![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 9 months ago
Closed 9 months ago
#16672 closed defect (duplicate)
Crash on Mac waking from sleep
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-13.0-arm64-arm-64bit
ChimeraX Version: 1.8rc202405312319 (2024-05-31 23:19:45 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x000000020c61e500 (most recent call first):
File "/Applications/ChimeraX-1.8-rc2024.05.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 307 in event_loop
File "/Applications/ChimeraX-1.8-rc2024.05.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
File "/Applications/ChimeraX-1.8-rc2024.05.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.surface._surface, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, psutil._psutil_osx, psutil._psutil_posix, PIL._imagingmath, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.mlp._mlp, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 62)
{"app_name":"ChimeraX","timestamp":"2025-01-23 09:16:10.00 +0800","app_version":"1.8.0","slice_uuid":"17982d98-65bc-3327-8526-577ec996453c","build_version":"1.8.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 13.0 (22A8380)","roots_installed":0,"name":"ChimeraX","incident_id":"F7A274B8-2C42-4965-A854-837CBD22C875"}
{
"uptime" : 940000,
"procRole" : "Background",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "Mac14,9",
"coalitionID" : 108778,
"osVersion" : {
"train" : "macOS 13.0",
"build" : "22A8380",
"releaseType" : "User"
},
"captureTime" : "2025-01-23 09:16:04.6291 +0800",
"incident" : "F7A274B8-2C42-4965-A854-837CBD22C875",
"pid" : 44038,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-01-22 17:18:55.2879 +0800",
"procStartAbsTime" : 21277181683796,
"procExitAbsTime" : 22655471290693,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.8-rc2024.05.31.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"5A8E51FF-AD96-59E9-A6DC-0328C3B508F1","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "98748426-6024-9D56-0A5C-BCAEAF1373E8",
"sip" : "enabled",
"vmRegionInfo" : "0x50901a845348 is not in any region. Bytes after previous region: 88098814055241 Bytes before following region: 16973265874104\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL ...(unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600008000000 [128.0M] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000001, 0x000050901a845348","rawCodes":[1,88579850392392],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x000050901a845348"},
"vmregioninfo" : "0x50901a845348 is not in any region. Bytes after previous region: 88098814055241 Bytes before following region: 16973265874104\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL ...(unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600008000000 [128.0M] rw-\/rwx SM=PRV ",
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
"threads" : [{"triggered":true,"id":9575937,"threadState":{"x":[{"value":0},{"value":0},{"value":1},{"value":4832131736},{"value":99},{"value":98},{"value":105553168342016},{"value":0},{"value":17850619100349352185},{"value":17850619091962932729},{"value":14757395258967641293},{"value":4294967286},{"value":4832131666},{"value":0},{"value":54},{"value":4294967280},{"value":328},{"value":8879528632},{"value":0},{"value":11},{"value":8797676800,"symbolLocation":0,"symbol":"_main_thread"},{"value":259},{"value":8797677024,"symbolLocation":224,"symbol":"_main_thread"},{"value":1},{"value":4353984048,"symbolLocation":0,"symbol":"faulthandler_handlers"},{"value":8759844864,"symbolLocation":0,"symbol":"OBJC_IVAR_$_NSTableView._tvFlagsExtra"},{"value":8759844864,"symbolLocation":0,"symbol":"OBJC_IVAR_$_NSTableView._tvFlagsExtra"},{"value":4},{"value":0}],"flavor":"ARM_THREAD_STATE64","lr":{"value":7263018220},"cpsr":{"value":1073745920},"fp":{"value":4832131808},"sp":{"value":4832131776},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":7262794276,"matchesCrashFrame":1},"far":{"value":5326823432}},"name":"CrBrowserMain","queue":"com.apple.main-thread","frames":[{"imageOffset":37412,"symbol":"__pthread_kill","symbolLocation":8,"imageIndex":0},{"imageOffset":27884,"symbol":"pthread_kill","symbolLocation":288,"imageIndex":1},{"imageOffset":268880,"symbol":"raise","symbolLocation":32,"imageIndex":2},{"imageOffset":2417160,"symbol":"faulthandler_fatal_error","symbolLocation":392,"imageIndex":3},{"imageOffset":17060,"symbol":"_sigtramp","symbolLocation":56,"imageIndex":4},{"imageOffset":343184,"imageIndex":5},{"imageOffset":343184,"imageIndex":5},{"imageOffset":378896,"symbol":"_NSViewHierarchyDidChangeBackingProperties","symbolLocation":244,"imageIndex":6},{"imageOffset":8460692,"symbol":"-[NSWindow _postWindowDidChangeBackingPropertiesAndDisplayWindowForPreviousBackingScaleFactor:previousColorSpace:]","symbolLocation":192,"imageIndex":6},{"imageOffset":2105016,"symbol":"__67-[NSWindow _updateSettingsSendingScreenChangeNotificationToScreen:]_block_invoke","symbolLocation":448,"imageIndex":6},{"imageOffset":509644,"symbol":"NSPerformVisuallyAtomicChange","symbolLocation":108,"imageIndex":6},{"imageOffset":2104556,"symbol":"-[NSWindow _updateSettingsSendingScreenChangeNotificationToScreen:]","symbolLocation":96,"imageIndex":6},{"imageOffset":514984,"symbol":"-[NSWindow _setFrameCommon:display:fromServer:]","symbolLocation":1852,"imageIndex":6},{"imageOffset":8435504,"symbol":"-[NSWindow(NSScreenLayout) _setFrame:fromAdjustmentToScreen:anchorIfNeeded:animate:]","symbolLocation":576,"imageIndex":6},{"imageOffset":3291704,"symbol":"-[NSWindow _adjustWindowToScreen]","symbolLocation":1100,"imageIndex":6},{"imageOffset":3420744,"symbol":"-[NSWindow _displayChangedSoAdjustWindows:]","symbolLocation":100,"imageIndex":6},{"imageOffset":11179912,"symbol":"___NSApplicationPerformScreenInvalidationReactions_block_invoke","symbolLocation":72,"imageIndex":6},{"imageOffset":216116,"symbol":"-[NSApplication enumerateWindowsWithOptions:usingBlock:]","symbolLocation":236,"imageIndex":6},{"imageOffset":11178724,"symbol":"___NSApplicationReactToScreenInvalidation_block_invoke","symbolLocation":756,"imageIndex":6},{"imageOffset":11177424,"symbol":"_NSApplicationReactToScreenInvalidation","symbolLocation":292,"imageIndex":6},{"imageOffset":11177896,"symbol":"-[NSApplication(ScreenHandling) _reactToDisplayChanges:]","symbolLocation":372,"imageIndex":6},{"imageOffset":6683676,"symbol":"_NSCGSDisplayConfigurationUpdateAndInvokeObservers","symbolLocation":416,"imageIndex":6},{"imageOffset":6684584,"symbol":"_NSCGSDisplayConfigurationDidReconfigureNotificationHandler","symbolLocation":308,"imageIndex":6},{"imageOffset":46276,"symbol":"(anonymous namespace)::notify_datagram_handler(unsigned int, CGSDatagramType, void*, unsigned long, void*)","symbolLocation":896,"imageIndex":7},{"imageOffset":3368308,"symbol":"CGSDatagramReadStream::dispatchMainQueueDatagrams()","symbolLocation":228,"imageIndex":7},{"imageOffset":3368048,"symbol":"invocation function for block in CGSDatagramReadStream::mainQueueWakeup()","symbolLocation":28,"imageIndex":7},{"imageOffset":10716,"symbol":"_dispatch_call_block_and_release","symbolLocation":32,"imageIndex":8},{"imageOffset":17668,"symbol":"_dispatch_client_callout","symbolLocation":20,"imageIndex":8},{"imageOffset":77084,"symbol":"_dispatch_main_queue_drain","symbolLocation":928,"imageIndex":8},{"imageOffset":76140,"symbol":"_dispatch_main_queue_callback_4CF","symbolLocation":44,"imageIndex":8},{"imageOffset":798060,"symbol":"__CFRUNLOOP_IS_SERVICING_THE_MAIN_DISPATCH_QUEUE__","symbolLocation":16,"imageIndex":9},{"imageOffset":526316,"symbol":"__CFRunLoopRun","symbolLocation":2036,"imageIndex":9},{"imageOffset":522404,"symbol":"CFRunLoopRunSpecific","symbolLocation":612,"imageIndex":9},{"imageOffset":205756,"symbol":"RunCurrentEventLoopInMode","symbolLocation":292,"imageIndex":10},{"imageOffset":205312,"symbol":"ReceiveNextEventCommon","symbolLocation":672,"imageIndex":10},{"imageOffset":204616,"symbol":"_BlockUntilNextEventMatchingListInModeWithFilter","symbolLocation":72,"imageIndex":10},{"imageOffset":235056,"symbol":"_DPSNextEvent","symbolLocation":632,"imageIndex":6},{"imageOffset":231360,"symbol":"-[NSApplication(NSEvent) _nextEventMatchingEventMask:untilDate:inMode:dequeue:]","symbolLocation":728,"imageIndex":6},{"imageOffset":183280,"symbol":"-[NSApplication run]","symbolLocation":464,"imageIndex":6},{"imageOffset":81772,"imageIndex":5},{"imageOffset":573772,"symbol":"QEventLoop::exec(QFlags)","symbolLocation":540,"imageIndex":11},{"imageOffset":535260,"symbol":"QCoreApplication::exec()","symbolLocation":112,"imageIndex":11},{"imageOffset":2507676,"symbol":"meth_QApplication_exec(_object*, _object*)","symbolLocation":96,"imageIndex":12},{"imageOffset":1004504,"symbol":"cfunction_call","symbolLocation":96,"imageIndex":3},{"imageOffset":594156,"symbol":"_PyObject_MakeTpCall","symbolLocation":128,"imageIndex":3},{"imageOffset":1789244,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":54984,"imageIndex":3},{"imageOffset":1729512,"symbol":"PyEval_EvalCode","symbolLocation":276,"imageIndex":3},{"imageOffset":1707120,"symbol":"builtin_exec","symbolLocation":428,"imageIndex":3},{"imageOffset":1007044,"symbol":"cfunction_vectorcall_FASTCALL_KEYWORDS","symbolLocation":80,"imageIndex":3},{"imageOffset":1788292,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":54032,"imageIndex":3},{"imageOffset":1811404,"symbol":"_PyEval_Vector","symbolLocation":156,"imageIndex":3},{"imageOffset":2389028,"symbol":"pymain_run_module","symbolLocation":256,"imageIndex":3},{"imageOffset":2387652,"symbol":"Py_RunMain","symbolLocation":1784,"imageIndex":3},{"imageOffset":2392180,"symbol":"pymain_main","symbolLocation":52,"imageIndex":3},{"imageOffset":2392116,"symbol":"Py_Main","symbolLocation":36,"imageIndex":3},{"imageOffset":15700,"symbol":"main","symbolLocation":128,"imageIndex":13},{"imageOffset":24144,"symbol":"start","symbolLocation":2544,"imageIndex":14}]},{"id":9576059,"name":"ThreadPoolServiceThread","frames":[{"imageOffset":51208,"symbol":"kevent64","symbolLocation":8,"imageIndex":0},{"imageOffset":66705848,"imageIndex":15},{"imageOffset":66705328,"imageIndex":15},{"imageOffset":66336288,"imageIndex":15},{"imageOffset":66064512,"imageIndex":15},{"imageOffset":66483648,"imageIndex":15},{"imageOffset":66384288,"imageIndex":15},{"imageOffset":66484032,"imageIndex":15},{"imageOffset":66589352,"imageIndex":15},{"imageOffset":28780,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":7724,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":9576060,"name":"ThreadPoolForegroundWorker","frames":[{"imageOffset":3568,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":0},{"imageOffset":75992,"symbol":"mach_msg2_internal","symbolLocation":80,"imageIndex":0},{"imageOffset":38456,"symbol":"mach_msg_overwrite","symbolLocation":540,"imageIndex":0},{"imageOffset":4460,"symbol":"mach_msg","symbolLocation":24,"imageIndex":0},{"imageOffset":66741424,"imageIndex":15},{"imageOffset":66197236,"imageIndex":15},{"imageOffset":66429892,"imageIndex":15},{"imageOffset":66433464,"imageIndex":15},{"imageOffset":66432016,"imageIndex":15},{"imageOffset":66431744,"imageIndex":15},{"imageOffset":66589352,"imageIndex":15},{"imageOffset":28780,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":7724,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":9576061,"name":"ThreadPoolBackgroundWorker","frames":[{"imageOffset":3568,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":0},{"imageOffset":75992,"symbol":"mach_msg2_internal","symbolLocation":80,"imageIndex":0},{"imageOffset":38456,"symbol":"mach_msg_overwrite","symbolLocation":540,"imageIndex":0},{"imageOffset":4460,"symbol":"mach_msg","symbolLocation":24,"imageIndex":0},{"imageOffset":66741424,"imageIndex":15},{"imageOffset":66197236,"imageIndex":15},{"imageOffset":66429892,"imageIndex":15},{"imageOffset":66433464,"imageIndex":15},{"imageOffset":66431884,"imageIndex":15},{"imageOffset":66431792,"imageIndex":15},{"imageOffset":66589352,"imageIndex":15},{"imageOffset":28780,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":7724,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":9576062,"name":"Chrome_IOThread","frames":[{"imageOffset":51208,"symbol":"kevent64","symbolLocation":8,"imageIndex":0},{"imageOffset":66705848,"imageIndex":15},{"imageOffset":66705328,"imageIndex":15},{"imageOffset":66336288,"imageIndex":15},{"imageOffset":66064512,"imageIndex":15},{"imageOffset":66483648,"imageIndex":15},{"imageOffset":42148336,"imageIndex":15},{"imageOffset":66484032,"imageIndex":15},{"imageOffset":66589352,"imageIndex":15},{"imageOffset":28780,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":7724,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":9576063,"name":"NetworkConfigWatcher","frames":[{"imageOffset":3568,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":0},{"imageOffset":75992,"symbol":"mach_msg2_internal","symbolLocation":80,"imageIndex":0},{"imageOffset":38456,"symbol":"mach_msg_overwrite","symbolLocation":540,"imageIndex":0},{"imageOffset":4460,"symbol":"mach_msg","symbolLocation":24,"imageIndex":0},{"imageOffset":66741424,"imageIndex":15},{"imageOffset":66197236,"imageIndex":15},{"imageOffset":66197084,"imageIndex":15},{"imageOffset":65870644,"imageIndex":15},{"imageOffset":66336288,"imageIndex":15},{"imageOffset":66064512,"imageIndex":15},{"imageOffset":66483648,"imageIndex":15},{"imageOffset":66484032,"imageIndex":15},{"imageOffset":66589352,"imageIndex":15},{"imageOffset":28780,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":7724,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":9576067,"name":"Chrome_InProcGpuThread","frames":[{"imageOffset":3568,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":0},{"imageOffset":75992,"symbol":"mach_msg2_internal","symbolLocation":80,"imageIndex":0},{"imageOffset":38456,"symbol":"mach_msg_overwrite","symbolLocation":540,"imageIndex":0},{"imageOffset":4460,"symbol":"mach_msg","symbolLocation":24,"imageIndex":0},{"imageOffset":66741424,"imageIndex":15},{"imageOffset":66197236,"imageIndex":15},{"imageOffset":66197084,"imageIndex":15},{"imageOffset":65870644,"imageIndex":15},{"imageOffset":66336288,"imageIndex":15},{"imageOffset":66064512,"imageIndex":15},{"imageOffset":66483648,"imageIndex":15},{"imageOffset":66484032,"imageIndex":15},{"imageOffset":66589352,"imageIndex":15},{"imageOffset":28780,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":7724,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":9576068,"name":"Chrome_ChildIOThread","frames":[{"imageOffset":51208,"symbol":"kevent64","symbolLocation":8,"imageIndex":0},{"imageOffset":66705848,"imageIndex":15},{"imageOffset":66705328,"imageIndex":15},{"imageOffset":66336288,"imageIndex":15},{"imageOffset":66064512,"imageIndex":15},{"imageOffset":66483648,"imageIndex":15},{"imageOffset":107949588,"imageIndex":15},{"imageOffset":66484032,"imageIndex":15},{"imageOffset":66589352,"imageIndex":15},{"imageOffset":28780,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":7724,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":9576069,"name":"CompositorTileWorker1","frames":[{"imageOffset":17892,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":0},{"imageOffset":30264,"symbol":"_pthread_cond_wait","symbolLocation":1232,"imageIndex":1},{"imageOffset":66586532,"imageIndex":15},{"imageOffset":99447652,"imageIndex":15},{"imageOffset":66589352,"imageIndex":15},{"imageOffset":28780,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":7724,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":9576070,"name":"ThreadPoolSingleThreadSharedForeground0","frames":[{"imageOffset":3568,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":0},{"imageOffset":75992,"symbol":"mach_msg2_internal","symbolLocation":80,"imageIndex":0},{"imageOffset":38456,"symbol":"mach_msg_overwrite","symbolLocation":540,"imageIndex":0},{"imageOffset":4460,"symbol":"mach_msg","symbolLocation":24,"imageIndex":0},{"imageOffset":66741424,"imageIndex":15},{"imageOffset":66197236,"imageIndex":15},{"imageOffset":66429892,"imageIndex":15},{"imageOffset":66432404,"imageIndex":15},{"imageOffset":66432060,"imageIndex":15},{"imageOffset":66431816,"imageIndex":15},{"imageOffset":66589352,"imageIndex":15},{"imageOffset":28780,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":7724,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":9576071,"name":"NetworkConfigWatcher","frames":[{"imageOffset":3568,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":0},{"imageOffset":75992,"symbol":"mach_msg2_internal","symbolLocation":80,"imageIndex":0},{"imageOffset":38456,"symbol":"mach_msg_overwrite","symbolLocation":540,"imageIndex":0},{"imageOffset":4460,"symbol":"mach_msg","symbolLocation":24,"imageIndex":0},{"imageOffset":66741424,"imageIndex":15},{"imageOffset":66197236,"imageIndex":15},{"imageOffset":66197084,"imageIndex":15},{"imageOffset":65870644,"imageIndex":15},{"imageOffset":66336288,"imageIndex":15},{"imageOffset":66064512,"imageIndex":15},{"imageOffset":66483648,"imageIndex":15},{"imageOffset":66484032,"imageIndex":15},{"imageOffset":66589352,"imageIndex":15},{"imageOffset":28780,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":7724,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":9576072,"name":"VizCompositorThread","frames":[{"imageOffset":3568,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":0},{"imageOffset":75992,"symbol":"mach_msg2_internal","symbolLocation":80,"imageIndex":0},{"imageOffset":38456,"symbol":"mach_msg_overwrite","symbolLocation":540,"imageIndex":0},{"imageOffset":4460,"symbol":"mach_msg","symbolLocation":24,"imageIndex":0},{"imageOffset":66741424,"imageIndex":15},{"imageOffset":66197236,"imageIndex":15},{"imageOffset":65870544,"imageIndex":15},{"imageOffset":66336288,"imageIndex":15},{"imageOffset":66064512,"imageIndex":15},{"imageOffset":66483648,"imageIndex":15},{"imageOffset":66484032,"imageIndex":15},{"imageOffset":66589352,"imageIndex":15},{"imageOffset":28780,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":7724,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":9576073,"name":"NetworkService","frames":[{"imageOffset":51208,"symbol":"kevent64","symbolLocation":8,"imageIndex":0},{"imageOffset":66705848,"imageIndex":15},{"imageOffset":66705328,"imageIndex":15},{"imageOffset":66336288,"imageIndex":15},{"imageOffset":66064512,"imageIndex":15},{"imageOffset":66483648,"imageIndex":15},{"imageOffset":66484032,"imageIndex":15},{"imageOffset":66589352,"imageIndex":15},{"imageOffset":28780,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":7724,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":9576074,"name":"NetworkConfigWatcher","frames":[{"imageOffset":3568,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":0},{"imageOffset":75992,"symbol":"mach_msg2_internal","symbolLocation":80,"imageIndex":0},{"imageOffset":38456,"symbol":"mach_msg_overwrite","symbolLocation":540,"imageIndex":0},{"imageOffset":4460,"symbol":"mach_msg","symbolLocation":24,"imageIndex":0},{"imageOffset":66741424,"imageIndex":15},{"imageOffset":66197236,"imageIndex":15},{"imageOffset":66197084,"imageIndex":15},{"imageOffset":65870644,"imageIndex":15},{"imageOffset":66336288,"imageIndex":15},{"imageOffset":66064512,"imageIndex":15},{"imageOffset":66483648,"imageIndex":15},{"imageOffset":66484032,"imageIndex":15},{"imageOffset":66589352,"imageIndex":15},{"imageOffset":28780,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":7724,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":9576076,"name":"ThreadPoolSingleThreadForegroundBlocking1","frames":[{"imageOffset":3568,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":0},{"imageOffset":75992,"symbol":"mach_msg2_internal","symbolLocation":80,"imageIndex":0},{"imageOffset":38456,"symbol":"mach_msg_overwrite","symbolLocation":540,"imageIndex":0},{"imageOffset":4460,"symbol":"mach_msg","symbolLocation":24,"imageIndex":0},{"imageOffset":66741424,"imageIndex":15},{"imageOffset":66197236,"imageIndex":15},{"imageOffset":66429892,"imageIndex":15},{"imageOffset":66433464,"imageIndex":15},{"imageOffset":66432104,"imageIndex":15},{"imageOffset":66431804,"imageIndex":15},{"imageOffset":66589352,"imageIndex":15},{"imageOffset":28780,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":7724,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":9576095,"name":"NetworkConfigWatcher","frames":[{"imageOffset":3568,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":0},{"imageOffset":75992,"symbol":"mach_msg2_internal","symbolLocation":80,"imageIndex":0},{"imageOffset":38456,"symbol":"mach_msg_overwrite","symbolLocation":540,"imageIndex":0},{"imageOffset":4460,"symbol":"mach_msg","symbolLocation":24,"imageIndex":0},{"imageOffset":66741424,"imageIndex":15},{"imageOffset":66197236,"imageIndex":15},{"imageOffset":66197084,"imageIndex":15},{"imageOffset":65870644,"imageIndex":15},{"imageOffset":66336288,"imageIndex":15},{"imageOffset":66064512,"imageIndex":15},{"imageOffset":66483648,"imageIndex":15},{"imageOffset":66484032,"imageIndex":15},{"imageOffset":66589352,"imageIndex":15},{"imageOffset":28780,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":7724,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":9576127,"name":"com.apple.NSEventThread","frames":[{"imageOffset":3568,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":0},{"imageOffset":75992,"symbol":"mach_msg2_internal","symbolLocation":80,"imageIndex":0},{"imageOffset":38456,"symbol":"mach_msg_overwrite","symbolLocation":540,"imageIndex":0},{"imageOffset":4460,"symbol":"mach_msg","symbolLocation":24,"imageIndex":0},{"imageOffset":531420,"symbol":"__CFRunLoopServiceMachPort","symbolLocation":160,"imageIndex":9},{"imageOffset":525512,"symbol":"__CFRunLoopRun","symbolLocation":1232,"imageIndex":9},{"imageOffset":522404,"symbol":"CFRunLoopRunSpecific","symbolLocation":612,"imageIndex":9},{"imageOffset":1454664,"symbol":"_NSEventThread","symbolLocation":172,"imageIndex":6},{"imageOffset":28780,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":7724,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":9576129,"name":"MemoryInfra","frames":[{"imageOffset":3568,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":0},{"imageOffset":75992,"symbol":"mach_msg2_internal","symbolLocation":80,"imageIndex":0},{"imageOffset":38456,"symbol":"mach_msg_overwrite","symbolLocation":540,"imageIndex":0},{"imageOffset":4460,"symbol":"mach_msg","symbolLocation":24,"imageIndex":0},{"imageOffset":66741424,"imageIndex":15},{"imageOffset":66197236,"imageIndex":15},{"imageOffset":66197084,"imageIndex":15},{"imageOffset":65870644,"imageIndex":15},{"imageOffset":66336288,"imageIndex":15},{"imageOffset":66064512,"imageIndex":15},{"imageOffset":66483648,"imageIndex":15},{"imageOffset":66484032,"imageIndex":15},{"imageOffset":66589352,"imageIndex":15},{"imageOffset":28780,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":7724,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":9576130,"name":"ThreadPoolSingleThreadSharedBackgroundBlocking2","frames":[{"imageOffset":3568,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":0},{"imageOffset":75992,"symbol":"mach_msg2_internal","symbolLocation":80,"imageIndex":0},{"imageOffset":38456,"symbol":"mach_msg_overwrite","symbolLocation":540,"imageIndex":0},{"imageOffset":4460,"symbol":"mach_msg","symbolLocation":24,"imageIndex":0},{"imageOffset":66741424,"imageIndex":15},{"imageOffset":66197236,"imageIndex":15},{"imageOffset":66429892,"imageIndex":15},{"imageOffset":66432404,"imageIndex":15},{"imageOffset":66431928,"imageIndex":15},{"imageOffset":66431840,"imageIndex":15},{"imageOffset":66589352,"imageIndex":15},{"imageOffset":28780,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":7724,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":9576152,"frames":[{"imageOffset":17892,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":0},{"imageOffset":30264,"symbol":"_pthread_cond_wait","symbolLocation":1232,"imageIndex":1},{"imageOffset":51908,"symbol":"std::__1::condition_variable::wait(std::__1::unique_lock&)","symbolLocation":28,"imageIndex":16},{"imageOffset":95156600,"imageIndex":15},{"imageOffset":95160968,"imageIndex":15},{"imageOffset":28780,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":7724,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":9576153,"frames":[{"imageOffset":17892,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":0},{"imageOffset":30264,"symbol":"_pthread_cond_wait","symbolLocation":1232,"imageIndex":1},{"imageOffset":51908,"symbol":"std::__1::condition_variable::wait(std::__1::unique_lock&)","symbolLocation":28,"imageIndex":16},{"imageOffset":95156600,"imageIndex":15},{"imageOffset":95160968,"imageIndex":15},{"imageOffset":28780,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":7724,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":9576154,"frames":[{"imageOffset":17892,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":0},{"imageOffset":30264,"symbol":"_pthread_cond_wait","symbolLocation":1232,"imageIndex":1},{"imageOffset":51908,"symbol":"std::__1::condition_variable::wait(std::__1::unique_lock&)","symbolLocation":28,"imageIndex":16},{"imageOffset":95156600,"imageIndex":15},{"imageOffset":95160968,"imageIndex":15},{"imageOffset":28780,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":7724,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":9576155,"frames":[{"imageOffset":17892,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":0},{"imageOffset":30264,"symbol":"_pthread_cond_wait","symbolLocation":1232,"imageIndex":1},{"imageOffset":51908,"symbol":"std::__1::condition_variable::wait(std::__1::unique_lock&)","symbolLocation":28,"imageIndex":16},{"imageOffset":95156600,"imageIndex":15},{"imageOffset":95160968,"imageIndex":15},{"imageOffset":28780,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":7724,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":9576156,"frames":[{"imageOffset":17892,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":0},{"imageOffset":30264,"symbol":"_pthread_cond_wait","symbolLocation":1232,"imageIndex":1},{"imageOffset":51908,"symbol":"std::__1::condition_variable::wait(std::__1::unique_lock&)","symbolLocation":28,"imageIndex":16},{"imageOffset":95156600,"imageIndex":15},{"imageOffset":95160968,"imageIndex":15},{"imageOffset":28780,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":7724,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":9576157,"frames":[{"imageOffset":17892,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":0},{"imageOffset":30264,"symbol":"_pthread_cond_wait","symbolLocation":1232,"imageIndex":1},{"imageOffset":51908,"symbol":"std::__1::condition_variable::wait(std::__1::unique_lock&)","symbolLocation":28,"imageIndex":16},{"imageOffset":95156600,"imageIndex":15},{"imageOffset":95160968,"imageIndex":15},{"imageOffset":28780,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":7724,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":9576158,"frames":[{"imageOffset":17892,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":0},{"imageOffset":30264,"symbol":"_pthread_cond_wait","symbolLocation":1232,"imageIndex":1},{"imageOffset":51908,"symbol":"std::__1::condition_variable::wait(std::__1::unique_lock&)","symbolLocation":28,"imageIndex":16},{"imageOffset":95156600,"imageIndex":15},{"imageOffset":95160968,"imageIndex":15},{"imageOffset":28780,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":7724,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":9576159,"frames":[{"imageOffset":17892,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":0},{"imageOffset":30264,"symbol":"_pthread_cond_wait","symbolLocation":1232,"imageIndex":1},{"imageOffset":51908,"symbol":"std::__1::condition_variable::wait(std::__1::unique_lock&)","symbolLocation":28,"imageIndex":16},{"imageOffset":95156600,"imageIndex":15},{"imageOffset":95160968,"imageIndex":15},{"imageOffset":28780,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":7724,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":9576160,"frames":[{"imageOffset":17892,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":0},{"imageOffset":30264,"symbol":"_pthread_cond_wait","symbolLocation":1232,"imageIndex":1},{"imageOffset":51908,"symbol":"std::__1::condition_variable::wait(std::__1::unique_lock&)","symbolLocation":28,"imageIndex":16},{"imageOffset":95156600,"imageIndex":15},{"imageOffset":95160968,"imageIndex":15},{"imageOffset":28780,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":7724,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":9576161,"frames":[{"imageOffset":17892,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":0},{"imageOffset":30264,"symbol":"_pthread_cond_wait","symbolLocation":1232,"imageIndex":1},{"imageOffset":51908,"symbol":"std::__1::condition_variable::wait(std::__1::unique_lock&)","symbolLocation":28,"imageIndex":16},{"imageOffset":95156600,"imageIndex":15},{"imageOffset":95160968,"imageIndex":15},{"imageOffset":28780,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":7724,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":9576162,"frames":[{"imageOffset":17892,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":0},{"imageOffset":30264,"symbol":"_pthread_cond_wait","symbolLocation":1232,"imageIndex":1},{"imageOffset":51908,"symbol":"std::__1::condition_variable::wait(std::__1::unique_lock&)","symbolLocation":28,"imageIndex":16},{"imageOffset":95156600,"imageIndex":15},{"imageOffset":95160968,"imageIndex":15},{"imageOffset":28780,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":7724,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":9576163,"frames":[{"imageOffset":17892,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":0},{"imageOffset":30264,"symbol":"_pthread_cond_wait","symbolLocation":1232,"imageIndex":1},{"imageOffset":51908,"symbol":"std::__1::condition_variable::wait(std::__1::unique_lock&)","symbolLocation":28,"imageIndex":16},{"imageOffset":95156600,"imageIndex":15},{"imageOffset":95160968,"imageIndex":15},{"imageOffset":28780,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":7724,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":9711211,"frames":[{"imageOffset":17892,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":0},{"imageOffset":30264,"symbol":"_pthread_cond_wait","symbolLocation":1232,"imageIndex":1},{"imageOffset":1502040,"symbol":"blas_thread_server","symbolLocation":360,"imageIndex":17},{"imageOffset":28780,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":7724,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":9711212,"frames":[{"imageOffset":17892,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":0},{"imageOffset":30264,"symbol":"_pthread_cond_wait","symbolLocation":1232,"imageIndex":1},{"imageOffset":1502040,"symbol":"blas_thread_server","symbolLocation":360,"imageIndex":17},{"imageOffset":28780,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":7724,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":9711213,"frames":[{"imageOffset":17892,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":0},{"imageOffset":30264,"symbol":"_pthread_cond_wait","symbolLocation":1232,"imageIndex":1},{"imageOffset":1502040,"symbol":"blas_thread_server","symbolLocation":360,"imageIndex":17},{"imageOffset":28780,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":7724,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":9711214,"frames":[{"imageOffset":17892,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":0},{"imageOffset":30264,"symbol":"_pthread_cond_wait","symbolLocation":1232,"imageIndex":1},{"imageOffset":1502040,"symbol":"blas_thread_server","symbolLocation":360,"imageIndex":17},{"imageOffset":28780,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":7724,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":9711215,"frames":[{"imageOffset":17892,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":0},{"imageOffset":30264,"symbol":"_pthread_cond_wait","symbolLocation":1232,"imageIndex":1},{"imageOffset":1502040,"symbol":"blas_thread_server","symbolLocation":360,"imageIndex":17},{"imageOffset":28780,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":7724,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":9711216,"frames":[{"imageOffset":17892,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":0},{"imageOffset":30264,"symbol":"_pthread_cond_wait","symbolLocation":1232,"imageIndex":1},{"imageOffset":1502040,"symbol":"blas_thread_server","symbolLocation":360,"imageIndex":17},{"imageOffset":28780,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":7724,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":9711217,"frames":[{"imageOffset":17892,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":0},{"imageOffset":30264,"symbol":"_pthread_cond_wait","symbolLocation":1232,"imageIndex":1},{"imageOffset":1502040,"symbol":"blas_thread_server","symbolLocation":360,"imageIndex":17},{"imageOffset":28780,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":7724,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":9711218,"frames":[{"imageOffset":17892,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":0},{"imageOffset":30264,"symbol":"_pthread_cond_wait","symbolLocation":1232,"imageIndex":1},{"imageOffset":1502040,"symbol":"blas_thread_server","symbolLocation":360,"imageIndex":17},{"imageOffset":28780,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":7724,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":9711219,"frames":[{"imageOffset":17892,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":0},{"imageOffset":30264,"symbol":"_pthread_cond_wait","symbolLocation":1232,"imageIndex":1},{"imageOffset":1502040,"symbol":"blas_thread_server","symbolLocation":360,"imageIndex":17},{"imageOffset":28780,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":7724,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":9711220,"frames":[{"imageOffset":17892,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":0},{"imageOffset":30264,"symbol":"_pthread_cond_wait","symbolLocation":1232,"imageIndex":1},{"imageOffset":1502040,"symbol":"blas_thread_server","symbolLocation":360,"imageIndex":17},{"imageOffset":28780,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":7724,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":9711221,"frames":[{"imageOffset":17892,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":0},{"imageOffset":30264,"symbol":"_pthread_cond_wait","symbolLocation":1232,"imageIndex":1},{"imageOffset":1502040,"symbol":"blas_thread_server","symbolLocation":360,"imageIndex":17},{"imageOffset":28780,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":1},{"imageOffset":7724,"symbol":"thread_start","symbolLocation":8,"imageIndex":1}]},{"id":9773715,"frames":[{"imageOffset":7704,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":1}]},{"id":9798684,"frames":[{"imageOffset":7704,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":1}]},{"id":10129651,"frames":[{"imageOffset":7704,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":1}]},{"id":10129653,"frames":[{"imageOffset":7704,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":1}]},{"id":10193302,"frames":[{"imageOffset":7704,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":1}]},{"id":10193303,"frames":[{"imageOffset":7704,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":1}]}],
"usedImages" : [
{
"source" : "P",
"arch" : "arm64e",
"base" : 7262756864,
"size" : 233468,
"uuid" : "cc8c9730-0055-3658-bb1c-1b49a5eadccd",
"path" : "\/usr\/lib\/system\/libsystem_kernel.dylib",
"name" : "libsystem_kernel.dylib"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 7262990336,
"size" : 53244,
"uuid" : "1712c255-a808-3763-b5e4-8c3faeb3dd68",
"path" : "\/usr\/lib\/system\/libsystem_pthread.dylib",
"name" : "libsystem_pthread.dylib"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 7261708288,
"size" : 528372,
"uuid" : "93b31654-aeb0-3829-a447-3c3cb85016b7",
"path" : "\/usr\/lib\/system\/libsystem_c.dylib",
"name" : "libsystem_c.dylib"
},
{
"source" : "P",
"arch" : "arm64",
"base" : 4349706240,
"CFBundleShortVersionString" : "3.11.4, (c) 2001-2023 Python Software Foundation.",
"CFBundleIdentifier" : "org.python.python",
"size" : 3948544,
"uuid" : "88bffd37-99d8-36ab-9b95-9f54b30bd667",
"path" : "\/Applications\/ChimeraX-1.8-rc2024.05.31.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/Python",
"name" : "Python",
"CFBundleVersion" : "3.11.4"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 7263191040,
"size" : 32764,
"uuid" : "09a49a5d-2c19-33bb-ad50-219b2739ff1f",
"path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
"name" : "libsystem_platform.dylib"
},
{
"source" : "P",
"arch" : "arm64",
"base" : 5907415040,
"size" : 638976,
"uuid" : "68fd5eb3-4cdf-3190-8b80-e5378d6b4c9d",
"path" : "\/Applications\/ChimeraX-1.8-rc2024.05.31.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/plugins\/platforms\/libqcocoa.dylib",
"name" : "libqcocoa.dylib"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 7316484096,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.AppKit",
"size" : 15761408,
"uuid" : "47f20729-e102-3a52-a31d-8be7277f85fb",
"path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
"name" : "AppKit",
"CFBundleVersion" : "2299"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 7343542272,
"CFBundleShortVersionString" : "1.600.0",
"CFBundleIdentifier" : "com.apple.SkyLight",
"size" : 4288512,
"uuid" : "dfc7d410-2140-38b6-a249-721aef98b34e",
"path" : "\/System\/Library\/PrivateFrameworks\/SkyLight.framework\/Versions\/A\/SkyLight",
"name" : "SkyLight"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 7261401088,
"size" : 294912,
"uuid" : "32e65f15-e8fb-35d6-8bda-b0d046a41d56",
"path" : "\/usr\/lib\/system\/libdispatch.dylib",
"name" : "libdispatch.dylib"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 7263404032,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.CoreFoundation",
"size" : 5079040,
"uuid" : "da41d167-77ad-3bee-8a4c-ccc1399ee15e",
"path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
"name" : "CoreFoundation",
"CFBundleVersion" : "1953.1"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 7421485056,
"CFBundleShortVersionString" : "2.1.1",
"CFBundleIdentifier" : "com.apple.HIToolbox",
"size" : 3358720,
"uuid" : "8384f6fe-bb4d-3b01-b6b4-54011042b722",
"path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
"name" : "HIToolbox"
},
{
"source" : "P",
"arch" : "arm64",
"base" : 4443865088,
"size" : 4849664,
"uuid" : "113c92ac-6022-34c0-8532-0a96c67af294",
"path" : "\/Applications\/ChimeraX-1.8-rc2024.05.31.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtCore.framework\/Versions\/A\/QtCore",
"name" : "QtCore"
},
{
"source" : "P",
"arch" : "arm64",
"base" : 4455137280,
"size" : 3112960,
"uuid" : "ee8cff87-6a5d-38d1-8403-031c9916b0fb",
"path" : "\/Applications\/ChimeraX-1.8-rc2024.05.31.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/QtWidgets.abi3.so",
"name" : "QtWidgets.abi3.so"
},
{
"source" : "P",
"arch" : "arm64",
"base" : 4334862336,
"CFBundleShortVersionString" : "1.8.0",
"CFBundleIdentifier" : "edu.ucsf.cgl.ChimeraX",
"size" : 16384,
"uuid" : "17982d98-65bc-3327-8526-577ec996453c",
"path" : "\/Applications\/ChimeraX-1.8-rc2024.05.31.app\/Contents\/MacOS\/ChimeraX",
"name" : "ChimeraX",
"CFBundleVersion" : "1.8.0.0"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 7259676672,
"size" : 566452,
"uuid" : "b7142778-f6ba-31ca-820c-34b24d90f149",
"path" : "\/usr\/lib\/dyld",
"name" : "dyld"
},
{
"source" : "P",
"arch" : "arm64",
"base" : 6140051456,
"size" : 165756928,
"uuid" : "72eb72da-af14-3e6d-a878-889044e69fe6",
"path" : "\/Applications\/ChimeraX-1.8-rc2024.05.31.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtWebEngineCore.framework\/Versions\/A\/QtWebEngineCore",
"name" : "QtWebEngineCore"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 7262236672,
"size" : 421876,
"uuid" : "14267a9b-21bf-34c7-a706-8083a7ea551d",
"path" : "\/usr\/lib\/libc++.1.dylib",
"name" : "libc++.1.dylib"
},
{
"source" : "P",
"arch" : "arm64",
"base" : 4461838336,
"size" : 21299200,
"uuid" : "9854a721-2573-3169-81ec-19ea40ce8077",
"path" : "\/Applications\/ChimeraX-1.8-rc2024.05.31.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/numpy\/.dylibs\/libopenblas64_.0.dylib",
"name" : "libopenblas64_.0.dylib"
},
{
"size" : 0,
"source" : "A",
"base" : 0,
"uuid" : "00000000-0000-0000-0000-000000000000"
}
],
"vmSummary" : "ReadOnly portion of Libraries: Total=1.6G resident=0K(0%) swapped_out_or_unallocated=1.6G(100%)\nWritable regions: Total=4.0G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=4.0G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 2048K 16 \nActivity Tracing 256K 1 \nCG backing stores 7680K 8 \nCG image 880K 46 \nColorSync 640K 29 \nCoreAnimation 1984K 94 \nCoreGraphics 80K 5 \nCoreServices 624K 2 \nCoreUI image data 4432K 32 \nFoundation 48K 2 \nKernel Alloc Once 32K 1 \nMALLOC 2.1G 981 \nMALLOC guard page 192K 10 \nMALLOC_MEDIUM (reserved) 792.0M 12 reserved VM address space (unallocated)\nMALLOC_NANO (reserved) 384.0M 1 reserved VM address space (unallocated)\nMach message 64K 2 \nOpenGL GLSL 384K 4 \nSTACK GUARD 752K 47 \nStack 160.2M 48 \nStack Guard 56.0M 1 \nVM_ALLOCATE 337.1M 388 \nVM_ALLOCATE (reserved) 256.0M 1 reserved VM address space (unallocated)\n__AUTH 1938K 369 \n__AUTH_CONST 25.0M 600 \n__CTF 756 1 \n__DATA 20.7M 754 \n__DATA_CONST 38.7M 758 \n__DATA_DIRTY 2030K 238 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__LINKEDIT 791.9M 158 \n__OBJC_CONST 4847K 337 \n__OBJC_RO 65.1M 1 \n__OBJC_RW 1981K 1 \n__TEXT 843.2M 780 \ndyld private memory 560K 4 \nmapped file 209.9M 68 \nshared memory 3264K 32 \n=========== ======= ======= \nTOTAL 6.0G 5834 \nTOTAL, minus reserved VM space 4.6G 5834 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "6112e3d2fc54bc3389840661",
"factorPackIds" : {
"SIRI_TEXT_TO_SPEECH" : "6407d37503b3136e9aacb281"
},
"deploymentId" : 240000478
},
{
"rolloutId" : "6112d17137f5d11121dcd4e2",
"factorPackIds" : {
},
"deploymentId" : 240000570
}
],
"experiments" : [
]
},
"reportNotes" : [
"dyld_process_snapshot_create_for_process failed with 5"
]
}
===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
> camera ortho
> cofr centerOfView
> mousemode alt rightMode "contour level"
> mousemode alt leftMode "translate selected models"
> mousemode shift leftMode "rotate selected models"
> alias cofron cofr centerofview showpivot true
> alias cofroff cofr centerofview showpivot false
> alias symclip cofr centerofview; clip near -$1 far $1 position cofr
> alias cootmode surface cap false; surface style solid; lighting full;
> graphics silhouettes false; style stick; ~rib; color ##num_residues gold;
> color byhet ; disp; ~disp @H*; style solvent ball; size ballscale 0.1; size
> stickradius 0.07; transparency 70; cofr centerofview; clip near -10 far 10
> position cofr; color ##~num_residues cornflower blue
> alias cootmode_mesh surface cap false; surface style mesh; lighting full;
> graphics silhouettes false; style stick; ~rib; color ##num_residues gold;
> color byhet ; disp; ~disp @H*; style solvent ball; size ballscale 0.1; size
> stickradius 0.07; cofr centerofview; clip near -10 far 10 position cofr;
> color ##~num_residues #3d60ffff; transparency 50
> alias ca_and_sidechains ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1;
> disp @P&nucleic&$1; style $1 stick; disp sidechain&$1; disp
> ~backbone&nucleic&$1; size stickradius 0.1; size pseudobondradius 0.1
> alias ca_trace ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1; disp
> @P&nucleic&$1; style $1 stick; size stickradius 0.1; size pseudobondradius
> 0.1
> alias map_sphere_15 surface unzone ##~num_residues; sel; close #10000;
> marker #10000 position cofr; sel ~sel; surface zone ##~num_residues
> nearAtoms sel distance 15; close #10000
> alias map_unsphere surface unzone ##~num_residues
> alias hidemaps surface unzone ##~num_residues; sel; close #10000; marker
> #10000 position cofr; sel ~sel; surface zone ##~num_residues nearAtoms sel
> distance 0; close #10000
> alias showmaps surface unzone ##~num_residues
> alias caps_off surface cap false
> alias caps_on surface cap true
> alias selbetween ks ri
> alias rock_movie cofr showpivot false; movie record; rock y 30; wait 136;
> movie encode /Users/peiqiangfeng/Desktop/rock_movie.mp4; stop
> alias helixmap color byattribute r:helix_lipophilicity palette lipophilicity
> buttonpanel Shortcuts rows 3 columns 4
> buttonpanel Shortcuts add Vol_Viewer command "tool show 'Volume Viewer'"
> buttonpanel Shortcuts add Model_Panel command "tool show Models"
> buttonpanel Shortcuts add Log command "tool show Log"
> buttonpanel Shortcuts add default_disp command default_mol_display
> buttonpanel Shortcuts add map_sphere command map_sphere_15
> buttonpanel Shortcuts add map_unsphere command map_unsphere
> buttonpanel Shortcuts add cofron command cofron
> buttonpanel Shortcuts add cofroff command cofroff
> buttonpanel Shortcuts add cootmode command cootmode
> buttonpanel Shortcuts add cootmode_mesh command cootmode_mesh
> buttonpanel Shortcuts add mark_cofr command "marker #10000 position cofr"
> buttonpanel Shortcuts add hidemaps command hidemaps
> buttonpanel Shortcuts add showmaps command showmaps
> buttonpanel Shortcuts add caps_off command caps_off
> buttonpanel Shortcuts add caps_on command caps_on
> buttonpanel Shortcuts add previous_model command prevmodel
> buttonpanel Shortcuts add next_model command nextmodel
> runscript /Users/peiqiangfeng/Desktop/ChimeraX_py/chimerax_startup.py
> runscript /Users/peiqiangfeng/Desktop/ChimeraX_py/helixmlp.py
> volume defaultvalues limitVoxelCount false voxelLimitForPlane
> 1000000000000000 voxelLimitForOpen 1000000000000000 saveSettings true
Saved volume settings
UCSF ChimeraX version: 1.8rc202405312319 (2024-05-31)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/peiqiangfeng/Downloads/cryosparc_P32_J107_007_volume_map_sharp.mrc
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc as #1, grid size
280,280,280, pixel 0.92, shown at level 0.0348, step 1, values float32
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 0 atomic models, 1 maps.
> surface dust #1 size 9.2
> volume #1 level 0.1342
> volume #1 level 0.12
> open /Users/peiqiangfeng/Downloads/BASS2_2025_af3-coot-0.pdb
Chain information for BASS2_2025_af3-coot-0.pdb #2
---
Chain | Description
A | No description available
> fitmap #2 inMap #1
Fit molecule BASS2_2025_af3-coot-0.pdb (#2) to map
cryosparc_P32_J107_007_volume_map_sharp.mrc (#1) using 2402 atoms
average map value = 0.2364, steps = 48
shifted from previous position = 0.144
rotated from previous position = 0.439 degrees
atoms outside contour = 844, contour level = 0.12
Position of BASS2_2025_af3-coot-0.pdb (#2) relative to
cryosparc_P32_J107_007_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99997076 0.00764313 -0.00026276 -0.85064195
-0.00764298 0.99997063 0.00056603 0.95481804
0.00026708 -0.00056401 0.99999981 0.07664955
Axis -0.07368095 -0.03454680 -0.99668332
Axis point 124.28517026 112.22078632 0.00000000
Rotation angle (degrees) 0.43937623
Shift along axis -0.04670513
> fitmap #2 inMap #1
Fit molecule BASS2_2025_af3-coot-0.pdb (#2) to map
cryosparc_P32_J107_007_volume_map_sharp.mrc (#1) using 2402 atoms
average map value = 0.2363, steps = 44
shifted from previous position = 0.0193
rotated from previous position = 0.0292 degrees
atoms outside contour = 842, contour level = 0.12
Position of BASS2_2025_af3-coot-0.pdb (#2) relative to
cryosparc_P32_J107_007_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99997385 0.00721176 -0.00053269 -0.76749599
-0.00721145 0.99997383 0.00058013 0.91095516
0.00053686 -0.00057627 0.99999969 0.04377154
Axis -0.07970253 -0.07371669 -0.99408921
Axis point 125.42482878 107.42455122 0.00000000
Rotation angle (degrees) 0.41565513
Shift along axis -0.04949405
> fitmap #2 inMap #1
Fit molecule BASS2_2025_af3-coot-0.pdb (#2) to map
cryosparc_P32_J107_007_volume_map_sharp.mrc (#1) using 2402 atoms
average map value = 0.2363, steps = 76
shifted from previous position = 0.00352
rotated from previous position = 0.0088 degrees
atoms outside contour = 845, contour level = 0.12
Position of BASS2_2025_af3-coot-0.pdb (#2) relative to
cryosparc_P32_J107_007_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99997294 0.00734249 -0.00045829 -0.79476282
-0.00734224 0.99997289 0.00054932 0.92889104
0.00046231 -0.00054594 0.99999974 0.04944318
Axis -0.07423345 -0.06239528 -0.99528701
Axis point 125.70079312 109.19181745 0.00000000
Rotation angle (degrees) 0.42268265
Shift along axis -0.04817059
> fitmap #2 inMap #1
Fit molecule BASS2_2025_af3-coot-0.pdb (#2) to map
cryosparc_P32_J107_007_volume_map_sharp.mrc (#1) using 2402 atoms
average map value = 0.2363, steps = 40
shifted from previous position = 0.00578
rotated from previous position = 0.0011 degrees
atoms outside contour = 845, contour level = 0.12
Position of BASS2_2025_af3-coot-0.pdb (#2) relative to
cryosparc_P32_J107_007_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99997306 0.00732550 -0.00046670 -0.79222012
-0.00732525 0.99997302 0.00055253 0.92073787
0.00047074 -0.00054910 0.99999974 0.04732007
Axis -0.07482915 -0.06367597 -0.99516128
Axis point 124.88830788 109.07913635 0.00000000
Rotation angle (degrees) 0.42175764
Shift along axis -0.04643882
> fitmap #2 inMap #1
Fit molecule BASS2_2025_af3-coot-0.pdb (#2) to map
cryosparc_P32_J107_007_volume_map_sharp.mrc (#1) using 2402 atoms
average map value = 0.2363, steps = 44
shifted from previous position = 0.0088
rotated from previous position = 0.0109 degrees
atoms outside contour = 844, contour level = 0.12
Position of BASS2_2025_af3-coot-0.pdb (#2) relative to
cryosparc_P32_J107_007_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99997438 0.00714041 -0.00051015 -0.76531226
-0.00714013 0.99997436 0.00054636 0.90576366
0.00051404 -0.00054271 0.99999972 0.04250603
Axis -0.07584827 -0.07132965 -0.99456479
Axis point 125.97912865 108.15128779 0.00000000
Rotation angle (degrees) 0.41134652
Shift along axis -0.04883520
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> open 9JCZ
Fetching url http://files.rcsb.org/download/9jcz.cif failed:
HTTP Error 404: Not Found
> transparency 50
> show atoms
> color byhetero
> open /Users/peiqiangfeng/Downloads/BASS2_phenix-coot-0.pdb
Chain information for BASS2_phenix-coot-0.pdb #3
---
Chain | Description
A | No description available
> tool show Models
> close #2
> select add #3
2371 atoms, 2419 bonds, 319 residues, 1 model selected
> select add #1
2371 atoms, 2419 bonds, 319 residues, 3 models selected
> fitmap #3 inMap #1
Fit molecule BASS2_phenix-coot-0.pdb (#3) to map
cryosparc_P32_J107_007_volume_map_sharp.mrc (#1) using 2371 atoms
average map value = 0.2767, steps = 28
shifted from previous position = 0.0438
rotated from previous position = 0.047 degrees
atoms outside contour = 575, contour level = 0.12
Position of BASS2_phenix-coot-0.pdb (#3) relative to
cryosparc_P32_J107_007_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99999990 0.00043449 -0.00011857 -0.05700117
-0.00043457 0.99999967 -0.00068630 0.19354619
0.00011827 0.00068635 0.99999976 -0.08757505
Axis 0.83606106 -0.14425351 -0.52933243
Axis point 0.00000000 150.22865499 275.80189148
Rotation angle (degrees) 0.04703401
Shift along axis -0.02921986
> fitmap #3 inMap #1
Fit molecule BASS2_phenix-coot-0.pdb (#3) to map
cryosparc_P32_J107_007_volume_map_sharp.mrc (#1) using 2371 atoms
average map value = 0.2767, steps = 48
shifted from previous position = 0.00534
rotated from previous position = 0.00385 degrees
atoms outside contour = 575, contour level = 0.12
Position of BASS2_phenix-coot-0.pdb (#3) relative to
cryosparc_P32_J107_007_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99999989 0.00043829 -0.00016054 -0.04943512
-0.00043839 0.99999970 -0.00063393 0.18152075
0.00016026 0.00063400 0.99999979 -0.08780127
Axis 0.80528101 -0.20374597 -0.55678548
Axis point 0.00000000 163.08878156 277.29535571
Rotation angle (degrees) 0.04510680
Shift along axis -0.02790681
> fitmap #3 inMap #1
Fit molecule BASS2_phenix-coot-0.pdb (#3) to map
cryosparc_P32_J107_007_volume_map_sharp.mrc (#1) using 2371 atoms
average map value = 0.2767, steps = 48
shifted from previous position = 0.00217
rotated from previous position = 0.00811 degrees
atoms outside contour = 575, contour level = 0.12
Position of BASS2_phenix-coot-0.pdb (#3) relative to
cryosparc_P32_J107_007_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99999983 0.00057475 -0.00013088 -0.06982266
-0.00057483 0.99999965 -0.00061041 0.19577458
0.00013053 0.00061049 0.99999981 -0.08090758
Axis 0.71936341 -0.15402649 -0.67734196
Axis point 0.00000000 161.01096633 314.17707650
Rotation angle (degrees) 0.04862115
Shift along axis -0.02558024
> select clear
> volume #1 level 0.1058
> volume #1 level 0.08448
> cootmode_mesh
Changed 2371 atom styles
Changed 0 atom styles
Changed 1 ball scales
Changed 2419 bond radii
> color ##~num_residues #3d60ffff; transparency 50
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> set bgColor black
> select ions
2 atoms, 2 residues, 1 model selected
> style sel sphere
Changed 2 atom styles
> style sel ball
Changed 2 atom styles
> style sel stick
Changed 2 atom styles
> style sel ball
Changed 2 atom styles
> style sel ball
Changed 2 atom styles
> style sel ball
Changed 2 atom styles
> style sel sphere
Changed 2 atom styles
> transparency 0
> select #1
2 models selected
> select clear
> volume #1 level 0.12
> select ligand
6 atoms, 5 bonds, 1 residue, 1 model selected
> color sel byhetero
> style sel ball
Changed 6 atom styles
> style sel sphere
Changed 6 atom styles
> style sel ball
Changed 6 atom styles
> select clear
> select add #3
2371 atoms, 2419 bonds, 319 residues, 1 model selected
> mlp sel
Map values for surface "BASS2_phenix-coot-0.pdb_A SES surface": minimum
-31.28, mean 0.5773, maximum 23.32
To also show corresponding color key, enter the above mlp command and add key
true
> caps_on
> surface cap true
> caps_on
> caps_off
> surface cap false
> select clear
> select add #3.1
2363 atoms, 316 residues, 1 model selected
> transparency sel 50
> select clear
> hide #3.1 models
> view
> volume #1 level 0.08448
> cootmode_mesh
Changed 2371 atom styles
Changed 0 atom styles
Changed 1 ball scales
Changed 2419 bond radii
> color ##~num_residues #3d60ffff; transparency 50
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> view
> cootmode
Changed 2371 atom styles
Changed 0 atom styles
Changed 1 ball scales
Changed 2419 bond radii
> color ##~num_residues cornflower blue
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> lighting soft
> lighting full
> lighting simple
> lighting flat
> graphics silhouettes false
> lighting soft
> lighting simple
> marker #10000 position cofr
> cofroff
> cofron
> cofroff
> default_mol_display
Unknown command: default_mol_display
> map_unsphere
> surface unzone ##~num_residues
Missing or invalid "surfaces" argument: invalid surfaces specifier
> map_sphere_15
> surface unzone ##~num_residues; sel; close #10000; marker #10000 position
> cofr; sel ~sel; surface zone ##~num_residues nearAtoms sel distance 15;
> close #10000
Missing or invalid "surfaces" argument: invalid surfaces specifier
> tool show Models
> close #10000
> show #3.1 models
> select add #3.1
2363 atoms, 316 residues, 1 model selected
> map_sphere_15
> surface unzone ##~num_residues; sel; close #10000; marker #10000 position
> cofr; sel ~sel; surface zone ##~num_residues nearAtoms sel distance 15;
> close #10000
Missing or invalid "surfaces" argument: invalid surfaces specifier
> hide #!3 models
> ui tool show "Side View"
> view sel
> tool show Models
> show #!3 models
> hide #3.1 models
> select subtract #3.1
1 model selected
> select ligand
6 atoms, 5 bonds, 1 residue, 1 model selected
> tool show Log
> style sel stick
Changed 6 atom styles
> style sel ball
Changed 6 atom styles
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue PYR (net charge -1) with am1-bcc method
Running ANTECHAMBER command:
/Applications/ChimeraX-1.8-rc2024.05.31.app/Contents/bin/amber20/bin/antechamber
-ek qm_theory='AM1', -i
/var/folders/hn/x3ztvv2n1ll3wlkllltf7nyw0000gp/T/tmpybdusft4/ante.in.mol2 -fi
mol2 -o
/var/folders/hn/x3ztvv2n1ll3wlkllltf7nyw0000gp/T/tmpybdusft4/ante.out.mol2 -fo
mol2 -c bcc -nc -1 -j 5 -s 2 -dr n
(PYR) ``
(PYR) `Welcome to antechamber 20.0: molecular input file processor.`
(PYR) ``
(PYR) `Info: Finished reading file
(/var/folders/hn/x3ztvv2n1ll3wlkllltf7nyw0000gp/T/tmpybdusft4/ante.in.mol2);
atoms read (9), bonds read (8).`
(PYR) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(PYR) `Running:
/Applications/ChimeraX-1.8-rc2024.05.31.app/Contents/bin/amber20/bin/bondtype
-j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(PYR) ``
(PYR) ``
(PYR) `Running:
/Applications/ChimeraX-1.8-rc2024.05.31.app/Contents/bin/amber20/bin/atomtype
-i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(PYR) `Info: Total number of electrons: 46; net charge: -1`
(PYR) ``
(PYR) `Running:
/Applications/ChimeraX-1.8-rc2024.05.31.app/Contents/bin/amber20/bin/sqm -O -i
sqm.in -o sqm.out`
(PYR) ``
(PYR) `Running:
/Applications/ChimeraX-1.8-rc2024.05.31.app/Contents/bin/amber20/bin/am1bcc -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
/Applications/ChimeraX-1.8-rc2024.05.31.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT
-s 2 -j 1`
(PYR) ``
(PYR) `Running:
/Applications/ChimeraX-1.8-rc2024.05.31.app/Contents/bin/amber20/bin/atomtype
-f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`
(PYR) ``
Charges for residue PYR determined
Coulombic values for BASS2_phenix-coot-0.pdb_A SES surface #3.2: minimum,
-9.71, mean -6.28, maximum -2.04
To also show corresponding color key, enter the above coulombic command and
add key true
> mlp sel
mlp: no amino acids specified
> mlp sel
mlp: no amino acids specified
> show #3.1 models
> hide #3.1 models
> hide #3.2 models
> show #3.2 models
> color bfactor sel
6 atoms, 1 residues, 1 surfaces, atom bfactor range 20 to 20
> hide #3.2 models
> show #3.2 models
> hide #3.2 models
> select subtract #3.2
1 model selected
> color byhetero
> show #3.2 models
> close #3.2
> select add #3
2371 atoms, 2419 bonds, 319 residues, 1 model selected
> color bfactor sel
2371 atoms, 319 residues, 1 surfaces, atom bfactor range 0.8 to 127
> select subtract #3
1 model selected
> show cartoons
> vop gaussian #1 sdev 2.76
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc gaussian as #2, grid size
280,280,280, pixel 0.92, shown at step 1, values float32
> vop gaussian #2 sdev 2.76
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc gaussian as #4, grid size
280,280,280, pixel 0.92, shown at step 1, values float32
> vop gaussian #4 sdev 2.76
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc gaussian as #5, grid size
280,280,280, pixel 0.92, shown at step 1, values float32
> close #5
> close #4
> show #!2 models
> close #2
> rainbow
> select ions
2 atoms, 2 residues, 1 model selected
> style sel sphere
Changed 2 atom styles
> select ligand
6 atoms, 5 bonds, 1 residue, 1 model selected
> color sel bynucleotide
> rainbow sel
> color sel byhetero
> style sel sphere
Changed 6 atom styles
> hide sel atoms
> show sel atoms
> select add #3
2371 atoms, 2419 bonds, 319 residues, 1 model selected
> hide sel atoms
> select ligand
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> show #!1 models
> select add #3
2371 atoms, 2419 bonds, 319 residues, 1 model selected
Alignment identifier is 3/A
> select /A:402
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:402-407
52 atoms, 52 bonds, 6 residues, 1 model selected
> select clear
> hide #!3 models
> hide #!1 models
> show #!3 models
> select ions
2 atoms, 2 residues, 1 model selected
> style sel sphere
Changed 2 atom styles
> show sel atoms
> hide #!3 models
> show #!3 models
> open /Users/peiqiangfeng/Downloads/BASS2_2025_af3.pdb
Chain information for BASS2_2025_af3.pdb #2
---
Chain | Description
A | No description available
> show #3.1 models
> hide #3.1 models
> hide #2 models
> show #2 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #2 models
> show #!1 models
> ui tool show "Color Zone"
> color zone #1 near #3 distance 3.55
> transparency #1.1 0
> color zone #1 near #3 distance 2.43
> volume #1 level 0.1013
> volume #1 level 0.0901
> color zone #1 near #3 distance 2.43
> volume splitbyzone #1
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 0 as #4.1, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 1 as #4.2, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 2 as #4.3, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 3 as #4.4, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 4 as #4.5, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 5 as #4.6, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 6 as #4.7, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 7 as #4.8, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 8 as #4.9, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 9 as #4.10, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 10 as #4.11, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 11 as #4.12, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 12 as #4.13, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 13 as #4.14, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 14 as #4.15, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 15 as #4.16, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 16 as #4.17, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 17 as #4.18, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 18 as #4.19, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 19 as #4.20, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 20 as #4.21, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 21 as #4.22, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 22 as #4.23, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 23 as #4.24, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 24 as #4.25, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 25 as #4.26, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 26 as #4.27, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 27 as #4.28, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 28 as #4.29, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 29 as #4.30, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 30 as #4.31, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 31 as #4.32, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 32 as #4.33, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 33 as #4.34, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 34 as #4.35, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 35 as #4.36, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 36 as #4.37, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 37 as #4.38, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 38 as #4.39, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 39 as #4.40, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 40 as #4.41, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 41 as #4.42, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 42 as #4.43, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 43 as #4.44, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 44 as #4.45, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 45 as #4.46, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 46 as #4.47, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 47 as #4.48, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 48 as #4.49, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 49 as #4.50, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 50 as #4.51, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 51 as #4.52, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 52 as #4.53, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 53 as #4.54, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 54 as #4.55, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 55 as #4.56, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 56 as #4.57, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 57 as #4.58, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 58 as #4.59, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 59 as #4.60, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 60 as #4.61, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 61 as #4.62, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 62 as #4.63, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 63 as #4.64, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 64 as #4.65, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 65 as #4.66, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 66 as #4.67, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 67 as #4.68, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 68 as #4.69, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 69 as #4.70, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 70 as #4.71, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 71 as #4.72, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 72 as #4.73, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 73 as #4.74, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 74 as #4.75, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 75 as #4.76, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 76 as #4.77, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 77 as #4.78, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 78 as #4.79, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 79 as #4.80, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 80 as #4.81, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 81 as #4.82, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 82 as #4.83, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 83 as #4.84, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 84 as #4.85, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 85 as #4.86, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 86 as #4.87, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 87 as #4.88, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 88 as #4.89, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 89 as #4.90, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 90 as #4.91, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 91 as #4.92, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 92 as #4.93, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 93 as #4.94, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 94 as #4.95, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 95 as #4.96, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 96 as #4.97, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 97 as #4.98, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 98 as #4.99, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 99 as #4.100, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 100 as #4.101, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 101 as #4.102, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 102 as #4.103, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 103 as #4.104, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 104 as #4.105, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 105 as #4.106, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 106 as #4.107, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 107 as #4.108, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 108 as #4.109, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 109 as #4.110, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 110 as #4.111, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 111 as #4.112, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 112 as #4.113, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 113 as #4.114, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 114 as #4.115, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 115 as #4.116, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 116 as #4.117, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 117 as #4.118, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 118 as #4.119, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 119 as #4.120, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 120 as #4.121, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 121 as #4.122, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 122 as #4.123, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 123 as #4.124, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 124 as #4.125, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 125 as #4.126, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 126 as #4.127, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 127 as #4.128, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 128 as #4.129, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 129 as #4.130, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 130 as #4.131, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 131 as #4.132, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 132 as #4.133, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 133 as #4.134, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 134 as #4.135, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 135 as #4.136, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 136 as #4.137, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 137 as #4.138, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 138 as #4.139, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 139 as #4.140, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 140 as #4.141, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 141 as #4.142, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 142 as #4.143, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 143 as #4.144, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 144 as #4.145, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 145 as #4.146, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 146 as #4.147, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 147 as #4.148, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 148 as #4.149, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 149 as #4.150, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 150 as #4.151, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 151 as #4.152, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 152 as #4.153, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 153 as #4.154, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 154 as #4.155, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 155 as #4.156, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 156 as #4.157, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 157 as #4.158, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 158 as #4.159, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 159 as #4.160, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 160 as #4.161, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 161 as #4.162, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 162 as #4.163, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 163 as #4.164, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 164 as #4.165, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 165 as #4.166, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 166 as #4.167, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 167 as #4.168, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 168 as #4.169, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 169 as #4.170, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 170 as #4.171, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 171 as #4.172, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 172 as #4.173, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 173 as #4.174, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 174 as #4.175, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 175 as #4.176, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 176 as #4.177, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 177 as #4.178, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 178 as #4.179, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 179 as #4.180, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 180 as #4.181, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 181 as #4.182, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 182 as #4.183, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 183 as #4.184, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 184 as #4.185, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 185 as #4.186, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 186 as #4.187, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 187 as #4.188, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 188 as #4.189, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 189 as #4.190, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 190 as #4.191, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 191 as #4.192, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 192 as #4.193, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 193 as #4.194, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 194 as #4.195, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 195 as #4.196, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 196 as #4.197, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 197 as #4.198, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 198 as #4.199, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 199 as #4.200, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 200 as #4.201, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 201 as #4.202, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 202 as #4.203, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 203 as #4.204, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 204 as #4.205, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 205 as #4.206, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 206 as #4.207, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 207 as #4.208, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 208 as #4.209, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 209 as #4.210, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 210 as #4.211, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 211 as #4.212, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 212 as #4.213, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 213 as #4.214, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 214 as #4.215, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 215 as #4.216, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 216 as #4.217, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 217 as #4.218, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 218 as #4.219, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 219 as #4.220, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 220 as #4.221, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 221 as #4.222, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 222 as #4.223, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 223 as #4.224, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 224 as #4.225, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 225 as #4.226, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 226 as #4.227, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 227 as #4.228, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 228 as #4.229, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 229 as #4.230, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 230 as #4.231, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 231 as #4.232, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 232 as #4.233, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 233 as #4.234, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 234 as #4.235, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 235 as #4.236, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 236 as #4.237, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 237 as #4.238, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 238 as #4.239, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 239 as #4.240, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 240 as #4.241, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 241 as #4.242, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 242 as #4.243, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 243 as #4.244, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 244 as #4.245, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 245 as #4.246, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 246 as #4.247, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 247 as #4.248, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 248 as #4.249, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 249 as #4.250, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 250 as #4.251, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 251 as #4.252, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 252 as #4.253, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 253 as #4.254, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 254 as #4.255, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 255 as #4.256, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 256 as #4.257, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 257 as #4.258, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 258 as #4.259, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 259 as #4.260, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 260 as #4.261, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 261 as #4.262, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 262 as #4.263, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 263 as #4.264, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 264 as #4.265, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 265 as #4.266, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 266 as #4.267, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 267 as #4.268, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 268 as #4.269, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 269 as #4.270, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 270 as #4.271, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 271 as #4.272, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 272 as #4.273, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 273 as #4.274, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 274 as #4.275, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 275 as #4.276, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 276 as #4.277, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 277 as #4.278, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 278 as #4.279, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 279 as #4.280, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 280 as #4.281, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 281 as #4.282, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 282 as #4.283, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 283 as #4.284, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 284 as #4.285, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 285 as #4.286, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 286 as #4.287, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 287 as #4.288, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 288 as #4.289, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 289 as #4.290, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 290 as #4.291, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 291 as #4.292, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 292 as #4.293, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 293 as #4.294, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 294 as #4.295, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 295 as #4.296, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 296 as #4.297, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 297 as #4.298, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 298 as #4.299, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 299 as #4.300, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 300 as #4.301, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 301 as #4.302, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 302 as #4.303, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 303 as #4.304, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 304 as #4.305, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 305 as #4.306, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 306 as #4.307, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 307 as #4.308, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 308 as #4.309, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 309 as #4.310, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 310 as #4.311, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 311 as #4.312, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 312 as #4.313, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 313 as #4.314, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 314 as #4.315, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 315 as #4.316, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 316 as #4.317, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 317 as #4.318, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 318 as #4.319, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 319 as #4.320, grid size
280,280,280, pixel 0.92, shown at level 0.0901, step 1, values float32
> tool show 'Volume Viewer'
> close session
> open
> /Users/peiqiangfeng/Downloads/cryosparc_P32_J107_007_volume_map_sharp.mrc
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc as #1, grid size
280,280,280, pixel 0.92, shown at level 0.0348, step 1, values float32
> surface dust #1 size 9.2
> volume #1 level 0.09658
> open /Users/peiqiangfeng/Downloads/BASS2_phenix-coot-0.pdb
Chain information for BASS2_phenix-coot-0.pdb #2
---
Chain | Description
A | No description available
> fitmap #2 inMap #1
Fit molecule BASS2_phenix-coot-0.pdb (#2) to map
cryosparc_P32_J107_007_volume_map_sharp.mrc (#1) using 2371 atoms
average map value = 0.2767, steps = 28
shifted from previous position = 0.0438
rotated from previous position = 0.047 degrees
atoms outside contour = 444, contour level = 0.09658
Position of BASS2_phenix-coot-0.pdb (#2) relative to
cryosparc_P32_J107_007_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99999990 0.00043449 -0.00011857 -0.05700117
-0.00043457 0.99999967 -0.00068630 0.19354619
0.00011827 0.00068635 0.99999976 -0.08757505
Axis 0.83606106 -0.14425351 -0.52933243
Axis point 0.00000000 150.22865499 275.80189148
Rotation angle (degrees) 0.04703401
Shift along axis -0.02921986
> fitmap #2 inMap #1
Fit molecule BASS2_phenix-coot-0.pdb (#2) to map
cryosparc_P32_J107_007_volume_map_sharp.mrc (#1) using 2371 atoms
average map value = 0.2767, steps = 48
shifted from previous position = 0.00534
rotated from previous position = 0.00385 degrees
atoms outside contour = 442, contour level = 0.09658
Position of BASS2_phenix-coot-0.pdb (#2) relative to
cryosparc_P32_J107_007_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99999989 0.00043829 -0.00016054 -0.04943512
-0.00043839 0.99999970 -0.00063393 0.18152075
0.00016026 0.00063400 0.99999979 -0.08780127
Axis 0.80528101 -0.20374597 -0.55678548
Axis point 0.00000000 163.08878156 277.29535571
Rotation angle (degrees) 0.04510680
Shift along axis -0.02790681
> fitmap #2 inMap #1
Fit molecule BASS2_phenix-coot-0.pdb (#2) to map
cryosparc_P32_J107_007_volume_map_sharp.mrc (#1) using 2371 atoms
average map value = 0.2767, steps = 48
shifted from previous position = 0.00217
rotated from previous position = 0.00811 degrees
atoms outside contour = 440, contour level = 0.09658
Position of BASS2_phenix-coot-0.pdb (#2) relative to
cryosparc_P32_J107_007_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99999983 0.00057475 -0.00013088 -0.06982266
-0.00057483 0.99999965 -0.00061041 0.19577458
0.00013053 0.00061049 0.99999981 -0.08090758
Axis 0.71936341 -0.15402649 -0.67734196
Axis point 0.00000000 161.01096633 314.17707650
Rotation angle (degrees) 0.04862115
Shift along axis -0.02558024
> fitmap #2 inMap #1
Fit molecule BASS2_phenix-coot-0.pdb (#2) to map
cryosparc_P32_J107_007_volume_map_sharp.mrc (#1) using 2371 atoms
average map value = 0.2767, steps = 36
shifted from previous position = 0.0149
rotated from previous position = 0.0255 degrees
atoms outside contour = 438, contour level = 0.09658
Position of BASS2_phenix-coot-0.pdb (#2) relative to
cryosparc_P32_J107_007_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99999955 0.00093567 0.00012508 -0.14510616
-0.00093559 0.99999934 -0.00066094 0.23880356
-0.00012569 0.00066083 0.99999977 -0.05470226
Axis 0.57351363 0.10880828 -0.81193773
Axis point 256.63140543 147.34524401 0.00000000
Rotation angle (degrees) 0.06602451
Shift along axis -0.01282173
> fitmap #2 inMap #1
Fit molecule BASS2_phenix-coot-0.pdb (#2) to map
cryosparc_P32_J107_007_volume_map_sharp.mrc (#1) using 2371 atoms
average map value = 0.2767, steps = 44
shifted from previous position = 0.0159
rotated from previous position = 0.0248 degrees
atoms outside contour = 442, contour level = 0.09658
Position of BASS2_phenix-coot-0.pdb (#2) relative to
cryosparc_P32_J107_007_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99999984 0.00055341 -0.00007908 -0.07732116
-0.00055346 0.99999964 -0.00064477 0.19653421
0.00007872 0.00064482 0.99999979 -0.07920252
Axis 0.75556797 -0.09245295 -0.64851330
Axis point 0.00000000 148.30022917 301.11085995
Rotation angle (degrees) 0.04889574
Shift along axis -0.02522767
> volume #1 level 0.08534
> fitmap #2 inMap #1
Fit molecule BASS2_phenix-coot-0.pdb (#2) to map
cryosparc_P32_J107_007_volume_map_sharp.mrc (#1) using 2371 atoms
average map value = 0.2767, steps = 44
shifted from previous position = 0.017
rotated from previous position = 0.0324 degrees
atoms outside contour = 372, contour level = 0.085341
Position of BASS2_phenix-coot-0.pdb (#2) relative to
cryosparc_P32_J107_007_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99999943 0.00104714 0.00019184 -0.16870109
-0.00104701 0.99999922 -0.00068573 0.25642508
-0.00019256 0.00068553 0.99999975 -0.04902301
Axis 0.54146625 0.15178503 -0.82690725
Axis point 246.51945845 155.09330547 0.00000000
Rotation angle (degrees) 0.07255099
Shift along axis -0.01188698
> fitmap #2 inMap #1
Fit molecule BASS2_phenix-coot-0.pdb (#2) to map
cryosparc_P32_J107_007_volume_map_sharp.mrc (#1) using 2371 atoms
average map value = 0.2767, steps = 36
shifted from previous position = 0.0123
rotated from previous position = 0.0189 degrees
atoms outside contour = 373, contour level = 0.085341
Position of BASS2_phenix-coot-0.pdb (#2) relative to
cryosparc_P32_J107_007_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99999966 0.00082706 -0.00004802 -0.10708144
-0.00082709 0.99999938 -0.00074412 0.24890300
0.00004740 0.00074416 0.99999972 -0.08466587
Axis 0.66823711 -0.04284450 -0.74271361
Axis point 299.85059982 113.97332731 0.00000000
Rotation angle (degrees) 0.06380368
Shift along axis -0.01933742
> ui tool show "Color Zone"
> color zone #1 near #2 distance 2.7
> color bychain
> color zone #1 near #2 distance 2.7
> volume splitbyzone #1
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 0 as #3.1, grid size
280,280,280, pixel 0.92, shown at level 0.0853, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 1 as #3.2, grid size
280,280,280, pixel 0.92, shown at level 0.0853, step 1, values float32
Opened cryosparc_P32_J107_007_volume_map_sharp.mrc 2 as #3.3, grid size
280,280,280, pixel 0.92, shown at level 0.0853, step 1, values float32
> fitmap #2 inMap #3.2
Fit molecule BASS2_phenix-coot-0.pdb (#2) to map
cryosparc_P32_J107_007_volume_map_sharp.mrc 1 (#3.2) using 2371 atoms
average map value = 0.2765, steps = 40
shifted from previous position = 0.01
rotated from previous position = 0.0116 degrees
atoms outside contour = 374, contour level = 0.085341
Position of BASS2_phenix-coot-0.pdb (#2) relative to
cryosparc_P32_J107_007_volume_map_sharp.mrc 1 (#3.2) coordinates:
Matrix rotation and translation
0.99999961 0.00087682 0.00012509 -0.13708788
-0.00087674 0.99999940 -0.00065023 0.23175670
-0.00012566 0.00065012 0.99999978 -0.05271803
Axis 0.59175479 0.11410753 -0.79800109
Axis point 265.87873831 147.95578464 0.00000000
Rotation angle (degrees) 0.06295230
Shift along axis -0.01260818
> fitmap #2 inMap #3.2
Fit molecule BASS2_phenix-coot-0.pdb (#2) to map
cryosparc_P32_J107_007_volume_map_sharp.mrc 1 (#3.2) using 2371 atoms
average map value = 0.2765, steps = 44
shifted from previous position = 0.0107
rotated from previous position = 0.0207 degrees
atoms outside contour = 375, contour level = 0.085341
Position of BASS2_phenix-coot-0.pdb (#2) relative to
cryosparc_P32_J107_007_volume_map_sharp.mrc 1 (#3.2) coordinates:
Matrix rotation and translation
0.99999982 0.00058563 -0.00008948 -0.07596746
-0.00058568 0.99999963 -0.00063243 0.19693317
0.00008911 0.00063248 0.99999980 -0.07863570
Axis 0.72982784 -0.10303929 -0.67582115
Axis point 0.00000000 148.56699388 307.62269477
Rotation angle (degrees) 0.04965163
Shift along axis -0.02259135
> surface dust #3.2 size 9.2
> show #!3.1 models
> hide #!3.1 models
> show #!3.3 models
> hide #!3.3 models
> show #!3.3 models
> hide #2 models
> view
> show #2 models
> color #3.2 #d6d6d6ff models
> select add #2
2371 atoms, 2419 bonds, 319 residues, 1 model selected
> select subtract #2
Nothing selected
> open
> /Users/peiqiangfeng/Downloads/fold_2025_01_22_21_25/fold_2025_01_22_21_25_model_0.cif
Chain information for fold_2025_01_22_21_25_model_0.cif #4
---
Chain | Description
A | .
B | .
> hide #2 models
> hide #!3.2 models
> hide #!3.3 models
> hide #!3 models
> select add #4
5487 atoms, 5628 bonds, 710 residues, 1 model selected
> view sel
> color sel bychain
> select subtract #4
Nothing selected
Alignment identifier is 2/A
Alignment identifier is 4/A
Alignment identifier is 4/B
> select
> #4/A:22-25,29-31,37-44,52-58,64-70,77-79,87-92,97-102,111-118,123-126,130-134,143-147,158-168,174-177,186-189,192-194,197-207,217-222,227-232,264-268,283-289,299-304,307-309,313-319,324-332,344-349,357-361,372-376,387-397,403-408,411-413,416-418,429-438,447-453,461-467
1716 atoms, 1725 bonds, 211 residues, 1 model selected
> select #4/B:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/B:1-5
39 atoms, 39 bonds, 5 residues, 1 model selected
> select #4/B:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/B:1-22
175 atoms, 179 bonds, 22 residues, 1 model selected
> select
> #4/B:23-26,29-33,38-44,57-62,69-72,86-91,94-99,108-114,126-131,138-142,153-161,168-174,177-179,183-187,199-206,215-222,229-234
806 atoms, 807 bonds, 102 residues, 1 model selected
> select #4/B:43
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #4/B:43-58
125 atoms, 126 bonds, 16 residues, 1 model selected
> select #4/B:74
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/B:74-80
58 atoms, 58 bonds, 7 residues, 1 model selected
> select #4/B:113
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #4/B:113-120
61 atoms, 64 bonds, 8 residues, 1 model selected
> select #4/A:50
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/A:50-54
50 atoms, 52 bonds, 5 residues, 1 model selected
> select #4/A:58
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/A:50-58
89 atoms, 93 bonds, 9 residues, 1 model selected
> select #4/A:46
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #4/A:46-54
86 atoms, 89 bonds, 9 residues, 1 model selected
> select #4/A:69
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #4/A:69-85
141 atoms, 146 bonds, 17 residues, 1 model selected
> select #4/A:118
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/A:118-125
66 atoms, 68 bonds, 8 residues, 1 model selected
> select #4/A:217
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #4/A:217-218
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #4/A:264
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #4/A:264-267
32 atoms, 32 bonds, 4 residues, 1 model selected
> select #4/A:234
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/A:234-238
33 atoms, 34 bonds, 5 residues, 1 model selected
> select #4/A:241
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #4/A:241-246
43 atoms, 44 bonds, 6 residues, 1 model selected
> select #4/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/A:1-7
58 atoms, 59 bonds, 7 residues, 1 model selected
> select #4/A:246
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/A:246-249
29 atoms, 30 bonds, 4 residues, 1 model selected
> select #4/B:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/B:1-22
175 atoms, 179 bonds, 22 residues, 1 model selected
> select #4/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/A:1-20
156 atoms, 159 bonds, 20 residues, 1 model selected
> select #4/B:21-22
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #4/B:21-22
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #4/B:22
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/B:22-23
16 atoms, 15 bonds, 2 residues, 1 model selected
> select #4/B:21
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #4/B:21-22
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #4/A:21
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #4/A:21
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #4/A:44
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #4/A:44-53
86 atoms, 88 bonds, 10 residues, 1 model selected
> open 7RXC
Summary of feedback from opening 7RXC fetched from pdb
---
note | Fetching compressed mmCIF 7rxc from http://files.rcsb.org/download/7rxc.cif
7rxc title:
CryoEM structure of KDELR with Legobody [more info...]
Chain information for 7rxc #5
---
Chain | Description | UniProt
B | Maltodextrin-binding protein,Immunoglobulin G-binding protein A,Immunoglobulin G-binding protein G | A0A4Z0THX4_ECOLX 2-359, SPA_STAAN 360-467, SPG1_STRSG 479-536
H | Fab_8D3_2 heavy chain |
K | ER lumen protein-retaining receptor 2 | ERD22_CHICK 1-212
L | Fab_8D3_2 light chain |
N | Nb_KR |
Non-standard residues in 7rxc #5
---
GLC — alpha-D-glucopyranose (alpha-D-glucose; D-glucose; glucose)
POV — (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl
2-(trimethylammonio)ethyl phosphate (POPC)
> hide sel atoms
> show sel cartoons
> select add #5
9446 atoms, 9684 bonds, 8 pseudobonds, 1194 residues, 3 models selected
> select add #4
14847 atoms, 15224 bonds, 8 pseudobonds, 1894 residues, 3 models selected
> select subtract #5
5487 atoms, 5628 bonds, 710 residues, 1 model selected
> select subtract #4
Nothing selected
> select add #5
9360 atoms, 9596 bonds, 8 pseudobonds, 1184 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> split 35
Expected a structures specifier or a keyword
> split #5
Split 7rxc (#5) into 6 models
Chain information for 7rxc B #5.2
---
Chain | Description
B | No description available
Chain information for 7rxc H #5.3
---
Chain | Description
H | No description available
Chain information for 7rxc K #5.4
---
Chain | Description
K | No description available
Chain information for 7rxc L #5.5
---
Chain | Description
L | No description available
Chain information for 7rxc N #5.6
---
Chain | Description
N | No description available
> close #5.6
> close #5.1
> hide #4 models
> show #4 models
> select add #4
5487 atoms, 5628 bonds, 710 residues, 1 model selected
> select subtract #4
Nothing selected
> select add #4
5487 atoms, 5628 bonds, 710 residues, 1 model selected
> select subtract #4
Nothing selected
> select add #5.2
3433 atoms, 3511 bonds, 4 pseudobonds, 439 residues, 2 models selected
> close #5.2
> select add #5.4
1726 atoms, 1771 bonds, 206 residues, 1 model selected
> close #5.4
> mmaker #4 to #5
Specify a single 'to' model only
> select add #4
5487 atoms, 5628 bonds, 710 residues, 1 model selected
> mmaker #4 to #5.3
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 7rxc H, chain H (#5.3) with fold_2025_01_22_21_25_model_0.cif,
chain A (#4), sequence alignment score = 633.4
RMSD between 180 pruned atom pairs is 0.877 angstroms; (across all 200 pairs:
1.766)
> select subtract #4
Nothing selected
> hide #4 models
> show #4 models
> color #4 #00fdffff
> color #4#!5.3,5 bychain
> select add #5.5
1588 atoms, 1625 bonds, 2 pseudobonds, 204 residues, 2 models selected
Alignment identifier is 5.5/L
> select #5.5/L:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5.5/L:1-3
24 atoms, 23 bonds, 3 residues, 1 model selected
> select #4/B:21
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #4/B:21-22
15 atoms, 14 bonds, 2 residues, 1 model selected
> color #5.5 #ffd479ff
> color #5.5 #d783ffff
> color #5.5 #ff40ffff
> color #5.5 #0433ffff
> color #5.5 #00fdffff
> select #5.5/L:25
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5.5/L:25
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #4/B:44
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #4/B:44
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #4/B:53
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #4/B:53-56
31 atoms, 31 bonds, 4 residues, 1 model selected
> select #4/B:57
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/B:57
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5.5/L:39
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5.5/L:39
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5.5/L:36
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5.5/L:36-38
28 atoms, 28 bonds, 3 residues, 1 model selected
> select #5.5/L:39
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5.5/L:39-40
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #4/B:59
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #4/B:59-62
43 atoms, 45 bonds, 4 residues, 1 model selected
> select #5.5/L:41
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #5.5/L:41-44
44 atoms, 46 bonds, 4 residues, 1 model selected
> select #4/A:256
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #4/A:256-472
1720 atoms, 1762 bonds, 217 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select add #5.3
1582 atoms, 1626 bonds, 2 pseudobonds, 207 residues, 2 models selected
Alignment identifier is 5.3/H
> select #5.3/H:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5.3/H:1-3
24 atoms, 23 bonds, 3 residues, 1 model selected
> select #4/A:21
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #4/A:21
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #4/A:20
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/A:20-22
25 atoms, 24 bonds, 3 residues, 1 model selected
> select #5.3/H:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5.3/H:1-3
24 atoms, 23 bonds, 3 residues, 1 model selected
> select clear
> select add #5.3
1582 atoms, 1626 bonds, 2 pseudobonds, 207 residues, 2 models selected
> select add #5.5
3170 atoms, 3251 bonds, 4 pseudobonds, 411 residues, 4 models selected
> show sel atoms
> style sel stick
Changed 3170 atom styles
> color sel byhetero
> select clear
> select #4/A:227
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #4/A:227-235
71 atoms, 71 bonds, 9 residues, 1 model selected
> select #5.3/H:221
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5.3/H:221-223
23 atoms, 23 bonds, 3 residues, 1 model selected
> select #4/A:233
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/A:233
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/A:233
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/A:233-235
24 atoms, 24 bonds, 3 residues, 1 model selected
> select #5.3/H:190
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5.3/H:190-193
27 atoms, 26 bonds, 4 residues, 1 model selected
> select #5.3/H:186
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #5.3/H:186-193
59 atoms, 59 bonds, 8 residues, 1 model selected
> select #4/A:217
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #4/A:217-220
26 atoms, 25 bonds, 4 residues, 1 model selected
> select #5.3/H:215
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5.3/H:215-223
72 atoms, 72 bonds, 9 residues, 1 model selected
> select #4/A:227
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #4/A:227-235
71 atoms, 71 bonds, 9 residues, 1 model selected
> select #5.3/H:212
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #5.3/H:212-214
21 atoms, 21 bonds, 3 residues, 1 model selected
> select #4/A:223
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/A:223-226
24 atoms, 24 bonds, 4 residues, 1 model selected
> select #4/A:217
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #4/A:217-222
41 atoms, 41 bonds, 6 residues, 1 model selected
> select #5.3/H:205
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5.3/H:205-209
37 atoms, 36 bonds, 5 residues, 1 model selected
> select #4/A:208
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #4/A:208-216
69 atoms, 71 bonds, 9 residues, 1 model selected
> select #5.3/H:194
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5.3/H:194-204
33 atoms, 33 bonds, 1 pseudobond, 4 residues, 2 models selected
> select #4/A:208
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #4/A:208-210
19 atoms, 18 bonds, 3 residues, 1 model selected
> select
> #4/A:22-25,29-31,37-44,52-58,64-70,77-79,87-92,97-102,111-118,123-126,130-134,143-147,158-168,174-177,186-189,192-194,197-207,217-222,227-232
890 atoms, 896 bonds, 111 residues, 1 model selected
> select #4/A:207
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/A:197-207
81 atoms, 82 bonds, 11 residues, 1 model selected
> select #4/A:186
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #4/A:186-189
35 atoms, 36 bonds, 4 residues, 1 model selected
> select #4/A:192
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/A:192
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/A:192
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/A:192-194
25 atoms, 24 bonds, 3 residues, 1 model selected
> select #5.3/H:179
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5.3/H:179-182
30 atoms, 29 bonds, 4 residues, 1 model selected
> select clear
> hide #4#!5.3,5 atoms
> hide #!5.5 models
> hide #!5.3 models
> select #4/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/A:1-19
147 atoms, 150 bonds, 19 residues, 1 model selected
> show #!5.3 models
> select #5.3/H:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5.3/H:1-3
24 atoms, 23 bonds, 3 residues, 1 model selected
> select #4/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/A:1-19
147 atoms, 150 bonds, 19 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #4/B:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/B:1-22
175 atoms, 179 bonds, 22 residues, 1 model selected
> show #!5.5 models
> select #5.5/L:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5.5/L:1-3
24 atoms, 23 bonds, 3 residues, 1 model selected
> select #4/B:21
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #4/B:21-22
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #4/B:21-22
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #4/B:21-24
30 atoms, 29 bonds, 4 residues, 1 model selected
> select #5.5/L:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5.5/L:1-5
39 atoms, 38 bonds, 5 residues, 1 model selected
> select
> #5.5/L:4-7,10-14,19-25,39-44,51-55,59-60,68-73,76-81,90-96,102-103,107-112,119-123,134-144,150-154,164-168,178-187,197-202,211-214
809 atoms, 811 bonds, 102 residues, 1 model selected
> select #5.5/L:4
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5.5/L:4-7
30 atoms, 29 bonds, 4 residues, 1 model selected
> select #4/B:84
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/B:84-104
156 atoms, 157 bonds, 21 residues, 1 model selected
> select #4/B:23
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/B:23-26
31 atoms, 30 bonds, 4 residues, 1 model selected
> select #5.5/L:3
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5.5/L:3-4
16 atoms, 15 bonds, 2 residues, 1 model selected
> select #4/B:19-20
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #4/B:20-22
23 atoms, 22 bonds, 3 residues, 1 model selected
> select #5.5/L:2
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5.5/L:2-3
16 atoms, 15 bonds, 2 residues, 1 model selected
> select #4/B:21
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #4/B:21-22
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #4/B:20
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/B:20
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/B:19
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #4/B:1-19
152 atoms, 156 bonds, 19 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #4/B:235-236
19 atoms, 18 bonds, 2 residues, 1 model selected
> select #4/B:235-238
35 atoms, 34 bonds, 4 residues, 1 model selected
> select #5.3/H:221
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5.3/H:221-223
23 atoms, 23 bonds, 3 residues, 1 model selected
> select #4/A:233
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/A:233-235
24 atoms, 24 bonds, 3 residues, 1 model selected
> select #4/A:236
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #4/A:236-255
143 atoms, 148 bonds, 20 residues, 1 model selected
> delete atoms sel
> delete bonds sel
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
> camera ortho
> cofr centerOfView
> mousemode alt rightMode "contour level"
> mousemode alt leftMode "translate selected models"
> mousemode shift leftMode "rotate selected models"
> alias cofron cofr centerofview showpivot true
> alias cofroff cofr centerofview showpivot false
> alias symclip cofr centerofview; clip near -$1 far $1 position cofr
> alias cootmode surface cap false; surface style solid; lighting full;
> graphics silhouettes false; style stick; ~rib; color ##num_residues gold;
> color byhet ; disp; ~disp @H*; style solvent ball; size ballscale 0.1; size
> stickradius 0.07; transparency 70; cofr centerofview; clip near -10 far 10
> position cofr; color ##~num_residues cornflower blue
> alias cootmode_mesh surface cap false; surface style mesh; lighting full;
> graphics silhouettes false; style stick; ~rib; color ##num_residues gold;
> color byhet ; disp; ~disp @H*; style solvent ball; size ballscale 0.1; size
> stickradius 0.07; cofr centerofview; clip near -10 far 10 position cofr;
> color ##~num_residues #3d60ffff; transparency 50
> alias ca_and_sidechains ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1;
> disp @P&nucleic&$1; style $1 stick; disp sidechain&$1; disp
> ~backbone&nucleic&$1; size stickradius 0.1; size pseudobondradius 0.1
> alias ca_trace ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1; disp
> @P&nucleic&$1; style $1 stick; size stickradius 0.1; size pseudobondradius
> 0.1
> alias map_sphere_15 surface unzone ##~num_residues; sel; close #10000;
> marker #10000 position cofr; sel ~sel; surface zone ##~num_residues
> nearAtoms sel distance 15; close #10000
> alias map_unsphere surface unzone ##~num_residues
> alias hidemaps surface unzone ##~num_residues; sel; close #10000; marker
> #10000 position cofr; sel ~sel; surface zone ##~num_residues nearAtoms sel
> distance 0; close #10000
> alias showmaps surface unzone ##~num_residues
> alias caps_off surface cap false
> alias caps_on surface cap true
> alias selbetween ks ri
> alias rock_movie cofr showpivot false; movie record; rock y 30; wait 136;
> movie encode /Users/peiqiangfeng/Desktop/rock_movie.mp4; stop
> alias helixmap color byattribute r:helix_lipophilicity palette lipophilicity
> buttonpanel Shortcuts rows 3 columns 4
> buttonpanel Shortcuts add Vol_Viewer command "tool show 'Volume Viewer'"
> buttonpanel Shortcuts add Model_Panel command "tool show Models"
> buttonpanel Shortcuts add Log command "tool show Log"
> buttonpanel Shortcuts add default_disp command default_mol_display
> buttonpanel Shortcuts add map_sphere command map_sphere_15
> buttonpanel Shortcuts add map_unsphere command map_unsphere
> buttonpanel Shortcuts add cofron command cofron
> buttonpanel Shortcuts add cofroff command cofroff
> buttonpanel Shortcuts add cootmode command cootmode
> buttonpanel Shortcuts add cootmode_mesh command cootmode_mesh
> buttonpanel Shortcuts add mark_cofr command "marker #10000 position cofr"
> buttonpanel Shortcuts add hidemaps command hidemaps
> buttonpanel Shortcuts add showmaps command showmaps
> buttonpanel Shortcuts add caps_off command caps_off
> buttonpanel Shortcuts add caps_on command caps_on
> buttonpanel Shortcuts add previous_model command prevmodel
> buttonpanel Shortcuts add next_model command nextmodel
> runscript /Users/peiqiangfeng/Desktop/ChimeraX_py/chimerax_startup.py
> runscript /Users/peiqiangfeng/Desktop/ChimeraX_py/helixmlp.py
> volume defaultvalues limitVoxelCount false voxelLimitForPlane
> 1000000000000000 voxelLimitForOpen 1000000000000000 saveSettings true
Saved volume settings
UCSF ChimeraX version: 1.8rc202405312319 (2024-05-31)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 83
OpenGL renderer: Apple M2 Pro
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac14,9
Model Number: MPHF3LL/A
Chip: Apple M2 Pro
Total Number of Cores: 12 (8 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 8419.41.10
OS Loader Version: 8419.41.10
Software:
System Software Overview:
System Version: macOS 13.0 (22A8380)
Kernel Version: Darwin 22.1.0
Time since boot: 11 days, 5 hours, 3 minutes
Graphics/Displays:
Apple M2 Pro:
Chipset Model: Apple M2 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 19
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
U27P2G6B:
Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus)
UI Looks like: 2560 x 1440 @ 30.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57
ChimeraX-AtomicLibrary: 14.0.5
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-clix: 0.1.7
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: 1.8rc202405312319
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.16
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.4
ChimeraX-PDB: 2.7.5
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: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.45
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4
traitlets: 5.14.2
typing-extensions: 4.12.0
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
Change History (2)
comment:1 by , 9 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash on Mac waking from sleep |
comment:2 by , 9 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
Note:
See TracTickets
for help on using tickets.
