models"
> view matrix models
> #17,-0.89523,0.44561,6.7934e-05,427.17,-0.44517,-0.89433,-0.044681,563.57,-0.019849,-0.04003,0.999,21.146
> ui mousemode right "rotate selected models"
> view matrix models
> #17,-0.47251,0.86599,-0.16369,212.93,-0.87354,-0.48482,-0.04334,627.18,-0.11689,0.12251,0.98556,22.738
> view matrix models
> #17,-0.46584,0.87322,-0.14312,203.79,-0.87369,-0.47953,-0.082009,635.38,-0.14024,0.08684,0.9863,39.467
> view matrix models
> #17,-0.46756,0.88374,-0.019893,172.12,-0.88389,-0.46768,-0.0015532,616.91,-0.010676,0.016857,0.9998,4.3843
> fitmap #17 inMap #1.1
Fit molecule combination (#17) to map
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) using 33780 atoms
average map value = 0.01657, steps = 196
shifted from previous position = 8.66
rotated from previous position = 16.9 degrees
atoms outside contour = 28536, contour level = 0.033162
Position of combination (#17) relative to
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) coordinates:
Matrix rotation and translation
-0.19195294 0.98140336 0.00122133 41.38432771
-0.98136374 -0.19193360 -0.00930995 587.53282874
-0.00890240 -0.00298564 0.99995590 0.46391723
Axis 0.00322208 0.00515779 -0.99998151
Axis point 262.56350360 276.73403491 0.00000000
Rotation angle (degrees) 101.06750063
Shift along axis 2.69980687
> ui mousemode right "translate selected models"
> view matrix models
> #17,-0.19195,0.9814,0.0012213,40.044,-0.98136,-0.19193,-0.00931,589.52,-0.0089024,-0.0029856,0.99996,36.113
> fitmap #17 inMap #1.1
Fit molecule combination (#17) to map
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) using 33780 atoms
average map value = 0.01791, steps = 80
shifted from previous position = 4.86
rotated from previous position = 0.651 degrees
atoms outside contour = 28024, contour level = 0.033162
Position of combination (#17) relative to
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) coordinates:
Matrix rotation and translation
-0.18270821 0.98316498 0.00207464 37.16758709
-0.98305348 -0.18265458 -0.01559271 587.23745022
-0.01495126 -0.00488840 0.99987626 42.95155303
Axis 0.00544382 0.00865876 -0.99994769
Axis point 262.92091076 278.27079917 0.00000000
Rotation angle (degrees) 100.52958842
Shift along axis -37.66222630
> ui mousemode right select
> select clear
> combine #12,14
Remapping chain ID 'B' in copy of copy of copy of mMIP.pdb #14 to 'F'
Remapping chain ID 'I' in copy of copy of copy of mMIP.pdb #14 to 'M'
> select add #18
33780 atoms, 34555 bonds, 5 pseudobonds, 4280 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #18,0.95143,-0.30774,0.0089491,29.725,0.30773,0.95147,0.0027385,31.014,-0.0093575,0.00014845,0.99996,18.702
> fitmap #18 inMap #1.1
Fit molecule combination (#18) to map
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) using 33780 atoms
average map value = 0.0539, steps = 284
shifted from previous position = 11.6
rotated from previous position = 9.73 degrees
atoms outside contour = 20989, contour level = 0.033162
Position of combination (#18) relative to
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) coordinates:
Matrix rotation and translation
0.88606217 -0.46342271 0.01154214 81.94349086
0.46315726 0.88605153 0.01995085 -24.45721374
-0.01947261 -0.01233187 0.99973434 23.54299380
Axis -0.03480013 0.03343329 0.99883490
Axis point 92.51162554 155.56762230 0.00000000
Rotation angle (degrees) 27.63455309
Shift along axis 19.84623440
> ui mousemode right select
> select clear
> select add #18
33780 atoms, 34555 bonds, 5 pseudobonds, 4280 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #18,0.88606,-0.46342,0.011542,79.125,0.46316,0.88605,0.019951,-23.29,-0.019473,-0.012332,0.99973,23.043
> fitmap #18 inMap #1.1
Fit molecule combination (#18) to map
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) using 33780 atoms
average map value = 0.0601, steps = 268
shifted from previous position = 1.61
rotated from previous position = 11.3 degrees
atoms outside contour = 19659, contour level = 0.033162
Position of combination (#18) relative to
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) coordinates:
Matrix rotation and translation
0.77878484 -0.62728335 0.00312637 159.62792323
0.62727014 0.77878988 0.00430041 -54.32746429
-0.00513237 -0.00138802 0.99998587 15.21207519
Axis -0.00453408 0.00658280 0.99996805
Axis point 157.00903224 199.20696745 0.00000000
Rotation angle (degrees) 38.85096442
Shift along axis 14.13019601
> ui mousemode right select
> select clear
> ui mousemode right translate
> select add #13
6756 atoms, 6911 bonds, 1 pseudobond, 856 residues, 2 models selected
> select subtract #13
Nothing selected
> select add #14
6756 atoms, 6911 bonds, 1 pseudobond, 856 residues, 2 models selected
> select subtract #14
Nothing selected
> hide #!1 models
> combine #15
> select add #19
6756 atoms, 6911 bonds, 1 pseudobond, 856 residues, 2 models selected
> show #!1 models
> ui mousemode right "translate selected models"
> view matrix models
> #19,0.928,0.37257,0.00021964,-128.53,-0.37257,0.928,-0.0029528,93.424,-0.001304,0.0026584,1,-223.74
> fitmap #19 inMap #1.1
Fit molecule copy of copy of copy of copy of mMIP.pdb (#19) to map
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) using 6756 atoms
average map value = 0.04699, steps = 132
shifted from previous position = 6.57
rotated from previous position = 24.1 degrees
atoms outside contour = 3818, contour level = 0.033162
Position of copy of copy of copy of copy of mMIP.pdb (#19) relative to
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) coordinates:
Matrix rotation and translation
0.69527060 0.71864073 0.01242166 -129.84753010
-0.71865323 0.69535578 -0.00422819 271.84628200
-0.01167603 -0.00598713 0.99991391 -216.44469674
Axis -0.00122361 0.01676364 -0.99985873
Axis point 251.47565000 286.94307088 0.00000000
Rotation angle (degrees) 45.95125175
Shift along axis 221.13013689
> combine #19
> view matrix models
> #19,0.69527,0.71864,0.012422,-177.39,-0.71865,0.69536,-0.0042282,255.75,-0.011676,-0.0059871,0.99991,-213.91
> view matrix models
> #19,0.69527,0.71864,0.012422,-179.19,-0.71865,0.69536,-0.0042282,254.74,-0.011676,-0.0059871,0.99991,-209.18
> fitmap #20 inMap #1.1
Fit molecule copy of copy of copy of copy of copy of mMIP.pdb (#20) to map
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) using 6756 atoms
average map value = 0.04699, steps = 40
shifted from previous position = 0.00402
rotated from previous position = 0.013 degrees
atoms outside contour = 3816, contour level = 0.033162
Position of copy of copy of copy of copy of copy of mMIP.pdb (#20) relative to
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) coordinates:
Matrix rotation and translation
0.69542748 0.71848898 0.01241843 -129.86861265
-0.71850078 0.69551296 -0.00428509 271.76777536
-0.01171597 -0.00594269 0.99991371 -216.44114025
Axis -0.00115336 0.01679273 -0.99985833
Axis point 251.45364269 286.99041394 0.00000000
Rotation angle (degrees) 45.93874108
Shift along axis 221.12398487
> view matrix models
> #19,0.69527,0.71864,0.012422,-178.89,-0.71865,0.69536,-0.0042282,261.93,-0.011676,-0.0059871,0.99991,-209.48
> fitmap #20 inMap #1.1
Fit molecule copy of copy of copy of copy of copy of mMIP.pdb (#20) to map
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) using 6756 atoms
average map value = 0.04699, steps = 48
shifted from previous position = 0.0074
rotated from previous position = 0.00959 degrees
atoms outside contour = 3820, contour level = 0.033162
Position of copy of copy of copy of copy of copy of mMIP.pdb (#20) relative to
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) coordinates:
Matrix rotation and translation
0.69536855 0.71854355 0.01255987 -129.90722454
-0.71855666 0.69545546 -0.00424659 271.78795436
-0.01178619 -0.00607203 0.99991211 -216.39135109
Axis -0.00127004 0.01693865 -0.99985572
Axis point 251.39726178 286.98315528 0.00000000
Rotation angle (degrees) 45.94344635
Shift along axis 221.12884016
> view matrix models
> #19,0.69527,0.71864,0.012422,-180.29,-0.71865,0.69536,-0.0042282,267.95,-0.011676,-0.0059871,0.99991,-206.69
> fitmap #20 inMap #1.1
Fit molecule copy of copy of copy of copy of copy of mMIP.pdb (#20) to map
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) using 6756 atoms
average map value = 0.047, steps = 28
shifted from previous position = 0.0217
rotated from previous position = 0.0421 degrees
atoms outside contour = 3808, contour level = 0.033162
Position of copy of copy of copy of copy of copy of mMIP.pdb (#20) relative to
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) coordinates:
Matrix rotation and translation
0.69554773 0.71837981 0.01199240 -129.74039638
-0.71838499 0.69563025 -0.00464276 271.82119325
-0.01167754 -0.00538590 0.99991731 -216.57782319
Axis -0.00051716 0.01647224 -0.99986419
Axis point 251.66821453 287.10024367 0.00000000
Rotation angle (degrees) 45.92912660
Shift along axis 221.09300848
> view matrix models
> #19,0.69527,0.71864,0.012422,-184.77,-0.71865,0.69536,-0.0042282,265.6,-0.011676,-0.0059871,0.99991,-213.91
> fitmap #20 inMap #1.1
Fit molecule copy of copy of copy of copy of copy of mMIP.pdb (#20) to map
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) using 6756 atoms
average map value = 0.047, steps = 44
shifted from previous position = 0.0201
rotated from previous position = 0.0246 degrees
atoms outside contour = 3819, contour level = 0.033162
Position of copy of copy of copy of copy of copy of mMIP.pdb (#20) relative to
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) coordinates:
Matrix rotation and translation
0.69556138 0.71836150 0.01229335 -129.85008341
-0.71837194 0.69564571 -0.00433745 271.69944317
-0.01166767 -0.00581424 0.99991503 -216.48831772
Axis -0.00102774 0.01667511 -0.99986043
Axis point 251.48084555 287.01887579 0.00000000
Rotation angle (degrees) 45.92805692
Shift along axis 221.12217190
> fitmap #19 inMap #1.1
Fit molecule copy of copy of copy of copy of mMIP.pdb (#19) to map
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) using 6756 atoms
average map value = 0.0242, steps = 144
shifted from previous position = 7.29
rotated from previous position = 27.8 degrees
atoms outside contour = 5127, contour level = 0.033162
Position of copy of copy of copy of copy of mMIP.pdb (#19) relative to
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) coordinates:
Matrix rotation and translation
0.27989392 0.96002981 0.00147331 -78.76596403
-0.96000243 0.27989711 -0.00727654 452.62020727
-0.00739807 0.00062227 0.99997244 -210.57996062
Axis 0.00411382 0.00462035 -0.99998086
Axis point 261.24373181 278.91082498 0.00000000
Rotation angle (degrees) 73.74685351
Shift along axis 212.34316488
> select subtract #19
Nothing selected
> hide #!1 models
> combine #18
> select add #21
33780 atoms, 34555 bonds, 5 pseudobonds, 4280 residues, 2 models selected
> show #!1 models
> view matrix models
> #21,0.77878,-0.62728,0.0031264,107.47,0.62727,0.77879,0.0043004,-52.825,-0.0051324,-0.001388,0.99999,14.869
> fitmap #21 inMap #1.1
Fit molecule copy of combination (#21) to map
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) using 33780 atoms
average map value = 0.03306, steps = 132
shifted from previous position = 6.71
rotated from previous position = 1.48 degrees
atoms outside contour = 23844, contour level = 0.033162
Position of copy of combination (#21) relative to
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) coordinates:
Matrix rotation and translation
0.76290093 -0.64650884 -0.00291382 120.30300561
0.64651056 0.76287001 0.00731003 -50.42745423
-0.00250313 -0.00746065 0.99996904 14.75429938
Axis -0.01142266 -0.00031760 0.99993471
Axis point 128.98149204 139.01530296 0.00000000
Rotation angle (degrees) 40.28213266
Shift along axis 13.39517164
> view matrix models
> #21,0.7629,-0.64651,-0.0029138,116.45,0.64651,0.76287,0.00731,-50.167,-0.0025031,-0.0074607,0.99997,8.3401
> fitmap #21 inMap #1.1
Fit molecule copy of combination (#21) to map
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) using 33780 atoms
average map value = 0.03428, steps = 92
shifted from previous position = 6.58
rotated from previous position = 1.67 degrees
atoms outside contour = 23612, contour level = 0.033162
Position of copy of combination (#21) relative to
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) coordinates:
Matrix rotation and translation
0.78085806 -0.62470372 0.00244108 103.89248144
0.62469984 0.78086185 0.00221019 -45.38135287
-0.00328686 -0.00020090 0.99999458 0.39692860
Axis -0.00192977 0.00458448 0.99998763
Axis point 116.63158139 125.39318365 0.00000000
Rotation angle (degrees) 38.66086914
Shift along axis -0.01161494
> view matrix models
> #21,0.78086,-0.6247,0.0024411,101.64,0.6247,0.78086,0.0022102,-49.183,-0.0032869,-0.0002009,0.99999,0.76612
> view matrix models
> #21,0.78086,-0.6247,0.0024411,103.13,0.6247,0.78086,0.0022102,-47.679,-0.0032869,-0.0002009,0.99999,1.9671
> fitmap #21 inMap #1.1
Fit molecule copy of combination (#21) to map
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) using 33780 atoms
average map value = 0.03429, steps = 76
shifted from previous position = 2.9
rotated from previous position = 0.501 degrees
atoms outside contour = 23597, contour level = 0.033162
Position of copy of combination (#21) relative to
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) coordinates:
Matrix rotation and translation
0.78629491 -0.61784690 0.00234998 100.27042055
0.61784275 0.78629834 0.00229112 -44.07511402
-0.00326334 -0.00034958 0.99999462 0.42777996
Axis -0.00213699 0.00454261 0.99998740
Axis point 113.85006090 122.91088875 0.00000000
Rotation angle (degrees) 38.15948972
Shift along axis 0.01328137
> ui mousemode right translate
> select add #12
60804 atoms, 62199 bonds, 9 pseudobonds, 7704 residues, 4 models selected
> select subtract #21
27024 atoms, 27644 bonds, 4 pseudobonds, 3424 residues, 2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #12,0.95056,-0.31028,-0.013065,68.648,0.31045,0.95049,0.013818,-7.4782,0.008131,-0.017191,0.99982,23.127
> view matrix models
> #12,0.95096,-0.30908,0.012172,63.106,0.30914,0.95101,-0.0036414,-3.5763,-0.010451,0.0072258,0.99992,24.33
> ui mousemode right translate
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #12,0.94854,-0.31391,0.041559,59.189,0.31463,0.94914,-0.011803,-3.5352,-0.03574,0.024271,0.99907,29.96
> view matrix models
> #12,0.95186,-0.30347,0.043221,55.168,0.30428,0.95249,-0.013431,-0.1243,-0.037092,0.025936,0.99898,30.094
> view matrix models
> #12,0.95653,-0.29154,-0.0071929,60.835,0.29163,0.95627,0.022435,-3.5437,0.00033774,-0.023557,0.99972,27.551
> view matrix models
> #12,0.98515,-0.17102,0.015264,17.354,0.1709,0.98525,0.0086594,37.573,-0.016519,-0.0059222,0.99985,29.694
> fitmap #12 inMap #1.1
Fit molecule copy of combination (#12) to map
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) using 27024 atoms
average map value = 0.07142, steps = 68
shifted from previous position = 1.95
rotated from previous position = 0.512 degrees
atoms outside contour = 16349, contour level = 0.033162
Position of copy of combination (#12) relative to
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) coordinates:
Matrix rotation and translation
0.98428426 -0.17628369 0.01041885 18.21216227
0.17625703 0.98433820 0.00343118 37.72041326
-0.01086053 -0.00154086 0.99993984 27.02973678
Axis -0.01407645 0.06024444 0.99808440
Axis point -193.18177269 122.84908368 0.00000000
Rotation angle (degrees) 10.17228645
Shift along axis 28.99404110
> view matrix models
> #12,0.68107,-0.73011,-0.055529,274.65,0.72706,0.68331,-0.06694,-83.343,0.086817,0.0052171,0.99621,-10.303
> fitmap #12 inMap #1.1
Fit molecule copy of combination (#12) to map
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) using 27024 atoms
average map value = 0.1813, steps = 240
shifted from previous position = 2.63
rotated from previous position = 20.4 degrees
atoms outside contour = 6296, contour level = 0.033162
Position of copy of combination (#12) relative to
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) coordinates:
Matrix rotation and translation
0.39547743 -0.91846630 -0.00415484 414.70478352
0.91847472 0.39547956 0.00033083 -104.22047056
0.00133929 -0.00394695 0.99999132 22.49425611
Axis -0.00232874 -0.00299089 0.99999282
Axis point 286.50241902 263.00199113 0.00000000
Rotation angle (degrees) 66.70445099
Shift along axis 21.84006730
> select subtract #12
Nothing selected
> select add #13
6756 atoms, 6911 bonds, 1 pseudobond, 856 residues, 2 models selected
> select subtract #13
Nothing selected
> select add #14
6756 atoms, 6911 bonds, 1 pseudobond, 856 residues, 2 models selected
> select subtract #14
Nothing selected
> select add #15
6756 atoms, 6911 bonds, 1 pseudobond, 856 residues, 2 models selected
> select subtract #15
Nothing selected
> select add #16
6756 atoms, 6911 bonds, 1 pseudobond, 856 residues, 2 models selected
> select subtract #16
Nothing selected
> select add #18
33780 atoms, 34555 bonds, 5 pseudobonds, 4280 residues, 2 models selected
> close #18
> select add #21
33780 atoms, 34555 bonds, 5 pseudobonds, 4280 residues, 2 models selected
> close #21
> hide #!1 models
> combine #12,14
Remapping chain ID 'B' in copy of copy of copy of mMIP.pdb #14 to 'F'
Remapping chain ID 'I' in copy of copy of copy of mMIP.pdb #14 to 'M'
> select add #14
6756 atoms, 6911 bonds, 1 pseudobond, 856 residues, 2 models selected
> select add #12
33780 atoms, 34555 bonds, 5 pseudobonds, 4280 residues, 4 models selected
> select subtract #12
6756 atoms, 6911 bonds, 1 pseudobond, 856 residues, 2 models selected
> select subtract #14
Nothing selected
> select add #16
6756 atoms, 6911 bonds, 1 pseudobond, 856 residues, 2 models selected
> select subtract #16
Nothing selected
> select add #18
33780 atoms, 34555 bonds, 5 pseudobonds, 4280 residues, 2 models selected
> show #!1 models
> ui mousemode right "translate selected models"
> view matrix models
> #18,0.39548,-0.91847,-0.0041548,391.86,0.91847,0.39548,0.00033083,-61.349,0.0013393,-0.003947,0.99999,17.009
> view matrix models
> #18,0.39548,-0.91847,-0.0041548,376.6,0.91847,0.39548,0.00033083,-73.639,0.0013393,-0.003947,0.99999,19.239
> fitmap #18 inMap #1.1
Fit molecule combination (#18) to map
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) using 33780 atoms
average map value = 0.101, steps = 248
shifted from previous position = 8.19
rotated from previous position = 23.4 degrees
atoms outside contour = 12500, contour level = 0.033162
Position of combination (#18) relative to
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) coordinates:
Matrix rotation and translation
-0.00120286 -0.99997416 -0.00708817 538.94908965
0.99999892 -0.00119682 -0.00085618 -13.28514814
0.00084767 -0.00708919 0.99997451 14.24127601
Axis -0.00311651 -0.00396792 0.99998727
Axis point 276.10634935 262.55672068 0.00000000
Rotation angle (degrees) 90.06947604
Shift along axis 12.61416877
> combine #18
> select subtract #18
Nothing selected
> select add #21
33780 atoms, 34555 bonds, 5 pseudobonds, 4280 residues, 2 models selected
> view matrix models
> #21,-0.0012029,-0.99997,-0.0070882,490.37,1,-0.0011968,-0.00085618,-18.727,0.00084767,-0.0070892,0.99997,18.737
> view matrix models
> #21,-0.0012029,-0.99997,-0.0070882,487.99,1,-0.0011968,-0.00085618,-16.81,0.00084767,-0.0070892,0.99997,10.834
> fitmap #21 inMap #1.1
Fit molecule copy of combination (#21) to map
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) using 33780 atoms
average map value = 0.05597, steps = 340
shifted from previous position = 12.9
rotated from previous position = 25.4 degrees
atoms outside contour = 17879, contour level = 0.033162
Position of copy of combination (#21) relative to
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) coordinates:
Matrix rotation and translation
-0.42959365 -0.90298497 -0.00821209 624.86464353
0.90302128 -0.42958918 -0.00239117 130.57074241
-0.00136864 -0.00844292 0.99996342 6.00394474
Axis -0.00335086 -0.00378923 0.99998721
Axis point 271.20018359 262.65113487 0.00000000
Rotation angle (degrees) 115.44279338
Shift along axis 3.41527099
> combine #21
> select subtract #21
Nothing selected
> select add #22
33780 atoms, 34555 bonds, 5 pseudobonds, 4280 residues, 2 models selected
> view matrix models
> #22,-0.42959,-0.90298,-0.0082121,581.58,0.90302,-0.42959,-0.0023912,138.79,-0.0013686,-0.0084429,0.99996,63.504
> view matrix models
> #22,-0.42959,-0.90298,-0.0082121,571.18,0.90302,-0.42959,-0.0023912,133.6,-0.0013686,-0.0084429,0.99996,69.381
> view matrix models
> #22,-0.42959,-0.90298,-0.0082121,580.41,0.90302,-0.42959,-0.0023912,123.84,-0.0013686,-0.0084429,0.99996,73.036
> view matrix models
> #22,-0.42959,-0.90298,-0.0082121,576.44,0.90302,-0.42959,-0.0023912,115.44,-0.0013686,-0.0084429,0.99996,74.706
> ui mousemode right select
> select clear
> select #22/K
3374 atoms, 3451 bonds, 427 residues, 1 model selected
> select #22/F
3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected
> delete atoms (#!22 & sel)
> delete bonds (#!22 & sel)
> undo
Undo failed, probably because structures have been modified.
> fitmap #22 inMap #1.1
Fit molecule copy of copy of combination (#22) to map
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) using 30398 atoms
average map value = 0.02916, steps = 264
shifted from previous position = 2.78
rotated from previous position = 28.1 degrees
atoms outside contour = 21704, contour level = 0.033162
Position of copy of copy of combination (#22) relative to
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) coordinates:
Matrix rotation and translation
-0.80387257 -0.59473385 -0.00897490 642.98685850
0.59479470 -0.80384427 -0.00732480 317.85442028
-0.00285812 -0.01122643 0.99993290 77.76277501
Axis -0.00327992 -0.00514209 0.99998140
Axis point 269.15610307 265.17125528 0.00000000
Rotation angle (degrees) 143.50338205
Shift along axis 74.01794744
> select #21/F
3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected
> combine #21,F
Expected a keyword
> combine #21 chain F
Expected a keyword
> combine #21/F
> select add #23
37162 atoms, 38015 bonds, 6 pseudobonds, 4709 residues, 4 models selected
> select add #21
67560 atoms, 69110 bonds, 10 pseudobonds, 8560 residues, 4 models selected
> select subtract #21
33780 atoms, 34555 bonds, 5 pseudobonds, 4280 residues, 2 models selected
> select #23/F
3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected
> select ~sel & ##selected
30398 atoms, 31095 bonds, 4 pseudobonds, 3851 residues, 2 models selected
> delete atoms (#!23 & sel)
> delete bonds (#!23 & sel)
> select add #23
3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected
Drag select of 1.1 cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc , 5714
residues, 7 pseudobonds
> ui mousemode right select
> select clear
> select add #23
3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #23,-0.42959,-0.90298,-0.0082121,586.77,0.90302,-0.42959,-0.0023912,83.501,-0.0013686,-0.0084429,0.99996,-320.28
> view matrix models
> #23,-0.42959,-0.90298,-0.0082121,556.83,0.90302,-0.42959,-0.0023912,103.87,-0.0013686,-0.0084429,0.99996,-328.1
> view matrix models
> #23,-0.42959,-0.90298,-0.0082121,570.1,0.90302,-0.42959,-0.0023912,111.07,-0.0013686,-0.0084429,0.99996,-327.98
> fitmap #23 inMap #1.1
Fit molecule copy of copy of combination (#23) to map
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) using 3382 atoms
average map value = 0.01308, steps = 180
shifted from previous position = 14
rotated from previous position = 32.9 degrees
atoms outside contour = 2973, contour level = 0.033162
Position of copy of copy of combination (#23) relative to
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) coordinates:
Matrix rotation and translation
-0.52942860 -0.67404595 -0.51513824 766.06264894
0.79718952 -0.60296644 -0.03033719 203.02877966
-0.29016241 -0.42672419 0.85657005 -49.88052356
Axis -0.25735777 -0.14606755 0.95521267
Axis point 336.21048140 268.85362634 0.00000000
Rotation angle (degrees) 129.63633520
Shift along axis -274.45459932
> view matrix models
> #23,-0.52943,-0.67405,-0.51514,763.46,0.79719,-0.60297,-0.030337,202.11,-0.29016,-0.42672,0.85657,-47.97
> ui mousemode right "rotate selected models"
> view matrix models
> #23,-0.82462,-0.56346,0.050188,608.53,0.55267,-0.82139,-0.14098,390.69,0.12066,-0.088519,0.98874,-335.4
> ui mousemode right "translate selected models"
> view matrix models
> #23,-0.82462,-0.56346,0.050188,614.38,0.55267,-0.82139,-0.14098,392.57,0.12066,-0.088519,0.98874,-341.27
> volume #1.1 level 0.001
> volume #1.1 level 0.003
> volume #1.1 level 0.004
> fitmap #23 inMap #1.1
Fit molecule copy of copy of combination (#23) to map
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) using 3382 atoms
average map value = 0.01274, steps = 96
shifted from previous position = 3.6
rotated from previous position = 16.7 degrees
atoms outside contour = 1812, contour level = 0.004
Position of copy of copy of combination (#23) relative to
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) coordinates:
Matrix rotation and translation
-0.87017564 -0.44942131 -0.20202685 713.98361465
0.47070005 -0.87942587 -0.07107466 408.76977632
-0.14572517 -0.15694148 0.97679760 -223.22976300
Axis -0.09274550 -0.06081193 0.99383106
Axis point 298.45853927 282.12040068 0.00000000
Rotation angle (degrees) 152.42454274
Shift along axis -312.92951996
> view matrix models
> #23,-0.87018,-0.44942,-0.20203,714.41,0.4707,-0.87943,-0.071075,409.36,-0.14573,-0.15694,0.9768,-229.75
> fitmap #23 inMap #1.1
Fit molecule copy of copy of combination (#23) to map
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) using 3382 atoms
average map value = 0.01257, steps = 64
shifted from previous position = 3.36
rotated from previous position = 7.76 degrees
atoms outside contour = 1838, contour level = 0.004
Position of copy of copy of combination (#23) relative to
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) coordinates:
Matrix rotation and translation
-0.87354920 -0.48065584 -0.07669265 671.47024620
0.48652745 -0.86687837 -0.10868732 415.44877038
-0.01424201 -0.13225680 0.99111317 -287.61505607
Axis -0.02431137 -0.06441638 0.99762693
Axis point 281.14529676 284.41867596 0.00000000
Rotation angle (degrees) 151.00443136
Shift along axis -330.01859062
> combine #22,23
> select subtract #23
Nothing selected
> select add #24
33780 atoms, 34555 bonds, 5 pseudobonds, 4280 residues, 2 models selected
> view matrix models
> #24,-0.80387,-0.59473,-0.0089749,612.49,0.59479,-0.80384,-0.0073248,280.95,-0.0028581,-0.011226,0.99993,74.57
> fitmap #24 inMap #1.1
Fit molecule combination (#24) to map
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) using 33780 atoms
average map value = 0.01205, steps = 384
shifted from previous position = 9.8
rotated from previous position = 27.2 degrees
atoms outside contour = 18208, contour level = 0.004
Position of combination (#24) relative to
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) coordinates:
Matrix rotation and translation
-0.98697450 -0.16069695 -0.00760400 572.12203713
0.16077362 -0.98693156 -0.01085994 486.58996009
-0.00575947 -0.01194101 0.99991212 69.67555414
Axis -0.00336280 -0.00573767 0.99997789
Axis point 266.48122736 266.64522925 0.00000000
Rotation angle (degrees) 170.75021625
Shift along axis 64.95818797
> volume #1.1 level 0.005
> combine #24
> select subtract #24
Nothing selected
> select add #25
33780 atoms, 34555 bonds, 5 pseudobonds, 4280 residues, 2 models selected
> view matrix models
> #25,-0.98697,-0.1607,-0.007604,551.3,0.16077,-0.98693,-0.01086,438.35,-0.0057595,-0.011941,0.99991,67.639
> ui mousemode right translate
> ui mousemode right "translate selected models"
> view matrix models
> #25,-0.98697,-0.1607,-0.007604,551.63,0.16077,-0.98693,-0.01086,437.99,-0.0057595,-0.011941,0.99991,60.543
> fitmap #25 inMap #1.1
Fit molecule copy of combination (#25) to map
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) using 33780 atoms
average map value = 0.009276, steps = 628
shifted from previous position = 4.62
rotated from previous position = 28.9 degrees
atoms outside contour = 22263, contour level = 0.005
Position of copy of combination (#25) relative to
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) coordinates:
Matrix rotation and translation
-0.94154414 0.33686184 -0.00432765 422.49183700
-0.33679215 -0.94150302 -0.01196275 611.53282250
-0.00810429 -0.00980594 0.99991908 60.63488626
Axis 0.00320160 0.00560609 -0.99997916
Axis point 264.41741689 269.27191030 0.00000000
Rotation angle (degrees) 160.31589794
Shift along axis -55.85266880
> combine #25
> select subtract #25
Nothing selected
> select add #26
33780 atoms, 34555 bonds, 5 pseudobonds, 4280 residues, 2 models selected
> view matrix models
> #26,-0.94154,0.33686,-0.0043277,446.93,-0.33679,-0.9415,-0.011963,569.93,-0.0081043,-0.0098059,0.99992,52.542
> view matrix models
> #26,-0.94154,0.33686,-0.0043277,428.59,-0.33679,-0.9415,-0.011963,556.36,-0.0081043,-0.0098059,0.99992,53.504
> fitmap #26 inMap #1.1
Fit molecule copy of copy of combination (#26) to map
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) using 33780 atoms
average map value = 0.007022, steps = 104
shifted from previous position = 3.31
rotated from previous position = 2 degrees
atoms outside contour = 25242, contour level = 0.005
Position of copy of copy of combination (#26) relative to
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) coordinates:
Matrix rotation and translation
-0.95026704 0.31141250 -0.00384925 439.65229916
-0.31111051 -0.94976568 -0.03399137 550.87260223
-0.01424122 -0.03110334 0.99941472 59.48970101
Axis 0.00463854 0.01669081 -0.99984994
Axis point 264.00014804 240.82107314 0.00000000
Rotation angle (degrees) 161.86191257
Shift along axis -48.24691788
> ui mousemode right "rotate selected models"
> view matrix models
> #26,-0.60937,0.79282,-0.010013,200.53,-0.79197,-0.60923,-0.040335,651.95,-0.038079,-0.016649,0.99914,65.063
> ui mousemode right "translate selected models"
> view matrix models
> #26,-0.60937,0.79282,-0.010013,204.74,-0.79197,-0.60923,-0.040335,653.98,-0.038079,-0.016649,0.99914,65.144
> fitmap #26 inMap #1.1
Fit molecule copy of copy of combination (#26) to map
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) using 33780 atoms
average map value = 0.009403, steps = 84
shifted from previous position = 5.42
rotated from previous position = 1.76 degrees
atoms outside contour = 22377, contour level = 0.005
Position of copy of copy of combination (#26) relative to
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) coordinates:
Matrix rotation and translation
-0.60102643 0.79922908 0.00034392 199.56459754
-0.79916027 -0.60096892 -0.01338786 654.35871538
-0.01049328 -0.00832131 0.99991032 51.55653882
Axis 0.00316970 0.00677989 -0.99997199
Axis point 263.27041174 277.50609625 0.00000000
Rotation angle (degrees) 126.94459845
Shift along axis -46.48605565
> ui mousemode right select
> select clear
> volume #1.1 level 0.0337
> hide #!1 models
> view orient
> show #!1 models
> select add #8
6756 atoms, 6911 bonds, 1 pseudobond, 856 residues, 2 models selected
> select subtract #8
Nothing selected
> hide #!1 models
> show #!1 models
> select add #17
33780 atoms, 34555 bonds, 5 pseudobonds, 4280 residues, 2 models selected
> close #17
> hide #!1 models
> combine #11,19
Remapping chain ID 'B' in copy of copy of copy of copy of mMIP.pdb #19 to 'F'
Remapping chain ID 'I' in copy of copy of copy of copy of mMIP.pdb #19 to 'M'
> show #!1 models
> select add #26
33780 atoms, 34555 bonds, 5 pseudobonds, 4280 residues, 2 models selected
> select subtract #26
Nothing selected
> select add #17
33780 atoms, 34555 bonds, 5 pseudobonds, 4280 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #17,0.28989,0.95705,0.0047441,-121.68,-0.95701,0.28992,-0.0087206,474.47,-0.0097214,-0.0020121,0.99995,107.23
> view matrix models
> #17,0.28989,0.95705,0.0047441,-132.86,-0.95701,0.28992,-0.0087206,466.95,-0.0097214,-0.0020121,0.99995,108.49
> ui mousemode right "rotate selected models"
> view matrix models
> #17,-0.078654,0.99622,-0.036905,2.5,-0.99687,-0.078283,0.01138,565.11,0.0084475,0.037685,0.99925,92.477
> view matrix models
> #17,-0.082784,0.99656,0.0043514,-2.7379,-0.99653,-0.08274,-0.0094033,569.4,-0.0090109,-0.0051147,0.99995,108.95
> fitmap #17 inMap #1.1
Fit molecule combination (#17) to map
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) using 33780 atoms
average map value = 0.01866, steps = 136
shifted from previous position = 12.2
rotated from previous position = 5.86 degrees
atoms outside contour = 27889, contour level = 0.0337
Position of combination (#17) relative to
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) coordinates:
Matrix rotation and translation
-0.18396201 0.98293286 0.00098391 37.36525773
-0.98288208 -0.18394209 -0.01039835 586.20602886
-0.01003990 -0.00287997 0.99994545 120.79298247
Axis 0.00382447 0.00560762 -0.99997696
Axis point 262.52417572 277.74486119 0.00000000
Rotation angle (degrees) 100.60163059
Shift along axis -117.36007511
> ui mousemode right select
> select clear
> ui mousemode right translate
> hide #!1 models
> select add #26
33780 atoms, 34555 bonds, 5 pseudobonds, 4280 residues, 2 models selected
> select #26/F
3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected
> delete atoms (#!26 & sel)
> delete bonds (#!26 & sel)
> select #25/F
3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected
> delete atoms (#!25 & sel)
> delete bonds (#!25 & sel)
> show #!1 models
> select #24/F
3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected
> delete atoms (#!24 & sel)
> delete bonds (#!24 & sel)
> select #23/F
3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected
> delete atoms (#!23 & sel)
> delete bonds (#!23 & sel)
> hide #!1 models
> save /Users/jojudernatz/Desktop/mMIP_Model/250225_mMIP_J325_tubulinbuild.cxs
> select #2/A#3/A#4/A#9/A
13528 atoms, 13840 bonds, 4 pseudobonds, 1716 residues, 8 models selected
> color sel ivory
> select
> #2/B#3/B#4/B#5/B#6/B#7/B#8/B#9/B#10/B#11/B#12/B#13/B#14/B#15/B#16/B#17/B#18/B#19/B#20/B#21/B#22/B#24/B#25/B#26/B
81168 atoms, 83040 bonds, 24 pseudobonds, 10296 residues, 48 models selected
> color sel ivory
> select #17/F#18/F#21/F
10146 atoms, 10380 bonds, 3 pseudobonds, 1287 residues, 6 models selected
> color sel ivory
> select #10/K#11/K#12/K#17/K#18/K#21/K#22/K#24/K#25/K#26/K
33740 atoms, 34510 bonds, 4270 residues, 10 models selected
> select #17/M#18/M#21/M#22/M#24/M#25/M#26/M
23618 atoms, 24157 bonds, 2989 residues, 7 models selected
> select #10/L#11/L#12/L#17/L#18/L#21/L#22/L#24/L#25/L#26/L
33740 atoms, 34510 bonds, 4270 residues, 10 models selected
> select #10/J#11/J#12/J#17/J#18/J#21/J#22/J#24/J#25/J#26/J
33740 atoms, 34510 bonds, 4270 residues, 10 models selected
> select
> #2/I#3/I#4/I#5/I#6/I#7/I#8/I#9/I#10/I#11/I#12/I#13/I#14/I#15/I#16/I#17/I#18/I#19/I#20/I#21/I#22/I#24/I#25/I#26/I
80976 atoms, 82824 bonds, 10248 residues, 24 models selected
> select #2/H#3/H#4/H#9/H
13496 atoms, 13804 bonds, 1708 residues, 4 models selected
> select
> #2/I#3/I#4/I#5/I#6/I#7/I#8/I#9/I#10/I#11/I#12/I#13/I#14/I#15/I#16/I#17/I#18/I#19/I#20/I#21/I#22/I#24/I#25/I#26/I
80976 atoms, 82824 bonds, 10248 residues, 24 models selected
> color sel dim gray
> select #17/M#18/M#21/M#22/M#24/M#25/M#26/M
23618 atoms, 24157 bonds, 2989 residues, 7 models selected
> color sel dim gray
> select #10/K#11/K#12/K#17/K#18/K#21/K#22/K#24/K#25/K#26/K
33740 atoms, 34510 bonds, 4270 residues, 10 models selected
> color sel dim gray
> select #10/J#11/J#12/J#17/J#18/J#21/J#22/J#24/J#25/J#26/J
33740 atoms, 34510 bonds, 4270 residues, 10 models selected
> color sel dim gray
> select
> #2/B#3/B#4/B#5/B#6/B#7/B#8/B#9/B#10/B#11/B#12/B#13/B#14/B#15/B#16/B#17/B#18/B#19/B#20/B#21/B#22/B#24/B#25/B#26/B
81168 atoms, 83040 bonds, 24 pseudobonds, 10296 residues, 48 models selected
> select #2/C#3/C#4/C#9/C#10/C#11/C#12/C#17/C#18/C#21/C#22/C#24/C#25/C#26/C
39272 atoms, 40164 bonds, 10 pseudobonds, 4962 residues, 24 models selected
> color sel ivory
> select #2/D#3/D#4/D#9/D#10/D#11/D#12/D#17/D#18/D#21/D#22/D#24/D#25/D#26/D
35904 atoms, 36740 bonds, 10 pseudobonds, 4546 residues, 24 models selected
> color sel ivory
> select #10/E#11/E#12/E#17/E#18/E#21/E#22/E#24/E#25/E#26/E
33820 atoms, 34600 bonds, 10 pseudobonds, 4290 residues, 20 models selected
> color sel ivory
> select #10/E#11/E#12/E#17/E#18/E#21/E#22/E#24/E#25/E#26/E
33820 atoms, 34600 bonds, 10 pseudobonds, 4290 residues, 20 models selected
> select #17/F#18/F#21/F
10146 atoms, 10380 bonds, 3 pseudobonds, 1287 residues, 6 models selected
> select #2/H#3/H#4/H#9/H
13496 atoms, 13804 bonds, 1708 residues, 4 models selected
> color sel dim gray
> select #10/L#11/L#12/L#17/L#18/L#21/L#22/L#24/L#25/L#26/L
33740 atoms, 34510 bonds, 4270 residues, 10 models selected
> color sel dim gray
> ui mousemode right select
> select clear
> ui mousemode right "translate selected models"
> ui mousemode right translate
> select #2/C
1363 atoms, 1391 bonds, 168 residues, 1 model selected
> color sel #FFA200
> select #4/C
1363 atoms, 1391 bonds, 168 residues, 1 model selected
> color sel #FFA200
> select #3/C
1363 atoms, 1391 bonds, 168 residues, 1 model selected
> color sel #FFA200
> select #4/C
1363 atoms, 1391 bonds, 168 residues, 1 model selected
> select #2/C
1363 atoms, 1391 bonds, 168 residues, 1 model selected
> select #9/C
1363 atoms, 1391 bonds, 168 residues, 1 model selected
> color sel #FFA200
> select #2/D
521 atoms, 535 bonds, 64 residues, 1 model selected
> color sel #00BFFF
> select #3/D
521 atoms, 535 bonds, 64 residues, 1 model selected
> color sel #00BFFF
> select #4/D
521 atoms, 535 bonds, 64 residues, 1 model selected
> color sel #00BFFF
> select #9/D
521 atoms, 535 bonds, 64 residues, 1 model selected
> color sel #00BFFF
> ui mousemode right select
> select clear
> ui mousemode right translate
> view orient
> graphics ortho
Expected a keyword
> camera ortho
> view orient
> select #9/A
3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected
> hide #!26 models
> hide #!25 models
> hide #!24 models
> hide #!22 models
> hide #!17 models
> hide #!11 models
> hide #!19 models
> ui mousemode right select
> select clear
> ui mousemode right translate
> view orient
> turny90
Unknown command: turny90
> turn y 90
> show #!2-10,12-16,18,20-21 surfaces
> hide #!21 models
> hide #!20 models
> hide #!10 models
> view orient
> turn y 90
> view orient
> ui tool show "Side View"
> turn y 90
> save Surface_Top.tif pixelSize 0.1 transparentBackground true
> lighting soft
> cd /Users/jojudernatz/Desktop/mMIP_Model/ForFigures
Current working directory is: /Users/jojudernatz/Desktop/mMIP_Model/ForFigures
> save Surface_Top.tif pixelSize 0.1 transparentBackground true
> show #!10 models
> show #!11 models
> show #!17 models
> show #!19 models
> show #!20 models
> show #!21 models
> show #!22 models
> show #!24 models
> show #!25 models
> show #!26 models
> hide surfaces
> view orient
> select #2/A#3/A#4/A#9/A
13528 atoms, 13840 bonds, 4 pseudobonds, 1716 residues, 8 models selected
> color sel #AAFF7F
> select add #1
13528 atoms, 13840 bonds, 4 pseudobonds, 1716 residues, 15 models selected
> select
> #2/B#3/B#4/B#5/B#6/B#7/B#8/B#9/B#10/B#11/B#12/B#13/B#14/B#15/B#16/B#17/B#18/B#19/B#20/B#21/B#22/B#24/B#25/B#26/B
81168 atoms, 83040 bonds, 24 pseudobonds, 10296 residues, 48 models selected
> color sel #AAFF7F
> select #10/C
3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected
> color sel #AAFF7F
> select #12/C
3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected
> color sel #AAFF7F
> select #17/C
3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected
> color sel #AAFF7F
> select #18/C
3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected
> color sel #AAFF7F
> select #21/C
3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected
> color sel #AAFF7F
> select #22/C
3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected
> color sel #AAFF7F
> select #22/C
3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected
> select #22/C
3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected
> select #24/C
3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected
> color sel #AAFF7F
> select #25/C
3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected
> color sel #AAFF7F
> select #26/C
3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected
> color sel #AAFF7F
> select #10/E#11/E#12/E#17/E#18/E#21/E#22/E#24/E#25/E#26/E
33820 atoms, 34600 bonds, 10 pseudobonds, 4290 residues, 20 models selected
> color sel #AAFF7F
> select #17/F#18/F#21/F
10146 atoms, 10380 bonds, 3 pseudobonds, 1287 residues, 6 models selected
> color sel #AAFF7F
> select #11/C
3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected
> color sel #AAFF7F
> select #10/C
3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected
> select #10/J#11/J#12/J#17/J#18/J#21/J#22/J#24/J#25/J#26/J
33740 atoms, 34510 bonds, 4270 residues, 10 models selected
> select #10/E#11/E#12/E#17/E#18/E#21/E#22/E#24/E#25/E#26/E
33820 atoms, 34600 bonds, 10 pseudobonds, 4290 residues, 20 models selected
> select #2/D#3/D#4/D#9/D#10/D#11/D#12/D#17/D#18/D#21/D#22/D#24/D#25/D#26/D
35904 atoms, 36740 bonds, 10 pseudobonds, 4546 residues, 24 models selected
> select #10/D
3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected
> color sel #AAFF7F
> select #11/D
3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected
> color sel #AAFF7F
> select #12/D
3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected
> color sel #AAFF7F
> select #18/D
3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected
> color sel #AAFF7F
> select #21/D
3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected
> color sel #AAFF7F
> select #21/D
3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected
> select #22/D
3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected
> color sel #AAFF7F
> select #24/D
3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected
> color sel #AAFF7F
> select #25/D
3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected
> color sel #AAFF7F
> select #26/D
3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected
> color sel #AAFF7F
> select #17/D
3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected
> color sel #AAFF7F
> select
> #2/B#3/B#4/B#5/B#6/B#7/B#8/B#9/B#10/B#11/B#12/B#13/B#14/B#15/B#16/B#17/B#18/B#19/B#20/B#21/B#22/B#24/B#25/B#26/B
81168 atoms, 83040 bonds, 24 pseudobonds, 10296 residues, 48 models selected
> color sel lime
> color sel #AAFF7F
> select
> #2/I#3/I#4/I#5/I#6/I#7/I#8/I#9/I#10/I#11/I#12/I#13/I#14/I#15/I#16/I#17/I#18/I#19/I#20/I#21/I#22/I#24/I#25/I#26/I
80976 atoms, 82824 bonds, 10248 residues, 24 models selected
> color sel lime
> ui mousemode right select
> select clear
> select
> #2/I#3/I#4/I#5/I#6/I#7/I#8/I#9/I#10/I#11/I#12/I#13/I#14/I#15/I#16/I#17/I#18/I#19/I#20/I#21/I#22/I#24/I#25/I#26/I
80976 atoms, 82824 bonds, 10248 residues, 24 models selected
> color sel olive drab
> select #2/H#3/H#4/H#9/H
13496 atoms, 13804 bonds, 1708 residues, 4 models selected
> color sel olive drab
> select #17/F#18/F#21/F
10146 atoms, 10380 bonds, 3 pseudobonds, 1287 residues, 6 models selected
> select #10/J#11/J#12/J#17/J#18/J#21/J#22/J#24/J#25/J#26/J
33740 atoms, 34510 bonds, 4270 residues, 10 models selected
> color sel olive drab
> select #10/K#11/K#12/K#17/K#18/K#21/K#22/K#24/K#25/K#26/K
33740 atoms, 34510 bonds, 4270 residues, 10 models selected
> color sel olive drab
> select #10/L#11/L#12/L#17/L#18/L#21/L#22/L#24/L#25/L#26/L
33740 atoms, 34510 bonds, 4270 residues, 10 models selected
> color sel olive drab
> select #17/M#18/M#21/M#22/M#24/M#25/M#26/M
23618 atoms, 24157 bonds, 2989 residues, 7 models selected
> color sel olive drab
> select #2/D
521 atoms, 535 bonds, 64 residues, 1 model selected
> color sel #FFA200
> select #3/D
521 atoms, 535 bonds, 64 residues, 1 model selected
> color sel #FFA200
> select #4/D
521 atoms, 535 bonds, 64 residues, 1 model selected
> color sel #FFA200
> select #9/D
521 atoms, 535 bonds, 64 residues, 1 model selected
> color sel #FFA200
> ui mousemode right select
> select clear
> view orient
> select add #1
3 models selected
> color sel #FFA200
> show #!1 models
> color sel #AAFF7F
> color #1.1 #b2b2b2ff models
> color sel #AAFF7F
> color zone #1 near
> #2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26
> color zone #1 near
> #2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26 distance
> 4
> hide #!2 models
> hide #!4 models
> hide #!3 models
> hide #!5 models
> hide #!6 models
> hide #!7 models
> hide #!8 models
> hide #!9 models
> hide #!10 models
> hide #!11 models
> hide #!12 models
> hide #!13 models
> hide #!14 models
> hide #!15 models
> hide #!17 models
> hide #!16 models
> hide #!18 models
> hide #!19 models
> hide #!20 models
> hide #!21 models
> hide #!22 models
> hide #!24 models
> hide #!25 models
> hide #!26 models
> hide #!1 models
> show #!9 models
> show #!7 models
> show #!8 models
> hide #!8 models
> hide #!9 models
> show #!9 models
> hide #!7 models
> show #!2 models
> show #!3 models
> show #!4 models
> show #!5 models
> hide #!5 models
> show #!10 models
> hide #!10 models
> show #!11 models
> hide #!11 models
> show #!7 models
> hide #!7 models
> show #!8 models
> hide #!8 models
> show #!12 models
> show #!1 models
> show #!13 models
> hide #!13 models
> hide #!1 models
> show #!13 models
> hide #!13 models
> show #!13 models
> show #!14 models
> show #!15 models
> show #!16 models
> hide #!15 models
> hide #!13 models
> hide #!14 models
> show #!13 models
> show #!14 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!18 models
> hide #!18 models
> show #!19 models
> hide #!19 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!21 models
> hide #!21 models
> show #!22 models
> hide #!22 models
> show #!24 models
> hide #!24 models
> show #!26 models
> hide #!26 models
> show #!11 models
> hide #!11 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!5 models
> hide #!5 models
> show #!6 models
> show #!5 models
> show #!15 models
> show #!7 models
> show #!8 models
> hide #!9 models
> show #!9 models
> hide #!5 models
> hide #!4 models
> show #!4 models
> hide #!16 models
> show #!16 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> hide #!14 models
> show #!14 models
> hide #!13 models
> show #!13 models
> hide #!14 models
> show #!14 models
> hide #!12 models
> show #!12 models
> hide #!9 models
> show #!9 models
> hide #!8 models
> hide #!7 models
> hide #!6 models
> view orient
> volume zone #1 nearAtoms #2,3,4,9,12,13,14,16 range 4
> show #!1 models
> select #2/D
521 atoms, 535 bonds, 64 residues, 1 model selected
> color sel deep sky blue
> select #3/D
521 atoms, 535 bonds, 64 residues, 1 model selected
> color sel deep sky blue
> select #4/D
521 atoms, 535 bonds, 64 residues, 1 model selected
> color sel deep sky blue
> select #9/D
521 atoms, 535 bonds, 64 residues, 1 model selected
> color sel deep sky blue
> hide #!1 models
> show #!1 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> show #!3 models
> show #!2 models
> hide sel cartoons
> show #!4 models
> show sel cartoons
> color zone #1 near
> #2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26 distance
> 4
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!9 models
> select add #9
15396 atoms, 15748 bonds, 2 pseudobonds, 1944 residues, 3 models selected
> select subtract #9
6 models selected
> hide #!12 models
> hide #!13 models
> hide #!14 models
> hide #!16 models
> view orient
> turn y 90
Drag select of 1.1 cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc
> select clear
> ui mousemode right translate
> view orient
> turn y 90
> ui tool show "Side View"
> view orient
> turn y 90
> show #!13 models
> hide #!13 models
> show #!9 models
> hide #!9 models
> combine #9
> select #26/C
3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected
> show #!26 models
> hide #!26 models
> show #!9 models
> hide #!9 models
> combine #9
> hide #!23 models
> close #23
> select add #27
18778 atoms, 19208 bonds, 3 pseudobonds, 2373 residues, 4 models selected
> select #27/C
1363 atoms, 1391 bonds, 168 residues, 1 model selected
> select ~sel & ##selected
14033 atoms, 14357 bonds, 2 pseudobonds, 1776 residues, 2 models selected
> delete atoms (#!27 & sel)
> delete bonds (#!27 & sel)
> select add #27
1363 atoms, 1391 bonds, 168 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #27,1,0,0,-3.1829,0,1,0,-0.39177,0,0,1,-0.39631
> view matrix models #27,1,0,0,-3.5992,0,1,0,-0.062122,0,0,1,-1.3011
> view matrix models #27,1,0,0,-3.6142,0,1,0,-0.093856,0,0,1,-1.3889
> view matrix models #27,1,0,0,-7.0572,0,1,0,-0.67889,0,0,1,-0.81126
> volume zone #1 nearAtoms #2,3,4,9,12,13,14,16,27 range 4
> color zone #1 near
> #2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27
> distance 4
> hide #!27 models
> view orient
> turn y 90
> save greentubs_density_top.tif pixelSize 0.1 transparentBackground true
> color zone #1 near
> #2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27
> distance 4.2
> color zone #1 near
> #2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27
> distance 4.5
> color zone #1 near
> #2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27
> distance 4
> volume zone #1 nearAtoms #2,3,4,9,12,13,14,16,27 range 4.5
> volume zone #1 nearAtoms #2,3,4,9,12,13,14,16,27 range 5
> save
> /Users/jojudernatz/Desktop/mMIP_Model/250225_mMIP_J325_tubulinbuild_colors.cxs
> includeMaps true
> view orient
> turn y 90
> view orient
> turn y 90
> turn x 90
> turn z 90
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!10 models
> hide #!10 models
> show #!11 models
> hide #!11 models
> show #!12 models
> hide #!12 models
> show #!14 models
> hide #!14 models
> show #!13 models
> hide #!13 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!15 models
> show #!14 models
> hide #!14 models
> show #!18 models
> hide #!18 models
> show #!19 models
> hide #!19 models
> show #!21 models
> hide #!21 models
> show #!20 models
> hide #!20 models
> show #!19 models
> hide #!19 models
> show #!18 models
> hide #!18 models
> show #!17 models
> hide #!17 models
> show #!16 models
> hide #!16 models
> show #!14 models
> hide #!14 models
> show #!13 models
> hide #!13 models
> show #!12 models
> hide #!12 models
> show #!11 models
> hide #!11 models
> show #!10 models
> hide #!10 models
> show #!9 models
> hide #!9 models
> show #!8 models
> show #!7 models
> show #!6 models
> show #!5 models
> volume zone #1 nearAtoms #2,3,4,5,6,7,8,9,12,13,14,15,16,27 range 5
> hide #!15 models
> hide #!8 models
> hide #!7 models
> hide #!6 models
> hide #!5 models
> save greentubs_density_top2.tif pixelSize 0.1 transparentBackground true
> view orient
> hide #!1 models
> show #!2 models
> show #!3 models
> show #!4 models
> show #!5 models
> show #!6 models
> show #!7 models
> show #!27 models
> hide #!27 models
> show #!26 models
> select subtract #27
Nothing selected
> show #!25 models
> show #!24 models
> show #!22 models
> show #!21 models
> show #!20 models
> show #!19 models
> show #!18 models
> show #!17 models
> show #!16 models
> show #!15 models
> show #!14 models
> show #!13 models
> show #!12 models
> show #!11 models
> show #!9 models
> show #!10 models
> show #!8 models
> view orient
> select #26/M
3374 atoms, 3451 bonds, 427 residues, 1 model selected
> hide sel target a
> hide sel cartoons
> select #25/M
3374 atoms, 3451 bonds, 427 residues, 1 model selected
> hide sel cartoons
> select #24/M
3374 atoms, 3451 bonds, 427 residues, 1 model selected
> hide sel cartoons
> select #22/M
3374 atoms, 3451 bonds, 427 residues, 1 model selected
> hide sel cartoons
> save greentubs_SS_front.tif pixelSize 0.1 transparentBackground true
> show sel surfaces
> hide sel surfaces
> select add #22
30398 atoms, 31095 bonds, 4 pseudobonds, 3851 residues, 3 models selected
> select subtract #22
1 model selected
> show #!2-22,24-26 cartoons
> save greentubs_SS_front2.tif pixelSize 0.1 transparentBackground true
> show #!2-22,24-26 surfaces
> hide #!2-22,24-26 surfaces
> cartoon style width 2.5 thickness 0.7
> select #26/M
3374 atoms, 3451 bonds, 427 residues, 1 model selected
> hide sel cartoons
> select #25/M
3374 atoms, 3451 bonds, 427 residues, 1 model selected
> hide sel cartoons
> select #24/M
3374 atoms, 3451 bonds, 427 residues, 1 model selected
> hide sel cartoons
> select #22/M
3374 atoms, 3451 bonds, 427 residues, 1 model selected
> hide sel cartoons
> save greentubs_SS_front3.tif pixelSize 0.1 transparentBackground true
> ui mousemode right select
Drag select of 23 residues
> select clear
Drag select of 30 residues
> view orient
Drag select of 22 residues
> select clear
Drag select of 8 residues
> select clear
Drag select of 8 residues
> hide sel cartoons
Drag select of 5 residues
> hide sel cartoons
Drag select of 1 residues
Drag select of 3 residues
> hide sel cartoons
> select clear
Drag select of 7 residues
> select subtract #3/C:161
45 atoms, 6 residues, 2 models selected
> select add #3/C:163
53 atoms, 7 bonds, 7 residues, 2 models selected
> select add #3/C:161
62 atoms, 15 bonds, 8 residues, 2 models selected
> select subtract #3/C:161
53 atoms, 7 bonds, 7 residues, 2 models selected
> hide sel cartoons
> select clear
Drag select of 1 residues
> hide sel cartoons
Drag select of 1 residues
> hide sel cartoons
Drag select of 7 residues
> hide sel cartoons
> view orient
> turn x 90
> show #!1 models
> hide #1.1.1 models
> show #1.1.1 models
> hide #!1 models
> show #!1 models
> volume zone
Missing or invalid "volumes" argument: empty atom specifier
> volume #1.1 level 0.08317
> volume #1.1 level 0.07493
> volume #1.1 level 0.0337
> volume zone off
Missing or invalid "volumes" argument: invalid density maps specifier
> volume zone #1 off
Expected a keyword
> volume zone #1
Missing required "near_atoms" argument
> volume zone #1 nearAtoms #2-26
> hide #!1 models
> view orient
> select add #3
15450 atoms, 15748 bonds, 2 pseudobonds, 1951 residues, 4 models selected
> select subtract #3
54 atoms, 7 residues, 8 models selected
> view orient
> graphics silhouettes false
> graphics silhouettes true
> select #2/B
3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected
> hide sel cartoons
> show sel cartoons
> select #3/B
3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected
> hide sel cartoons
> select #13/B
3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected
> show sel cartoons
> hide sel cartoons
> select #13/I
3374 atoms, 3451 bonds, 427 residues, 1 model selected
> hide sel cartoons
> select #14/I
3374 atoms, 3451 bonds, 427 residues, 1 model selected
> hide sel cartoons
> select #14/B
3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected
> hide sel cartoons
> select #18/M
3374 atoms, 3451 bonds, 427 residues, 1 model selected
> hide sel cartoons
> select #18/F
3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected
> hide sel cartoons
> select #5/B
3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected
> hide sel cartoons
> select #10/B
3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected
> hide sel cartoons
> select #11/B
3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected
> hide sel cartoons
> select #17/B
3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected
> hide sel cartoons
> select #5/I
3374 atoms, 3451 bonds, 427 residues, 1 model selected
> hide sel cartoons
> select #10/I
3374 atoms, 3451 bonds, 427 residues, 1 model selected
> hide sel cartoons
> select #11/I
3374 atoms, 3451 bonds, 427 residues, 1 model selected
> hide sel cartoons
> select #17/I
3374 atoms, 3451 bonds, 427 residues, 1 model selected
> hide sel cartoons
> view orient
> select #3/I
3374 atoms, 3451 bonds, 427 residues, 1 model selected
> hide sel cartoons
> view orient
> save greentubs_SS_front.tif pixelSize 0.1 transparentBackground true
> ui mousemode right select
Drag select of 46105 residues, 53 pseudobonds
> show sel surfaces
> save greentubs_SS_front2.tif pixelSize 0.1 transparentBackground true
> hide sel surfaces
> show sel surfaces
> select clear
> save greentubs_SS_front2.tif pixelSize 0.1 transparentBackground true
> hide #!2-22,24-26 surfaces
> view orient
> ui tool show "Show Sequence Viewer"
> sequence chain #9/D #2/D #3/D #4/D
Alignment identifier is 1
> select #9/D:68 #2/D:68 #3/D:68 #4/D:68
36 atoms, 32 bonds, 4 residues, 4 models selected
> select #9/D #2/D #3/D #4/D
2084 atoms, 2140 bonds, 256 residues, 4 models selected
1 [ID: 1] region 4 chains [1-64] RMSD: 146.177
> select #9/D:117 #2/D:117 #3/D:117 #4/D:117
28 atoms, 28 bonds, 4 residues, 4 models selected
> select #9/D:117-121 #2/D:117-121 #3/D:117-121 #4/D:117-121
164 atoms, 168 bonds, 20 residues, 4 models selected
1 [ID: 1] region 4 chains [50-54] RMSD: 146.184
> ui mousemode right translate
> show sel atoms
> style sel stick
Changed 164 atom styles
> color sel byhetero
> show #!1 models
> volume zone #1 nearAtoms #9/C,D
> select add #4
15519 atoms, 15874 bonds, 2 pseudobonds, 1959 residues, 9 models selected
> select add #3
30874 atoms, 31580 bonds, 4 pseudobonds, 3898 residues, 15 models selected
> select add #2
46229 atoms, 47286 bonds, 6 pseudobonds, 5837 residues, 21 models selected
> select subtract #2
30833 atoms, 31538 bonds, 4 pseudobonds, 3893 residues, 24 models selected
> select subtract #3
15437 atoms, 15790 bonds, 2 pseudobonds, 1949 residues, 16 models selected
> select subtract #4
41 atoms, 42 bonds, 5 residues, 8 models selected
> select add #9
15396 atoms, 15748 bonds, 2 pseudobonds, 1944 residues, 3 models selected
> select subtract #9
6 models selected
> select add #9
15396 atoms, 15748 bonds, 2 pseudobonds, 1944 residues, 2 models selected
> select ~sel
419115 atoms, 428722 bonds, 59 pseudobonds, 53076 residues, 50 models selected
> hide sel & #!2-8,10-22,24-26 cartoons
> hide sel & #!2-8,10-22,24-26 atoms
> ui mousemode right select
> select clear
> view orient
> volume zone #1 nearAtoms #9/C,D range 6
> color #1 #b2b2b24e models
> select clear
> ui mousemode right translate
> select #9/D:101 #2/D:101 #3/D:101 #4/D:101
32 atoms, 28 bonds, 4 residues, 4 models selected
> select #9/D:101-109 #2/D:101-109 #3/D:101-109 #4/D:101-109
308 atoms, 320 bonds, 36 residues, 4 models selected
1 [ID: 1] region 4 chains [34-42] RMSD: 146.185
> select #9/D:74-75 #2/D:74-75 #3/D:74-75 #4/D:74-75
76 atoms, 76 bonds, 8 residues, 4 models selected
> select #9/D:74-78 #2/D:74-78 #3/D:74-78 #4/D:74-78
188 atoms, 196 bonds, 20 residues, 4 models selected
1 [ID: 1] region 4 chains [7-11] RMSD: 146.199
> select #9/D:74 #2/D:74 #3/D:74 #4/D:74
44 atoms, 44 bonds, 4 residues, 4 models selected
> select #9/D:74 #2/D:74 #3/D:74 #4/D:74
44 atoms, 44 bonds, 4 residues, 4 models selected
1 [ID: 1] region 4 chains [7] RMSD: 146.189
> show sel atoms
> color sel byhetero
> style sel stick
Changed 44 atom styles
> select add #9
15429 atoms, 15781 bonds, 2 pseudobonds, 1947 residues, 9 models selected
> select subtract #9
33 atoms, 33 bonds, 3 residues, 12 models selected
> hide sel atoms
> hide #!1 models
> ui mousemode right select
> select #9/D:118
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #9/D:120
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #9/D:121
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #9/D:117
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #9/D:68 #2/D:68 #3/D:68 #4/D:68
36 atoms, 32 bonds, 4 residues, 4 models selected
> select #9/D:68 #2/D:68 #3/D:68 #4/D:68
36 atoms, 32 bonds, 4 residues, 4 models selected
1 [ID: 1] region 4 chains [1] RMSD: 146.156
> show sel atoms
> style sel stick
Changed 36 atom styles
> show #!1 models
> select #1.1
2 models selected
> hide #!1 models
> select #9/D:78
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #9/D:79
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #9/D:82 #2/D:82 #3/D:82 #4/D:82
32 atoms, 28 bonds, 4 residues, 4 models selected
> select #9/D:82 #2/D:82 #3/D:82 #4/D:82
32 atoms, 28 bonds, 4 residues, 4 models selected
1 [ID: 1] region 4 chains [15] RMSD: 146.204
> show sel atoms
> style sel stick
Changed 32 atom styles
> select #9/D:77
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #9/D:78
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #9/D:72 #2/D:72 #3/D:72 #4/D:72
28 atoms, 24 bonds, 4 residues, 4 models selected
> select #9/D:72-77 #2/D:72-77 #3/D:72-77 #4/D:72-77
220 atoms, 224 bonds, 24 residues, 4 models selected
1 [ID: 1] region 4 chains [5-10] RMSD: 146.191
> select #9/D:75 #2/D:75 #3/D:75 #4/D:75
32 atoms, 28 bonds, 4 residues, 4 models selected
> select #9/D:75-81 #2/D:75-81 #3/D:75-81 #4/D:75-81
228 atoms, 236 bonds, 28 residues, 4 models selected
1 [ID: 1] region 4 chains [8-14] RMSD: 146.207
> select #9/D:75 #2/D:75 #3/D:75 #4/D:75
32 atoms, 28 bonds, 4 residues, 4 models selected
> select #9/D:75-79 #2/D:75-79 #3/D:75-79 #4/D:75-79
180 atoms, 184 bonds, 20 residues, 4 models selected
1 [ID: 1] region 4 chains [8-12] RMSD: 146.204
> select #9/D:76 #2/D:76 #3/D:76 #4/D:76
48 atoms, 48 bonds, 4 residues, 4 models selected
> select #9/D:76 #2/D:76 #3/D:76 #4/D:76
48 atoms, 48 bonds, 4 residues, 4 models selected
1 [ID: 1] region 4 chains [9] RMSD: 146.198
> show sel atoms
> style sel stick
Changed 48 atom styles
> select add #9
15432 atoms, 15784 bonds, 2 pseudobonds, 1947 residues, 9 models selected
> select subtract #9
36 atoms, 36 bonds, 3 residues, 12 models selected
> hide sel atoms
> color sel byhetero
> select clear
> color #!2-22,24-26 byhetero
> select add #2
15396 atoms, 15748 bonds, 2 pseudobonds, 1944 residues, 2 models selected
> select add #3
30792 atoms, 31496 bonds, 4 pseudobonds, 3888 residues, 10 models selected
> select add #4
46188 atoms, 47244 bonds, 6 pseudobonds, 5832 residues, 18 models selected
> hide sel atoms
> select clear
> select #9/D:130
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #9/D:129
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #9/D:125-126 #2/D:125-126 #3/D:125-126 #4/D:125-126
56 atoms, 60 bonds, 8 residues, 4 models selected
> select #9/D:125-126 #2/D:125-126 #3/D:125-126 #4/D:125-126
56 atoms, 60 bonds, 8 residues, 4 models selected
1 [ID: 1] region 4 chains [58-59] RMSD: 146.142
> select #9/D:125 #2/D:125 #3/D:125 #4/D:125
28 atoms, 28 bonds, 4 residues, 4 models selected
> select #9/D:125 #2/D:125 #3/D:125 #4/D:125
28 atoms, 28 bonds, 4 residues, 4 models selected
> show sel atoms
> color sel byhetero
> style sel stick
Changed 28 atom styles
> select add #9
15417 atoms, 15769 bonds, 2 pseudobonds, 1947 residues, 9 models selected
> select subtract #9
21 atoms, 21 bonds, 3 residues, 12 models selected
> hide sel atoms
> select clear
> select #9/C:153
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 5 atom styles
> select #9/C:154
10 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 10 atom styles
> show #!1 models
> hide #!1 models
> select clear
> select #9/D:78
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #9/D:79
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> select #9/C:91
7 atoms, 7 bonds, 1 residue, 1 model selected
> style sel stick
Changed 7 atom styles
> show sel atoms
> select #9/C:90
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 7 atom styles
> color sel byhetero
> select #9/D:79
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #9/D:71 #2/D:71 #3/D:71 #4/D:71
44 atoms, 40 bonds, 4 residues, 4 models selected
> select #9/D:71-76 #2/D:71-76 #3/D:71-76 #4/D:71-76
228 atoms, 232 bonds, 24 residues, 4 models selected
1 [ID: 1] region 4 chains [4-9] RMSD: 146.184
> select #9/D:75
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> style sel stick
Changed 8 atom styles
> select clear
> show #!1 models
> select #1.1
2 models selected
> hide #!1 models
> select #9/D:78
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #9/D:77
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> style sel stick
Changed 9 atom styles
> select clear
> select #9/D:77
9 atoms, 8 bonds, 1 residue, 1 model selected
> show #!1 models
> select clear
> hide #!1 models
> select #9/C:156
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> select #9/C:154
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #9/C:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> show #!1 models
> select #9/D:103
4 atoms, 3 bonds, 1 residue, 1 model selected
> hide #!1 models
> select #9/D:115
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #9/D:117
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #9/D:116
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #9/D:116
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> select #9/D:104
14 atoms, 15 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 14 atom styles
> show #!1 models
> hide #!1 models
> select #9/C:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #9/C:158
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> select clear
> select #9/C:159
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #9/C:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> select #9/C:92
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #9/D:104
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #9/D:69-71,91-96,104-109,112-117 #2/D:69-71,91-96,104-109,112-117
> #3/D:69-71,91-96,104-109,112-117 #4/D:69-71,91-96,104-109,112-117
724 atoms, 732 bonds, 84 residues, 4 models selected
> select clear
> select #9/D:105
14 atoms, 15 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 14 atom styles
> select #9/D:103
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel atoms
> show #!1 models
> hide #!1 models
> select #9/D:115
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 7 atom styles
> select #9/D:116
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #9/D:79
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #9/D:68
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #9/D:82
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #9/C:156
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #9/C:90
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #9/D:77
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #9/D:105
14 atoms, 15 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #9/D:75
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #9/D:76
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #9/C:90
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #9/C:91
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #9/C:92
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #9/C:89
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel atoms
> select #9/C:90
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #9/C:91
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #9/C:92
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add #9/C:91
14 atoms, 13 bonds, 2 residues, 2 models selected
> select add #9/C:90
21 atoms, 19 bonds, 3 residues, 2 models selected
> hide sel cartoons
> show sel atoms
> style sel stick
Changed 21 atom styles
> hide sel atoms
> show sel cartoons
> select #9/C:91
7 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> show #!1 models
> select #1.1
2 models selected
> hide #!1 models
> show #!1 models
> hide #!1 models
> select #9/D:79
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #9/D:79
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #9/D:77
9 atoms, 8 bonds, 1 residue, 1 model selected
> show #!1 models
> select #1.1
2 models selected
> hide #!1 models
> select #9/D:119
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #9/C:156
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> select #9/C:153
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #9/C:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> show #!1 models
> select clear
> save
> /Users/jojudernatz/Desktop/mMIP_Model/250225_mMIP_J325_tubulinbuild_close.cxs
> includeMaps true
> volume #1.1 level 0.037
> volume #1.1 level 0.005
> hide #!1 models
> select #9/C:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> show #!1 models
> hide #!1 models
> hide sel atoms
> select clear
> select #9/C:158
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #9/D:79
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #9/C:91
7 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #9/D:74
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #9/C:156
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #9/D:117
7 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #9/D:115
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #9/D:116
11 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel atoms
> show #!1 models
> select #9/C:160
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel cartoons
Drag select of 1.1 cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc , 4
atoms, 5 residues, 4 bonds
> select clear
> ui mousemode right translate
> hide #!1 models
> ui mousemode right select
> select #9/D:74
11 atoms, 11 bonds, 1 residue, 1 model selected
> select add #9/C:153
16 atoms, 15 bonds, 2 residues, 2 models selected
> hide sel atoms
> show #!1 models
> select clear
> ui mousemode right translate
> hide #!1 models
> ui mousemode right select
> select #9/C:150
9 atoms, 8 bonds, 1 residue, 1 model selected
> show #!1 models
> hide #!1 models
> show sel atoms
> style sel sphere
Changed 9 atom styles
> style sel stick
Changed 9 atom styles
> select #9/C:149
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> show #!1 models
> hide sel atoms
> hide #!1 models
> select #9/C:150
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #9/D:76
12 atoms, 12 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #9/D:104
14 atoms, 15 bonds, 1 residue, 1 model selected
> hide sel atoms
> show #!1 models
> view orient
> volume zone #1 nearAtoms #9/C,D range 5
> volume #1.1 level 0.0337
> volume zone #1 nearAtoms #9/C,D range 4
> select clear
> hide #!2-22,24-26 atoms
> volume zone #1 nearAtoms #9/C,D range 4.4
> volume zone #1 nearAtoms #9/C,D range 4
> volume zone #1 nearAtoms #9/C,D range 3.5
> color zone #1 near #9/C,D range 4
Expected a keyword
> color zone #1 near #9/C,D distance 4
> hide #!2-22,24-26 atoms
> color #!2-22,24-26 bychain
> undo
> color zone #1 near #9/C,D distance 4
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> select #9/C
1363 atoms, 1391 bonds, 168 residues, 1 model selected
> color sel #FFA200
> select #4/D
521 atoms, 535 bonds, 64 residues, 1 model selected
> select #9/D
521 atoms, 535 bonds, 64 residues, 1 model selected
> color sel deep sky blue
> select clear
> ui mousemode right translate
> color zone #1 near #9/C,D distance 4
> color #1.1.1 #b2b2b21d
> view orient
> color zone #1 near #9/C,D distance 4
> hide #!9 models
> show #!9 models
> color zone #1 near #9 distance 4
> select #9/A
3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected
> color sel #AAFF7F
> select #9/B
3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected
> color sel #AAFF7F
> select #9/H
3374 atoms, 3451 bonds, 427 residues, 1 model selected
> color sel olive drab
> select #9/I
3374 atoms, 3451 bonds, 427 residues, 1 model selected
> color sel olive drab
> ui mousemode right select
> ui mousemode right "translate selected models"
> ui mousemode right translate
> color zone #1 near #9 distance 4
> volume zone #1 nearAtoms #9 range 3.5
> hide #!9 models
> show #!27 models
> volume zone #1 nearAtoms #9,27 range 3.5
> hide #!27 models
> color zone #1 near #9,27 distance 4
> view
> view orient
> volume zone #1 nearAtoms #9,27 range 4
> volume zone #1 nearAtoms #9,27 range 5
> view orient
> turn y 90
> color zone #1 near #9,27 distance 5
> view orient
> turn y 90
> turn x 90
> turn y 90
> turn y -45
> turn y 5
> turn x 5
> turn y 5
> turn y -5
> turn z -5
> volume #1.1 level 0.04195
> view orient
> turn z 90
> turn y 90
> hide #!1 models
> show #!9 models
> ui mousemode right select
> select clear
> view orient
> turn y 90
> hide #!10 models
> show #!10 models
> show #!27 models
> hide #!27 models
> hide #!26 models
> show #!26 models
> hide #!26 models
> show #!26 models
> view orient
> turn x 90
> show #!2-22,24-26 cartoons
> view orient
> turn y 90
> turn x 90
> turn z 90
> turn x 90
> ui mousemode right clip
> save greentubs_SS_top.tif pixelSize 0.1 transparentBackground true
> view orient
> hide #!8 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> hide #!7 models
> show #!6 models
> hide #!10 models
> hide #!11 models
> hide #!12 models
> hide #!13 models
> hide #!14 models
> hide #!15 models
> hide #!16 models
> hide #!17 models
> show #!17 models
> hide #!18 models
> hide #!17 models
> hide #!19 models
> hide #!20 models
> hide #!21 models
> hide #!22 models
> hide #!24 models
> hide #!25 models
> hide #!26 models
> hide #!6 models
> hide #!9 models
> show #!9 models
> view orient
> open /Users/jojudernatz/Downloads/pdb8ou0.ent
pdb8ou0.ent title:
Bovine sperm endpiece singlet microtubules (one tubulin dimer and associated
microtubule inner proteins) [more info...]
Chain information for pdb8ou0.ent #23
---
Chain | Description | UniProt
A | α-tubulin 3 | TBA3_BOVIN 1-450
B | tubulin β-2C chain | TBB4B_BOVIN 1-455
C | sperm acrosome associated 9 |
D | stabilizer of axonemal microtubules 1 |
Non-standard residues in pdb8ou0.ent #23
---
GDP — guanosine-5'-diphosphate
GTP — guanosine-5'-triphosphate
MG — magnesium ion
> select add #23
8139 atoms, 8322 bonds, 7 pseudobonds, 1030 residues, 4 models selected
> ui mousemode right "translate selected models"
> view matrix models #23,1,0,0,-63.846,0,1,0,14.323,0,0,1,0
> view matrix models #23,1,0,0,168.66,0,1,0,27.315,0,0,1,6.913
> view matrix models
> #23,0.98541,0.088231,0.14557,127.01,-0.15324,0.087534,0.9843,82.47,0.074104,-0.99225,0.099777,364.15
> view matrix models
> #23,0.86937,0.48809,0.07724,77.288,0.41645,-0.80778,0.41719,255.74,0.26602,-0.33053,-0.90553,358.61
> view matrix models
> #23,0.71893,0.68416,0.12272,58.641,0.63872,-0.5806,-0.50492,322.81,-0.27419,0.44138,-0.8544,296.84
> view matrix models
> #23,0.78783,0.61051,0.081225,67.349,0.61386,-0.7677,-0.18386,311.68,-0.049889,0.19471,-0.97959,324.93
> view matrix models
> #23,0.78783,0.61051,0.081225,62.882,0.61386,-0.7677,-0.18386,360.97,-0.049889,0.19471,-0.97959,399.78
> view matrix models
> #23,0.78783,0.61051,0.081225,76.733,0.61386,-0.7677,-0.18386,322.84,-0.049889,0.19471,-0.97959,357.66
> view matrix models
> #23,0.78783,0.61051,0.081225,42.312,0.61386,-0.7677,-0.18386,318.76,-0.049889,0.19471,-0.97959,409.7
> view matrix models
> #23,0.78783,0.61051,0.081225,48.674,0.61386,-0.7677,-0.18386,348.66,-0.049889,0.19471,-0.97959,418.53
> ui tool show Matchmaker
> matchmaker #!23 to #9
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker mMIP.pdb, chain A (#9) with pdb8ou0.ent, chain A (#23), sequence
alignment score = 2098.3
RMSD between 423 pruned atom pairs is 0.947 angstroms; (across all 427 pairs:
0.972)
> ui mousemode right select
> select clear
> show #!1 models
> hide #!1 models
Drag select of 10 residues
> select subtract #9/C:159
73 atoms, 9 residues, 2 models selected
> hide sel cartoons
> show #!1 models
> hide #!1 models
> select add #9/C:159
80 atoms, 7 bonds, 10 residues, 2 models selected
> select add #9/C:158
88 atoms, 14 bonds, 11 residues, 2 models selected
> hide sel cartoons
> show #!1 models
> hide #!1 models
> select #9/C:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel cartoons
Drag select of 377 residues, 64 atoms, 5 pseudobonds, 61 bonds
Drag select of 2 residues
> select clear
> ui mousemode right translate
> view orient
> show #!1 models
> hide #!1 models
> hide #!9,23 atoms
> select #23/B
3365 atoms, 3442 bonds, 427 residues, 1 model selected
> hide sel cartoons
> select #23/A
3374 atoms, 3451 bonds, 6 pseudobonds, 430 residues, 3 models selected
> hide sel cartoons
> select #23/D
164 atoms, 168 bonds, 20 residues, 1 model selected
> hide sel cartoons
> show sel cartoons
> hide sel cartoons
> select #23/C
1236 atoms, 1261 bonds, 1 pseudobond, 153 residues, 2 models selected
> color sel dim grey
> ui mousemode right select
> select clear
> hbonds #!9,23 reveal true
3460 hydrogen bonds found
> ~hbonds
> hide #!9,23 atoms
> select clear
> select #9/C:92
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #23/C:93
7 atoms, 6 bonds, 1 residue, 1 model selected
Drag select of 36 residues
> select clear
> view orient
> select clear
Drag select of 1 pseudobonds
> hide #!9,23 cartoons
> show #!9,23 cartoons
> hide #!9,23 atoms
No visible atoms selected
> select clear
> ~label #9,23 residues
> ~label #9,23 atoms
> label delete
> select clear
Drag select of 7 residues
> select clear
Drag select of 8 residues
> hide sel cartoons
Drag select of 3 residues
> select add #9/C:157
35 atoms, 8 bonds, 4 residues, 2 models selected
> hide sel cartoons
> select #23/D
164 atoms, 168 bonds, 20 residues, 1 model selected
> hide sel cartoons
> select #9/D
521 atoms, 535 bonds, 64 residues, 1 model selected
> hide sel cartoons
> select #9/D
521 atoms, 535 bonds, 64 residues, 1 model selected
> show sel cartoons
> select #23/A
3374 atoms, 3451 bonds, 6 pseudobonds, 430 residues, 3 models selected
> hide sel cartoons
> select #23/A
3374 atoms, 3451 bonds, 6 pseudobonds, 430 residues, 3 models selected
> show sel cartoons
> color sel ivory
> select #23/B
3365 atoms, 3442 bonds, 427 residues, 1 model selected
> color sel dim grey
> select clear
> select #23/A
3374 atoms, 3451 bonds, 6 pseudobonds, 430 residues, 3 models selected
> color sel dim grey
> select clear
> view orient
> turn y 90
> turn y -90
> turn x -90
> turn z -90
> turn y -90
> morph #23,9 frames 40
models have different number of chains, 4 (Morph - pdb8ou0.ent #/A,Morph -
pdb8ou0.ent #/B,Morph - pdb8ou0.ent #/C,Morph - pdb8ou0.ent #/D) and 6
(mMIP.pdb #9/A,mMIP.pdb #9/B,mMIP.pdb #9/C,mMIP.pdb #9/D,mMIP.pdb
#9/H,mMIP.pdb #9/I)
> combine #9
> hide #!28 models
> show #!28 models
> show #!27 models
> hide #!27 models
> hide #!9 models
> select #28/A
3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected
> select #28/B
3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected
> delete atoms (#!28 & sel)
> delete bonds (#!28 & sel)
> select #28/C
1363 atoms, 1391 bonds, 168 residues, 1 model selected
> select #28/D
521 atoms, 535 bonds, 64 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #28/I
3374 atoms, 3451 bonds, 427 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #28/C
1363 atoms, 1391 bonds, 168 residues, 1 model selected
> color sel ivory
> select #23/C
1236 atoms, 1261 bonds, 1 pseudobond, 153 residues, 2 models selected
> color sel ivory
> select clear
> show #!9 models
> view orient
> turn z -90
> turn y -90
> morph #23,28 frames 40
models have different number of chains, 4 (Morph - pdb8ou0.ent #/A,Morph -
pdb8ou0.ent #/B,Morph - pdb8ou0.ent #/C,Morph - pdb8ou0.ent #/D) and 3 (copy
of mMIP.pdb #28/A,copy of mMIP.pdb #28/C,copy of mMIP.pdb #28/H)
> select add #28
8119 atoms, 8302 bonds, 1 pseudobond, 1024 residues, 2 models selected
> hide #!28 models
> show #!28 models
> hide #!9 models
> hide #!23 models
> show #!9 models
> hide #!9 models
> select clear
> show #!23 models
> morph #23,28 frames 40
models have different number of chains, 4 (Morph - pdb8ou0.ent #/A,Morph -
pdb8ou0.ent #/B,Morph - pdb8ou0.ent #/C,Morph - pdb8ou0.ent #/D) and 3 (copy
of mMIP.pdb #28/A,copy of mMIP.pdb #28/C,copy of mMIP.pdb #28/H)
> select #23/D
164 atoms, 168 bonds, 20 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> view orient
> turn z -90
> turn y -90
> show #!9 models
> morph #23,28 frames 40
Computed 41 frame morph #29
> coordset #29 1,41
> hide #!9 models
> close #29
> show #!28 models
> show #!27 models
> hide #!27 models
> show #!23 models
> ui tool show Matchmaker
> matchmaker #!23 to #28
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker copy of mMIP.pdb, chain A (#28) with pdb8ou0.ent, chain A (#23),
sequence alignment score = 2098.3
RMSD between 423 pruned atom pairs is 0.947 angstroms; (across all 427 pairs:
0.972)
> morph #23,28 cartesian true frames 40
Computed 41 frame morph #29
> coordset #29 1,41
> view orient
> show #!28 models
> view orient
> close #29
> show #!23 models
> view orient
> select #23/A
3374 atoms, 3451 bonds, 6 pseudobonds, 430 residues, 3 models selected
> delete atoms (#!23 & sel)
> delete bonds (#!23 & sel)
> select #23/B
3365 atoms, 3442 bonds, 427 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #28/A
3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected
> delete atoms (#!28 & sel)
> delete bonds (#!28 & sel)
> select #28/H
3374 atoms, 3451 bonds, 427 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> show #!9 models
> morph #23,28 frames 40
Computed 41 frame morph #29
> coordset #29 1,41
> label delete
> select add #29
1223 atoms, 1245 bonds, 1 pseudobond, 153 residues, 2 models selected
> color sel ivory
> select clear
Drag select of 105 residues
> select clear
> ui mousemode right translate
> view orient
> turn y -90
> turn z -90
> turn y -90
> movie record
> movie encode /Users/jojudernatz/Desktop/movie1.mp4 framerate 25.0
Movie saved to /Users/jojudernatz/Desktop/movie1.mp4
> movie record
> movie encode /Users/jojudernatz/Desktop/movie2.mp4 framerate 25.0
Error processing trigger "new frame":
Movie encoding failed because no images were recorded.
> movie record
> movie encode /Users/jojudernatz/Desktop/movie2.mp4 framerate 25.0
Error processing trigger "new frame":
Movie encoding failed because no images were recorded.
> movie record
> movie encode /Users/jojudernatz/Desktop/movie2.mp4 framerate 25.0
Error processing trigger "new frame":
Movie encoding failed because no images were recorded.
> turn y -90
> movie record
> movie encode /Users/jojudernatz/Desktop/movie2.mp4 framerate 25.0
Error processing trigger "new frame":
Movie encoding failed because no images were recorded.
> movie record
Already recording a movie
> movie encode
Movie saved to /Users/jojudernatz/Desktop/movie.mp4
> select add #29
1223 atoms, 1245 bonds, 1 pseudobond, 153 residues, 2 models selected
> show sel atoms
> show #!28 models
> hide #!28 models
> select add #28
2586 atoms, 2636 bonds, 1 pseudobond, 321 residues, 3 models selected
> show sel & #!29 atoms
> select subtract #29
1363 atoms, 1391 bonds, 168 residues, 1 model selected
> select subtract #28
Nothing selected
> select add #28
1363 atoms, 1391 bonds, 168 residues, 1 model selected
> select subtract #28
Nothing selected
> select add #27
1363 atoms, 1391 bonds, 168 residues, 1 model selected
> select subtract #27
Nothing selected
> select add #9
15396 atoms, 15748 bonds, 2 pseudobonds, 1944 residues, 2 models selected
> select subtract #9
6 models selected
> hide #!9 models
> show #!28 models
> select add #28
1363 atoms, 1391 bonds, 168 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 1363 atom styles
> show sel cartoons
> hide sel atoms
> ui mousemode right select
Drag select of 3 residues
Drag select of 6 residues
> select add #28/C:159
80 atoms, 7 bonds, 10 residues, 1 model selected
> select add #28/C:158
88 atoms, 14 bonds, 11 residues, 1 model selected
> hide sel cartoons
Drag select of 65 residues, 90 atoms, 77 bonds
> select clear
> select add #28
1363 atoms, 1391 bonds, 168 residues, 1 model selected
> show sel atoms
Drag select of 30 atoms, 29 bonds
> select add #28/C:166@O
31 atoms, 30 bonds, 5 residues, 1 model selected
> hide sel atoms
Drag select of 40 atoms, 39 bonds
> hide sel atoms
Drag select of 5 atoms, 2 bonds
Drag select of 7 atoms, 7 bonds
> select add #28/C:159@CA
82 atoms, 78 bonds, 11 residues, 1 model selected
> hide sel atoms
Drag select of 4 atoms, 4 bonds
> select add #28/C:158@CD1
87 atoms, 83 bonds, 11 residues, 1 model selected
> hide sel atoms
Drag select of 4 atoms, 1 residues, 3 bonds
> select add #28/C:157@CG
95 atoms, 88 bonds, 12 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> select clear
Drag select of 2 atoms, 1 bonds
> hide sel atoms
> view orient
> select clear
> turn y -90
> show #!9 models
> view orient
> turn z -90
> turn y -90
> ui mousemode right translate
> ui mousemode right select
Drag select of 22 residues, 1 atoms
> select subtract #28/C:131@NH2
183 atoms, 22 residues, 2 models selected
> show sel atoms
> style sel stick
Changed 183 atom styles
> select clear
> open /Users/jojudernatz/Downloads/mMIP_real_space_refined_013-coot-0.pdb
Summary of feedback from opening
/Users/jojudernatz/Downloads/mMIP_real_space_refined_013-coot-0.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY H 10 HIS H 28 1 19
Start residue of secondary structure not found: HELIX 2 2 ASP H 41 GLN H 43 1
3
Start residue of secondary structure not found: HELIX 3 3 ILE H 47 VAL H 49 1
3
Start residue of secondary structure not found: HELIX 4 4 GLY H 71 SER H 78 1
8
Start residue of secondary structure not found: HELIX 5 5 PRO H 87 ASN H 89 1
3
43 messages similar to the above omitted
End residue of secondary structure not found: HELIX 72 72 GLY B 144 ASP B 160
1 17
Start residue of secondary structure not found: HELIX 73 73 GLU B 183 THR B
194 1 12
Start residue of secondary structure not found: HELIX 74 74 ASN B 206 ARG B
215 1 10
Start residue of secondary structure not found: HELIX 75 75 TYR B 224 ILE B
238 1 15
Start residue of secondary structure not found: HELIX 76 76 THR B 239 SER B
241 1 3
Start residue of secondary structure not found: HELIX 77 77 LEU B 252 PHE B
255 1 4
42 messages similar to the above omitted
Chain information for mMIP_real_space_refined_013-coot-0.pdb #30
---
Chain | Description
A AA | No description available
B | No description available
C | No description available
D | No description available
> style #!9,28-30 stick
Changed 33305 atom styles
> hide #!28 models
> hide #!29 models
> show #!9,30 cartoons
> hide #!9,30 atoms
> dssp true
Expected a structures specifier or a keyword
> dssp #30 true
Expected a keyword
> dssp #30
Computing secondary structure
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!1 models
> hide #!1 models
> select clear
> ui mousemode right translate
===== Log before crash end =====
Log:
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
OpenGL version: 4.1 Metal - 89.3
OpenGL renderer: Apple M4 Pro
OpenGL vendor: Apple
Python: 3.11.4
Locale: 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: Mac16,7
Model Number: Z1FU000R8Y/A
Chip: Apple M4 Pro
Total Number of Cores: 14 (10 performance and 4 efficiency)
Memory: 48 GB
System Firmware Version: 11881.81.4
OS Loader Version: 11881.81.4
Software:
System Software Overview:
System Version: macOS 15.3.1 (24D70)
Kernel Version: Darwin 24.3.0
Time since boot: 12 days, 1 hour, 57 minutes
Graphics/Displays:
Apple M4 Pro:
Chipset Model: Apple M4 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 20
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
HP Z24nf G2:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 75.00Hz
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-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-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
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 , 8 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash moving window between screens |
comment:2 by , 8 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
Note:
See TracTickets
for help on using tickets.
