id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 18293 Crash on exit chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-12.0.1-arm64-arm-64bit ChimeraX Version: 1.10.dev202501170719 (2025-01-17 07:19:08 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. {""app_name"":""ChimeraX"",""timestamp"":""2025-07-27 13:29:19.00 +0200"",""app_version"":""1.10.0"",""slice_uuid"":""18de835b-eddc-3f3a-93bb-285f33da630d"",""build_version"":""1.10.0.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":0,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 12.0.1 (21A559)"",""incident_id"":""52587DBC-B810-439D-AEB6-B386E3C3F81C"",""name"":""ChimeraX""} { ""uptime"" : 100000, ""procLaunch"" : ""2025-07-27 13:17:32.7846 +0200"", ""procRole"" : ""Foreground"", ""version"" : 2, ""userID"" : 501, ""deployVersion"" : 210, ""modelCode"" : ""MacBookPro17,1"", ""procStartAbsTime"" : 2568798599057, ""coalitionID"" : 5105, ""osVersion"" : { ""train"" : ""macOS 12.0.1"", ""build"" : ""21A559"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2025-07-27 13:29:03.4726 +0200"", ""incident"" : ""52587DBC-B810-439D-AEB6-B386E3C3F81C"", ""bug_type"" : ""309"", ""pid"" : 22437, ""procExitAbsTime"" : 2585375018573, ""translated"" : false, ""cpuType"" : ""ARM-64"", ""procName"" : ""ChimeraX"", ""procPath"" : ""\/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX"", ""bundleInfo"" : {""CFBundleShortVersionString"":""1.10.0"",""CFBundleVersion"":""1.10.0.0"",""CFBundleIdentifier"":""edu.ucsf.cgl.ChimeraX""}, ""storeInfo"" : {""deviceIdentifierForVendor"":""1BC2B4F8-1EB7-5220-8FE0-B7CDC7F38667"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""8A55B74B-F213-3D41-5EA1-03E1CFE59D77"", ""wakeTime"" : 706, ""sleepWakeUUID"" : ""94FE8F5C-0BDA-4877-B7F5-8675867E012D"", ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0 is not in any region. Bytes before following region: 4303994880\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10089c000-1008a0000 [ 16K] r-x\/r-x SM=COW ...acOS\/ChimeraX"", ""isCorpse"" : 1, ""exception"" : {""codes"":""0x0000000000000001, 0x0000000000000000"",""rawCodes"":[1,0],""type"":""EXC_BAD_ACCESS"",""signal"":""SIGSEGV"",""subtype"":""KERN_INVALID_ADDRESS at 0x0000000000000000""}, ""vmregioninfo"" : ""0 is not in any region. Bytes before following region: 4303994880\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10089c000-1008a0000 [ 16K] r-x\/r-x SM=COW ...acOS\/ChimeraX"", ""extMods"" : {""caller"":{""thread_create"":0,""thread_set_state"":0,""task_for_pid"":0},""system"":{""thread_create"":0,""thread_set_state"":0,""task_for_pid"":0},""targeted"":{""thread_create"":0,""thread_set_state"":0,""task_for_pid"":0},""warnings"":0}, ""faultingThread"" : 0, ""threads"" : [{""triggered"":true,""id"":4150698,""threadState"":{""x"":[{""value"":0},{""value"":0},{""value"":1},{""value"":5369133720},{""value"":99},{""value"":95},{""value"":14},{""value"":0},{""value"":10368207727661735449},{""value"":10368207731952606105},{""value"":14757395258967641293},{""value"":4294967286},{""value"":5369133650},{""value"":0},{""value"":54},{""value"":874496},{""value"":328},{""value"":8386573616},{""value"":5700303168},{""value"":11},{""value"":4307715456,""symbolLocation"":0,""symbol"":""_main_thread""},{""value"":259},{""value"":316},{""value"":1},{""value"":4326458928,""symbolLocation"":0,""symbol"":""faulthandler_handlers""},{""value"":0},{""value"":27},{""value"":88},{""value"":0}],""flavor"":""ARM_THREAD_STATE64"",""lr"":{""value"":6872535388},""cpsr"":{""value"":1073741824},""fp"":{""value"":5369133792},""sp"":{""value"":5369133760},""esr"":{""value"":1442840704,""description"":"" Address size fault""},""pc"":{""value"":6872324536,""matchesCrashFrame"":1},""far"":{""value"":4326459092}},""name"":""CrBrowserMain"",""queue"":""com.apple.main-thread"",""frames"":[{""imageOffset"":39352,""symbol"":""__pthread_kill"",""symbolLocation"":8,""imageIndex"":0},{""imageOffset"":29020,""symbol"":""pthread_kill"",""symbolLocation"":288,""imageIndex"":1},{""imageOffset"":269476,""symbol"":""raise"",""symbolLocation"":32,""imageIndex"":2},{""imageOffset"":2417160,""symbol"":""faulthandler_fatal_error"",""symbolLocation"":392,""imageIndex"":3},{""imageOffset"":17636,""symbol"":""_sigtramp"",""symbolLocation"":56,""imageIndex"":4},{""imageOffset"":367252,""imageIndex"":5},{""imageOffset"":3638384,""symbol"":""-[NSTouch dealloc]"",""symbolLocation"":48,""imageIndex"":6},{""imageOffset"":394100,""symbol"":""__RELEASE_OBJECTS_IN_THE_SET__"",""symbolLocation"":148,""imageIndex"":7},{""imageOffset"":393872,""symbol"":""-[__NSSetM dealloc]"",""symbolLocation"":148,""imageIndex"":7},{""imageOffset"":1991660,""symbol"":""-[NSEvent dealloc]"",""symbolLocation"":68,""imageIndex"":6},{""imageOffset"":86980,""imageIndex"":5},{""imageOffset"":134552,""imageIndex"":5},{""imageOffset"":135076,""imageIndex"":5},{""imageOffset"":556296,""symbol"":""QGuiApplicationPrivate::~QGuiApplicationPrivate()"",""symbolLocation"":492,""imageIndex"":8},{""imageOffset"":37408,""symbol"":""QApplicationPrivate::~QApplicationPrivate()"",""symbolLocation"":12,""imageIndex"":9},{""imageOffset"":896912,""symbol"":""QObject::~QObject()"",""symbolLocation"":2180,""imageIndex"":10},{""imageOffset"":535368,""symbol"":""QGuiApplication::~QGuiApplication()"",""symbolLocation"":652,""imageIndex"":8},{""imageOffset"":45336,""symbol"":""QApplication::~QApplication()"",""symbolLocation"":1096,""imageIndex"":9},{""imageOffset"":1430396,""symbol"":""sipQApplication::~sipQApplication()"",""symbolLocation"":52,""imageIndex"":11},{""imageOffset"":1376780,""symbol"":""cleanup_on_exit(_object*, _object*)"",""symbolLocation"":68,""imageIndex"":12},{""imageOffset"":1007332,""symbol"":""cfunction_vectorcall_NOARGS"",""symbolLocation"":88,""imageIndex"":3},{""imageOffset"":2409280,""symbol"":""atexit_callfuncs"",""symbolLocation"":492,""imageIndex"":3},{""imageOffset"":2194280,""symbol"":""Py_FinalizeEx"",""symbolLocation"":104,""imageIndex"":3},{""imageOffset"":2386344,""symbol"":""Py_RunMain"",""symbolLocation"":476,""imageIndex"":3},{""imageOffset"":2392180,""symbol"":""pymain_main"",""symbolLocation"":52,""imageIndex"":3},{""imageOffset"":2392116,""symbol"":""Py_Main"",""symbolLocation"":36,""imageIndex"":3},{""imageOffset"":15764,""symbol"":""main"",""symbolLocation"":128,""imageIndex"":13},{""imageOffset"":20724,""symbol"":""start"",""symbolLocation"":520,""imageIndex"":14}]},{""id"":4150761,""name"":""ThreadPoolForegroundWorker"",""frames"":[{""imageOffset"":6484,""symbol"":""mach_msg_trap"",""symbolLocation"":8,""imageIndex"":0},{""imageOffset"":7424,""symbol"":""mach_msg"",""symbolLocation"":76,""imageIndex"":0},{""imageOffset"":77624492,""imageIndex"":15},{""imageOffset"":77121252,""imageIndex"":15},{""imageOffset"":77356364,""imageIndex"":15},{""imageOffset"":77353696,""imageIndex"":15},{""imageOffset"":77353132,""imageIndex"":15},{""imageOffset"":77352848,""imageIndex"":15},{""imageOffset"":77514920,""imageIndex"":15},{""imageOffset"":29932,""symbol"":""_pthread_start"",""symbolLocation"":148,""imageIndex"":1},{""imageOffset"":8912,""symbol"":""thread_start"",""symbolLocation"":8,""imageIndex"":1}]},{""id"":4150762,""name"":""ThreadPoolBackgroundWorker"",""frames"":[{""imageOffset"":6484,""symbol"":""mach_msg_trap"",""symbolLocation"":8,""imageIndex"":0},{""imageOffset"":7424,""symbol"":""mach_msg"",""symbolLocation"":76,""imageIndex"":0},{""imageOffset"":77624492,""imageIndex"":15},{""imageOffset"":77121252,""imageIndex"":15},{""imageOffset"":77356364,""imageIndex"":15},{""imageOffset"":77353696,""imageIndex"":15},{""imageOffset"":77353000,""imageIndex"":15},{""imageOffset"":77352908,""imageIndex"":15},{""imageOffset"":77514920,""imageIndex"":15},{""imageOffset"":29932,""symbol"":""_pthread_start"",""symbolLocation"":148,""imageIndex"":1},{""imageOffset"":8912,""symbol"":""thread_start"",""symbolLocation"":8,""imageIndex"":1}]},{""id"":4150765,""name"":""ThreadPoolForegroundWorker"",""frames"":[{""imageOffset"":6484,""symbol"":""mach_msg_trap"",""symbolLocation"":8,""imageIndex"":0},{""imageOffset"":7424,""symbol"":""mach_msg"",""symbolLocation"":76,""imageIndex"":0},{""imageOffset"":77624492,""imageIndex"":15},{""imageOffset"":77121252,""imageIndex"":15},{""imageOffset"":77356364,""imageIndex"":15},{""imageOffset"":77353696,""imageIndex"":15},{""imageOffset"":77353132,""imageIndex"":15},{""imageOffset"":77352848,""imageIndex"":15},{""imageOffset"":77514920,""imageIndex"":15},{""imageOffset"":29932,""symbol"":""_pthread_start"",""symbolLocation"":148,""imageIndex"":1},{""imageOffset"":8912,""symbol"":""thread_start"",""symbolLocation"":8,""imageIndex"":1}]},{""id"":4150766,""name"":""ThreadPoolForegroundWorker"",""frames"":[{""imageOffset"":6484,""symbol"":""mach_msg_trap"",""symbolLocation"":8,""imageIndex"":0},{""imageOffset"":7424,""symbol"":""mach_msg"",""symbolLocation"":76,""imageIndex"":0},{""imageOffset"":77624492,""imageIndex"":15},{""imageOffset"":77121252,""imageIndex"":15},{""imageOffset"":77356364,""imageIndex"":15},{""imageOffset"":77353696,""imageIndex"":15},{""imageOffset"":77353132,""imageIndex"":15},{""imageOffset"":77352848,""imageIndex"":15},{""imageOffset"":77514920,""imageIndex"":15},{""imageOffset"":29932,""symbol"":""_pthread_start"",""symbolLocation"":148,""imageIndex"":1},{""imageOffset"":8912,""symbol"":""thread_start"",""symbolLocation"":8,""imageIndex"":1}]},{""id"":4150767,""name"":""ThreadPoolForegroundWorker"",""frames"":[{""imageOffset"":6484,""symbol"":""mach_msg_trap"",""symbolLocation"":8,""imageIndex"":0},{""imageOffset"":7424,""symbol"":""mach_msg"",""symbolLocation"":76,""imageIndex"":0},{""imageOffset"":77624492,""imageIndex"":15},{""imageOffset"":77121252,""imageIndex"":15},{""imageOffset"":77356364,""imageIndex"":15},{""imageOffset"":77353696,""imageIndex"":15},{""imageOffset"":77353132,""imageIndex"":15},{""imageOffset"":77352848,""imageIndex"":15},{""imageOffset"":77514920,""imageIndex"":15},{""imageOffset"":29932,""symbol"":""_pthread_start"",""symbolLocation"":148,""imageIndex"":1},{""imageOffset"":8912,""symbol"":""thread_start"",""symbolLocation"":8,""imageIndex"":1}]},{""id"":4150768,""name"":""ThreadPoolForegroundWorker"",""frames"":[{""imageOffset"":6484,""symbol"":""mach_msg_trap"",""symbolLocation"":8,""imageIndex"":0},{""imageOffset"":7424,""symbol"":""mach_msg"",""symbolLocation"":76,""imageIndex"":0},{""imageOffset"":77624492,""imageIndex"":15},{""imageOffset"":77121252,""imageIndex"":15},{""imageOffset"":77356364,""imageIndex"":15},{""imageOffset"":77353696,""imageIndex"":15},{""imageOffset"":77353132,""imageIndex"":15},{""imageOffset"":77352848,""imageIndex"":15},{""imageOffset"":77514920,""imageIndex"":15},{""imageOffset"":29932,""symbol"":""_pthread_start"",""symbolLocation"":148,""imageIndex"":1},{""imageOffset"":8912,""symbol"":""thread_start"",""symbolLocation"":8,""imageIndex"":1}]},{""id"":4150772,""name"":""ThreadPoolSingleThreadSharedForeground0"",""frames"":[{""imageOffset"":6484,""symbol"":""mach_msg_trap"",""symbolLocation"":8,""imageIndex"":0},{""imageOffset"":7424,""symbol"":""mach_msg"",""symbolLocation"":76,""imageIndex"":0},{""imageOffset"":77624492,""imageIndex"":15},{""imageOffset"":77121252,""imageIndex"":15},{""imageOffset"":77356364,""imageIndex"":15},{""imageOffset"":77353696,""imageIndex"":15},{""imageOffset"":77353176,""imageIndex"":15},{""imageOffset"":77352932,""imageIndex"":15},{""imageOffset"":77514920,""imageIndex"":15},{""imageOffset"":29932,""symbol"":""_pthread_start"",""symbolLocation"":148,""imageIndex"":1},{""imageOffset"":8912,""symbol"":""thread_start"",""symbolLocation"":8,""imageIndex"":1}]},{""id"":4150775,""name"":""NetworkService"",""frames"":[{""imageOffset"":51784,""symbol"":""kevent64"",""symbolLocation"":8,""imageIndex"":0},{""imageOffset"":77650208,""imageIndex"":15},{""imageOffset"":77649684,""imageIndex"":15},{""imageOffset"":77251124,""imageIndex"":15},{""imageOffset"":76997832,""imageIndex"":15},{""imageOffset"":77411004,""imageIndex"":15},{""imageOffset"":77411388,""imageIndex"":15},{""imageOffset"":77514920,""imageIndex"":15},{""imageOffset"":29932,""symbol"":""_pthread_start"",""symbolLocation"":148,""imageIndex"":1},{""imageOffset"":8912,""symbol"":""thread_start"",""symbolLocation"":8,""imageIndex"":1}]},{""id"":4150776,""name"":""NetworkNotificationThreadMac"",""frames"":[{""imageOffset"":6484,""symbol"":""mach_msg_trap"",""symbolLocation"":8,""imageIndex"":0},{""imageOffset"":7424,""symbol"":""mach_msg"",""symbolLocation"":76,""imageIndex"":0},{""imageOffset"":544312,""symbol"":""__CFRunLoopServiceMachPort"",""symbolLocation"":372,""imageIndex"":7},{""imageOffset"":537328,""symbol"":""__CFRunLoopRun"",""symbolLocation"":1212,""imageIndex"":7},{""imageOffset"":534164,""symbol"":""CFRunLoopRunSpecific"",""symbolLocation"":600,""imageIndex"":7},{""imageOffset"":413200,""symbol"":""-[NSRunLoop(NSRunLoop) runMode:beforeDate:]"",""symbolLocation"":236,""imageIndex"":16},{""imageOffset"":77855292,""imageIndex"":15},{""imageOffset"":77849548,""imageIndex"":15},{""imageOffset"":77251124,""imageIndex"":15},{""imageOffset"":76997832,""imageIndex"":15},{""imageOffset"":77411004,""imageIndex"":15},{""imageOffset"":77411388,""imageIndex"":15},{""imageOffset"":77514920,""imageIndex"":15},{""imageOffset"":29932,""symbol"":""_pthread_start"",""symbolLocation"":148,""imageIndex"":1},{""imageOffset"":8912,""symbol"":""thread_start"",""symbolLocation"":8,""imageIndex"":1}]},{""id"":4150777,""name"":""NetworkConfigWatcher"",""frames"":[{""imageOffset"":6484,""symbol"":""mach_msg_trap"",""symbolLocation"":8,""imageIndex"":0},{""imageOffset"":7424,""symbol"":""mach_msg"",""symbolLocation"":76,""imageIndex"":0},{""imageOffset"":77624492,""imageIndex"":15},{""imageOffset"":77121252,""imageIndex"":15},{""imageOffset"":77121132,""imageIndex"":15},{""imageOffset"":76786520,""imageIndex"":15},{""imageOffset"":77251124,""imageIndex"":15},{""imageOffset"":76997832,""imageIndex"":15},{""imageOffset"":77411004,""imageIndex"":15},{""imageOffset"":77411388,""imageIndex"":15},{""imageOffset"":77514920,""imageIndex"":15},{""imageOffset"":29932,""symbol"":""_pthread_start"",""symbolLocation"":148,""imageIndex"":1},{""imageOffset"":8912,""symbol"":""thread_start"",""symbolLocation"":8,""imageIndex"":1}]},{""id"":4150778,""name"":""ThreadPoolSingleThreadForegroundBlocking1"",""frames"":[{""imageOffset"":6484,""symbol"":""mach_msg_trap"",""symbolLocation"":8,""imageIndex"":0},{""imageOffset"":7424,""symbol"":""mach_msg"",""symbolLocation"":76,""imageIndex"":0},{""imageOffset"":77624492,""imageIndex"":15},{""imageOffset"":77121252,""imageIndex"":15},{""imageOffset"":77356364,""imageIndex"":15},{""imageOffset"":77353696,""imageIndex"":15},{""imageOffset"":77353220,""imageIndex"":15},{""imageOffset"":77352920,""imageIndex"":15},{""imageOffset"":77514920,""imageIndex"":15},{""imageOffset"":29932,""symbol"":""_pthread_start"",""symbolLocation"":148,""imageIndex"":1},{""imageOffset"":8912,""symbol"":""thread_start"",""symbolLocation"":8,""imageIndex"":1}]},{""id"":4150815,""name"":""ThreadPoolBackgroundWorker"",""frames"":[{""imageOffset"":6484,""symbol"":""mach_msg_trap"",""symbolLocation"":8,""imageIndex"":0},{""imageOffset"":7424,""symbol"":""mach_msg"",""symbolLocation"":76,""imageIndex"":0},{""imageOffset"":77624492,""imageIndex"":15},{""imageOffset"":77121252,""imageIndex"":15},{""imageOffset"":77356364,""imageIndex"":15},{""imageOffset"":77353696,""imageIndex"":15},{""imageOffset"":77353000,""imageIndex"":15},{""imageOffset"":77352908,""imageIndex"":15},{""imageOffset"":77514920,""imageIndex"":15},{""imageOffset"":29932,""symbol"":""_pthread_start"",""symbolLocation"":148,""imageIndex"":1},{""imageOffset"":8912,""symbol"":""thread_start"",""symbolLocation"":8,""imageIndex"":1}]},{""id"":4150816,""name"":""MemoryInfra"",""frames"":[{""imageOffset"":6484,""symbol"":""mach_msg_trap"",""symbolLocation"":8,""imageIndex"":0},{""imageOffset"":7424,""symbol"":""mach_msg"",""symbolLocation"":76,""imageIndex"":0},{""imageOffset"":77624492,""imageIndex"":15},{""imageOffset"":77121252,""imageIndex"":15},{""imageOffset"":77121132,""imageIndex"":15},{""imageOffset"":76786520,""imageIndex"":15},{""imageOffset"":77251124,""imageIndex"":15},{""imageOffset"":76997832,""imageIndex"":15},{""imageOffset"":77411004,""imageIndex"":15},{""imageOffset"":77411388,""imageIndex"":15},{""imageOffset"":77514920,""imageIndex"":15},{""imageOffset"":29932,""symbol"":""_pthread_start"",""symbolLocation"":148,""imageIndex"":1},{""imageOffset"":8912,""symbol"":""thread_start"",""symbolLocation"":8,""imageIndex"":1}]},{""id"":4150817,""name"":""ThreadPoolSingleThreadSharedBackgroundBlocking2"",""frames"":[{""imageOffset"":6484,""symbol"":""mach_msg_trap"",""symbolLocation"":8,""imageIndex"":0},{""imageOffset"":7424,""symbol"":""mach_msg"",""symbolLocation"":76,""imageIndex"":0},{""imageOffset"":77624492,""imageIndex"":15},{""imageOffset"":77121252,""imageIndex"":15},{""imageOffset"":77356364,""imageIndex"":15},{""imageOffset"":77353696,""imageIndex"":15},{""imageOffset"":77353044,""imageIndex"":15},{""imageOffset"":77352956,""imageIndex"":15},{""imageOffset"":77514920,""imageIndex"":15},{""imageOffset"":29932,""symbol"":""_pthread_start"",""symbolLocation"":148,""imageIndex"":1},{""imageOffset"":8912,""symbol"":""thread_start"",""symbolLocation"":8,""imageIndex"":1}]},{""id"":4150838,""name"":""com.apple.NSEventThread"",""frames"":[{""imageOffset"":6484,""symbol"":""mach_msg_trap"",""symbolLocation"":8,""imageIndex"":0},{""imageOffset"":7424,""symbol"":""mach_msg"",""symbolLocation"":76,""imageIndex"":0},{""imageOffset"":544312,""symbol"":""__CFRunLoopServiceMachPort"",""symbolLocation"":372,""imageIndex"":7},{""imageOffset"":537328,""symbol"":""__CFRunLoopRun"",""symbolLocation"":1212,""imageIndex"":7},{""imageOffset"":534164,""symbol"":""CFRunLoopRunSpecific"",""symbolLocation"":600,""imageIndex"":7},{""imageOffset"":1764388,""symbol"":""_NSEventThread"",""symbolLocation"":196,""imageIndex"":6},{""imageOffset"":29932,""symbol"":""_pthread_start"",""symbolLocation"":148,""imageIndex"":1},{""imageOffset"":8912,""symbol"":""thread_start"",""symbolLocation"":8,""imageIndex"":1}]},{""id"":4150864,""frames"":[{""imageOffset"":20672,""symbol"":""__psynch_cvwait"",""symbolLocation"":8,""imageIndex"":0},{""imageOffset"":31412,""symbol"":""_pthread_cond_wait"",""symbolLocation"":1228,""imageIndex"":1},{""imageOffset"":1502040,""symbol"":""blas_thread_server"",""symbolLocation"":360,""imageIndex"":17},{""imageOffset"":29932,""symbol"":""_pthread_start"",""symbolLocation"":148,""imageIndex"":1},{""imageOffset"":8912,""symbol"":""thread_start"",""symbolLocation"":8,""imageIndex"":1}]},{""id"":4150865,""frames"":[{""imageOffset"":20672,""symbol"":""__psynch_cvwait"",""symbolLocation"":8,""imageIndex"":0},{""imageOffset"":31412,""symbol"":""_pthread_cond_wait"",""symbolLocation"":1228,""imageIndex"":1},{""imageOffset"":1502040,""symbol"":""blas_thread_server"",""symbolLocation"":360,""imageIndex"":17},{""imageOffset"":29932,""symbol"":""_pthread_start"",""symbolLocation"":148,""imageIndex"":1},{""imageOffset"":8912,""symbol"":""thread_start"",""symbolLocation"":8,""imageIndex"":1}]},{""id"":4150866,""frames"":[{""imageOffset"":20672,""symbol"":""__psynch_cvwait"",""symbolLocation"":8,""imageIndex"":0},{""imageOffset"":31412,""symbol"":""_pthread_cond_wait"",""symbolLocation"":1228,""imageIndex"":1},{""imageOffset"":1502040,""symbol"":""blas_thread_server"",""symbolLocation"":360,""imageIndex"":17},{""imageOffset"":29932,""symbol"":""_pthread_start"",""symbolLocation"":148,""imageIndex"":1},{""imageOffset"":8912,""symbol"":""thread_start"",""symbolLocation"":8,""imageIndex"":1}]},{""id"":4150867,""frames"":[{""imageOffset"":20672,""symbol"":""__psynch_cvwait"",""symbolLocation"":8,""imageIndex"":0},{""imageOffset"":31412,""symbol"":""_pthread_cond_wait"",""symbolLocation"":1228,""imageIndex"":1},{""imageOffset"":1502040,""symbol"":""blas_thread_server"",""symbolLocation"":360,""imageIndex"":17},{""imageOffset"":29932,""symbol"":""_pthread_start"",""symbolLocation"":148,""imageIndex"":1},{""imageOffset"":8912,""symbol"":""thread_start"",""symbolLocation"":8,""imageIndex"":1}]},{""id"":4150868,""frames"":[{""imageOffset"":20672,""symbol"":""__psynch_cvwait"",""symbolLocation"":8,""imageIndex"":0},{""imageOffset"":31412,""symbol"":""_pthread_cond_wait"",""symbolLocation"":1228,""imageIndex"":1},{""imageOffset"":1502040,""symbol"":""blas_thread_server"",""symbolLocation"":360,""imageIndex"":17},{""imageOffset"":29932,""symbol"":""_pthread_start"",""symbolLocation"":148,""imageIndex"":1},{""imageOffset"":8912,""symbol"":""thread_start"",""symbolLocation"":8,""imageIndex"":1}]},{""id"":4150869,""frames"":[{""imageOffset"":20672,""symbol"":""__psynch_cvwait"",""symbolLocation"":8,""imageIndex"":0},{""imageOffset"":31412,""symbol"":""_pthread_cond_wait"",""symbolLocation"":1228,""imageIndex"":1},{""imageOffset"":1502040,""symbol"":""blas_thread_server"",""symbolLocation"":360,""imageIndex"":17},{""imageOffset"":29932,""symbol"":""_pthread_start"",""symbolLocation"":148,""imageIndex"":1},{""imageOffset"":8912,""symbol"":""thread_start"",""symbolLocation"":8,""imageIndex"":1}]},{""id"":4150870,""frames"":[{""imageOffset"":20672,""symbol"":""__psynch_cvwait"",""symbolLocation"":8,""imageIndex"":0},{""imageOffset"":31412,""symbol"":""_pthread_cond_wait"",""symbolLocation"":1228,""imageIndex"":1},{""imageOffset"":1502040,""symbol"":""blas_thread_server"",""symbolLocation"":360,""imageIndex"":17},{""imageOffset"":29932,""symbol"":""_pthread_start"",""symbolLocation"":148,""imageIndex"":1},{""imageOffset"":8912,""symbol"":""thread_start"",""symbolLocation"":8,""imageIndex"":1}]},{""id"":4158975,""frames"":[{""imageOffset"":8892,""symbol"":""start_wqthread"",""symbolLocation"":0,""imageIndex"":1}]},{""id"":4159079,""frames"":[{""imageOffset"":8892,""symbol"":""start_wqthread"",""symbolLocation"":0,""imageIndex"":1}]},{""id"":4159107,""frames"":[{""imageOffset"":8892,""symbol"":""start_wqthread"",""symbolLocation"":0,""imageIndex"":1}]},{""id"":4159110,""frames"":[{""imageOffset"":8892,""symbol"":""start_wqthread"",""symbolLocation"":0,""imageIndex"":1}]},{""id"":4159111,""frames"":[{""imageOffset"":8892,""symbol"":""start_wqthread"",""symbolLocation"":0,""imageIndex"":1}]},{""id"":4159648,""frames"":[{""imageOffset"":8892,""symbol"":""start_wqthread"",""symbolLocation"":0,""imageIndex"":1}]},{""id"":4159649,""queue"":""com.apple.root.user-interactive-qos"",""frames"":[{""imageOffset"":6568,""symbol"":""semaphore_timedwait_trap"",""symbolLocation"":8,""imageIndex"":0},{""imageOffset"":16824,""symbol"":""_dispatch_sema4_timedwait"",""symbolLocation"":64,""imageIndex"":18},{""imageOffset"":18364,""symbol"":""_dispatch_semaphore_wait_slow"",""symbolLocation"":76,""imageIndex"":18},{""imageOffset"":9626304,""symbol"":""__22-[NSCGSLocalFence set]_block_invoke_2"",""symbolLocation"":180,""imageIndex"":6},{""imageOffset"":15404,""symbol"":""CA::Transaction::run_commit_handlers(CATransactionPhase)"",""symbolLocation"":120,""imageIndex"":19},{""imageOffset"":1452936,""symbol"":""CA::Context::commit_transaction(CA::Transaction*, double, double*)"",""symbolLocation"":748,""imageIndex"":19},{""imageOffset"":11640,""symbol"":""CA::Transaction::commit()"",""symbolLocation"":680,""imageIndex"":19},{""imageOffset"":601728,""symbol"":""NSPerformVisuallyAtomicChange"",""symbolLocation"":160,""imageIndex"":6},{""imageOffset"":4600360,""symbol"":""__30-[NSAnimation _runInNewThread]_block_invoke"",""symbolLocation"":116,""imageIndex"":6},{""imageOffset"":7776,""symbol"":""_dispatch_call_block_and_release"",""symbolLocation"":32,""imageIndex"":18},{""imageOffset"":15276,""symbol"":""_dispatch_client_callout"",""symbolLocation"":20,""imageIndex"":18},{""imageOffset"":87100,""symbol"":""_dispatch_root_queue_drain"",""symbolLocation"":684,""imageIndex"":18},{""imageOffset"":88920,""symbol"":""_dispatch_worker_thread2"",""symbolLocation"":164,""imageIndex"":18},{""imageOffset"":13684,""symbol"":""_pthread_wqthread"",""symbolLocation"":228,""imageIndex"":1},{""imageOffset"":8900,""symbol"":""start_wqthread"",""symbolLocation"":8,""imageIndex"":1}]}], ""usedImages"" : [ { ""source"" : ""P"", ""arch"" : ""arm64e"", ""base"" : 6872285184, ""size"" : 221184, ""uuid"" : ""c8524c02-b14f-30bd-a228-c44b4a448e68"", ""path"" : ""\/usr\/lib\/system\/libsystem_kernel.dylib"", ""name"" : ""libsystem_kernel.dylib"" }, { ""source"" : ""P"", ""arch"" : ""arm64e"", ""base"" : 6872506368, ""size"" : 53248, ""uuid"" : ""4786e19a-9312-38e6-80ef-9c1394548118"", ""path"" : ""\/usr\/lib\/system\/libsystem_pthread.dylib"", ""name"" : ""libsystem_pthread.dylib"" }, { ""source"" : ""P"", ""arch"" : ""arm64e"", ""base"" : 6871240704, ""size"" : 528384, ""uuid"" : ""002a39ae-6431-3b2e-85e7-c45fc2f95ad0"", ""path"" : ""\/usr\/lib\/system\/libsystem_c.dylib"", ""name"" : ""libsystem_c.dylib"" }, { ""source"" : ""P"", ""arch"" : ""arm64"", ""base"" : 4322181120, ""CFBundleShortVersionString"" : ""3.11.4, (c) 2001-2023 Python Software Foundation."", ""CFBundleIdentifier"" : ""org.python.python"", ""size"" : 3948544, ""uuid"" : ""88bffd37-99d8-36ab-9b95-9f54b30bd667"", ""path"" : ""\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/Python"", ""name"" : ""Python"", ""CFBundleVersion"" : ""3.11.4"" }, { ""source"" : ""P"", ""arch"" : ""arm64e"", ""base"" : 6872612864, ""size"" : 32768, ""uuid"" : ""06ce953d-f22a-3724-b6d5-829b45179897"", ""path"" : ""\/usr\/lib\/system\/libsystem_platform.dylib"", ""name"" : ""libsystem_platform.dylib"" }, { ""source"" : ""P"", ""arch"" : ""arm64"", ""base"" : 4816977920, ""size"" : 688128, ""uuid"" : ""41d18909-c4c7-3b88-9995-ae4bf56f0f5f"", ""path"" : ""\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/plugins\/platforms\/libqcocoa.dylib"", ""name"" : ""libqcocoa.dylib"" }, { ""source"" : ""P"", ""arch"" : ""arm64e"", ""base"" : 6918529024, ""CFBundleShortVersionString"" : ""6.9"", ""CFBundleIdentifier"" : ""com.apple.AppKit"", ""size"" : 15409152, ""uuid"" : ""518f4e68-c324-320f-9d7f-85c224eae972"", ""path"" : ""\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit"", ""name"" : ""AppKit"", ""CFBundleVersion"" : ""2113"" }, { ""source"" : ""P"", ""arch"" : ""arm64e"", ""base"" : 6872825856, ""CFBundleShortVersionString"" : ""6.9"", ""CFBundleIdentifier"" : ""com.apple.CoreFoundation"", ""size"" : 5521408, ""uuid"" : ""b2ff96d0-ae99-31ef-9014-fc9964b4f3e0"", ""path"" : ""\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation"", ""name"" : ""CoreFoundation"", ""CFBundleVersion"" : ""1855.105"" }, { ""source"" : ""P"", ""arch"" : ""arm64"", ""base"" : 4536418304, ""size"" : 7192576, ""uuid"" : ""a8ea0a9b-1cec-33c6-98cc-0263b2b04f58"", ""path"" : ""\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtGui.framework\/Versions\/A\/QtGui"", ""name"" : ""QtGui"" }, { ""source"" : ""P"", ""arch"" : ""arm64"", ""base"" : 4549476352, ""size"" : 4866048, ""uuid"" : ""c25ee3e6-f552-32f6-9638-d0c3c2b9e88b"", ""path"" : ""\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtWidgets.framework\/Versions\/A\/QtWidgets"", ""name"" : ""QtWidgets"" }, { ""source"" : ""P"", ""arch"" : ""arm64"", ""base"" : 4415111168, ""size"" : 4816896, ""uuid"" : ""33a8a2c3-65f0-3e8b-9d5d-2fe2096a312b"", ""path"" : ""\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtCore.framework\/Versions\/A\/QtCore"", ""name"" : ""QtCore"" }, { ""source"" : ""P"", ""arch"" : ""arm64"", ""base"" : 4427038720, ""size"" : 3112960, ""uuid"" : ""01bdab74-5f85-357d-9ac4-a9ed2dc92340"", ""path"" : ""\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/QtWidgets.abi3.so"", ""name"" : ""QtWidgets.abi3.so"" }, { ""source"" : ""P"", ""arch"" : ""arm64"", ""base"" : 4423041024, ""size"" : 1818624, ""uuid"" : ""3d5b3918-05dc-3af6-9acc-86261296227e"", ""path"" : ""\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/QtCore.abi3.so"", ""name"" : ""QtCore.abi3.so"" }, { ""source"" : ""P"", ""arch"" : ""arm64"", ""base"" : 4303994880, ""CFBundleShortVersionString"" : ""1.10.0"", ""CFBundleIdentifier"" : ""edu.ucsf.cgl.ChimeraX"", ""size"" : 16384, ""uuid"" : ""18de835b-eddc-3f3a-93bb-285f33da630d"", ""path"" : ""\/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX"", ""name"" : ""ChimeraX"", ""CFBundleVersion"" : ""1.10.0.0"" }, { ""source"" : ""P"", ""arch"" : ""arm64e"", ""base"" : 4307255296, ""size"" : 393216, ""uuid"" : ""86a8ba48-8bb4-3b30-9cda-051f73c74f44"", ""path"" : ""\/usr\/lib\/dyld"", ""name"" : ""dyld"" }, { ""source"" : ""P"", ""arch"" : ""arm64"", ""base"" : 6168625152, ""size"" : 181551104, ""uuid"" : ""ab75c71e-3aa9-3a7f-981c-e8c6c2177118"", ""path"" : ""\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtWebEngineCore.framework\/Versions\/A\/QtWebEngineCore"", ""name"" : ""QtWebEngineCore"" }, { ""source"" : ""P"", ""arch"" : ""arm64e"", ""base"" : 6888517632, ""CFBundleShortVersionString"" : ""6.9"", ""CFBundleIdentifier"" : ""com.apple.Foundation"", ""size"" : 4120576, ""uuid"" : ""de039f1b-ffe5-3644-a8cf-7ba52c32cd73"", ""path"" : ""\/System\/Library\/Frameworks\/Foundation.framework\/Versions\/C\/Foundation"", ""name"" : ""Foundation"", ""CFBundleVersion"" : ""1855.105"" }, { ""source"" : ""P"", ""arch"" : ""arm64"", ""base"" : 4479516672, ""size"" : 21299200, ""uuid"" : ""9854a721-2573-3169-81ec-19ea40ce8077"", ""path"" : ""\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/numpy\/.dylibs\/libopenblas64_.0.dylib"", ""name"" : ""libopenblas64_.0.dylib"" }, { ""source"" : ""P"", ""arch"" : ""arm64e"", ""base"" : 6870691840, ""size"" : 290816, ""uuid"" : ""3d7a56a3-23bf-3077-b5c6-9ce65ce7333e"", ""path"" : ""\/usr\/lib\/system\/libdispatch.dylib"", ""name"" : ""libdispatch.dylib"" }, { ""source"" : ""P"", ""arch"" : ""arm64e"", ""base"" : 6988857344, ""CFBundleShortVersionString"" : ""1.11"", ""CFBundleIdentifier"" : ""com.apple.QuartzCore"", ""size"" : 3137536, ""uuid"" : ""b7469cdd-ceae-3cb7-bb88-6c8d274d546a"", ""path"" : ""\/System\/Library\/Frameworks\/QuartzCore.framework\/Versions\/A\/QuartzCore"", ""name"" : ""QuartzCore"", ""CFBundleVersion"" : ""962.57.1"" } ], ""sharedCache"" : { ""base"" : 6869336064, ""size"" : 3072180224, ""uuid"" : ""a6162d66-93e3-3251-93cc-b11f7c8c830e"" }, ""vmSummary"" : ""ReadOnly portion of Libraries: Total=1.3G resident=0K(0%) swapped_out_or_unallocated=1.3G(100%)\nWritable regions: Total=2.7G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=2.7G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 1408K 11 \nActivity Tracing 256K 1 \nCG backing stores 3136K 8 \nCG image 1952K 68 \nColorSync 576K 29 \nCoreAnimation 5216K 123 \nCoreGraphics 48K 3 \nCoreUI image data 5776K 57 \nFoundation 48K 2 \nKernel Alloc Once 32K 1 \nMALLOC 1.5G 259 \nMALLOC guard page 192K 10 \nMALLOC_MEDIUM (reserved) 576.0M 8 reserved VM address space (unallocated)\nMALLOC_NANO (reserved) 128.0M 1 reserved VM address space (unallocated)\nOpenGL GLSL 384K 4 \nSTACK GUARD 464K 29 \nStack 128.2M 30 \nStack Guard 56.0M 1 \nVM_ALLOCATE 240.6M 172 \nVM_ALLOCATE (reserved) 96.0M 1 reserved VM address space (unallocated)\n__AUTH 2619K 337 \n__AUTH_CONST 20.4M 542 \n__CTF 759 1 \n__DATA 27.3M 696 \n__DATA_CONST 29.5M 705 \n__DATA_DIRTY 1949K 242 \n__FONT_DATA 4K 1 \n__GLSLBUILTINS 5176K 1 \n__LINKEDIT 601.0M 161 \n__OBJC_CONST 3921K 311 \n__OBJC_RO 81.8M 1 \n__OBJC_RW 3088K 1 \n__TEXT 762.9M 722 \n__UNICODE 588K 1 \ndyld private memory 1072K 3 \nmapped file 234.6M 60 \nshared memory 1440K 19 \n=========== ======= ======= \nTOTAL 4.5G 4622 \nTOTAL, minus reserved VM space 3.7G 4622 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""60da5e84ab0ca017dace9abf"", ""factorPackIds"" : { }, ""deploymentId"" : 240000008 }, { ""rolloutId"" : ""607844aa04477260f58a8077"", ""factorPackIds"" : { ""SIRI_MORPHUN_ASSETS"" : ""6103050cbfe6dc472e1c982a"" }, ""deploymentId"" : 240000066 }, { ""rolloutId"" : ""602ad4dac86151000cf27e46"", ""factorPackIds"" : { ""SIRI_DICTATION_ASSETS"" : ""61ae8d06da72d16a4beb762e"" }, ""deploymentId"" : 240000305 }, { ""rolloutId"" : ""601d9415f79519000ccd4b69"", ""factorPackIds"" : { ""SIRI_TEXT_TO_SPEECH"" : ""61ef3bd729647d394933a0a6"" }, ""deploymentId"" : 240000416 }, { ""rolloutId"" : ""5fb4245a1bbfe8005e33a1e1"", ""factorPackIds"" : { }, ""deploymentId"" : 240000021 }, { ""rolloutId"" : ""5f72dc58705eff005a46b3a9"", ""factorPackIds"" : { }, ""deploymentId"" : 240000015 }, { ""rolloutId"" : ""60f8ddccefea4203d95cbeef"", ""factorPackIds"" : { }, ""deploymentId"" : 240000025 }, { ""rolloutId"" : ""5fc94383418129005b4e9ae0"", ""factorPackIds"" : { }, ""deploymentId"" : 240000614 }, { ""rolloutId"" : ""60186475825c62000ccf5450"", ""factorPackIds"" : { }, ""deploymentId"" : 240000083 }, { ""rolloutId"" : ""5ffde50ce2aacd000d47a95f"", ""factorPackIds"" : { }, ""deploymentId"" : 240000486 } ], ""experiments"" : [ ] } } Log: UCSF ChimeraX version: 1.10.dev202501170719 (2025-01-17) © 2016-2025 Regents of the University of California. All rights reserved. > open /Users/usuario/Desktop/fold_paper/ak1b_2_f6_2_paegreen5.cxs Log from Sat Jul 26 18:22:59 2025UCSF ChimeraX version: 1.8rc202405312319 (2024-05-31) © 2016-2024 Regents of the University of California. All rights reserved. > open /Users/usuario/Desktop/fragmentoG160/F2.cxs Log from Fri Jul 25 10:55:12 2025 Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.8rc202405312319 (2024-05-31) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/usuario/Downloads/fold_g160_1copia/fold_g160_1copia_model_0.cif Chain information for fold_g160_1copia_model_0.cif #1 --- Chain | Description A | . > set bgColor white > preset cartoons/nucleotides cylinders/stubs Using preset: Cartoons/Nucleotides / Cylinders/Stubs Changed 0 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick ~worm cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect cartoon style protein modeh tube rad 2 sides 24 thick 0.6 cartoon style nucleic x round width 1.6 thick 1.6 nucleotides stubs > ui tool show ""Color Actions"" > color indian red [Repeated 1 time(s)] > color fire brick > color indian red > transparency 80 target ac > transparency 50 target ac > transparency 60 target ac > transparency 80 target ac > select :1-393 2937 atoms, 2990 bonds, 393 residues, 1 model selected > ui tool show ""Color Actions"" > color sel red > color sel medium violet red [Repeated 2 time(s)] > color sel medium orchid > color sel medium violet red > transparency sel 0 target ac > select add #1 11715 atoms, 11835 bonds, 1498 residues, 1 model selected > select subtract #1 Nothing selected > select :1-393 2937 atoms, 2990 bonds, 393 residues, 1 model selected > color sel purple > graphics selection color black width 0.8 > graphics selection color black width 3 > graphics selection color black width 1.2 > save /Users/usuario/Desktop/fragmentoG160/F2.cxs ——— End of log from Fri Jul 25 10:55:12 2025 ——— opened ChimeraX session > save /Users/usuario/Desktop/fragmentoG160/f2.png width 864 height 611 > supersample 3 > open ""/Users/usuario/Dropbox > (Personal)/alphafold_paper/fold_ak1b_2short_f6_2-2/fold_ak1b_2short_f6_2_model_0.cif"" Chain information for fold_ak1b_2short_f6_2_model_0.cif #2 --- Chain | Description A B | . C D | . > open ""/Users/usuario/Dropbox > (Personal)/alphafold_paper/fold_ak1b_2short_f6_2-2/fold_ak1b_2short_f6_2_model_1.cif"" Chain information for fold_ak1b_2short_f6_2_model_1.cif #3 --- Chain | Description A B | . C D | . > open ""/Users/usuario/Dropbox > (Personal)/alphafold_paper/fold_ak1b_2short_f6_2-2/fold_ak1b_2short_f6_2_model_2.cif"" Chain information for fold_ak1b_2short_f6_2_model_2.cif #4 --- Chain | Description A B | . C D | . > open ""/Users/usuario/Dropbox > (Personal)/alphafold_paper/fold_ak1b_2short_f6_2-2/fold_ak1b_2short_f6_2_model_3.cif"" Chain information for fold_ak1b_2short_f6_2_model_3.cif #5 --- Chain | Description A B | . C D | . > open ""/Users/usuario/Dropbox > (Personal)/alphafold_paper/fold_ak1b_2short_f6_2-2/fold_ak1b_2short_f6_2_model_4.cif"" Chain information for fold_ak1b_2short_f6_2_model_4.cif #6 --- Chain | Description A B | . C D | . > close #1 > ui tool show Matchmaker > matchmaker #3-6 to #2 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_ak1b_2short_f6_2_model_0.cif, chain C (#2) with fold_ak1b_2short_f6_2_model_1.cif, chain C (#3), sequence alignment score = 651 RMSD between 78 pruned atom pairs is 0.606 angstroms; (across all 128 pairs: 6.488) Matchmaker fold_ak1b_2short_f6_2_model_0.cif, chain C (#2) with fold_ak1b_2short_f6_2_model_2.cif, chain C (#4), sequence alignment score = 651 RMSD between 72 pruned atom pairs is 0.524 angstroms; (across all 128 pairs: 12.583) Matchmaker fold_ak1b_2short_f6_2_model_0.cif, chain C (#2) with fold_ak1b_2short_f6_2_model_3.cif, chain C (#5), sequence alignment score = 651 RMSD between 73 pruned atom pairs is 0.577 angstroms; (across all 128 pairs: 8.942) Matchmaker fold_ak1b_2short_f6_2_model_0.cif, chain C (#2) with fold_ak1b_2short_f6_2_model_4.cif, chain C (#6), sequence alignment score = 651 RMSD between 72 pruned atom pairs is 0.483 angstroms; (across all 128 pairs: 17.400) > select #2/A 980 atoms, 986 bonds, 120 residues, 1 model selected > select #2/A:1-120 980 atoms, 986 bonds, 120 residues, 1 model selected > select #2/A:1-120 980 atoms, 986 bonds, 120 residues, 1 model selected > select :A,B Nothing selected > select /A,/B Expected an objects specifier or a keyword > select A,B Expected an objects specifier or a keyword > select A Expected an objects specifier or a keyword > color bychain > color bypolymer > select > #2/A#2/B#2/C#2/D#3/A#3/B#3/C#3/D#4/A#4/B#4/C#4/D#5/A#5/B#5/C#5/D#6/A#6/B#6/C#6/D 19470 atoms, 19760 bonds, 2480 residues, 5 models selected > color sel bypolymer Alignment identifier is 1 Alignment identifier is 2 > select #2/A-B:1 #3/A-B:1 #4/A-B:1 #5/A-B:1 #6/A-B:1 80 atoms, 70 bonds, 10 residues, 5 models selected > select #2/A-B #3/A-B #4/A-B #5/A-B #6/A-B 9800 atoms, 9860 bonds, 1200 residues, 5 models selected . [ID: 1] region 10 chains [1-120] RMSD: 1.517 > color sel cornflower blue > transparency sel 30 > transparency sel 80 > transparency sel 30 target ac > select #2/C-D:1 #3/C-D:1 #4/C-D:1 #5/C-D:1 #6/C-D:1 90 atoms, 80 bonds, 10 residues, 5 models selected > select #2/C-D #3/C-D #4/C-D #5/C-D #6/C-D 9670 atoms, 9900 bonds, 1280 residues, 5 models selected . [ID: 2] region 10 chains [1-128] RMSD: 12.546 > ui tool show ""Color Actions"" > color sel gold > color sel yellow > color sel royal blue > color sel light pink [Repeated 1 time(s)] > color sel light coral > color sel violet > color sel light goldenrod yellow > color sel old lace > color sel light yellow > color sel lemon chiffon > color sel moccasin > color sel pale green > color sel moccasin > color sel navajo white > color sel peach puff [Repeated 1 time(s)] > color sel navajo white > color sel moccasin > transparency sel 30 target ac > graphics silhouettes true color black width 1 depthJump 0.01 > hide #3 models > show #3 models > select add #3 11630 atoms, 11872 bonds, 1520 residues, 5 models selected > select subtract #3 7736 atoms, 7920 bonds, 1024 residues, 4 models selected > select add #4 9696 atoms, 9892 bonds, 1264 residues, 4 models selected > select subtract #4 5802 atoms, 5940 bonds, 768 residues, 3 models selected > select add #3 9696 atoms, 9892 bonds, 1264 residues, 4 models selected > select add #4 13590 atoms, 13844 bonds, 1760 residues, 5 models selected > select add #5 15550 atoms, 15816 bonds, 2000 residues, 5 models selected > select add #6 17510 atoms, 17788 bonds, 2240 residues, 5 models selected > select subtract #6 13616 atoms, 13836 bonds, 1744 residues, 4 models selected > select add #6 17510 atoms, 17788 bonds, 2240 residues, 5 models selected > select subtract #6 13616 atoms, 13836 bonds, 1744 residues, 4 models selected > select subtract #5 9722 atoms, 9884 bonds, 1248 residues, 3 models selected > select subtract #4 5828 atoms, 5932 bonds, 752 residues, 2 models selected > select subtract #3 1934 atoms, 1980 bonds, 256 residues, 1 model selected > select add #3 5828 atoms, 5932 bonds, 752 residues, 2 models selected > select add #2 7788 atoms, 7904 bonds, 992 residues, 2 models selected > select subtract #3 3894 atoms, 3952 bonds, 496 residues, 1 model selected > select add #3 7788 atoms, 7904 bonds, 992 residues, 2 models selected > select add #4 11682 atoms, 11856 bonds, 1488 residues, 3 models selected > select add #5 15576 atoms, 15808 bonds, 1984 residues, 4 models selected > select add #6 19470 atoms, 19760 bonds, 2480 residues, 5 models selected > graphics silhouettes true color black width 1 depthJump 0.01 > graphics silhouettes true color black width 5 depthJump 0.01 > graphics silhouettes true color black width 1.2 depthJump 0.01 > graphics silhouettes true color black width 1.2 depthJump 0.03 > graphics silhouettes true color black width 1.2 depthJump 0.4 > graphics silhouettes true color black width 1.2 depthJump 6 > graphics silhouettes true color black width 1.2 depthJump 0.01 > save /Users/usuario/Desktop/fold_paper/ak1b_2_f6_2.cxs > color bfactor palette > 0,#FF7D45:50,#FF7D45:50.00001,#FFDB13:70,#FFDB13:70.00001,#65CBF3:90,#65CBF3:90.00001,#0053D6:100,#0053D6 > key true > key #ff7d45:0 #ff7d45:50 #ffdb13:50 #ffdb13:70 #65cbf3:70 #65cbf3:90 > #0053d6:90 #0053d6:100 showTool true > ui mousemode right ""color key"" 19470 atoms, 2480 residues, atom bfactor range 17.7 to 95.2 > key size 0.26000,0.05000 > key size 0.27000,0.05000 > key size 0.28000,0.05000 > key size 0.29000,0.05000 > key size 0.30000,0.05000 > key size 0.31000,0.05000 Key is partially or completely offscreen > key size 0.32000,0.05000 Key is partially or completely offscreen > key size 0.32000,0.04000 Key is partially or completely offscreen > key size 0.32000,0.03000 Key is partially or completely offscreen > key pos 0.69000,0.08000 Key is partially or completely offscreen > key pos 0.68000,0.08000 > key pos 0.69000,0.08000 Key is partially or completely offscreen > key pos 0.70000,0.08000 Key is partially or completely offscreen > key pos 0.71000,0.08000 Key is partially or completely offscreen > key pos 0.72000,0.08000 Key is partially or completely offscreen > key pos 0.73000,0.08000 Key is partially or completely offscreen > key pos 0.73000,0.07000 Key is partially or completely offscreen > key pos 0.73000,0.06000 Key is partially or completely offscreen > key pos 0.73000,0.05000 Key is partially or completely offscreen > key pos 0.73000,0.04000 Key is partially or completely offscreen > key pos 0.73000,0.03000 Key is partially or completely offscreen > key pos 0.73000,0.02000 Key is partially or completely offscreen > key pos 0.73000,0.01000 Key is partially or completely offscreen > key pos 0.73000,0.00000 Key is partially or completely offscreen > key pos 0.73000,-0.01000 Key is partially or completely offscreen > key pos 0.73000,-0.02000 Key is partially or completely offscreen > key pos 0.73000,-0.03000 Key is partially or completely offscreen > key pos 0.73000,-0.04000 Key is partially or completely offscreen > key pos 0.73000,-0.05000 Key is partially or completely offscreen > key pos 0.73000,-0.06000 Key is partially or completely offscreen > key pos 0.73000,-0.07000 Key is partially or completely offscreen > key pos 0.73000,-0.08000 Key is partially or completely offscreen > save /Users/usuario/Desktop/fold_paper/ak1b_2_f6_2bfactor.cxs > undo > alphafold contacts #1/A toAtoms #1/D distance 5 maxPae 5 palette paegreen No alphafold specified for alphafold contacts > rename #1.1 ""AB contacts"" > alphafold contacts #1/B toAtoms #1/C distance 5 maxPae 5 palette paegreen No alphafold specified for alphafold contacts > rename #1.2 ""BC contacts"" > alphafold contacts #1/A toAtoms #1/C distance 5 maxPae 5 palette paegreen No alphafold specified for alphafold contacts > rename #1.3 ""CD contacts"" > alphafold contacts #1/B toAtoms #1/D distance 5 maxPae 5 palette paegreen No alphafold specified for alphafold contacts > alphafold contacts #2/A toAtoms #2/D distance 5 maxPae 5 palette paegreen Structure fold_ak1b_2short_f6_2_model_0.cif #2 does not have PAE data opened > rename #2.1 ""AB contacts"" > alphafold contacts #2/B toAtoms #2/C distance 5 maxPae 5 palette paegreen Structure fold_ak1b_2short_f6_2_model_0.cif #2 does not have PAE data opened > rename #2.2 ""BC contacts"" > alphafold contacts #2/A toAtoms #2/C distance 5 maxPae 5 palette paegreen Structure fold_ak1b_2short_f6_2_model_0.cif #2 does not have PAE data opened > rename #2.3 ""CD contacts"" > alphafold contacts #2/B toAtoms #2/D distance 5 maxPae 5 palette paegreen Structure fold_ak1b_2short_f6_2_model_0.cif #2 does not have PAE data opened > alphafold contacts #3/A toAtoms #3/D distance 5 maxPae 5 palette paegreen Structure fold_ak1b_2short_f6_2_model_1.cif #3 does not have PAE data opened > rename #3.1 ""AB contacts"" > alphafold contacts #3/B toAtoms #3/C distance 5 maxPae 5 palette paegreen Structure fold_ak1b_2short_f6_2_model_1.cif #3 does not have PAE data opened > rename #3.2 ""BC contacts"" > alphafold contacts #3/A toAtoms #3/C distance 5 maxPae 5 palette paegreen Structure fold_ak1b_2short_f6_2_model_1.cif #3 does not have PAE data opened > rename #3.3 ""CD contacts"" > alphafold contacts #3/B toAtoms #3/D distance 5 maxPae 5 palette paegreen Structure fold_ak1b_2short_f6_2_model_1.cif #3 does not have PAE data opened > alphafold contacts #4/A toAtoms #4/D distance 5 maxPae 5 palette paegreen Structure fold_ak1b_2short_f6_2_model_2.cif #4 does not have PAE data opened > rename #4.1 ""AB contacts"" > alphafold contacts #4/B toAtoms #4/C distance 5 maxPae 5 palette paegreen Structure fold_ak1b_2short_f6_2_model_2.cif #4 does not have PAE data opened > rename #4.2 ""BC contacts"" > alphafold contacts #4/A toAtoms #4/C distance 5 maxPae 5 palette paegreen Structure fold_ak1b_2short_f6_2_model_2.cif #4 does not have PAE data opened > rename #4.3 ""CD contacts"" > alphafold contacts #4/B toAtoms #4/D distance 5 maxPae 5 palette paegreen Structure fold_ak1b_2short_f6_2_model_2.cif #4 does not have PAE data opened > alphafold contacts #5/A toAtoms #5/D distance 5 maxPae 5 palette paegreen Structure fold_ak1b_2short_f6_2_model_3.cif #5 does not have PAE data opened > rename #5.1 ""AB contacts"" > alphafold contacts #5/B toAtoms #5/C distance 5 maxPae 5 palette paegreen Structure fold_ak1b_2short_f6_2_model_3.cif #5 does not have PAE data opened > rename #5.2 ""BC contacts"" > alphafold contacts #5/A toAtoms #5/C distance 5 maxPae 5 palette paegreen Structure fold_ak1b_2short_f6_2_model_3.cif #5 does not have PAE data opened > rename #5.3 ""CD contacts"" > alphafold contacts #5/B toAtoms #5/D distance 5 maxPae 5 palette paegreen Structure fold_ak1b_2short_f6_2_model_3.cif #5 does not have PAE data opened > ui tool show ""AlphaFold Error Plot"" > alphafold pae #2 file ""/Users/usuario/Dropbox > (Personal)/alphafold_paper/fold_ak1b_2short_f6_2-2/fold_ak1b_2short_f6_2_full_data_0.json"" > ui tool show ""AlphaFold Error Plot"" > alphafold pae #2 file ""/Users/usuario/Dropbox > (Personal)/alphafold_paper/fold_ak1b_2short_f6_2-2/fold_ak1b_2short_f6_2_full_data_1.json"" > alphafold pae #2 file ""/Users/usuario/Dropbox > (Personal)/alphafold_paper/fold_ak1b_2short_f6_2-2/fold_ak1b_2short_f6_2_full_data_2.json"" > alphafold pae #2 file ""/Users/usuario/Dropbox > (Personal)/alphafold_paper/fold_ak1b_2short_f6_2-2/fold_ak1b_2short_f6_2_full_data_0.json"" > alphafold pae #3 file ""/Users/usuario/Dropbox > (Personal)/alphafold_paper/fold_ak1b_2short_f6_2-2/fold_ak1b_2short_f6_2_full_data_1.json"" > alphafold pae #3 file ""/Users/usuario/Dropbox > (Personal)/alphafold_paper/fold_ak1b_2short_f6_2-2/fold_ak1b_2short_f6_2_full_data_2.json"" > open ""/Users/usuario/Dropbox > (Personal)/alphafold_paper/fold_ak1b_2short_f6_2-2/fold_ak1b_2short_f6_2_full_data_1.json"" Failed opening file /Users/usuario/Dropbox (Personal)/alphafold_paper/fold_ak1b_2short_f6_2-2/fold_ak1b_2short_f6_2_full_data_1.json: Opening an AlphaFold PAE file requires specifying the structure to associate. Did not find an open structure from the same directory. To specify the structure use menu Tools / Structure Prediction / AlphaFold Error Plot or use the open command, for example open /Users/usuario/Dropbox (Personal)/alphafold_paper/fold_ak1b_2short_f6_2-2/fold_ak1b_2short_f6_2_full_data_1.json format pae structure #1 > open ""/Users/usuario/Dropbox > (Personal)/alphafold_paper/fold_ak1b_2short_f6_2-2/fold_ak1b_2short_f6_2_full_data_2.json"" Failed opening file /Users/usuario/Dropbox (Personal)/alphafold_paper/fold_ak1b_2short_f6_2-2/fold_ak1b_2short_f6_2_full_data_2.json: Opening an AlphaFold PAE file requires specifying the structure to associate. Did not find an open structure from the same directory. To specify the structure use menu Tools / Structure Prediction / AlphaFold Error Plot or use the open command, for example open /Users/usuario/Dropbox (Personal)/alphafold_paper/fold_ak1b_2short_f6_2-2/fold_ak1b_2short_f6_2_full_data_2.json format pae structure #1 > open ""/Users/usuario/Dropbox > (Personal)/alphafold_paper/fold_ak1b_2short_f6_2-2/fold_ak1b_2short_f6_2_full_data_3.json"" Failed opening file /Users/usuario/Dropbox (Personal)/alphafold_paper/fold_ak1b_2short_f6_2-2/fold_ak1b_2short_f6_2_full_data_3.json: Opening an AlphaFold PAE file requires specifying the structure to associate. Did not find an open structure from the same directory. To specify the structure use menu Tools / Structure Prediction / AlphaFold Error Plot or use the open command, for example open /Users/usuario/Dropbox (Personal)/alphafold_paper/fold_ak1b_2short_f6_2-2/fold_ak1b_2short_f6_2_full_data_3.json format pae structure #1 > open ""/Users/usuario/Dropbox > (Personal)/alphafold_paper/fold_ak1b_2short_f6_2-2/fold_ak1b_2short_f6_2_full_data_4.json"" Failed opening file /Users/usuario/Dropbox (Personal)/alphafold_paper/fold_ak1b_2short_f6_2-2/fold_ak1b_2short_f6_2_full_data_4.json: Opening an AlphaFold PAE file requires specifying the structure to associate. Did not find an open structure from the same directory. To specify the structure use menu Tools / Structure Prediction / AlphaFold Error Plot or use the open command, for example open /Users/usuario/Dropbox (Personal)/alphafold_paper/fold_ak1b_2short_f6_2-2/fold_ak1b_2short_f6_2_full_data_4.json format pae structure #1 > open ""/Users/usuario/Dropbox > (Personal)/alphafold_paper/fold_ak1b_2short_f6_2-2/fold_ak1b_2short_f6_2_full_data_0.json"" Failed opening file /Users/usuario/Dropbox (Personal)/alphafold_paper/fold_ak1b_2short_f6_2-2/fold_ak1b_2short_f6_2_full_data_0.json: Opening an AlphaFold PAE file requires specifying the structure to associate. Did not find an open structure from the same directory. To specify the structure use menu Tools / Structure Prediction / AlphaFold Error Plot or use the open command, for example open /Users/usuario/Dropbox (Personal)/alphafold_paper/fold_ak1b_2short_f6_2-2/fold_ak1b_2short_f6_2_full_data_0.json format pae structure #1 > alphafold pae #3 file ""/Users/usuario/Dropbox > (Personal)/alphafold_paper/fold_ak1b_2short_f6_2-2/fold_ak1b_2short_f6_2_full_data_1.json"" > alphafold pae #4 file ""/Users/usuario/Dropbox > (Personal)/alphafold_paper/fold_ak1b_2short_f6_2-2/fold_ak1b_2short_f6_2_full_data_2.json"" > alphafold pae #5 file ""/Users/usuario/Dropbox > (Personal)/alphafold_paper/fold_ak1b_2short_f6_2-2/fold_ak1b_2short_f6_2_full_data_3.json"" > alphafold pae #6 file ""/Users/usuario/Dropbox > (Personal)/alphafold_paper/fold_ak1b_2short_f6_2-2/fold_ak1b_2short_f6_2_full_data_4.json"" > close #1 > ui mousemode right translate > alphafold contacts #2/A toAtoms #2/D distance 5 maxPae 5 palette paegreen Found 56 residue or atom pairs within distance 5 with pae <= 5 > rename #2.1 ""AB contacts"" > alphafold contacts #2/B toAtoms #2/C distance 5 maxPae 5 palette paegreen Found 57 residue or atom pairs within distance 5 with pae <= 5 > rename #2.2 ""BC contacts"" > alphafold contacts #2/A toAtoms #2/C distance 5 maxPae 5 palette paegreen Found 50 residue or atom pairs within distance 5 with pae <= 5 > rename #2.3 ""CD contacts"" > alphafold contacts #2/B toAtoms #2/D distance 5 maxPae 5 palette paegreen Found 49 residue or atom pairs within distance 5 with pae <= 5 > alphafold contacts #3/A toAtoms #3/D distance 5 maxPae 5 palette paegreen Found 55 residue or atom pairs within distance 5 with pae <= 5 > rename #3.1 ""AB contacts"" > alphafold contacts #3/B toAtoms #3/C distance 5 maxPae 5 palette paegreen Found 55 residue or atom pairs within distance 5 with pae <= 5 > rename #3.2 ""BC contacts"" > alphafold contacts #3/A toAtoms #3/C distance 5 maxPae 5 palette paegreen Found 49 residue or atom pairs within distance 5 with pae <= 5 > rename #3.3 ""CD contacts"" > alphafold contacts #3/B toAtoms #3/D distance 5 maxPae 5 palette paegreen Found 49 residue or atom pairs within distance 5 with pae <= 5 > alphafold contacts #4/A toAtoms #4/D distance 5 maxPae 5 palette paegreen Found 52 residue or atom pairs within distance 5 with pae <= 5 > rename #4.1 ""AB contacts"" > alphafold contacts #4/B toAtoms #4/C distance 5 maxPae 5 palette paegreen Found 55 residue or atom pairs within distance 5 with pae <= 5 > rename #4.2 ""BC contacts"" > alphafold contacts #4/A toAtoms #4/C distance 5 maxPae 5 palette paegreen Found 48 residue or atom pairs within distance 5 with pae <= 5 > rename #4.3 ""CD contacts"" > alphafold contacts #4/B toAtoms #4/D distance 5 maxPae 5 palette paegreen Found 47 residue or atom pairs within distance 5 with pae <= 5 > alphafold contacts #5/A toAtoms #5/D distance 5 maxPae 5 palette paegreen Found 51 residue or atom pairs within distance 5 with pae <= 5 > rename #5.1 ""AB contacts"" > alphafold contacts #5/B toAtoms #5/C distance 5 maxPae 5 palette paegreen Found 54 residue or atom pairs within distance 5 with pae <= 5 > rename #5.2 ""BC contacts"" > alphafold contacts #5/A toAtoms #5/C distance 5 maxPae 5 palette paegreen Found 50 residue or atom pairs within distance 5 with pae <= 5 > rename #5.3 ""CD contacts"" > alphafold contacts #5/B toAtoms #5/D distance 5 maxPae 5 palette paegreen Found 49 residue or atom pairs within distance 5 with pae <= 5 > alphafold contacts #6/A toAtoms #6/D distance 5 maxPae 5 palette paegreen Found 53 residue or atom pairs within distance 5 with pae <= 5 > rename #5.1 ""AB contacts"" > alphafold contacts #6/B toAtoms #6/C distance 5 maxPae 5 palette paegreen Found 55 residue or atom pairs within distance 5 with pae <= 5 > rename #5.2 ""BC contacts"" > alphafold contacts #6/A toAtoms #6/C distance 5 maxPae 5 palette paegreen Found 48 residue or atom pairs within distance 5 with pae <= 5 > rename #5.3 ""CD contacts"" > alphafold contacts #6/B toAtoms #6/D distance 5 maxPae 5 palette paegreen Found 48 residue or atom pairs within distance 5 with pae <= 5 > select #2/A-B:1 #3/A-B:1 #4/A-B:1 #5/A-B:1 #6/A-B:1 80 atoms, 70 bonds, 10 residues, 5 models selected > select #2/A-B #3/A-B #4/A-B #5/A-B #6/A-B 9800 atoms, 9860 bonds, 1200 residues, 5 models selected . [ID: 1] region 10 chains [1-120] RMSD: 1.517 > ui tool show ""Color Actions"" > color sel misty rose > color sel plum > color sel light salmon > color sel plum > color sel violet > select #2/C-D:1 #3/C-D:1 #4/C-D:1 #5/C-D:1 #6/C-D:1 90 atoms, 80 bonds, 10 residues, 5 models selected > select #2/C-D #3/C-D #4/C-D #5/C-D #6/C-D 9670 atoms, 9900 bonds, 1280 residues, 5 models selected . [ID: 2] region 10 chains [1-128] RMSD: 12.546 > transparency sel 0 target ac > save /Users/usuario/Desktop/fold_paper/ak1b_2_f6_2_paegreen5.cxs ——— End of log from Sat Jul 26 18:22:59 2025 ——— > view name session-start opened ChimeraX session OpenGL version: 4.1 Metal - 76.1 OpenGL renderer: Apple M1 OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.8.0, Qt 6.8.1 Qt runtime version: 6.8.1 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro17,1 Chip: Apple M1 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 16 GB System Firmware Version: 7429.41.5 OS Loader Version: 7429.41.5 Software: System Software Overview: System Version: macOS 12.0.1 (21A559) Kernel Version: Darwin 21.1.0 Time since boot: 5 days 21:16 Graphics/Displays: Apple M1: Chipset Model: Apple M1 Type: GPU Bus: Built-In Total Number of Cores: 8 Vendor: Apple (0x106b) Metal Family: Supported, Metal GPUFamily Apple 7 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal VA2715-QHD: Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition) UI Looks like: 2560 x 1440 @ 60.00Hz Mirror: Off Online: Yes Rotation: Supported Automatically Adjust Brightness: Yes Installed Packages: alabaster: 1.0.0 anyio: 4.8.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 auditwheel: 6.2.0 babel: 2.16.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 3.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.1 ChimeraX-AddCharge: 1.5.18 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.16.2 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.60 ChimeraX-AtomicLibrary: 14.1.11 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.2 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.4.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.3 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.8 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.10.dev202501170719 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.4 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.7 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.4.1 ChimeraX-Hbonds: 2.5 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.3 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.5.1 ChimeraX-Label: 1.1.14 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.3 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.6 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.2 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.18 ChimeraX-ModelPanel: 1.5 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-MutationScores: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.14 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.7 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.2 ChimeraX-ProfileGrids: 1.0.1 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.3 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.3 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.7 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.15 ChimeraX-Shape: 1.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.0 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.19.1 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.43 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.4 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.3.1 coverage: 7.6.10 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.12 decorator: 5.1.1 docutils: 0.21.2 executing: 2.1.0 filelock: 3.15.4 fonttools: 4.55.3 funcparserlib: 2.0.0a0 glfw: 2.8.0 grako: 3.16.5 h11: 0.14.0 h5py: 3.12.1 html2text: 2024.2.26 httpcore: 1.0.7 httpx: 0.28.1 idna: 3.10 ihm: 1.3 imagecodecs: 2024.6.1 imagesize: 1.4.1 iniconfig: 2.0.0 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.5 jedi: 0.19.1 Jinja2: 3.1.5 jupyter_client: 8.6.2 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.13 kiwisolver: 1.4.8 line_profiler: 4.1.3 lxml: 5.2.2 lz4: 4.3.3 MarkupSafe: 3.0.2 matplotlib: 3.9.2 matplotlib-inline: 0.1.7 msgpack: 1.0.8 ndindex: 1.9.2 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.2 numpy: 1.26.4 OpenMM: 8.2.0 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 10.4.0 pip: 24.2 pkginfo: 1.11.1 platformdirs: 4.3.6 pluggy: 1.5.0 prompt_toolkit: 3.0.48 psutil: 6.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.31 Pygments: 2.18.0 pynmrstar: 3.3.5 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.2.1 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.8.0 PyQt6-Qt6: 6.8.1 PyQt6-WebEngine-commercial: 6.8.0 PyQt6-WebEngine-Qt6: 6.8.1 PyQt6_sip: 13.9.1 pytest: 8.3.4 pytest-cov: 6.0.0 python-dateutil: 2.9.0.post0 pytz: 2024.2 pyzmq: 26.2.0 qtconsole: 5.5.2 QtPy: 2.4.2 qtshim: 1.1 RandomWords: 0.4.0 requests: 2.32.3 scipy: 1.14.0 setuptools: 72.1.0 sfftk-rw: 0.8.1 six: 1.16.0 sniffio: 1.3.1 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.6 Sphinx: 8.0.2 sphinx-autodoc-typehints: 2.2.3 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.10.2 tcia_utils: 1.5.1 tifffile: 2024.7.24 tinyarray: 1.2.4 tornado: 6.4.2 traitlets: 5.14.3 typing_extensions: 4.12.2 tzdata: 2024.2 urllib3: 2.3.0 wcwidth: 0.2.13 webcolors: 24.6.0 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.13 }}} " defect closed normal Window Toolkit can't reproduce all ChimeraX