![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 3 years ago
Closed 3 years ago
#8683 closed defect (can't reproduce)
Crash in Qt event loop look after saving image
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Input/Output | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.5 (2022-11-24 00:03:27 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 0x00007ff84a0c48c0 (most recent call first):
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 283 in event_loop
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 884 in init
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1035 in
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main
{"app_name":"ChimeraX","timestamp":"2023-03-21 17:21:22.00 +0800","app_version":"1.5.0","slice_uuid":"5df621ee-554e-36a8-b448-93b2334e5480","build_version":"1.5.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":1,"is_first_party":0,"bug_type":"309","os_version":"macOS 13.1 (22C65)","roots_installed":0,"name":"ChimeraX","incident_id":"4D0DF493-A928-48C3-9A62-ABEA801488CC"}
{
"uptime" : 570000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro16,3",
"coalitionID" : 16455,
"osVersion" : {
"train" : "macOS 13.1",
"build" : "22C65",
"releaseType" : "User"
},
"captureTime" : "2023-03-21 17:21:20.4519 +0800",
"incident" : "4D0DF493-A928-48C3-9A62-ABEA801488CC",
"pid" : 8110,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2023-03-21 17:14:53.1776 +0800",
"procStartAbsTime" : 571652617644149,
"procExitAbsTime" : 572039833605557,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.5.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.5.0","CFBundleVersion":"1.5.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"06719F3A-35A4-59AC-886F-30E8D7472281","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "FC927C24-F19B-A04D-921A-2F062A6DA2BE",
"throttleTimeout" : 2147483647,
"wakeTime" : 4595,
"bridgeVersion" : {"build":"20P2059","train":"7.1"},
"sleepWakeUUID" : "9F938BF2-1180-4703-B62D-03E172E8AA4E",
"sip" : "enabled",
"vmRegionInfo" : "0x83 is not in any region. Bytes before following region: 140737487208317\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n shared memory 7fffffee8000-7fffffee9000 [ 4K] r-x\/r-x SM=SHM ",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000083","rawCodes":[1,131],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000083"},
"vmregioninfo" : "0x83 is not in any region. Bytes before following region: 140737487208317\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n shared memory 7fffffee8000-7fffffee9000 [ 4K] r-x\/r-x SM=SHM ",
"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" : [{"queue":"com.apple.main-thread","instructionState":{"instructionStream":{"bytes":[65,95,93,195,102,46,15,31,132,0,0,0,0,0,102,144,72,139,64,16,72,133,192,15,132,251,254,255,255,72,139,64,8,72,139,72,120,72,133,201,116,230,72,139,73,16,72,133,201,116,221,72,139,121,24,76,137,254,232,33,62,52,0,65,180,1,233,212,254,255,255,102,15,31,132,0,0,0,0,0,85,72,137,229,65,87,65,86,65,85,65,84,83,72,131,236,40,137,117,212,76,139,103,24,76,139,111,32,76,139,127,40,77,133,228,116,6,240,65,131,4,36,1,77,133,255,15,142,241,0,0,0,69,49,246,76,137,101,200,235,32,72,137,223,232,155,251,255,255,102,46,15,31,132,0,0,0,0,0,144,73,131,198,1,77,57,247,15,132,200,0,0,0,75,139,92,245,0,72,133,219,116,233,72,139,123,8,246,71,48,1,116],"offset":187}},"frames":[{"imageOffset":33322,"symbol":"__pthread_kill","symbolLocation":10,"imageIndex":0},{"imageOffset":24443,"symbol":"pthread_kill","symbolLocation":263,"imageIndex":1},{"imageOffset":279856,"symbol":"raise","symbolLocation":26,"imageIndex":2},{"imageOffset":15389,"symbol":"_sigtramp","symbolLocation":29,"imageIndex":3},{"imageOffset":0,"imageIndex":4},{"imageOffset":390785,"symbol":"QWidget::event(QEvent*)","symbolLocation":2097,"imageIndex":5},{"imageOffset":1708804,"symbol":"QMainWindow::event(QEvent*)","symbolLocation":276,"imageIndex":5},{"imageOffset":612463,"symbol":"sipQMainWindow::event(QEvent*)","symbolLocation":191,"imageIndex":6},{"imageOffset":51847,"symbol":"QApplicationPrivate::notify_helper(QObject*, QEvent*)","symbolLocation":247,"imageIndex":5},{"imageOffset":55875,"symbol":"QApplication::notify(QObject*, QEvent*)","symbolLocation":499,"imageIndex":5},{"imageOffset":1282534,"symbol":"sipQApplication::notify(QObject*, QEvent*)","symbolLocation":230,"imageIndex":6},{"imageOffset":449594,"symbol":"QCoreApplication::notifyInternal2(QObject*, QEvent*)","symbolLocation":170,"imageIndex":7},{"imageOffset":489294,"imageIndex":5},{"imageOffset":477452,"imageIndex":5},{"imageOffset":51847,"symbol":"QApplicationPrivate::notify_helper(QObject*, QEvent*)","symbolLocation":247,"imageIndex":5},{"imageOffset":55875,"symbol":"QApplication::notify(QObject*, QEvent*)","symbolLocation":499,"imageIndex":5},{"imageOffset":1282534,"symbol":"sipQApplication::notify(QObject*, QEvent*)","symbolLocation":230,"imageIndex":6},{"imageOffset":449594,"symbol":"QCoreApplication::notifyInternal2(QObject*, QEvent*)","symbolLocation":170,"imageIndex":7},{"imageOffset":536965,"symbol":"QGuiApplicationPrivate::processWindowSystemEvent(QWindowSystemInterfacePrivate::WindowSystemEvent*)","symbolLocation":181,"imageIndex":8},{"imageOffset":917514,"imageIndex":8},{"imageOffset":299513,"imageIndex":9},{"imageOffset":513556,"symbol":"QMetaMethod::invoke(QObject*, Qt::ConnectionType, QGenericReturnArgument, QGenericArgument, QGenericArgument, QGenericArgument, QGenericArgument, QGenericArgument, QGenericArgument, QGenericArgument, QGenericArgument, QGenericArgument, QGenericArgument) const","symbolLocation":1284,"imageIndex":7},{"imageOffset":326252,"imageIndex":9},{"imageOffset":480227,"symbol":"__CFNOTIFICATIONCENTER_IS_CALLING_OUT_TO_AN_OBSERVER__","symbolLocation":120,"imageIndex":10},{"imageOffset":1111098,"symbol":"___CFXRegistrationPost_block_invoke","symbolLocation":88,"imageIndex":10},{"imageOffset":1110921,"symbol":"_CFXRegistrationPost","symbolLocation":536,"imageIndex":10},{"imageOffset":297241,"symbol":"_CFXNotificationPost","symbolLocation":735,"imageIndex":10},{"imageOffset":40748,"symbol":"-[NSNotificationCenter postNotificationName:object:userInfo:]","symbolLocation":82,"imageIndex":11},{"imageOffset":3861197,"symbol":"-[NSWindow(NSWindow_Theme) showDeminiaturizedWindow]","symbolLocation":151,"imageIndex":12},{"imageOffset":10058600,"symbol":"___NSWindowAddDockMessageHandlers_block_invoke_3","symbolLocation":305,"imageIndex":12},{"imageOffset":1730042,"symbol":"_NSCGSDockMessageReceive","symbolLocation":1799,"imageIndex":12},{"imageOffset":351754,"symbol":"DockCallback(unsigned int, unsigned int, void*, void*)","symbolLocation":1961,"imageIndex":13},{"imageOffset":101914,"symbol":"_DCXMaximizedWindows","symbolLocation":41,"imageIndex":14},{"imageOffset":101840,"symbol":"_XMaximizedWindows","symbolLocation":76,"imageIndex":14},{"imageOffset":42409,"symbol":"mshMIGPerform","symbolLocation":182,"imageIndex":14},{"imageOffset":524497,"symbol":"__CFRUNLOOP_IS_CALLING_OUT_TO_A_SOURCE1_PERFORM_FUNCTION__","symbolLocation":41,"imageIndex":10},{"imageOffset":524302,"symbol":"__CFRunLoopDoSource1","symbolLocation":540,"imageIndex":10},{"imageOffset":519307,"symbol":"__CFRunLoopRun","symbolLocation":2705,"imageIndex":10},{"imageOffset":514944,"symbol":"CFRunLoopRunSpecific","symbolLocation":560,"imageIndex":10},{"imageOffset":194406,"symbol":"RunCurrentEventLoopInMode","symbolLocation":292,"imageIndex":13},{"imageOffset":193910,"symbol":"ReceiveNextEventCommon","symbolLocation":679,"imageIndex":13},{"imageOffset":193203,"symbol":"_BlockUntilNextEventMatchingListInModeWithFilter","symbolLocation":70,"imageIndex":13},{"imageOffset":253747,"symbol":"_DPSNextEvent","symbolLocation":909,"imageIndex":12},{"imageOffset":249268,"symbol":"-[NSApplication(NSEvent) _nextEventMatchingEventMask:untilDate:inMode:dequeue:]","symbolLocation":1219,"imageIndex":12},{"imageOffset":193527,"symbol":"-[NSApplication run]","symbolLocation":586,"imageIndex":12},{"imageOffset":102572,"imageIndex":9},{"imageOffset":488230,"symbol":"QEventLoop::exec(QFlags)","symbolLocation":486,"imageIndex":7},{"imageOffset":451125,"symbol":"QCoreApplication::exec()","symbolLocation":133,"imageIndex":7},{"imageOffset":2252186,"symbol":"meth_QApplication_exec(_object*, _object*)","symbolLocation":90,"imageIndex":6},{"imageOffset":517917,"symbol":"cfunction_call","symbolLocation":125,"imageIndex":15},{"imageOffset":259511,"symbol":"_PyObject_MakeTpCall","symbolLocation":359,"imageIndex":15},{"imageOffset":1146524,"symbol":"call_function","symbolLocation":876,"imageIndex":15},{"imageOffset":1135266,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":25554,"imageIndex":15},{"imageOffset":261416,"symbol":"function_code_fastcall","symbolLocation":104,"imageIndex":15},{"imageOffset":269674,"symbol":"method_vectorcall","symbolLocation":202,"imageIndex":15},{"imageOffset":1146380,"symbol":"call_function","symbolLocation":732,"imageIndex":15},{"imageOffset":1135266,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":25554,"imageIndex":15},{"imageOffset":1149699,"symbol":"_PyEval_EvalCode","symbolLocation":2611,"imageIndex":15},{"imageOffset":261297,"symbol":"_PyFunction_Vectorcall","symbolLocation":289,"imageIndex":15},{"imageOffset":1146380,"symbol":"call_function","symbolLocation":732,"imageIndex":15},{"imageOffset":1135435,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":25723,"imageIndex":15},{"imageOffset":1149699,"symbol":"_PyEval_EvalCode","symbolLocation":2611,"imageIndex":15},{"imageOffset":1109419,"symbol":"PyEval_EvalCode","symbolLocation":139,"imageIndex":15},{"imageOffset":1096722,"symbol":"builtin_exec","symbolLocation":626,"imageIndex":15},{"imageOffset":516131,"symbol":"cfunction_vectorcall_FASTCALL","symbolLocation":195,"imageIndex":15},{"imageOffset":1146380,"symbol":"call_function","symbolLocation":732,"imageIndex":15},{"imageOffset":1135435,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":25723,"imageIndex":15},{"imageOffset":1149699,"symbol":"_PyEval_EvalCode","symbolLocation":2611,"imageIndex":15},{"imageOffset":261297,"symbol":"_PyFunction_Vectorcall","symbolLocation":289,"imageIndex":15},{"imageOffset":1146380,"symbol":"call_function","symbolLocation":732,"imageIndex":15},{"imageOffset":1135435,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":25723,"imageIndex":15},{"imageOffset":1149699,"symbol":"_PyEval_EvalCode","symbolLocation":2611,"imageIndex":15},{"imageOffset":261297,"symbol":"_PyFunction_Vectorcall","symbolLocation":289,"imageIndex":15},{"imageOffset":1566832,"symbol":"pymain_run_module","symbolLocation":208,"imageIndex":15},{"imageOffset":1564551,"symbol":"Py_RunMain","symbolLocation":1431,"imageIndex":15},{"imageOffset":1566095,"symbol":"pymain_main","symbolLocation":223,"imageIndex":15},{"imageOffset":1565851,"symbol":"Py_Main","symbolLocation":43,"imageIndex":15},{"imageOffset":3528,"symbol":"main","symbolLocation":120,"imageIndex":16},{"imageOffset":25360,"symbol":"start","symbolLocation":2432,"imageIndex":17}],"id":8033574,"triggered":true,"threadState":{"r13":{"value":140560138272272},"rax":{"value":0},"rflags":{"value":582},"cpu":{"value":0},"r14":{"value":11},"rsi":{"value":11},"r8":{"value":140560125222728},"cr2":{"value":140560153892272},"rdx":{"value":0},"r10":{"value":140704370936000,"symbolLocation":0,"symbol":"_main_thread"},"r9":{"value":8235507280786994059},"r15":{"value":22},"rbx":{"value":140704370936000,"symbolLocation":0,"symbol":"_main_thread"},"trap":{"value":133},"err":{"value":33554760},"r11":{"value":582},"rip":{"value":140703236997674,"matchesCrashFrame":1},"rbp":{"value":140560125221504},"rsp":{"value":140560125221464},"r12":{"value":259},"rcx":{"value":140560125221464},"flavor":"x86_THREAD_STATE","rdi":{"value":259}},"name":"CrBrowserMain"},{"id":8033596,"frames":[{"imageOffset":16666,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":0},{"imageOffset":26593,"symbol":"_pthread_cond_wait","symbolLocation":1243,"imageIndex":1},{"imageOffset":3445311,"symbol":"blas_thread_server","symbolLocation":207,"imageIndex":18},{"imageOffset":25177,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":7291,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":8033597,"frames":[{"imageOffset":16666,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":0},{"imageOffset":26593,"symbol":"_pthread_cond_wait","symbolLocation":1243,"imageIndex":1},{"imageOffset":3445311,"symbol":"blas_thread_server","symbolLocation":207,"imageIndex":18},{"imageOffset":25177,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":7291,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":8033598,"frames":[{"imageOffset":16666,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":0},{"imageOffset":26593,"symbol":"_pthread_cond_wait","symbolLocation":1243,"imageIndex":1},{"imageOffset":3445311,"symbol":"blas_thread_server","symbolLocation":207,"imageIndex":18},{"imageOffset":25177,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":7291,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":8033686,"name":"ThreadPoolServiceThread","frames":[{"imageOffset":44654,"symbol":"kevent64","symbolLocation":10,"imageIndex":0},{"imageOffset":66456106,"imageIndex":19},{"imageOffset":66455847,"imageIndex":19},{"imageOffset":65919580,"imageIndex":19},{"imageOffset":65624472,"imageIndex":19},{"imageOffset":66059960,"imageIndex":19},{"imageOffset":65958573,"imageIndex":19},{"imageOffset":66060362,"imageIndex":19},{"imageOffset":66222344,"imageIndex":19},{"imageOffset":25177,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":7291,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":8033688,"name":"ThreadPoolBackgroundWorker","frames":[{"imageOffset":5570,"symbol":"mach_msg2_trap","symbolLocation":10,"imageIndex":0},{"imageOffset":62980,"symbol":"mach_msg2_internal","symbolLocation":82,"imageIndex":0},{"imageOffset":34357,"symbol":"mach_msg_overwrite","symbolLocation":723,"imageIndex":0},{"imageOffset":6312,"symbol":"mach_msg","symbolLocation":19,"imageIndex":0},{"imageOffset":66252326,"imageIndex":19},{"imageOffset":66009023,"imageIndex":19},{"imageOffset":66011756,"imageIndex":19},{"imageOffset":66010589,"imageIndex":19},{"imageOffset":66222344,"imageIndex":19},{"imageOffset":25177,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":7291,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":8033689,"name":"Chrome_IOThread","frames":[{"imageOffset":44654,"symbol":"kevent64","symbolLocation":10,"imageIndex":0},{"imageOffset":66456106,"imageIndex":19},{"imageOffset":66455847,"imageIndex":19},{"imageOffset":65919580,"imageIndex":19},{"imageOffset":65624472,"imageIndex":19},{"imageOffset":66059960,"imageIndex":19},{"imageOffset":48386978,"imageIndex":19},{"imageOffset":66060362,"imageIndex":19},{"imageOffset":66222344,"imageIndex":19},{"imageOffset":25177,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":7291,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":8033690,"name":"NetworkConfigWatcher","frames":[{"imageOffset":5570,"symbol":"mach_msg2_trap","symbolLocation":10,"imageIndex":0},{"imageOffset":62980,"symbol":"mach_msg2_internal","symbolLocation":82,"imageIndex":0},{"imageOffset":34357,"symbol":"mach_msg_overwrite","symbolLocation":723,"imageIndex":0},{"imageOffset":6312,"symbol":"mach_msg","symbolLocation":19,"imageIndex":0},{"imageOffset":66252326,"imageIndex":19},{"imageOffset":66251759,"imageIndex":19},{"imageOffset":65421769,"imageIndex":19},{"imageOffset":65919580,"imageIndex":19},{"imageOffset":65624472,"imageIndex":19},{"imageOffset":66059960,"imageIndex":19},{"imageOffset":66060362,"imageIndex":19},{"imageOffset":66222344,"imageIndex":19},{"imageOffset":25177,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":7291,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":8033694,"name":"CompositorTileWorker1","frames":[{"imageOffset":16666,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":0},{"imageOffset":26593,"symbol":"_pthread_cond_wait","symbolLocation":1243,"imageIndex":1},{"imageOffset":66219291,"imageIndex":19},{"imageOffset":100616493,"imageIndex":19},{"imageOffset":66222344,"imageIndex":19},{"imageOffset":25177,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":7291,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":8033695,"name":"Chrome_InProcGpuThread","frames":[{"imageOffset":5386,"symbol":"_platform_bzero$VARIANT$Haswell","symbolLocation":74,"imageIndex":3},{"imageOffset":112949,"symbol":"nanov2_malloc_zero_on_alloc","symbolLocation":605,"imageIndex":20},{"imageOffset":72026,"symbol":"operator new(unsigned long)","symbolLocation":26,"imageIndex":21},{"imageOffset":71742464,"imageIndex":19},{"imageOffset":71672097,"imageIndex":19},{"imageOffset":70361372,"imageIndex":19},{"imageOffset":70361633,"imageIndex":19},{"imageOffset":70474467,"imageIndex":19},{"imageOffset":70500866,"imageIndex":19},{"imageOffset":70296722,"imageIndex":19},{"imageOffset":71000374,"imageIndex":19},{"imageOffset":71029017,"imageIndex":19},{"imageOffset":71027025,"imageIndex":19},{"imageOffset":70749966,"imageIndex":19},{"imageOffset":70393053,"imageIndex":19},{"imageOffset":70392688,"imageIndex":19},{"imageOffset":70435573,"imageIndex":19},{"imageOffset":70306312,"imageIndex":19},{"imageOffset":70305552,"imageIndex":19},{"imageOffset":70307949,"imageIndex":19},{"imageOffset":70277489,"imageIndex":19},{"imageOffset":71132809,"imageIndex":19},{"imageOffset":106587462,"imageIndex":19},{"imageOffset":106601864,"imageIndex":19},{"imageOffset":106566857,"imageIndex":19},{"imageOffset":106577356,"imageIndex":19},{"imageOffset":101422088,"imageIndex":19},{"imageOffset":107954770,"imageIndex":19},{"imageOffset":107954023,"imageIndex":19},{"imageOffset":107981788,"imageIndex":19},{"imageOffset":108022324,"imageIndex":19},{"imageOffset":101449557,"imageIndex":19},{"imageOffset":65816201,"imageIndex":19},{"imageOffset":65917583,"imageIndex":19},{"imageOffset":65916874,"imageIndex":19},{"imageOffset":65918994,"imageIndex":19},{"imageOffset":65421708,"imageIndex":19},{"imageOffset":65919580,"imageIndex":19},{"imageOffset":65624472,"imageIndex":19},{"imageOffset":66059960,"imageIndex":19},{"imageOffset":66060362,"imageIndex":19},{"imageOffset":66222344,"imageIndex":19},{"imageOffset":25177,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":7291,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":8033696,"name":"Chrome_ChildIOThread","frames":[{"imageOffset":44654,"symbol":"kevent64","symbolLocation":10,"imageIndex":0},{"imageOffset":66456106,"imageIndex":19},{"imageOffset":66455847,"imageIndex":19},{"imageOffset":65919580,"imageIndex":19},{"imageOffset":65624472,"imageIndex":19},{"imageOffset":66059960,"imageIndex":19},{"imageOffset":66060362,"imageIndex":19},{"imageOffset":66222344,"imageIndex":19},{"imageOffset":25177,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":7291,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":8033697,"name":"NetworkConfigWatcher","frames":[{"imageOffset":5570,"symbol":"mach_msg2_trap","symbolLocation":10,"imageIndex":0},{"imageOffset":62980,"symbol":"mach_msg2_internal","symbolLocation":82,"imageIndex":0},{"imageOffset":34357,"symbol":"mach_msg_overwrite","symbolLocation":723,"imageIndex":0},{"imageOffset":6312,"symbol":"mach_msg","symbolLocation":19,"imageIndex":0},{"imageOffset":66252326,"imageIndex":19},{"imageOffset":66251759,"imageIndex":19},{"imageOffset":65421769,"imageIndex":19},{"imageOffset":65919580,"imageIndex":19},{"imageOffset":65624472,"imageIndex":19},{"imageOffset":66059960,"imageIndex":19},{"imageOffset":66060362,"imageIndex":19},{"imageOffset":66222344,"imageIndex":19},{"imageOffset":25177,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":7291,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":8033698,"name":"VizCompositorThread","frames":[{"imageOffset":5570,"symbol":"mach_msg2_trap","symbolLocation":10,"imageIndex":0},{"imageOffset":62980,"symbol":"mach_msg2_internal","symbolLocation":82,"imageIndex":0},{"imageOffset":34357,"symbol":"mach_msg_overwrite","symbolLocation":723,"imageIndex":0},{"imageOffset":6312,"symbol":"mach_msg","symbolLocation":19,"imageIndex":0},{"imageOffset":66252326,"imageIndex":19},{"imageOffset":65421672,"imageIndex":19},{"imageOffset":65919580,"imageIndex":19},{"imageOffset":65624472,"imageIndex":19},{"imageOffset":66059960,"imageIndex":19},{"imageOffset":66060362,"imageIndex":19},{"imageOffset":66222344,"imageIndex":19},{"imageOffset":25177,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":7291,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":8033710,"name":"NetworkService","frames":[{"imageOffset":44654,"symbol":"kevent64","symbolLocation":10,"imageIndex":0},{"imageOffset":66456106,"imageIndex":19},{"imageOffset":66455847,"imageIndex":19},{"imageOffset":65919580,"imageIndex":19},{"imageOffset":65624472,"imageIndex":19},{"imageOffset":66059960,"imageIndex":19},{"imageOffset":66060362,"imageIndex":19},{"imageOffset":66222344,"imageIndex":19},{"imageOffset":25177,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":7291,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":8033711,"name":"NetworkConfigWatcher","frames":[{"imageOffset":5570,"symbol":"mach_msg2_trap","symbolLocation":10,"imageIndex":0},{"imageOffset":62980,"symbol":"mach_msg2_internal","symbolLocation":82,"imageIndex":0},{"imageOffset":34357,"symbol":"mach_msg_overwrite","symbolLocation":723,"imageIndex":0},{"imageOffset":6312,"symbol":"mach_msg","symbolLocation":19,"imageIndex":0},{"imageOffset":66252326,"imageIndex":19},{"imageOffset":66251759,"imageIndex":19},{"imageOffset":65421769,"imageIndex":19},{"imageOffset":65919580,"imageIndex":19},{"imageOffset":65624472,"imageIndex":19},{"imageOffset":66059960,"imageIndex":19},{"imageOffset":66060362,"imageIndex":19},{"imageOffset":66222344,"imageIndex":19},{"imageOffset":25177,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":7291,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":8033721,"name":"ThreadPoolSingleThreadForegroundBlocking0","frames":[{"imageOffset":5570,"symbol":"mach_msg2_trap","symbolLocation":10,"imageIndex":0},{"imageOffset":62980,"symbol":"mach_msg2_internal","symbolLocation":82,"imageIndex":0},{"imageOffset":34357,"symbol":"mach_msg_overwrite","symbolLocation":723,"imageIndex":0},{"imageOffset":6312,"symbol":"mach_msg","symbolLocation":19,"imageIndex":0},{"imageOffset":66252326,"imageIndex":19},{"imageOffset":66009023,"imageIndex":19},{"imageOffset":66011756,"imageIndex":19},{"imageOffset":66010829,"imageIndex":19},{"imageOffset":66222344,"imageIndex":19},{"imageOffset":25177,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":7291,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":8033748,"name":"NetworkConfigWatcher","frames":[{"imageOffset":5570,"symbol":"mach_msg2_trap","symbolLocation":10,"imageIndex":0},{"imageOffset":62980,"symbol":"mach_msg2_internal","symbolLocation":82,"imageIndex":0},{"imageOffset":34357,"symbol":"mach_msg_overwrite","symbolLocation":723,"imageIndex":0},{"imageOffset":6312,"symbol":"mach_msg","symbolLocation":19,"imageIndex":0},{"imageOffset":66252326,"imageIndex":19},{"imageOffset":66251759,"imageIndex":19},{"imageOffset":65421769,"imageIndex":19},{"imageOffset":65919580,"imageIndex":19},{"imageOffset":65624472,"imageIndex":19},{"imageOffset":66059960,"imageIndex":19},{"imageOffset":66060362,"imageIndex":19},{"imageOffset":66222344,"imageIndex":19},{"imageOffset":25177,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":7291,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":8033806,"name":"com.apple.NSEventThread","frames":[{"imageOffset":5570,"symbol":"mach_msg2_trap","symbolLocation":10,"imageIndex":0},{"imageOffset":62980,"symbol":"mach_msg2_internal","symbolLocation":82,"imageIndex":0},{"imageOffset":34357,"symbol":"mach_msg_overwrite","symbolLocation":723,"imageIndex":0},{"imageOffset":6312,"symbol":"mach_msg","symbolLocation":19,"imageIndex":0},{"imageOffset":523486,"symbol":"__CFRunLoopServiceMachPort","symbolLocation":145,"imageIndex":10},{"imageOffset":517962,"symbol":"__CFRunLoopRun","symbolLocation":1360,"imageIndex":10},{"imageOffset":514944,"symbol":"CFRunLoopRunSpecific","symbolLocation":560,"imageIndex":10},{"imageOffset":1696409,"symbol":"_NSEventThread","symbolLocation":132,"imageIndex":12},{"imageOffset":25177,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":7291,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":8033891,"name":"MemoryInfra","frames":[{"imageOffset":5570,"symbol":"mach_msg2_trap","symbolLocation":10,"imageIndex":0},{"imageOffset":62980,"symbol":"mach_msg2_internal","symbolLocation":82,"imageIndex":0},{"imageOffset":34357,"symbol":"mach_msg_overwrite","symbolLocation":723,"imageIndex":0},{"imageOffset":6312,"symbol":"mach_msg","symbolLocation":19,"imageIndex":0},{"imageOffset":66252326,"imageIndex":19},{"imageOffset":66251759,"imageIndex":19},{"imageOffset":65421769,"imageIndex":19},{"imageOffset":65919580,"imageIndex":19},{"imageOffset":65624472,"imageIndex":19},{"imageOffset":66059960,"imageIndex":19},{"imageOffset":66060362,"imageIndex":19},{"imageOffset":66222344,"imageIndex":19},{"imageOffset":25177,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":7291,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":8033892,"name":"ThreadPoolSingleThreadSharedBackgroundBlocking1","frames":[{"imageOffset":5570,"symbol":"mach_msg2_trap","symbolLocation":10,"imageIndex":0},{"imageOffset":62980,"symbol":"mach_msg2_internal","symbolLocation":82,"imageIndex":0},{"imageOffset":34357,"symbol":"mach_msg_overwrite","symbolLocation":723,"imageIndex":0},{"imageOffset":6312,"symbol":"mach_msg","symbolLocation":19,"imageIndex":0},{"imageOffset":66252326,"imageIndex":19},{"imageOffset":66009023,"imageIndex":19},{"imageOffset":66011034,"imageIndex":19},{"imageOffset":66010637,"imageIndex":19},{"imageOffset":66222344,"imageIndex":19},{"imageOffset":25177,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":7291,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":8034744,"name":"QFileInfoGatherer","frames":[{"imageOffset":16666,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":0},{"imageOffset":26593,"symbol":"_pthread_cond_wait","symbolLocation":1243,"imageIndex":1},{"imageOffset":2107627,"imageIndex":7},{"imageOffset":2107486,"symbol":"QWaitCondition::wait(QMutex*, QDeadlineTimer)","symbolLocation":94,"imageIndex":7},{"imageOffset":4529677,"symbol":"QFileInfoGatherer::run()","symbolLocation":125,"imageIndex":8},{"imageOffset":2066019,"imageIndex":7},{"imageOffset":25177,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":7291,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":8037466,"frames":[{"imageOffset":7256,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":1}]},{"id":8037673,"name":"ThreadPoolForegroundWorker","frames":[{"imageOffset":5570,"symbol":"mach_msg2_trap","symbolLocation":10,"imageIndex":0},{"imageOffset":62980,"symbol":"mach_msg2_internal","symbolLocation":82,"imageIndex":0},{"imageOffset":34357,"symbol":"mach_msg_overwrite","symbolLocation":723,"imageIndex":0},{"imageOffset":6312,"symbol":"mach_msg","symbolLocation":19,"imageIndex":0},{"imageOffset":66252326,"imageIndex":19},{"imageOffset":66009023,"imageIndex":19},{"imageOffset":66011756,"imageIndex":19},{"imageOffset":66010733,"imageIndex":19},{"imageOffset":66222344,"imageIndex":19},{"imageOffset":25177,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":1},{"imageOffset":7291,"symbol":"thread_start","symbolLocation":15,"imageIndex":1}]},{"id":8038503,"frames":[{"imageOffset":7256,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":1}]},{"id":8038551,"frames":[{"imageOffset":7256,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":1}]}],
"usedImages" : [
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703236964352,
"size" : 237560,
"uuid" : "7c3dcc95-9f42-3c7c-8796-476ff67b9cf7",
"path" : "\/usr\/lib\/system\/libsystem_kernel.dylib",
"name" : "libsystem_kernel.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703237201920,
"size" : 49144,
"uuid" : "5920e36f-53ec-33f0-b675-8ae48b58418c",
"path" : "\/usr\/lib\/system\/libsystem_pthread.dylib",
"name" : "libsystem_pthread.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703235948544,
"size" : 561152,
"uuid" : "376f7cb7-6dd2-3e00-976f-77dd755bdb0d",
"path" : "\/usr\/lib\/system\/libsystem_c.dylib",
"name" : "libsystem_c.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703237386240,
"size" : 40952,
"uuid" : "f314b62b-98f4-3a7c-8296-8739f8b6855a",
"path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
"name" : "libsystem_platform.dylib"
},
{
"size" : 0,
"source" : "A",
"base" : 0,
"uuid" : "00000000-0000-0000-0000-000000000000"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4676235264,
"size" : 4964352,
"uuid" : "f36760e5-d1e7-3a93-ae8c-1c3e55e3fc35",
"path" : "\/Applications\/ChimeraX-1.5.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/Qt6\/lib\/QtWidgets.framework\/Versions\/A\/QtWidgets",
"name" : "QtWidgets"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4450652160,
"size" : 2801664,
"uuid" : "babd94e3-ec19-3110-ab5b-11c39432d8c5",
"path" : "\/Applications\/ChimeraX-1.5.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/QtWidgets.abi3.so",
"name" : "QtWidgets.abi3.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4461907968,
"size" : 5259264,
"uuid" : "35b47b1c-6952-3d39-a5e7-711f3ca228f2",
"path" : "\/Applications\/ChimeraX-1.5.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/Qt6\/lib\/QtCore.framework\/Versions\/A\/QtCore",
"name" : "QtCore"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4682620928,
"size" : 6979584,
"uuid" : "49d915f7-1c6d-3bbd-b96f-064260e7d998",
"path" : "\/Applications\/ChimeraX-1.5.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/Qt6\/lib\/QtGui.framework\/Versions\/A\/QtGui",
"name" : "QtGui"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4696342528,
"size" : 655360,
"uuid" : "4bf756eb-ff87-3f7f-8c98-b1eda6463b81",
"path" : "\/Applications\/ChimeraX-1.5.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/Qt6\/plugins\/platforms\/libqcocoa.dylib",
"name" : "libqcocoa.dylib"
},
{
"source" : "P",
"arch" : "x86_64h",
"base" : 140703237603328,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.CoreFoundation",
"size" : 4825088,
"uuid" : "beb5fc0b-7196-3c1d-a59a-f62ada98f592",
"path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
"name" : "CoreFoundation",
"CFBundleVersion" : "1953.300"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703252779008,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.Foundation",
"size" : 10559479,
"uuid" : "ab5f8db8-b03b-33b6-98f7-ffaec27a8eab",
"path" : "\/System\/Library\/Frameworks\/Foundation.framework\/Versions\/C\/Foundation",
"name" : "Foundation",
"CFBundleVersion" : "1953.300"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703289556992,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.AppKit",
"size" : 16809984,
"uuid" : "00f4aa78-a19f-3a8e-9650-9f90b7beefd6",
"path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
"name" : "AppKit",
"CFBundleVersion" : "2299.30.116"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703398637568,
"CFBundleShortVersionString" : "2.1.1",
"CFBundleIdentifier" : "com.apple.HIToolbox",
"size" : 3112958,
"uuid" : "db45022f-3922-35b3-9a06-377f66ed0fbe",
"path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
"name" : "HIToolbox"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703330496512,
"CFBundleShortVersionString" : "1.22",
"CFBundleIdentifier" : "com.apple.HIServices",
"size" : 376817,
"uuid" : "38e5c75e-2b25-3bfd-a3f3-39d0a18bfaa1",
"path" : "\/System\/Library\/Frameworks\/ApplicationServices.framework\/Versions\/A\/Frameworks\/HIServices.framework\/Versions\/A\/HIServices",
"name" : "HIServices"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4395900928,
"CFBundleShortVersionString" : "3.9.11, (c) 2001-2021 Python Software Foundation.",
"CFBundleIdentifier" : "org.python.python",
"size" : 2527232,
"uuid" : "ef9cc1f4-5991-3213-9a9e-e68c578b6c1b",
"path" : "\/Applications\/ChimeraX-1.5.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/Python",
"name" : "Python",
"CFBundleVersion" : "3.9.11"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4391604224,
"CFBundleShortVersionString" : "1.5.0",
"CFBundleIdentifier" : "edu.ucsf.cgl.ChimeraX",
"size" : 4096,
"uuid" : "5df621ee-554e-36a8-b448-93b2334e5480",
"path" : "\/Applications\/ChimeraX-1.5.app\/Contents\/MacOS\/ChimeraX",
"name" : "ChimeraX",
"CFBundleVersion" : "1.5.0.0"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703233847296,
"size" : 609392,
"uuid" : "bb7a0970-8c62-3dce-a7a2-5cec9c501f11",
"path" : "\/usr\/lib\/dyld",
"name" : "dyld"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4478251008,
"size" : 64028672,
"uuid" : "24c9d5c5-4854-3af4-9550-cb0204044dfa",
"path" : "\/Applications\/ChimeraX-1.5.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/numpy\/.dylibs\/libopenblas64_.0.dylib",
"name" : "libopenblas64_.0.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4865794048,
"size" : 165052416,
"uuid" : "4aa1de3e-464c-340c-ab61-bcd39bfc7658",
"path" : "\/Applications\/ChimeraX-1.5.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/Qt6\/lib\/QtWebEngineCore.framework\/Versions\/A\/QtWebEngineCore",
"name" : "QtWebEngineCore"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703235461120,
"size" : 184320,
"uuid" : "f609f029-bcd0-3a54-b48a-99b3ce8378ce",
"path" : "\/usr\/lib\/system\/libsystem_malloc.dylib",
"name" : "libsystem_malloc.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703236874240,
"size" : 90104,
"uuid" : "1fa4a590-f60c-3813-a408-a407fbcd0e89",
"path" : "\/usr\/lib\/libc++abi.dylib",
"name" : "libc++abi.dylib"
}
],
"vmSummary" : "ReadOnly portion of Libraries: Total=1.1G resident=0K(0%) swapped_out_or_unallocated=1.1G(100%)\nWritable regions: Total=1.9G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=1.9G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 256K 2 \nActivity Tracing 256K 1 \nCG backing stores 960K 4 \nCG image 100K 18 \nColorSync 248K 29 \nCoreAnimation 44K 9 \nCoreGraphics 12K 2 \nCoreServices 624K 2 \nCoreUI image data 1760K 26 \nFoundation 16K 1 \nKernel Alloc Once 8K 1 \nMALLOC 1.5G 692 \nMALLOC guard page 32K 8 \nMALLOC_LARGE (reserved) 384K 1 reserved VM address space (unallocated)\nMach message 16K 3 \nOpenGL GLSL 384K 4 \nSTACK GUARD 96K 24 \nStack 140.2M 25 \nStack Guard 56.0M 1 \nVM_ALLOCATE 207.7M 105 \nVM_ALLOCATE (reserved) 32.0M 1 reserved VM address space (unallocated)\n__CTF 756 1 \n__DATA 46.5M 733 \n__DATA_CONST 40.6M 380 \n__DATA_DIRTY 1817K 223 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__LINKEDIT 212.2M 139 \n__OBJC_RO 65.4M 1 \n__OBJC_RW 1988K 2 \n__TEXT 894.0M 738 \ndyld private memory 416K 3 \nmapped file 551.4M 88 \nshared memory 2992K 28 \n=========== ======= ======= \nTOTAL 3.7G 3297 \nTOTAL, minus reserved VM space 3.7G 3297 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "6112e3d2fc54bc3389840661",
"factorPackIds" : {
"SIRI_TEXT_TO_SPEECH" : "63f8017d238e7b23a1f300f1"
},
"deploymentId" : 240000356
},
{
"rolloutId" : "63a0a6cfd1cdb67d083006d0",
"factorPackIds" : {
},
"deploymentId" : 240000003
}
],
"experiments" : [
]
},
"reportNotes" : [
"dyld_process_snapshot_create_for_process failed with 5"
]
}
===== Log before crash start =====
UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open "/Users/zhaixiuwen/Desktop/文章_PTH1R_arrestin/fig2/New
> Folder2/fig2a.cxs"
Log from Thu Nov 3 22:15:31 2022UCSF ChimeraX version: 1.4.dev202112080557
(2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "/Users/zhaixiuwen/Desktop/class b
> arrestin/PTH1R/文章/fig2/coupleing_comformation_3.cxs"
Log from Tue Oct 25 11:08:16 2022UCSF ChimeraX version: 1.4.dev202112080557
(2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "/Users/zhaixiuwen/Desktop/class b
> arrestin/PTH1R/文章/fig2/coupleing_comformation.cxs"
Log from Mon Oct 24 21:54:21 2022UCSF ChimeraX version: 1.4.dev202112080557
(2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "/Users/zhaixiuwen/Desktop/class b
> arrestin/PTH1R/文章/fig2/color_map_model.cxs"
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
restore_snapshot for "ZoneColor" returned None
[Repeated 1 time(s)]Log from Mon Oct 24 17:14:13 2022UCSF ChimeraX version:
1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open D:\\\AA_ZJU\\\arr\\\PTH1R\\\PTH1R_arrestin_composite_final.mrc
Opened PTH1R_arrestin_composite_final.mrc as #1, grid size 320,320,320, pixel
0.93, shown at level 8.64e-05, step 2, values float32
> volume #1 step 1
> volume #1 level 0.04086
> set bgColor white
> open D:/AA_ZJU/arr/PTH1R/PTH_arrestin-coot-15_real_space_refined_137.pdb
Summary of feedback from opening D:/AA_ZJU/arr/PTH1R/PTH_arrestin-
coot-15_real_space_refined_137.pdb
---
warnings | Ignored bad PDB record found on line 393
TER
Ignored bad PDB record found on line 3169
TER
Ignored bad PDB record found on line 4084
TER
Ignored bad PDB record found on line 4908
TER
Ignored bad PDB record found on line 7245
TER
Chain information for PTH_arrestin-coot-15_real_space_refined_137.pdb #2
---
Chain | Description
A | No description available
H | No description available
L | No description available
P | No description available
R | No description available
> hide #!2 models
> show #!2 models
> select /R
2336 atoms, 2401 bonds, 3 pseudobonds, 283 residues, 2 models selected
> ui tool show "Color Actions"
> color sel blue
> color sel cornflower blue
> color sel royal blue
> color sel dark slate gray
> color sel light pink
> color sel dark sea green
> color sel medium spring green
> color sel dodger blue
> color sel teal
> color sel dark cyan
> color sel steel blue
> select #2
7119 atoms, 7294 bonds, 4 pseudobonds, 890 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> hide #!1 models
> alias licorice cartoon style protein modeHelix default arrows false xsection
> oval width 2.5 thickness 1.2
> licorice
> lighting soft
> select /h
914 atoms, 939 bonds, 118 residues, 1 model selected
> color sel light gray
> select /l
823 atoms, 842 bonds, 108 residues, 1 model selected
> color sel light gray
> color sel silver
> select /h
914 atoms, 939 bonds, 118 residues, 1 model selected
> color sel silver
> color sel dark gray
> select /l
823 atoms, 842 bonds, 108 residues, 1 model selected
> color sel dark gray
> select /p
271 atoms, 276 bonds, 32 residues, 1 model selected
> color sel yellow
> color sel gold
> select /a
2775 atoms, 2836 bonds, 1 pseudobond, 349 residues, 2 models selected
> color sel brown
> select #2
7119 atoms, 7294 bonds, 4 pseudobonds, 890 residues, 2 models selected
> ~select #2
Nothing selected
> show #!1 models
> ui tool show "Color Zone"
> color zone #1 near #2 distance 5.58
> hide #!2 models
> color zone #1 near #2 distance 16.59
> color zone #1 near #2 distance 16.59
> hide #!1 models
> show #!2 models
> select /a
2775 atoms, 2836 bonds, 1 pseudobond, 349 residues, 2 models selected
> ui tool show "Color Actions"
> color sel brown
> color sel chocolate
> color sel coral
> color sel dark red
> color sel maroon
> color sel fire brick
> color sel magenta
> color sel deep pink
> color sel hot pink
> color sel purple
> color sel pale violet red
> color sel indian red
> color sel sienna
> color sel coral
> color sel indian red
> color sel maroon
> color sel salmon
> color sel red
> color sel maroon
> color sel dark red
> color sel medium violet red
> color zone #1 near #2 distance 16.59
> select #2
7119 atoms, 7294 bonds, 4 pseudobonds, 890 residues, 2 models selected
> ~select #2
Nothing selected
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!2 models
> show #!1 models
> select #1
2 models selected
> hide #!1 models
> show #!2 models
> select /r
2336 atoms, 2401 bonds, 3 pseudobonds, 283 residues, 2 models selected
> color (#!2 & sel) #e4ff83ff
> color (#!2 & sel) #d0ffa4ff
> color (#!2 & sel) #d0ffcfff
> color (#!2 & sel) #dbffe9ff
> color (#!2 & sel) #beffdbff
> color (#!2 & sel) #98ffe2ff
> color (#!2 & sel) #8afff5ff
> color (#!2 & sel) #6bffdfff
> color (#!2 & sel) #6fff85ff
> color (#!2 & sel) #6dff53ff
> color (#!2 & sel) #63ff33ff
> color (#!2 & sel) #69ff33ff
> color (#!2 & sel) #74ff33ff
> color (#!2 & sel) #7aff33ff
> color (#!2 & sel) #8eff59ff
> color (#!2 & sel) #8fff96ff
> color (#!2 & sel) #8bff59ff
> color (#!2 & sel) #82ff23ff
> color (#!2 & sel) #a3ff10ff
> color (#!2 & sel) #5dff05ff
> color (#!2 & sel) #07ffa0ff
> color (#!2 & sel) #15ff9eff
> color (#!2 & sel) #34ffb1ff
> color (#!2 & sel) #47ffacff
> color (#!2 & sel) #58ff87ff
> color (#!2 & sel) #75ffacff
> color (#!2 & sel) #8affd4ff
> color (#!2 & sel) #69ffd2ff
> color (#!2 & sel) #65ffadff
> color (#!2 & sel) #43ffa1ff
> color (#!2 & sel) #43ff88ff
> color (#!2 & sel) #2eff7bff
> color (#!2 & sel) #17ff6cff
> color (#!2 & sel) #17ff0bff
> color (#!2 & sel) #12c308ff
> color (#!2 & sel) #0e9907ff
> color (#!2 & sel) #0b7805ff
> color (#!2 & sel) #096304ff
> color (#!2 & sel) #0a7005ff
> color (#!2 & sel) #0e9e07ff
> color (#!2 & sel) #0c8706ff
> color (#!2 & sel) #11b608ff
> color (#!2 & sel) #13cc09ff
> color (#!2 & sel) #5fcc5dff
> color (#!2 & sel) #5fcc5eff
> color (#!2 & sel) #44cc5bff
> color (#!2 & sel) #30cc42ff
> color (#!2 & sel) #26cc26ff
> color (#!2 & sel) #37cc44ff
> color (#!2 & sel) #5ccca3ff
> color (#!2 & sel) #7eaaccff
> color (#!2 & sel) #7ea7ccff
> color (#!2 & sel) #759cbeff
> color (#!2 & sel) #7fa9ceff
> color (#!2 & sel) #769dbfff
> color (#!2 & sel) #7ca6caff
> select /a
2775 atoms, 2836 bonds, 1 pseudobond, 349 residues, 2 models selected
> color (#!2 & sel) #ca75aaff
> color (#!2 & sel) #ca5c82ff
> color (#!2 & sel) #ca4775ff
> color (#!2 & sel) #ca3eb0ff
> color (#!2 & sel) #ca1173ff
> color (#!2 & sel) #ca0aaaff
> color (#!2 & sel) #ca3fb7ff
> color (#!2 & sel) #ca71c9ff
> color (#!2 & sel) #ca9bbbff
> color (#!2 & sel) #ca8dadff
> color (#!2 & sel) #ca79aeff
> color (#!2 & sel) #ca79bfff
> color (#!2 & sel) #ca86b6ff
> color (#!2 & sel) #ca83c6ff
> color (#!2 & sel) #ca74c3ff
> color (#!2 & sel) #cab030ff
> color (#!2 & sel) #b9ca4eff
> color (#!2 & sel) #c7ca23ff
> color (#!2 & sel) #caca10ff
> color (#!2 & sel) #caba10ff
> color (#!2 & sel) #caa510ff
> color (#!2 & sel) #c0ca53ff
> color (#!2 & sel) #bbca71ff
> color (#!2 & sel) #afca35ff
> color (#!2 & sel) #ca68a4ff
> color zone #1 near #2 distance 16.59
> show #!1 models
> select #2
7119 atoms, 7294 bonds, 4 pseudobonds, 890 residues, 2 models selected
> ~select #2
Nothing selected
> hide #!1 models
> show #!1 models
> hide #!2 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!1 models
> show #!2 models
> hide #!1 models
> select /r
2336 atoms, 2401 bonds, 3 pseudobonds, 283 residues, 2 models selected
> ui tool show "Color Actions"
> color (#!2 & sel) #6eca69ff
> color (#!2 & sel) #55ca4dff
> color (#!2 & sel) #56ca4eff
> color (#!2 & sel) #34ca34ff
> color (#!2 & sel) #1bca35ff
> color (#!2 & sel) #8aca14ff
> color (#!2 & sel) #93ca14ff
> color (#!2 & sel) #61ca43ff
> color (#!2 & sel) #25ca33ff
> color (#!2 & sel) #25c732ff
> color (#!2 & sel) #26d034ff
> color (#!2 & sel) #2be73aff
> color (#!2 & sel) #2be83bff
> color (#!2 & sel) #2ef83fff
> color (#!2 & sel) #2efc40ff
> color (#!2 & sel) #2cef3cff
> color (#!2 & sel) #24c632ff
> color (#!2 & sel) #23bd30ff
> color (#!2 & sel) #22b92fff
> color (#!2 & sel) #1b9325ff
> color (#!2 & sel) #1c9626ff
> color (#!2 & sel) #1d9e28ff
> color (#!2 & sel) #1ea52aff
> color (#!2 & sel) #6ba58dff
> color (#!2 & sel) #74a580ff
> color (#!2 & sel) #74a58dff
> color (#!2 & sel) #6fa584ff
> color (#!2 & sel) #66a57bff
> color (#!2 & sel) #59a56cff
> color (#!2 & sel) #59a565ff
> color (#!2 & sel) #52a551ff
> color (#!2 & sel) #4da55fff
> color (#!2 & sel) #4da576ff
> color (#!2 & sel) #4ea777ff
> color (#!2 & sel) #4faa7aff
> color (#!2 & sel) #55b682ff
> color (#!2 & sel) #56b984ff
> color (#!2 & sel) #61cf94ff
> color (#!2 & sel) #61d095ff
> color (#!2 & sel) #60ce93ff
> color (#!2 & sel) #59bf89ff
> color (#!2 & sel) #58bd87ff
> color (#!2 & sel) #56b984ff
> color (#!2 & sel) #52af7dff
> color (#!2 & sel) #50ac7bff
> color (#!2 & sel) #51ad7cff
> color (#!2 & sel) #52af7dff
> color (#!2 & sel) #52b07eff
> color (#!2 & sel) #53b17fff
> color (#!2 & sel) #54b380ff
> select /p
271 atoms, 276 bonds, 32 residues, 1 model selected
> color sel #ffff7fff
> color sel #ffff00ff
> color sel #dada00ff
> color sel #e7e700ff
> color sel #dde775ff
> color sel #d2e74bff
> color sel #e7e725ff
> color sel #e7e711ff
> color sel #e79a57ff
> color sel #e79857ff
> color sel #e7a67aff
> color sel #e7d26cff
> color sel #dae76aff
> color sel #dae768ff
> color sel #dae761ff
> color sel #d9e75aff
> color sel #d9e759ff
> color sel #dbe759ff
> color sel #dbe75aff
> color sel #e1e767ff
> color sel #e1e774ff
> color sel #e1e775ff
> color sel #e5e775ff
> color sel #e7e775ff
> color sel #e7e375ff
> color sel #e7df75ff
> color sel #e7da75ff
> color sel #e7dd6fff
> color sel #e7e369ff
> color sel #e7e765ff
> color sel #e7e761ff
> color sel #e5e761ff
> color sel #dee72fff
> color sel #e7e725ff
> color sel #e7c725ff
> color sel #e7e12eff
> color sel #e7e248ff
> color sel #e7dc3dff
> color sel #e7d235ff
> color sel #ead535ff
> show #!1 models
> color zone #1 near #2 distance 16.59
> hide #!2 models
> show #!2 models
> hide #!1 models
> select /r
2336 atoms, 2401 bonds, 3 pseudobonds, 283 residues, 2 models selected
> color (#!2 & sel) #a8eaacff
> color (#!2 & sel) #8cea7bff
> color (#!2 & sel) #64ea5bff
> color (#!2 & sel) #74ea41ff
> color (#!2 & sel) #50a12dff
> color (#!2 & sel) #438726ff
> color (#!2 & sel) #346a1eff
> color (#!2 & sel) #418425ff
> color (#!2 & sel) #53a72eff
> color (#!2 & sel) #36a725ff
> color (#!2 & sel) #10a743ff
> color (#!2 & sel) #20a75fff
> color (#!2 & sel) #33a771ff
> color (#!2 & sel) #2f9a68ff
> color (#!2 & sel) #309c69ff
> color (#!2 & sel) #32a36eff
> color (#!2 & sel) #33a771ff
> color (#!2 & sel) #38b67bff
> color (#!2 & sel) #3bc182ff
> color (#!2 & sel) #3dc787ff
> color (#!2 & sel) #3eca89ff
> color (#!2 & sel) #3fce8bff
> color (#!2 & sel) #3fcf8cff
> color (#!2 & sel) #41d38fff
> color (#!2 & sel) #41d590ff
> color (#!2 & sel) #45e299ff
> color (#!2 & sel) #48ea9eff
> color (#!2 & sel) #47e79cff
> color (#!2 & sel) #3cc585ff
> color (#!2 & sel) #3bc182ff
> color (#!2 & sel) #2f9a68ff
> color (#!2 & sel) #2e9867ff
> color (#!2 & sel) #29875bff
> color (#!2 & sel) #277e55ff
> color (#!2 & sel) #247650ff
> color (#!2 & sel) #257952ff
> color (#!2 & sel) #288359ff
> color (#!2 & sel) #29875bff
> color (#!2 & sel) #2b8b5eff
> color (#!2 & sel) #2c9162ff
> color (#!2 & sel) #309c69ff
> color (#!2 & sel) #309d6aff
> color (#!2 & sel) #719d71ff
> color (#!2 & sel) #699d61ff
> color (#!2 & sel) #589d33ff
> color (#!2 & sel) #4b9d0cff
> color (#!2 & sel) #159d0cff
> color (#!2 & sel) #16a20cff
> color (#!2 & sel) #17a60cff
> color (#!2 & sel) #18ad0dff
> color (#!2 & sel) #18af0dff
> color (#!2 & sel) #19b90eff
> color (#!2 & sel) #1ac10eff
> color (#!2 & sel) #1bc50fff
> color (#!2 & sel) #1cce0fff
> color (#!2 & sel) #1cd00fff
> color (#!2 & sel) #1dd510ff
> color (#!2 & sel) #1dd810ff
> color (#!2 & sel) #1fe211ff
> color (#!2 & sel) #1fe511ff
> color (#!2 & sel) #1fe611ff
> color (#!2 & sel) #1fe711ff
> color (#!2 & sel) #1fe511ff
> color (#!2 & sel) #1fe211ff
> color (#!2 & sel) #1cd110ff
> color (#!2 & sel) #19b40dff
> color (#!2 & sel) #169e0cff
> color (#!2 & sel) #14930bff
> color (#!2 & sel) #138d0bff
> color (#!2 & sel) #13880aff
> color (#!2 & sel) #12870aff
> color (#!2 & sel) #138d0bff
> color (#!2 & sel) #159d0cff
> color (#!2 & sel) #16a10cff
> color (#!2 & sel) #17a70cff
> color (#!2 & sel) #1abc0eff
> color (#!2 & sel) #1abd0eff
> color (#!2 & sel) #96bd4cff
> color (#!2 & sel) #6ebd4cff
> color (#!2 & sel) #6fbf4dff
> color (#!2 & sel) #70c14eff
> color (#!2 & sel) #76cb52ff
> color (#!2 & sel) #79d054ff
> color (#!2 & sel) #78ce53ff
> color (#!2 & sel) #70c14eff
> color (#!2 & sel) #6ebd4cff
> color (#!2 & sel) #6ebc4cff
> color (#!2 & sel) #65ad46ff
> color (#!2 & sel) #64ab45ff
> color (#!2 & sel) #64ac45ff
> color (#!2 & sel) #6fbe4dff
> color (#!2 & sel) #6fbf4dff
> color (#!2 & sel) #73c550ff
> color (#!2 & sel) #73c650ff
> color (#!2 & sel) #72c34fff
> color (#!2 & sel) #6ebd4cff
> color (#!2 & sel) #6cba4bff
> color zone #1 near #2 distance 16.59
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> color (#!2 & sel) #63ba5aff
> select /r
2336 atoms, 2401 bonds, 3 pseudobonds, 283 residues, 2 models selected
> color sel real
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color selseal
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color sel seal
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color sel teal
> show #!1 models
> color zone #1 near #2 distance 16.59
> select #2
7119 atoms, 7294 bonds, 4 pseudobonds, 890 residues, 2 models selected
> ~select #2
Nothing selected
> hide #!2 models
> hide #!1 models
> show #!2 models
> select /R:225
10 atoms, 10 bonds, 1 residue, 1 model selected
> select up
226 atoms, 231 bonds, 27 residues, 1 model selected
> select up
2336 atoms, 2401 bonds, 283 residues, 1 model selected
> color sel #cce4f7ff
> color sel #ccccccff
> color sel #f0f0f0ff
> color sel #ffffffff
> color sel #fffeffff
> color sel #ffffffff
> color sel #fffdfcff
> color sel #355968ff
> color sel #385863ff
> color sel #5c8ea2ff
> color sel #5c8ea1ff
> select clear
> select /P:26
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
249 atoms, 253 bonds, 29 residues, 1 model selected
> select up
271 atoms, 276 bonds, 32 residues, 1 model selected
> color sel #cfe5f6ff
> color sel #ccccccff
> color sel #ffffffff
> color sel #d1ccd2ff
> color sel #f9f9f9ff
> color sel #ddc5d3ff
> color sel #8a274fff
> color sel #4b2537ff
> color sel #661734ff
> color sel #5b2a20ff
> color sel #fffdf4ff
> color sel #fffcf8ff
> color sel #e5d9c3ff
> color sel #755e2dff
> color sel #795b2dff
> color sel #775b33ff
> color sel #fcf7f6ff
> color sel #460923ff
> color sel #ae2b5fff
> color sel #aa3261ff
> color sel #9a335bff
> color sel #54162fff
> color sel #3e1326ff
> color sel #fdfef8ff
> color sel #fdffffff
> color sel #ffffffff
> color sel #cba944ff
> color sel #f0a738ff
> color sel #8e6f3cff
> color sel #fcf8eeff
> color sel #fcf7e2ff
> color sel #e3a726ff
> color sel #94643bff
> color sel #a66a36ff
> color sel #fcba25ff
> color sel #c6872eff
> color sel #c67f2fff
> color sel #c68132ff
> color sel #c68233ff
> color sel #c68234ff
> color sel #c68536ff
> color sel #c68c3aff
> color sel #c6943eff
> color sel #cc9940ff
> color sel #cf9b41ff
> color sel #d39e42ff
> color sel #dea646ff
> select clear
> select /A:234
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
122 atoms, 122 bonds, 15 residues, 1 model selected
> select up
2775 atoms, 2836 bonds, 349 residues, 1 model selected
> color sel #f0f0f0ff
> color sel #ccccccff
> color sel #787878ff
> color sel #ccccccff
> color sel #f0f0f0ff
> color sel #466c7bff
> color sel #ffffffff
> color sel #89204aff
> color sel #cbf7e9ff
> color sel #5e1437ff
> color sel #712043ff
> color sel #882651ff
> color sel #c69cacff
> color sel #b9a283ff
> color sel #8a6625ff
> color sel #836924ff
> color sel #da952eff
> color sel #de9533ff
> color sel #d08931ff
> color sel #f6a61fff
> color sel #f7b62aff
> select /P:26
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
249 atoms, 253 bonds, 29 residues, 1 model selected
> select up
271 atoms, 276 bonds, 32 residues, 1 model selected
> color sel #daebf9ff
> color sel #ccccccff
> color sel #ffffffff
> color sel #fbfbfbff
> color sel #feeffaff
> color sel #3b4f3dff
> color sel #e4d3dcff
> color sel #fbf9fcff
> color sel #f9f9fbff
> color sel #843558ff
> color sel #b82d64ff
> color sel #ac2b5dff
> color sel #ae3966ff
> select clear
> color zone #1 near #2 distance 16.59
> show #!1 models
> save D:/AA_ZJU/arr/PTH1R/color_map_model.cxs
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> hide #!1 models
> show #!2 models
> select /H:91
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
22 atoms, 21 bonds, 3 residues, 1 model selected
> select up
914 atoms, 939 bonds, 118 residues, 1 model selected
> select up
7119 atoms, 7294 bonds, 890 residues, 1 model selected
> select down
914 atoms, 939 bonds, 118 residues, 1 model selected
> color sel ae3966ff
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> ui tool show "Color Actions"
> color sel #aaee33ff
> color sel #ae3966ff
> color sel #aacc22ff
> color sel #ac2b5dff
> color sel #000000ff
> color sel #ccccccff
> color sel #69a2b8ff
> color sel #ffffffff
> color sel #3f616fff
> color sel #4f7587ff
> color sel #577e8fff
> color sel #5a899cff
> color sel #578696ff
> color sel #486e7eff
> color sel #4e7f8eff
> color sel #558393ff
> color sel #588797ff
> color sel #5a899aff
> color sel #5a8b9cff
> color sel #5b8b9cff
> color sel #59889aff
> color sel #568396ff
> color sel #558295ff
> color sel #568293ff
> color sel #6699aaff
> color sel #6498a9ff
> color sel #5e92a6ff
> color sel #5d90a3ff
> color sel #5b8da0ff
> color sel #598a9bff
> color sel #daebf9ff
> color sel #ccccccff
> color sel #ffffffff
> color sel #36545fff
> color sel #ffffffff
> color sel #64a4b5ff
> color sel #67a0b5ff
> color sel #ffffffff
> color sel #fbfcfeff
> color sel #9c999bff
> color sel #b22863ff
> color sel #9b2657ff
> color sel #573b46ff
> color sel #4c2b3aff
> color sel #88254eff
> color sel #a22d5fff
> color sel #9c2f5dff
> color sel #a02458ff
> color sel #9c2556ff
> color sel #88254eff
> color sel #3f1a2cff
> color sel #46162bff
> color sel #650e32ff
> color sel #9c2c5aff
> color sel #a12658ff
> color sel #9d1d50ff
> color sel #911947ff
> color sel #831140ff
> color sel #fff7fdff
> color sel #d4b4c3ff
> color sel #3a0a20ff
> color sel #882551ff
> color sel #9d2658ff
> color sel #620f32ff
> color sel #4d142cff
> color sel #4e172eff
> color sel #fdf7fbff
> color sel #eed1dfff
> color sel #922e53ff
> color sel #9c2d56ff
> color sel #a52a59ff
> color sel #ba2b61ff
> color sel #b7285fff
> color sel #b6295eff
> color sel #ac2d5dff
> color sel #a6305dff
> color sel #932751ff
> color sel #3a0e22ff
> color sel #4e1029ff
> color sel #51122bff
> color sel #480d26ff
> color sel #53132dff
> color sel #440e25ff
> color sel #560e2bff
> color sel #5c0e2eff
> color sel #6b1036ff
> color sel #88224cff
> color sel #b62661ff
> color sel #491129ff
> color sel #47152bff
> color sel #55132eff
> color sel #87274dff
> color sel #ac2357ff
> color sel #aa2759ff
> color sel #a42a5bff
> color sel #9b2c59ff
> color sel #ac3162ff
> color sel #ab3062ff
> color sel #aa295cff
> color sel #a82c60ff
> color sel #aa2e60ff
> color sel #8b2f53ff
> color sel #41061bff
> color sel #290a18ff
> color sel #5c3848ff
> color sel #652b43ff
> color sel #a9295aff
> color sel #a62d5dff
> color sel #9b2e5bff
> color sel #89264fff
> color sel #9b2e5bff
> color sel #a62d5dff
> color sel #681838ff
> color sel #648592ff
> color sel #ffffffff
> color sel #5a8a9dff
> color sel #6196aaff
> color sel #ffffffff
> color sel #6a233eff
> color sel #902f54ff
> color sel #9b335bff
> color sel #a53660ff
> color sel #ddecf9ff
> color sel #ccccccff
> color sel #bfbfbfff
> color sel #c6a45eff
> color sel #f0ba47ff
> color sel #eeb947ff
> color sel #cfa242ff
> color sel #c69b40ff
> color sel #fabc36ff
> color sel #dea72fff
> color sel #926c19ff
> color sel #795915ff
> color sel #c08e21ff
> color sel #ebad28ff
> color sel #e7aa27ff
> color sel #dea426ff
> color sel #aa7d1dff
> color sel #ffffffff
> color sel #ab8b45ff
> color sel #ffffffff
> color sel #eeb232ff
> color sel #f9ba34ff
> color sel #f6b934ff
> color sel #f6b933ff
> color sel #f4b733ff
> color sel #f5b833ff
> color sel #f3b633ff
> color sel #f9ba34ff
> color sel #f5b733ff
> color sel #f7b934ff
> color sel #fdbe35ff
> color sel #ffbf35ff
> color sel #febe35ff
> color sel #ffc136ff
> color sel #ffbf35ff
> color sel #ffc136ff
> color sel #fbbc34ff
> color sel #e7ae33ff
> color sel #e9af34ff
> color sel #c59b41ff
> color sel #ffffffff
> color sel #ffbe2cff
> color sel #d39b24ff
> color sel #ac893dff
> color sel #ffffffff
> color sel #dfa831ff
> color sel #e0a931ff
> color sel #e0a831ff
> color sel #e1a931ff
> color sel #dfa831ff
> color sel dark gray
> color sel light gray
> color sel dark gray
> color sel silver
> color sel dark gray
> color /r #598a9b
> color /p #598a9b
> color /p #598a9b
> color /p #598a9b
> color /p #a53660
> color /a #dfa831
> color zone #1 near #2 distance 16.59
> show #!1 models
> hide #!1 models
> save D:/AA_ZJU/arr/PTH1R/color_map_model.cxs
——— End of log from Mon Oct 24 17:14:13 2022 ———
opened ChimeraX session
> open "/Users/zhaixiuwen/Desktop/class b arrestin/pdb_class a
> arrestin/b1ar_arrestin_6tko.pdb"
b1ar_arrestin_6tko.pdb title:
Phosphorylated turkey Β1 adrenoceptor with bound agonist formoterol coupled to
arrestin-2 In lipid nanodisc. [more info...]
Chain information for b1ar_arrestin_6tko.pdb #1
---
Chain | Description | UniProt
A | β-1 adrenergic receptor | ADRB1_MELGA
B | β-arrestin-1 | ARRB1_HUMAN
H | FAB30 heavy chain |
L | FAB30 light chain |
Non-standard residues in b1ar_arrestin_6tko.pdb #1
---
H98 —
~{N}-[5-[(1~{R})-2-[[(2~{R})-1-(4-methoxyphenyl)propan-2-yl]amino]-1-oxidanyl-
ethyl]-2-oxidanyl-phenyl]methanamide
SEP — phosphoserine (phosphonoserine)
TPO — phosphothreonine (phosphonothreonine)
> open "/Users/zhaixiuwen/Desktop/class b arrestin/pdb_class a
> arrestin/m2r_arrestin.pdb"
m2r_arrestin.pdb title:
GPCR-β arrestin structure In lipid bilayer [more info...]
Chain information for m2r_arrestin.pdb #3
---
Chain | Description | UniProt
C | arrestin β-1 | ARRB1_RAT
H | FAB30 heavy chain | V9HW68_HUMAN
L | FAB30 light chain | Q7Z3Y4_HUMAN
R | muscarinic acetylcholine receptor M2, vasopressin V2 receptor chimera |
V2R_HUMAN
Non-standard residues in m2r_arrestin.pdb #3
---
2CU — 3-amino-5-chloro-N-
cyclopropyl-4-methyl-6-[2-(4-methylpiperazin-1-yl)-2-oxoethoxy]thieno[2,3-B]pyridine-2-carboxamide
(LY2119620 positive allosteric modulator of M2/M4RECEPTOR)
> open "/Users/zhaixiuwen/Desktop/class b arrestin/pdb_class a
> arrestin/NTSR1_arrestin_6pwc.pdb"
NTSR1_arrestin_6pwc.pdb title:
A complex structure of arrestin-2 bound to neurotensin receptor 1 [more
info...]
Chain information for NTSR1_arrestin_6pwc.pdb #4
---
Chain | Description | UniProt
A | β-arrestin-1 | ARRB1_HUMAN
B | neurotensin peptide |
H | FAB30 heavy chain |
L | FAB30 light chain |
R | neurotensin receptor type 1 | NTR1_HUMAN
> open "/Users/zhaixiuwen/Desktop/class b arrestin/pdb_class a
> arrestin/V2R_arrestin_7r0c.pdb"
V2R_arrestin_7r0c.pdb title:
Structure of the avp-V2R-ARRESTIN2-SCFV30 complex [more info...]
Chain information for V2R_arrestin_7r0c.pdb #5
---
Chain | Description | UniProt
A | vasopressin V2 receptor | V2R_HUMAN
B | AVP |
C | ARRESTIN2 | ARRB1_HUMAN
D | SCFV30 |
Non-standard residues in V2R_arrestin_7r0c.pdb #5
---
NH2 — amino group
> licorice
> show sel atoms
> hide sel atoms
> style sel stick
Changed 914 atom styles
> style sel stick
Changed 914 atom styles
> select clear
Drag select of 3444 residues, 19 pseudobonds, 5597 atoms, 174 bonds
> select clear
> licorice
> ui tool show Matchmaker
> matchmaker #!1 to #2/R pairing bs
Parameters
---
Chain pairing | bs
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 PTH_arrestin-coot-15_real_space_refined_137.pdb, chain R (#2) with
b1ar_arrestin_6tko.pdb, chain A (#1), sequence alignment score = 324.3
RMSD between 67 pruned atom pairs is 1.001 angstroms; (across all 265 pairs:
7.469)
> matchmaker #!3 to #2/R pairing bs
Parameters
---
Chain pairing | bs
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 PTH_arrestin-coot-15_real_space_refined_137.pdb, chain R (#2) with
m2r_arrestin.pdb, chain R (#3), sequence alignment score = 333.4
RMSD between 63 pruned atom pairs is 1.151 angstroms; (across all 258 pairs:
7.503)
> matchmaker #!4 to #2/R pairing bs
Parameters
---
Chain pairing | bs
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 PTH_arrestin-coot-15_real_space_refined_137.pdb, chain R (#2) with
NTSR1_arrestin_6pwc.pdb, chain R (#4), sequence alignment score = 323.1
RMSD between 39 pruned atom pairs is 1.210 angstroms; (across all 279 pairs:
10.909)
> matchmaker #!5 to #2/R pairing bs
Parameters
---
Chain pairing | bs
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 PTH_arrestin-coot-15_real_space_refined_137.pdb, chain R (#2) with
V2R_arrestin_7r0c.pdb, chain A (#5), sequence alignment score = 335.2
RMSD between 53 pruned atom pairs is 1.187 angstroms; (across all 262 pairs:
7.443)
> matchmaker #!5 to #2/R pairing bs
Parameters
---
Chain pairing | bs
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 PTH_arrestin-coot-15_real_space_refined_137.pdb, chain R (#2) with
V2R_arrestin_7r0c.pdb, chain A (#5), sequence alignment score = 335.2
RMSD between 53 pruned atom pairs is 1.187 angstroms; (across all 262 pairs:
7.443)
> style stick
Changed 33762 atom styles
> hide atoms
> show cartoons
> select clear
> ui tool show Matchmaker
> matchmaker #1/A to #2/R pairing ss
Parameters
---
Chain pairing | ss
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 PTH_arrestin-coot-15_real_space_refined_137.pdb, chain R (#2) with
b1ar_arrestin_6tko.pdb, chain A (#1), sequence alignment score = 324.3
RMSD between 67 pruned atom pairs is 1.001 angstroms; (across all 265 pairs:
7.469)
> matchmaker #3/R to #2/R pairing ss
Parameters
---
Chain pairing | ss
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 PTH_arrestin-coot-15_real_space_refined_137.pdb, chain R (#2) with
m2r_arrestin.pdb, chain R (#3), sequence alignment score = 333.4
RMSD between 63 pruned atom pairs is 1.151 angstroms; (across all 258 pairs:
7.503)
> matchmaker #4/R to #2/R pairing ss
Parameters
---
Chain pairing | ss
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 PTH_arrestin-coot-15_real_space_refined_137.pdb, chain R (#2) with
NTSR1_arrestin_6pwc.pdb, chain R (#4), sequence alignment score = 323.1
RMSD between 39 pruned atom pairs is 1.210 angstroms; (across all 279 pairs:
10.909)
> matchmaker #!1 to #2/A pairing bs
Parameters
---
Chain pairing | bs
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 PTH_arrestin-coot-15_real_space_refined_137.pdb, chain A (#2) with
b1ar_arrestin_6tko.pdb, chain B (#1), sequence alignment score = 1631.2
RMSD between 312 pruned atom pairs is 0.927 angstroms; (across all 344 pairs:
1.648)
> hide #!1 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> show #!1 models
> hide #!1 models
> select #2/R:218
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/R:346
8 atoms, 7 bonds, 1 residue, 1 model selected
> mmaker #1 to #2/R:218-346
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 PTH_arrestin-coot-15_real_space_refined_137.pdb, chain R (#2) with
b1ar_arrestin_6tko.pdb, chain A (#1), sequence alignment score = 128.6
RMSD between 49 pruned atom pairs is 0.951 angstroms; (across all 94 pairs:
7.948)
> show #!1 models
> show #!3 models
> show #!4 models
> show #!5 models
> mmaker #3 to #2/R:218-346
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 PTH_arrestin-coot-15_real_space_refined_137.pdb, chain R (#2) with
m2r_arrestin.pdb, chain R (#3), sequence alignment score = 143.2
RMSD between 20 pruned atom pairs is 1.296 angstroms; (across all 94 pairs:
11.774)
> mmaker #4 to #2/R:218-346
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 PTH_arrestin-coot-15_real_space_refined_137.pdb, chain R (#2) with
NTSR1_arrestin_6pwc.pdb, chain R (#4), sequence alignment score = 150.1
RMSD between 14 pruned atom pairs is 1.023 angstroms; (across all 100 pairs:
9.723)
> mmaker #5 to #2/R:218-346
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 PTH_arrestin-coot-15_real_space_refined_137.pdb, chain R (#2) with
V2R_arrestin_7r0c.pdb, chain A (#5), sequence alignment score = 136.4
RMSD between 50 pruned atom pairs is 1.171 angstroms; (across all 100 pairs:
10.686)
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> show #!2 models
> hide #!1 models
> select #2/R:218
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!3 models
> show #!2 models
> hide #!3 models
> hide #!2 models
> show #!5 models
> show #!2 models
> mmaker #5/R to #2/R:218-346
No molecules/chains to match specified
> mmaker #5/B to #2/R:218-346
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 PTH_arrestin-coot-15_real_space_refined_137.pdb, chain R (#2) with
V2R_arrestin_7r0c.pdb, chain B (#5), sequence alignment score = 0.5
RMSD between 4 pruned atom pairs is 1.499 angstroms; (across all 5 pairs:
4.532)
> mmaker #5/ to #2/R:218-346
> matchmaker #5/ to #2/R:218-346
Missing required "to" argument
> hide #!2 models
> select #5/A:72
5 atoms, 4 bonds, 1 residue, 1 model selected
> show #!2 models
> mmaker #5/A to #2/R:218-346
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 PTH_arrestin-coot-15_real_space_refined_137.pdb, chain R (#2) with
V2R_arrestin_7r0c.pdb, chain A (#5), sequence alignment score = 136.4
RMSD between 50 pruned atom pairs is 1.171 angstroms; (across all 100 pairs:
10.686)
> hide #!2 models
> hide #!5 models
> show #!1 models
Drag select of 154 residues, 2 pseudobonds
> select up
1340 atoms, 1369 bonds, 2 pseudobonds, 179 residues, 2 models selected
> select up
3135 atoms, 3214 bonds, 2 pseudobonds, 415 residues, 2 models selected
> hide sel cartoons
> hide #!1 models
> show #!2 models
Drag select of 58 residues
> select up
747 atoms, 765 bonds, 96 residues, 1 model selected
> select up
1737 atoms, 1781 bonds, 226 residues, 1 model selected
> hide sel cartoons
> hide #!2 models
> show #!3 models
Drag select of 64 residues
> select up
883 atoms, 901 bonds, 120 residues, 1 model selected
> select up
1627 atoms, 1671 bonds, 227 residues, 1 model selected
> hide sel cartoons
> hide #!3 models
> show #!4 models
Drag select of 157 residues, 2 pseudobonds
> select up
989 atoms, 992 bonds, 2 pseudobonds, 175 residues, 2 models selected
> select up
2093 atoms, 2107 bonds, 2 pseudobonds, 377 residues, 2 models selected
> select up
5879 atoms, 5939 bonds, 7 pseudobonds, 1055 residues, 2 models selected
> select down
2093 atoms, 2107 bonds, 2 pseudobonds, 377 residues, 2 models selected
> hide sel cartoons
> hide #!4 models
> show #!5 models
Drag select of 72 residues, 1 pseudobonds
> select up
718 atoms, 731 bonds, 1 pseudobond, 95 residues, 2 models selected
> select up
1750 atoms, 1795 bonds, 1 pseudobond, 229 residues, 2 models selected
> hide sel cartoons
> show #!2 models
> show #!4 models
> mmaker #4/A to #2/R:218-346
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 PTH_arrestin-coot-15_real_space_refined_137.pdb, chain R (#2) with
NTSR1_arrestin_6pwc.pdb, chain A (#4), sequence alignment score = 0
Fewer than 3 residues aligned; cannot match PTH_arrestin-
coot-15_real_space_refined_137.pdb, chain R with NTSR1_arrestin_6pwc.pdb,
chain A
> hide #!2 models
> hide #!5 models
> select #4/R:99
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #4/R:205
5 atoms, 4 bonds, 1 residue, 1 model selected
> show #!2 models
> mmaker #4/R:99-205 to #2/R:218-346
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 PTH_arrestin-coot-15_real_space_refined_137.pdb, chain R (#2) with
NTSR1_arrestin_6pwc.pdb, chain R (#4), sequence alignment score = 125.3
RMSD between 26 pruned atom pairs is 0.984 angstroms; (across all 100 pairs:
7.595)
> show #!1 models
> show #!3 models
> hide #!2 models
> hide #!4 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> select #3/R:56
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #3/R:167
4 atoms, 3 bonds, 1 residue, 1 model selected
> mmaker #3/R:56-166 to #2/R:218-346
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 PTH_arrestin-coot-15_real_space_refined_137.pdb, chain R (#2) with
m2r_arrestin.pdb, chain R (#3), sequence alignment score = 127.2
RMSD between 61 pruned atom pairs is 1.189 angstroms; (across all 100 pairs:
2.662)
> show #!2 models
> show #!1 models
> show #!4 models
> show #!5 models
> hide #!1 models
> hide #!3 models
> hide #!5 models
> hide #!2 models
> hide #!4 models
> show #!3 models
> hide #!3 models
> show #!2 models
> select #2/A:283
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
106 atoms, 107 bonds, 13 residues, 1 model selected
> select up
2775 atoms, 2836 bonds, 349 residues, 1 model selected
> select up
7119 atoms, 7294 bonds, 890 residues, 1 model selected
> select up
33762 atoms, 34494 bonds, 4739 residues, 5 models selected
> select clear
> select #4/B
27 atoms, 27 bonds, 5 residues, 1 model selected
> hide #!2 cartoons
> undo
> show #!1 models
> show #!3 models
> show #!4 models
> show #!5 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
Drag select of 637 residues, 2 pseudobonds
> color (#!1 & sel) yellow
> color (#!1 & sel) orange
> ui tool show "Color Actions"
> color sel sandy brown
> color sel khaki
> select clear
> hide #!1 models
> show #!2 models
> select #2/R:235
7 atoms, 6 bonds, 1 residue, 1 model selected
> select clear
Drag select of 664 residues, 3 pseudobonds
> select clear
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!2 models
> hide #!2 models
> hide #2.1 models
> show #!2 models
> show #!1 models
> show #!3 models
> show #!4 models
> hide #!4 models
> hide #!3 models
> hide #!2 models
> hide #!1 models
> show #!2 models
> show #!3 models
> hide #!3 models
> show #!3 models
> graphics silhouettes true
> hide #!3 models
> show #!1 models
> hide #!1 models
> show #!5 models
> graphics silhouettes false
> graphics silhouettes true
> open "/Users/zhaixiuwen/Desktop/class b arrestin/pdb_class a
> arrestin/rhodopsi_arrestin_4zwj.pdb"
rhodopsi_arrestin_4zwj.pdb title:
Crystal structure of rhodopsin bound to arrestin by femtosecond X-ray laser
[more info...]
Chain information for rhodopsi_arrestin_4zwj.pdb #6
---
Chain | Description | UniProt
A D | chimera protein of human rhodopsin, mouse S-arrestin, and T4 endolysin |
ARRS_MOUSE
B | chimera protein of human rhodopsin, mouse S-arrestin, and T4 endolysin |
ARRS_MOUSE
C | chimera protein of human rhodopsin, mouse S-arrestin, and T4 endolysin |
ARRS_MOUSE
> select #6/A
6565 atoms, 6725 bonds, 2 pseudobonds, 833 residues, 2 models selected
> hide sel cartoons
> select #6/B
5296 atoms, 5435 bonds, 2 pseudobonds, 673 residues, 2 models selected
> hide sel cartoons
> select #6/C
6231 atoms, 6385 bonds, 3 pseudobonds, 789 residues, 2 models selected
> hide sel cartoons
> mmaker #6/D to #2/R:218-346
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 PTH_arrestin-coot-15_real_space_refined_137.pdb, chain R (#2) with
rhodopsi_arrestin_4zwj.pdb, chain D (#6), sequence alignment score = 142.7
RMSD between 26 pruned atom pairs is 1.305 angstroms; (across all 94 pairs:
9.496)
> hide #!5 models
> hide #!2 models
> select #6/D:70
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #6/D:169
5 atoms, 4 bonds, 1 residue, 1 model selected
> show #!2 models
> mmaker #6/D:70-169 to #2/R:218-346
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 PTH_arrestin-coot-15_real_space_refined_137.pdb, chain R (#2) with
rhodopsi_arrestin_4zwj.pdb, chain D (#6), sequence alignment score = 143.4
RMSD between 60 pruned atom pairs is 1.167 angstroms; (across all 90 pairs:
3.378)
> show #!1 models
> show #!3 models
> show #!4 models
> hide #!4 models
> show #!4 models
> show #!5 models
Drag select of 4095 residues, 11 pseudobonds
> licorice
> hide #!1 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!3 models
> open "/Users/zhaixiuwen/Desktop/class b arrestin/pdb_class a
> arrestin/inactive_arrestin_1g4m.pdb"
inactive_arrestin_1g4m.pdb title:
Crystal structure of bovine β-arrestin 1 [more info...]
Chain information for inactive_arrestin_1g4m.pdb #7
---
Chain | Description | UniProt
A | β-ARRESTIN1 | ARRB1_BOVIN
B | β-ARRESTIN1 | ARRB1_BOVIN
> open /Users/zhaixiuwen/Desktop/pth1r/pdb+map/LAPTH-PTH1R-DNGs.pdb
LAPTH-PTH1R-DNGs.pdb title:
Cryo-em structure of parathyroid hormone receptor type 1 In complex with A
long-acting parathyroid hormone analog and G protein [more info...]
Chain information for LAPTH-PTH1R-DNGs.pdb #8
---
Chain | Description | UniProt
A | GS protein α subunit |
B | transducin β chain 1 | GBB1_RAT
G | G γ-I | GBG2_BOVIN
N | nanobody-35 |
P | long-acting parathyroid hormone analog |
R | parathyroid hormone/parathyroid hormone-related peptide receptor |
PTH1R_HUMAN
Non-standard residues in LAPTH-PTH1R-DNGs.pdb #8
---
CLR — cholesterol
PLM — palmitic acid
> select #7
5926 atoms, 5775 bonds, 4 pseudobonds, 982 residues, 2 models selected
> ~select #7
Nothing selected
> select #8
9424 atoms, 9646 bonds, 6 pseudobonds, 1158 residues, 2 models selected
> select #7
5926 atoms, 5775 bonds, 4 pseudobonds, 982 residues, 2 models selected
> hide #!3 models
> hide #!6 models
> select clear
Drag select of 713 residues, 9 pseudobonds, 9424 atoms, 254 bonds
> show sel cartoons
> style sel stick
Changed 15081 atom styles
> hide sel atoms
> show sel cartoons
> licorice
> ui tool show Matchmaker
> matchmaker #!8 to #2/R pairing bs
Parameters
---
Chain pairing | bs
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 PTH_arrestin-coot-15_real_space_refined_137.pdb, chain R (#2) with
LAPTH-PTH1R-DNGs.pdb, chain R (#8), sequence alignment score = 1380.9
RMSD between 251 pruned atom pairs is 0.706 angstroms; (across all 270 pairs:
1.054)
> matchmaker #!8 to #2/R pairing bs
Parameters
---
Chain pairing | bs
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 PTH_arrestin-coot-15_real_space_refined_137.pdb, chain R (#2) with
LAPTH-PTH1R-DNGs.pdb, chain R (#8), sequence alignment score = 1380.9
RMSD between 251 pruned atom pairs is 0.706 angstroms; (across all 270 pairs:
1.054)
> show #!2 models
> show #!1 models
> hide #!1 models
> hide #!2 models
> ui tool show Matchmaker
QMainWindowLayout::tabPosition called with out-of-bounds value '0'
> matchmaker #!7 to #2/A pairing bs
Parameters
---
Chain pairing | bs
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 PTH_arrestin-coot-15_real_space_refined_137.pdb, chain A (#2) with
inactive_arrestin_1g4m.pdb, chain B (#7), sequence alignment score = 1603.9
RMSD between 154 pruned atom pairs is 0.758 angstroms; (across all 345 pairs:
4.905)
> matchmaker #!7 to #2/A pairing bs
Parameters
---
Chain pairing | bs
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 PTH_arrestin-coot-15_real_space_refined_137.pdb, chain A (#2) with
inactive_arrestin_1g4m.pdb, chain B (#7), sequence alignment score = 1603.9
RMSD between 154 pruned atom pairs is 0.758 angstroms; (across all 345 pairs:
4.905)
> hide #!8 models
> show #!2 models
> select #7/A:15
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #7/A:81
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
111 atoms, 113 bonds, 13 residues, 1 model selected
> select up
2976 atoms, 2880 bonds, 511 residues, 1 model selected
> hide sel cartoons
> save "/Users/zhaixiuwen/Desktop/class b
> arrestin/PTH1R/文章/fig2/coupleing_comformation.cxs"
——— End of log from Mon Oct 24 21:54:21 2022 ———
opened ChimeraX session
> close #8
> close #7
> graphics silhouettes false
> select #2/R:1362
10 atoms, 9 bonds, 1 residue, 1 model selected
> select up
35 atoms, 34 bonds, 4 residues, 1 model selected
> select up
2336 atoms, 2401 bonds, 283 residues, 1 model selected
> select down
35 atoms, 34 bonds, 4 residues, 1 model selected
> select add #2/R:1356
44 atoms, 42 bonds, 5 residues, 1 model selected
> select add #2/R:1357
54 atoms, 51 bonds, 6 residues, 1 model selected
> select add #2/R:1359
65 atoms, 61 bonds, 7 residues, 1 model selected
> select add #2/R:1358
70 atoms, 65 bonds, 8 residues, 1 model selected
> select add #2/R:1360
81 atoms, 75 bonds, 9 residues, 1 model selected
> select add #2/R:1366
86 atoms, 79 bonds, 10 residues, 1 model selected
> select add #2/R:1365
94 atoms, 86 bonds, 11 residues, 1 model selected
> select add #2/R:1367
103 atoms, 94 bonds, 12 residues, 1 model selected
> select add #2/R:1368
111 atoms, 101 bonds, 13 residues, 1 model selected
> ui tool show "Color Actions"
> color sel dark red
> select clear
> hide #!2 models
> show #!1 models
> show #!2 models
> show #!3 models
> show #!5 models
> hide #!5 models
> hide #!3 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!2 models
> show #!3 models
> show #!5 models
> show #!4 models
> hide #!5 models
> hide #!4 models
> hide #!3 models
> hide #!2 models
Drag select of 217 residues
> select clear
> select #1/A:89
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
228 atoms, 230 bonds, 32 residues, 1 model selected
> select up
2266 atoms, 2323 bonds, 294 residues, 1 model selected
> ui tool show "Color Actions"
> color sel royal blue
> select clear
> color khaki
> undo
> hide #!1 models
> show #!3 models
> select #3/R:46
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
147 atoms, 146 bonds, 29 residues, 1 model selected
> select up
1689 atoms, 1726 bonds, 279 residues, 1 model selected
> color sel orchid
> select #3/C:357
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
77 atoms, 81 bonds, 12 residues, 1 model selected
> select up
2547 atoms, 2605 bonds, 359 residues, 1 model selected
> color sel cadet blue
> color sel dark cyan
> color sel forest green
> color sel lime green
> color sel green
> color sel dark turquoise
> color sel turquoise
> color sel cadet blue
> color sel steel blue
> color sel teal
> color sel medium aquamarine
> color sel dark cyan
> color sel dark green
> color sel light green
> color sel pale green
> color sel light salmon
> hide #!3 models
> show #!5 models
> select #5/A:86
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
245 atoms, 252 bonds, 32 residues, 1 model selected
> select up
2181 atoms, 2236 bonds, 284 residues, 1 model selected
> color sel orange
> color sel dark orange
> select #5/C:280
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
51 atoms, 51 bonds, 6 residues, 1 model selected
> select up
2810 atoms, 2872 bonds, 353 residues, 1 model selected
> color sel #b2d9adff
> color sel #7dbb8aff
[Repeated 2 time(s)]
> color sel #c8e5c5ff
> color sel #c9e5c7ff
[Repeated 1 time(s)]
> color sel #c7e3c5ff
> color sel #c6e2c4ff
> color sel #c5e0c3ff
> color sel #c3dfc2ff
> color sel #bed9bdff
> color sel #bed9bcff
> color sel #b4cdb2ff
> color sel #aac2a9ff
> color sel #a1b79fff
> color sel #879b86ff
> color sel #869985ff
> color sel #879a85ff
> color sel #90a48fff
> color sel #b1caafff
> color sel #b1cbb0ff
> color sel #b6d0b5ff
> color sel #b5ceb3ff
> color sel #9eb59dff
> color sel #778876ff
[Repeated 1 time(s)]
> color sel #798a78ff
> color sel #839582ff
> color sel #93a892ff
> color sel #a8c0a7ff
> color sel #b2cbb0ff
> color sel #b4cdb2ff
> color sel #b5ceb3ff
> color sel #b5cfb4ff
> color sel #b6d0b5ff
> color sel #b9d3b7ff
> color sel #b9d3b8ff
> color sel #bbd6baff
> color sel #bdd8bbff
> color sel #bed9bdff
> color sel #bfdabdff
> color sel #c2dec1ff
> color sel #c3dfc1ff
> color sel #dc01feff
[Repeated 1 time(s)]
> color sel #00fe82ff
> color sel #3e38ebff
> color sel #3d37ebff
> color sel medium sea green
> select clear
[Repeated 1 time(s)]
> show #!3 models
> hide #!5 models
> select #3/C:255
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
95 atoms, 96 bonds, 13 residues, 1 model selected
> select up
2547 atoms, 2605 bonds, 359 residues, 1 model selected
> color sel medium sea green
> select clear
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!5 models
> select #5/C:212
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
42 atoms, 44 bonds, 5 residues, 1 model selected
> select up
2810 atoms, 2872 bonds, 353 residues, 1 model selected
> color sel medium purple
> color sel magenta
> color sel rebecca purple
> color sel dark slate blue
> color sel medium slate blue
> select #5/C:362
10 atoms, 10 bonds, 1 residue, 1 model selected
> select up
126 atoms, 132 bonds, 15 residues, 1 model selected
> select up
2810 atoms, 2872 bonds, 353 residues, 1 model selected
> color sel light sky blue
> color sel sky blue
[Repeated 1 time(s)]
> color sel cornflower blue
> color sel dodger blue
> select clear
> show #!3 models
> hide #!3 models
> hide #!5 models
> show #!4 models
> select #4/R:86
11 atoms, 11 bonds, 1 residue, 1 model selected
> select up
200 atoms, 201 bonds, 33 residues, 1 model selected
> select up
1824 atoms, 1841 bonds, 323 residues, 1 model selected
> color sel plum
> color sel dark slate blue
> color sel slate blue
> color sel medium slate blue
> select clear
> select #4/A:260
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
38 atoms, 38 bonds, 7 residues, 1 model selected
> select up
1935 atoms, 1963 bonds, 350 residues, 1 model selected
> color sel thistle
> color sel light pink
> color sel teal
> color sel dark cyan
> color sel salmon
> select #4/R:68
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
200 atoms, 201 bonds, 33 residues, 1 model selected
> select up
1824 atoms, 1841 bonds, 323 residues, 1 model selected
> color sel salmon
> select clear
> select #4/A:258
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
60 atoms, 60 bonds, 11 residues, 1 model selected
> select up
1935 atoms, 1963 bonds, 350 residues, 1 model selected
> color sel slate blue
> color sel medium slate blue
> color sel deep pink
> color sel dark violet
> color sel blue violet
> color sel orchid
> color sel medium orchid
> color sel medium violet red
> color sel dark orchid
> color sel dark magenta
> color sel purple
> color sel pale violet red
> color sel dark slate gray
> color sel dark olive green
> select clear
> show #!1 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!5 models
> hide #!4 models
> hide #!5 models
> show #!4 models
> show #!3 models
> hide #!3 models
> select #4/A:317
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
156 atoms, 155 bonds, 30 residues, 1 model selected
> select up
1935 atoms, 1963 bonds, 350 residues, 1 model selected
> color sel pale violet red
> color sel hot pink
> color sel magenta
> color sel deep pink
> color sel dark violet
> color sel medium violet red
> color sel tomato
> select clear
> select #4/R:83
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
200 atoms, 201 bonds, 33 residues, 1 model selected
> select up
1824 atoms, 1841 bonds, 323 residues, 1 model selected
> color sel dark cyan
[Repeated 1 time(s)]
> color sel teal
> select clear
> show #!3 models
> hide #!3 models
> show #!3 models
> show #!2 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> hide #!3 models
> show #!5 models
> hide #!5 models
> show #!3 models
> hide #!3 models
> hide #!4 models
> show #!3 models
> hide #!3 models
> show #!4 models
> select clear
> select #4/B:10
7 atoms, 7 bonds, 1 residue, 1 model selected
> select up
27 atoms, 27 bonds, 5 residues, 1 model selected
> hide sel cartoons
> hide #!4 models
> show #!3 models
> show #!2 models
> hide #!3 models
> select #2/P:19
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
249 atoms, 253 bonds, 29 residues, 1 model selected
> select up
271 atoms, 276 bonds, 32 residues, 1 model selected
> hide sel cartoons
> show #!1 models
> hide #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!2 models
> select #2/R:1363
10 atoms, 9 bonds, 1 residue, 1 model selected
> select up
35 atoms, 34 bonds, 4 residues, 1 model selected
> select up
2336 atoms, 2401 bonds, 283 residues, 1 model selected
> select down
35 atoms, 34 bonds, 4 residues, 1 model selected
> select add #2/R:1356
44 atoms, 42 bonds, 5 residues, 1 model selected
> select add #2/R:1357
54 atoms, 51 bonds, 6 residues, 1 model selected
> select add #2/R:1358
59 atoms, 55 bonds, 7 residues, 1 model selected
> select add #2/R:1359
70 atoms, 65 bonds, 8 residues, 1 model selected
> select add #2/R:1360
81 atoms, 75 bonds, 9 residues, 1 model selected
> select add #2/R:1365
89 atoms, 82 bonds, 10 residues, 1 model selected
> select add #2/R:1366
94 atoms, 86 bonds, 11 residues, 1 model selected
> select add #2/R:1367
103 atoms, 94 bonds, 12 residues, 1 model selected
> select add #2/R:1368
111 atoms, 101 bonds, 13 residues, 1 model selected
> color sel #649aadff
> color sel #4f727eff
> select clear
> color #!2 #595959ff
> undo
> save "/Users/zhaixiuwen/Desktop/class b
> arrestin/PTH1R/文章/fig2/coupleing_comformation_2.cxs"
> show #!1 models
> show #!3 models
> show #!4 models
> show #!5 models
> hide #!5 models
> hide #!4 models
> hide #!3 models
> hide #!2 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!1 models
> select #1/B:282
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
45 atoms, 44 bonds, 5 residues, 1 model selected
> select up
2684 atoms, 2741 bonds, 344 residues, 1 model selected
> ui tool show "Color Actions"
> color sel medium slate blue
> color sel deep pink
> color sel magenta
> color sel hot pink
> color sel dark violet
> color sel old lace
> color sel light goldenrod yellow
> color sel khaki
> select clear
> show #!2 models
> graphics silhouettes true
> graphics silhouettes false
> show #!3 models
> show #!4 models
> show #!5 models
> show #!6 models
> hide #!1 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> show #!5 models
> show #!4 models
> show #!3 models
> show #!2 models
> show #!1 models
Drag select of 909 residues
> select up
8618 atoms, 8781 bonds, 1176 residues, 5 models selected
> select up
23047 atoms, 23544 bonds, 3218 residues, 5 models selected
> select clear
> hide #!5 models
> hide #!4 models
> hide #!3 models
> hide #!2 models
Drag select of 94 residues
> select up
1144 atoms, 1166 bonds, 148 residues, 1 model selected
> select up
2684 atoms, 2741 bonds, 344 residues, 1 model selected
> color sel byhetero
> style sel sphere
Changed 2684 atom styles
> show sel atoms
> style sel stick
Changed 2684 atom styles
> hide sel atoms
> coulombic sel
The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:
b1ar_arrestin_6tko.pdb #1/B LYS 17
b1ar_arrestin_6tko.pdb #1/B LYS 49
b1ar_arrestin_6tko.pdb #1/B GLU 92
b1ar_arrestin_6tko.pdb #1/B GLU 134
b1ar_arrestin_6tko.pdb #1/B HIS 159
b1ar_arrestin_6tko.pdb #1/B LEU 191
b1ar_arrestin_6tko.pdb #1/B MET 192
b1ar_arrestin_6tko.pdb #1/B SER 193
b1ar_arrestin_6tko.pdb #1/B ASP 194
b1ar_arrestin_6tko.pdb #1/B ASN 311
b1ar_arrestin_6tko.pdb #1/B SER 341
b1ar_arrestin_6tko.pdb #1/B LYS 357
b1ar_arrestin_6tko.pdb #1/B GLU 358
b1ar_arrestin_6tko.pdb #1/B GLU 359
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue HIS (net charge -3) with am1-bcc method
Running ANTECHAMBER command:
/Applications/ChimeraX_Daily.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/vw/c1xhdjbn1x1_7kwt2k41qdc40000gn/T/tmpl7wvsg0p/ante.in.mol2 -fi
mol2 -o
/var/folders/vw/c1xhdjbn1x1_7kwt2k41qdc40000gn/T/tmpl7wvsg0p/ante.out.mol2 -fo
mol2 -c bcc -nc -3 -j 5 -s 2 -dr n
(HIS) ``
(HIS) `Welcome to antechamber 20.0: molecular input file processor.`
(HIS) ``
(HIS) `Info: Finished reading file
(/var/folders/vw/c1xhdjbn1x1_7kwt2k41qdc40000gn/T/tmpl7wvsg0p/ante.in.mol2);
atoms read (19), bonds read (18).`
(HIS) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(HIS) `Running:
/Applications/ChimeraX_Daily.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(HIS) ``
(HIS) ``
(HIS) `Running:
/Applications/ChimeraX_Daily.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(HIS) `Info: Total number of electrons: 78; net charge: -3`
(HIS) ``
(HIS) `Running: /Applications/ChimeraX_Daily.app/Contents/bin/amber20/bin/sqm
-O -i sqm.in -o sqm.out`
(HIS) ``
(HIS) `Running:
/Applications/ChimeraX_Daily.app/Contents/bin/amber20/bin/am1bcc -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
/Applications/ChimeraX_Daily.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT
-s 2 -j 1`
(HIS) ``
(HIS) `Running:
/Applications/ChimeraX_Daily.app/Contents/bin/amber20/bin/atomtype -f ac -p
bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`
(HIS) ``
Charges for residue HIS determined
Coulombic values for b1ar_arrestin_6tko.pdb_B SES surface #1.2: minimum,
-21.09, mean -0.39, maximum 21.94
To also show corresponding color key, enter the above coulombic command and
add key true
> color sel khaki
> select clear
> hide #!1 models
> show #!2 models
> select #2/A:255
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
98 atoms, 99 bonds, 13 residues, 1 model selected
> select up
2775 atoms, 2836 bonds, 349 residues, 1 model selected
> color sel orange
> undo
> select clear
> select #2/A:232
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
122 atoms, 122 bonds, 15 residues, 1 model selected
> select up
2775 atoms, 2836 bonds, 349 residues, 1 model selected
> mlp sel
Map values for surface "PTH_arrestin-coot-15_real_space_refined_137.pdb_A SES
surface": minimum -25.77, mean -5.073, maximum 23.51
To also show corresponding color key, enter the above mlp command and add key
true
> color (#!2 & sel) #fbba2bff
> select clear
> hide #!2 models
> show #!1 models
> show #!2 models
> hide #!2 models
> hide #!1 models
> show #!3 models
> select #3/C:254
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
95 atoms, 96 bonds, 13 residues, 1 model selected
> select up
2547 atoms, 2605 bonds, 359 residues, 1 model selected
> mlp sel
Map values for surface "m2r_arrestin.pdb_C SES surface": minimum -24.92, mean
-3.832, maximum 24.04
To also show corresponding color key, enter the above mlp command and add key
true
> color sel medium sea green
> select clear
> hide #!3 models
> show #!4 models
> select #4/A:264
7 atoms, 7 bonds, 1 residue, 1 model selected
> select up
38 atoms, 38 bonds, 7 residues, 1 model selected
> select up
1935 atoms, 1963 bonds, 350 residues, 1 model selected
> mlp sel
Map values for surface "NTSR1_arrestin_6pwc.pdb_A SES surface": minimum
-27.66, mean -6.72, maximum 19.29
To also show corresponding color key, enter the above mlp command and add key
true
> color sel tomato
> select clear
> hide #!4 models
> show #!5 models
> select #5/C:279
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
51 atoms, 51 bonds, 6 residues, 1 model selected
> select up
2810 atoms, 2872 bonds, 353 residues, 1 model selected
> mlp sel
Map values for surface "V2R_arrestin_7r0c.pdb_C SES surface": minimum -28.3,
mean -3.537, maximum 23.78
To also show corresponding color key, enter the above mlp command and add key
true
> color sel dodger blue
> select clear
[Repeated 1 time(s)]
> hide #!5 models
> show #!6 models
> select #6/D:2346
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
101 atoms, 102 bonds, 13 residues, 1 model selected
> select up
6573 atoms, 6733 bonds, 833 residues, 1 model selected
> select clear
> hide #!6 models
> show #!1 models
> show #!2 models
> show #!3 models
> show #!4 models
> show #!5 models
> hide #!4 models
> hide #!1 models
> hide #!3 models
> hide #!5 models
> select clear
> windowsize 500 500
> select clear
> save "/Users/zhaixiuwen/Desktop/class b
> arrestin/PTH1R/文章/fig2/pth1r-arrestin.tif" width 500 height 500 supersample
> 3 transparentBackground true
> hide #!2 models
> show #!1 models
> show #!2 models
> hide #!2 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!1 models
> save "/Users/zhaixiuwen/Desktop/class b arrestin/PTH1R/文章/fig2/b1ar-
> arrestin.tif" width 500 height 500 supersample 3 transparentBackground true
> hide #!1 models
> show #!3 models
> save "/Users/zhaixiuwen/Desktop/class b
> arrestin/PTH1R/文章/fig2/m2r-arrestin.tif" width 500 height 500 supersample 3
> transparentBackground true
> hide #!3 models
> show #!4 models
> save "/Users/zhaixiuwen/Desktop/class b
> arrestin/PTH1R/文章/fig2/nst1r-arrestin.tif" width 500 height 500 supersample
> 3 transparentBackground true
> hide #!4 models
> show #!5 models
> show #!2 models
> hide #!2 models
> save "/Users/zhaixiuwen/Desktop/class b
> arrestin/PTH1R/文章/fig2/v2r-arrestin.tif" width 500 height 500 supersample 3
> transparentBackground true
> save "/Users/zhaixiuwen/Desktop/class b
> arrestin/PTH1R/文章/fig2/coupleing_comformation_3.cxs"
> save "/Users/zhaixiuwen/Desktop/class b
> arrestin/PTH1R/文章/fig2/v2r-arrestin.tif" width 500 height 500 supersample 3
> hide #!5 models
> show #!4 models
> hide #!4 models
> show #!3 models
> close #1.1
> hide #1.2 models
> show #1.2 models
> hide #1.2 models
> show #1.2 models
> close #2.1
> close #3.1
> close #4.1
> close #5.1
> close #6.1
> hide #!3 models
> windowsize 1000 1000
> save "/Users/zhaixiuwen/Desktop/class b arrestin/PTH1R/文章/fig2/b1ar-
> arrestin.tif" width 1000 height 1000 supersample 3
> hide #!1 models
> show #!2 models
> show #!1 models
> hide #!1 models
> show #!3 models
> hide #!3 models
> save "/Users/zhaixiuwen/Desktop/class b
> arrestin/PTH1R/文章/fig2/pth1r-arrestin.tif" width 1000 height 1000
> supersample 3
> hide #!2 models
> show #!3 models
> save "/Users/zhaixiuwen/Desktop/class b
> arrestin/PTH1R/文章/fig2/m2r-arrestin.tif" width 1000 height 1000 supersample
> 3
> hide #!3 models
> show #!4 models
> save "/Users/zhaixiuwen/Desktop/class b
> arrestin/PTH1R/文章/fig2/nst1r-arrestin.tif" width 1000 height 1000
> supersample 3
> hide #!4 models
> show #!5 models
> show #!2 models
> hide #!2 models
> save "/Users/zhaixiuwen/Desktop/class b
> arrestin/PTH1R/文章/fig2/v2r-arrestin.tif" width 1000 height 1000 supersample
> 3
> show #!4 models
> hide #!4 models
> show #!3 models
> show #!2 models
> show #!1 models
> ui tool show "Side View"
> hide #!5 models
> hide #!3 models
> hide #!2 models
> view orient
[Repeated 1 time(s)]
> view
> view orient
> graphics silhouettes true
> graphics silhouettes false
> show #!2 models
> show #!3 models
> hide #!1 models
> show #!1 models
> show #!5 models
> hide #!3 models
> hide #!2 models
> hide #!5 models
> show #!2 models
> hide #!2 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!4 models
> hide #!4 models
> show #!1 models
> select #1/A:1356
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
42 atoms, 41 bonds, 5 residues, 1 model selected
> select up
2266 atoms, 2323 bonds, 294 residues, 1 model selected
> select up
8085 atoms, 8278 bonds, 1053 residues, 1 model selected
> select clear
> mmaker
> matchmaker
Missing or invalid "matchAtoms" argument: empty atom specifier
> hide #!1 models
> show #!4 models
> save "/Users/zhaixiuwen/Desktop/class b
> arrestin/PTH1R/文章/fig2/nst1r-arrestin.tif" width 739 height 872 supersample
> 3
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!3 models
> save "/Users/zhaixiuwen/Desktop/class b
> arrestin/PTH1R/文章/fig2/m2r-arrestin.tif" width 739 height 872 supersample 3
> hide #!3 models
> show #!2 models
> save "/Users/zhaixiuwen/Desktop/class b
> arrestin/PTH1R/文章/fig2/pth1r-arrestin.tif" width 739 height 872 supersample
> 3
> hide #!2 models
> show #!1 models
> save "/Users/zhaixiuwen/Desktop/class b arrestin/PTH1R/文章/fig2/b1ar-
> arrestin.tif" width 739 height 872 supersample 3
> hide #!1 models
> show #!5 models
> save "/Users/zhaixiuwen/Desktop/class b
> arrestin/PTH1R/文章/fig2/v2r-arrestin.tif" width 739 height 872 supersample 3
> show #!2 models
> hide #!5 models
> show #!5 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> show #!1 models
> show #!3 models
> show #!4 models
> hide #!5 models
> show #!5 models
> hide #!1 models
> show #!1 models
Drag select of 557 residues
> select up
7579 atoms, 7749 bonds, 1095 residues, 5 models selected
> select up
10371 atoms, 10605 bonds, 1473 residues, 5 models selected
> select up
33762 atoms, 34494 bonds, 4739 residues, 5 models selected
> transparency sel 90 cartoons
> transparency sel 30 cartoons
> select clear
> undo
> transparency sel 10 cartoons
> select clear
[Repeated 2 time(s)]
> undo
[Repeated 1 time(s)]Drag select of 495 residues
> select up
7579 atoms, 7744 bonds, 1096 residues, 5 models selected
> select up
10371 atoms, 10605 bonds, 1473 residues, 5 models selected
> transparency sel 0 cartoons
> select clear
> show #6 models
> hide #6 models
> lighting simple
[Repeated 1 time(s)]
> lighting soft
> lighting flat
> lighting full
> lighting soft
> lighting full
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting soft
> select clear
> graphics silhouettes false
> cartoon style width 1.5 thickness 0.3
> undo
> cartoon style protein modeHelix default arrows false xsection oval width 2
> thickness 0.6
> cartoon style protein modeHelix default arrows false xsection oval width 1.5
> thickness 0.6
> cartoon style protein modeHelix default arrows false xsection oval width 1.0
> thickness 0.6
> cartoon style protein modeHelix default arrows false xsection oval width 1.5
> thickness 0.6
> 8
Unknown command: 8
> cartoon style protein modeHelix default arrows false xsection oval width 1.8
> thickness 0.6
> cartoon style protein modeHelix default arrows false xsection oval width 1.8
> thickness 2
> cartoon style protein modeHelix default arrows false xsection oval width 1.8
> thickness 1.5
> cartoon style protein modeHelix default arrows false xsection oval width 1.0
> thickness 1.5
> cartoon style protein modeHelix default arrows false xsection oval width 1.2
> thickness 1.5
> cartoon style protein modeHelix default arrows false xsection oval width 1.2
> thickness 1.0
> cartoon style protein modeHelix default arrows false xsection oval width 1.2
> thickness 1.2
> cartoon style protein modeHelix default arrows false xsection oval width 1.2
> thickness 1.5
> cartoon style protein modeHelix default arrows false xsection oval width 1.2
> thickness2
Expected a keyword
> cartoon style protein modeHelix default arrows false xsection oval width 1.2
> thickness 2
> cartoon style protein modeHelix default arrows false xsection oval width 1.2
> thickness 0.6
> cartoon style protein modeHelix default arrows false xsection oval width 2
> thickness 0.6
> cartoon style protein modeHelix default arrows false xsection oval width 2
> thickness 1
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> hide #!1.2 models
> cartoon style protein modeHelix default arrows false xsection oval width 2
> thickness 2
> show #!1.2 models
> hide #!1 models
> hide #!1.2 models
> show #!1 models
> hide #!1 models
> show #!1 models
> show #!1.2 models
> save "/Users/zhaixiuwen/Desktop/class b
> arrestin/PTH1R/文章/fig2/coupleing_comformation_3.cxs"
——— End of log from Tue Oct 25 11:08:16 2022 ———
opened ChimeraX session
> show #!2 models
> show #!3 models
> show #!4 models
> show #!5 models
> cartoon style protein modeHelix default arrows false xsection oval width 1.5
> thickness 2
[Repeated 1 time(s)]
> cartoon style protein modeHelix default arrows false xsection oval width 1
> thickness 2
> cartoon style protein modeHelix default arrows false xsection oval width 2
> thickness 1
> view orient
> cartoon style protein modeHelix default arrows false xsection oval width 2
> thickness 1.5
> cartoon style protein modeHelix default arrows false xsection oval width 2
> thickness 2
> cartoon style protein modeHelix default arrows false xsection oval width 2
> thickness 1
> cartoon style protein modeHelix default arrows false xsection oval width 2
> thickness 1。5
Invalid "thickness" argument: Expected a number
> cartoon style protein modeHelix default arrows false xsection oval width 2
> thickness 1.5
> select clear
> transparency 90 cartoons
> transparency 10 surfaces
> hide #!1 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> select #2
7119 atoms, 7294 bonds, 890 residues, 1 model selected
> transparency sel 0 surfaces
> transparency sel 0 cartoons
> show #!1 models
> show #!3 models
> show #!4 models
> select clear
> cartoon style protein modeHelix default arrows false xsection oval width 2
> thickness 1
> transparency sel 40 surfaces
> transparency 40 surfaces
> select clear
> hide #!1 models
> hide #!3 models
> hide #!4 models
> select #2/A:346@OE2
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> select up
62 atoms, 63 bonds, 8 residues, 2 models selected
> select up
2775 atoms, 2836 bonds, 349 residues, 2 models selected
> select up
7119 atoms, 7294 bonds, 890 residues, 2 models selected
> select down
2775 atoms, 2836 bonds, 349 residues, 2 models selected
> transparency sel 0 surfaces
> select clear
> show #!1 models
> show #!3 models
> show #!5 models
> select clear
> show #!4 models
> select clear
> transparency 60 cartoons
> select clear
> select #2
7119 atoms, 7294 bonds, 890 residues, 1 model selected
> transparency sel 0 cartoons
> select clear
> transparency 0 surfaces
> select clear
> select #1
8085 atoms, 8278 bonds, 1053 residues, 1 model selected
> hide #!2 models
> select clear
Drag select of b1ar_arrestin_6tko.pdb_B SES surface, 692 of 312740 triangles,
V2R_arrestin_7r0c.pdb_C SES surface, 772 of 386734 triangles, 20 residues
> select clear
Drag select of 239 residues
> select up
5064 atoms, 5168 bonds, 770 residues, 4 models selected
> select up
8035 atoms, 8204 bonds, 1190 residues, 4 models selected
> transparency 30 cartoons
> select clear
> show #!2 models
> select clear
[Repeated 1 time(s)]
> select #2
7119 atoms, 7294 bonds, 890 residues, 1 model selected
> transparency sel 0 cartoons
> select clear
> hide #!2 models
Drag select of 413 residues
> select up
5834 atoms, 5956 bonds, 880 residues, 4 models selected
> select up
8035 atoms, 8204 bonds, 1190 residues, 4 models selected
> select up
26643 atoms, 27200 bonds, 3849 residues, 4 models selected
> select down
8035 atoms, 8204 bonds, 1190 residues, 8 models selected
> transparency sel 90 cartoons
> select clear
> show #!2 models
> select clear
[Repeated 1 time(s)]
> hide #2.2 models
> hide #3.2 models
> hide #4.2 models
> hide #5.2 models
> hide #1.2 models
> select clear
Drag select of 1062 residues
> select up
9743 atoms, 9922 bonds, 1322 residues, 10 models selected
> select up
23047 atoms, 23544 bonds, 3218 residues, 10 models selected
> select down
9743 atoms, 9922 bonds, 1322 residues, 10 models selected
> transparency sel 0 cartoons
> select clear
> show #1.2 models
> show #2.2 models
> show #3.2 models
> show #4.2 models
> show #5.2 models
> show #6 models
> select #6/D:282
6 atoms, 5 bonds, 1 residue, 1 model selected
> hide #6 models
> graphics silhouettes true
> select clear
> graphics silhouettes false
> ui tool show "Side View"
> hide #1.2 models
> hide #!2 models
> hide #!3 models
> show #!3 models
> show #!2 models
> show #1.2 models
> hide #1.2 models
> hide #2.2 models
> hide #3.2 models
> hide #4.2 models
> hide #5.2 models
> show #1.2 models
> show #2.2 models
> show #3.2 models
> show #4.2 models
> show #5.2 models
> select clear
> save "/Users/zhaixiuwen/Desktop/class b arrestin/PTH1R/文章/fig2/New
> Folder2/fig2a.cxs"
——— End of log from Thu Nov 3 22:15:31 2022 ———
opened ChimeraX session
> open "/Users/zhaixiuwen/Desktop/文章_PTH1R_arrestin/fig2/New
> Folder2/fig2b_c.cxs"
opened ChimeraX session
> show #!2 models
> show #!3 models
> show #!4 models
> show #!5 models
> save "/Users/zhaixiuwen/Desktop/文章_PTH1R_arrestin/fig2/New
> Folder2/2ctif.tif" width 1085 height 1000 supersample 3
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 INTEL-20.2.48
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 645
OpenGL vendor: Intel Inc.
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro16,3
Processor Name: Quad-Core Intel Core i5
Processor Speed: 1.4 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 256 KB
L3 Cache: 6 MB
Hyper-Threading Technology: Enabled
Memory: 8 GB
System Firmware Version: 1916.60.2.0.0 (iBridge: 20.16.2059.0.0,0)
OS Loader Version: 564.40.4~55
Software:
System Software Overview:
System Version: macOS 13.1 (22C65)
Kernel Version: Darwin 22.2.0
Time since boot: 20天18小时
Graphics/Displays:
Intel Iris Plus Graphics 645:
Chipset Model: Intel Iris Plus Graphics 645
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3ea6
Revision ID: 0x0001
Metal Support: Metal 3
Displays:
Acer EH273U:
Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
UI Looks like: 2560 x 1440 @ 60.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: 941007943LAJ
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Connection Type: DVI or HDMI
Adapter Firmware Version: 2.55
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.1.0
Babel: 2.11.0
backcall: 0.2.0
blockdiag: 3.0.0
build: 0.8.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 2.1.1
ChimeraX-AddCharge: 1.4
ChimeraX-AddH: 2.2.1
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.6
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.41.5
ChimeraX-AtomicLibrary: 8.0.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.7.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.1
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.2
ChimeraX-CommandLine: 1.2.4
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.5
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.3
ChimeraX-DockPrep: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
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-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.1
ChimeraX-MatchMaker: 2.0.9
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.8
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.6
ChimeraX-ModelPanel: 1.3.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.1
ChimeraX-MouseModes: 1.1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.9.1
ChimeraX-PDB: 2.6.8
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
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
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.7.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.1.3
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.24.3
ChimeraX-uniprot: 2.2.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.1.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.1
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0.1
colorama: 0.4.5
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.32
debugpy: 1.6.4
decorator: 5.1.1
docutils: 0.19
entrypoints: 0.4
executing: 1.2.0
filelock: 3.7.1
fonttools: 4.38.0
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.33
imagecodecs: 2022.7.31
imagesize: 1.4.1
importlib-metadata: 5.1.0
ipykernel: 6.15.3
ipython: 8.4.0
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.1.2
jupyter-client: 7.3.4
jupyter-core: 5.1.0
kiwisolver: 1.4.4
line-profiler: 3.5.1
lxml: 4.9.1
lz4: 4.0.2
MarkupSafe: 2.1.1
matplotlib: 3.5.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.0
networkx: 2.8.5
numexpr: 2.8.4
numpy: 1.23.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.2.0
pip: 22.2.2
pkginfo: 1.8.3
platformdirs: 2.5.4
prompt-toolkit: 3.0.33
psutil: 5.9.1
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.12.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2022.6
pyzmq: 24.0.1
qtconsole: 5.3.1
QtPy: 2.3.0
RandomWords: 0.4.0
requests: 2.28.1
scipy: 1.9.0
setuptools: 65.1.1
setuptools-scm: 7.0.5
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 5.1.1
sphinx-autodoc-typehints: 1.19.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tifffile: 2022.7.31
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.2
traitlets: 5.3.0
typing-extensions: 4.4.0
urllib3: 1.26.13
wcwidth: 0.2.5
webcolors: 1.12
wheel: 0.37.1
wheel-filename: 1.4.1
zipp: 3.11.0
Change History (2)
comment:1 by , 3 years ago
| Component: | Unassigned → Input/Output |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash saving image |
comment:2 by , 3 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | assigned → closed |
| Summary: | Crash saving image → Crash in Qt event loop look after saving image |
Note:
See TracTickets
for help on using tickets.
