id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 6250 Crash in event loop chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Thread 0x00000003233f1000 (most recent call first): File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 576 in _handle_results File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x00000003223ee000 (most recent call first): File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 528 in _handle_tasks File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x00000003213eb000 (most recent call first): File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/selectors.py"", line 416 in select File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/connection.py"", line 936 in wait File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 499 in _wait_for_updates File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 519 in _handle_workers File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x00000003203e8000 (most recent call first): File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x000000031f3e5000 (most recent call first): File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x000000031e3e2000 (most recent call first): File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x000000031d3df000 (most recent call first): File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x000000031c3dc000 (most recent call first): File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x000000031b3d9000 (most recent call first): File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x000000031a3d6000 (most recent call first): File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x00000003193d3000 (most recent call first): File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Current thread 0x0000000205032e00 (most recent call first): File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py"", line 301 in event_loop File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py"", line 867 in init File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py"", line 1018 in File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py"", line 87 in _run_code File ""/Applications/ChimeraX-1.3.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"":""2022-02-25 13:04:03.00 -0800"",""app_version"":""1.3.0"",""slice_uuid"":""9596eff5-d2be-396c-9c4e-6177235c3dae"",""build_version"":""1.3.0.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":0,""is_first_party"":1,""bug_type"":""309"",""os_version"":""macOS 11.2.3 (20D91)"",""incident_id"":""82A6AF57-EA04-4250-B060-56098D99D063"",""name"":""ChimeraX""} { ""uptime"" : 52000, ""procLaunch"" : ""2022-02-25 12:49:54.2402 -0800"", ""procRole"" : ""Foreground"", ""exception"" : { ""type"" : ""EXC_BAD_ACCESS"", ""signal"" : ""SIGSEGV"", ""subtype"" : ""KERN_INVALID_ADDRESS at 0x0000000000000030"" }, ""userID"" : 502, ""modelCode"" : ""MacBookPro17,1"", ""coalitionID"" : 518, ""osVersion"" : { ""train"" : ""macOS 11.2.3"", ""build"" : ""20D91"", ""releaseType"" : """" }, ""captureTime"" : ""2022-02-25 13:03:56.6667 -0800"", ""incident"" : ""82A6AF57-EA04-4250-B060-56098D99D063"", ""pid"" : 5309, ""cpuType"" : ""ARM-64"", ""procName"" : ""ChimeraX"", ""procPath"" : ""\/Applications\/ChimeraX-1.3.app\/Contents\/MacOS\/ChimeraX"", ""bundleInfo"" : {""CFBundleShortVersionString"":""1.3.0"",""CFBundleVersion"":""1.3.0.0"",""CFBundleIdentifier"":""edu.ucsf.cgl.ChimeraX""}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""79245A4C-6733-338F-122B-EFE16B87EDCA"", ""wakeTime"" : 10921, ""sleepWakeUUID"" : ""C2629EAE-5471-4E15-ADBA-88F700904C37"", ""sip"" : ""enabled"", ""vmregioninfo"" : ""0x30 is not in any region. Bytes before following region: 4377808848\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 104f01000-104f02000 [ 4K] r-x\/r-x SM=COW ...acOS\/ChimeraX"", ""is_corpse"" : 1, ""extMods"" : {""caller"":{""thread_create"":0,""thread_set_state"":0,""task_for_pid"":0},""system"":{""thread_create"":0,""thread_set_state"":0,""task_for_pid"":45876},""targeted"":{""thread_create"":0,""thread_set_state"":0,""task_for_pid"":2},""warnings"":0}, ""threads"" : [{""triggered"":true,""id"":548930,""name"":""CrBrowserMain"",""queue"":""com.apple.main-thread"",""frames"":[[0,140731418618552],[1,29794],[2,64419],[3,15741],[0,0],[4,126171],[4,125894],[4,1460436]]},{""id"":549111,""name"":""ThreadPoolServiceThread"",""frames"":[[0,140731418618552],[1,40414],[5,45272263],[5,44783147],[5,44537803],[5,44829332],[5,44911229],[5,45211143],[6,26960],[6,9339]]},{""id"":549113,""name"":""ThreadPoolBackgroundWorker"",""frames"":[[0,140731418618552],[1,3710],[5,45229202],[5,44869496],[5,44872016],[5,44870724],[5,45211143],[6,26960],[6,9339]]},{""id"":549114,""name"":""Chrome_IOThread"",""frames"":[[0,140731418618552],[1,40414],[5,45272263],[5,44783147],[5,44537803],[5,111124230],[5,44911229],[5,45211143],[6,26960],[6,9339]]},{""id"":549115,""name"":""NetworkConfigWatcher"",""frames"":[[0,140731418618552],[1,3710],[5,45229202],[5,45228751],[5,44343771],[5,44783147],[5,44537803],[5,44911229],[5,45211143],[6,26960],[6,9339]]},{""id"":549119,""name"":""CompositorTileWorker1"",""frames"":[[0,140731418618552],[1,14562],[5,45194776],[5,64820728],[5,45211143],[6,26960],[6,9339]]},{""id"":549120,""name"":""Chrome_InProcGpuThread"",""frames"":[[0,140731418618552],[1,3710],[5,45229202],[5,44343823],[5,44783147],[5,44537803],[5,44911229],[5,45211143],[6,26960],[6,9339]]},{""id"":549121,""name"":""Chrome_ChildIOThread"",""frames"":[[0,140731418618552],[1,40414],[5,45272263],[5,44783147],[5,44537803],[5,44911229],[5,45211143],[6,26960],[6,9339]]},{""id"":549122,""name"":""NetworkConfigWatcher"",""frames"":[[0,140731418618552],[1,3710],[5,45229202],[5,45228751],[5,44343771],[5,44783147],[5,44537803],[5,44911229],[5,45211143],[6,26960],[6,9339]]},{""id"":549123,""name"":""VizCompositorThread"",""frames"":[[0,140731418618552],[1,3710],[5,45229202],[5,45228751],[5,44343771],[5,44783147],[5,44537803],[5,44911229],[5,45211143],[6,26960],[6,9339]]},{""id"":549145,""name"":""NetworkConfigWatcher"",""frames"":[[0,140731418618552],[1,3710],[5,45229202],[5,45228751],[5,44343771],[5,44783147],[5,44537803],[5,44911229],[5,45211143],[6,26960],[6,9339]]},{""id"":549146,""name"":""ThreadPoolSingleThreadForegroundBlocking0"",""frames"":[[0,140731418618552],[1,3710],[5,45229202],[5,45228751],[5,44869482],[5,44872016],[5,44870964],[5,45211143],[6,26960],[6,9339]]},{""id"":549205,""name"":""MemoryInfra"",""frames"":[[0,140731418618552],[1,3710],[5,45229202],[5,45228751],[5,44343771],[5,44783147],[5,44537803],[5,44911229],[5,45211143],[6,26960],[6,9339]]},{""id"":549234,""name"":""NetworkConfigWatcher"",""frames"":[[0,140731418618552],[1,3710],[5,45229202],[5,45228751],[5,44343771],[5,44783147],[5,44537803],[5,44911229],[5,45211143],[6,26960],[6,9339]]},{""id"":549261,""name"":""com.apple.rosetta.exceptionserver"",""frames"":[[7,8760],[7,50004],[7,53752]]},{""id"":549265,""frames"":[[0,140731418618552],[1,14562],[8,1485942],[9,5502],[9,4390],[8,502068],[8,1131916],[8,1121099],[8,1135235],[8,248017],[8,1122755],[8,248136],[8,1131916],[8,1120914],[8,248136],[8,1131916],[8,1120914],[8,248136],[8,256466],[8,1807302],[8,1485001],[6,26960],[6,9339]]},{""id"":549266,""frames"":[[0,140731418618552],[1,14562],[8,1485942],[9,5502],[9,4390],[8,502068],[8,1131916],[8,1121099],[8,1135235],[8,248017],[8,1122755],[8,248136],[8,1131916],[8,1120914],[8,248136],[8,1131916],[8,1120914],[8,248136],[8,256466],[8,1807302],[8,1485001],[6,26960],[6,9339]]},{""id"":549267,""frames"":[[0,140731418618552],[1,14562],[8,1485942],[9,5502],[9,4390],[8,502068],[8,1131916],[8,1121099],[8,1135235],[8,248017],[8,1122755],[8,248136],[8,1131916],[8,1120914],[8,248136],[8,1131916],[8,1120914],[8,248136],[8,256466],[8,1807302],[8,1485001],[6,26960],[6,9339]]},{""id"":549268,""frames"":[[0,140731418618552],[1,14562],[8,1485942],[9,5502],[9,4390],[8,502068],[8,1131916],[8,1121099],[8,1135235],[8,248017],[8,1122755],[8,248136],[8,1131916],[8,1120914],[8,248136],[8,1131916],[8,1120914],[8,248136],[8,256466],[8,1807302],[8,1485001],[6,26960],[6,9339]]},{""id"":549269,""frames"":[[0,140731418618552],[1,14562],[8,1485942],[9,5502],[9,4390],[8,502068],[8,1131916],[8,1121099],[8,1135235],[8,248017],[8,1122755],[8,248136],[8,1131916],[8,1120914],[8,248136],[8,1131916],[8,1120914],[8,248136],[8,256466],[8,1807302],[8,1485001],[6,26960],[6,9339]]},{""id"":549270,""frames"":[[0,140731418618552],[1,14562],[8,1485942],[9,5502],[9,4390],[8,502068],[8,1131916],[8,1121099],[8,1135235],[8,248017],[8,1122755],[8,248136],[8,1131916],[8,1120914],[8,248136],[8,1131916],[8,1120914],[8,248136],[8,256466],[8,1807302],[8,1485001],[6,26960],[6,9339]]},{""id"":549271,""frames"":[[0,140731418618552],[1,14562],[8,1485942],[9,5502],[9,4390],[8,502068],[8,1131916],[8,1121099],[8,1135235],[8,248017],[8,1122755],[8,248136],[8,1131916],[8,1120914],[8,248136],[8,1131916],[8,1120914],[8,248136],[8,256466],[8,1807302],[8,1485001],[6,26960],[6,9339]]},{""id"":549272,""frames"":[[0,140731418618552],[1,14562],[8,1485942],[9,5502],[9,4390],[8,502068],[8,1131916],[8,1121099],[8,1135235],[8,248017],[8,1122755],[8,248136],[8,1131916],[8,1120914],[8,248136],[8,1131916],[8,1120914],[8,248136],[8,256466],[8,1807302],[8,1485001],[6,26960],[6,9339]]},{""id"":549273,""frames"":[[0,140731418618552],[1,29950],[8,282735],[8,1131916],[8,1120914],[8,1135235],[8,248017],[8,1131916],[8,1120914],[8,1135235],[8,248017],[8,1131916],[8,1121249],[8,1135235],[8,248017],[8,1131916],[8,1120947],[8,248136],[8,256633],[8,1122755],[8,248136],[8,1131916],[8,1120914],[8,248136],[8,1131916],[8,1120914],[8,248136],[8,256466],[8,1807302],[8,1485001],[6,26960],[6,9339]]},{""id"":549274,""frames"":[[0,140731418618552],[1,14562],[8,1485942],[9,5502],[9,4390],[8,502068],[8,363450],[8,1119227],[8,248136],[8,1122755],[8,248136],[8,1131916],[8,1120914],[8,248136],[8,1131916],[8,1120914],[8,248136],[8,256466],[8,1807302],[8,1485001],[6,26960],[6,9339]]},{""id"":549276,""frames"":[[0,140731418618552],[1,14562],[8,1485942],[9,5502],[9,4390],[8,502068],[8,1131916],[8,1121099],[8,248136],[8,1122755],[8,248136],[8,1131916],[8,1120914],[8,248136],[8,1131916],[8,1120914],[8,248136],[8,256466],[8,1807302],[8,1485001],[6,26960],[6,9339]]},{""id"":549416,""name"":""com.apple.NSEventThread"",""frames"":[[0,140731418618552],[1,3710],[10,529677],[10,523254],[10,520162],[11,1853382],[6,26960],[6,9339]]},{""id"":549417,""name"":""ThreadPoolSingleThreadSharedBackgroundBlocking1"",""frames"":[[0,140731418618552],[1,3710],[5,45229202],[5,45228751],[5,44869482],[5,44871229],[5,44870772],[5,45211143],[6,26960],[6,9339]]},{""id"":549613,""frames"":[[0,140731418618552],[1,14562],[12,3377823],[6,26960],[6,9339]]},{""id"":549614,""frames"":[[0,140731418618552],[1,14562],[12,3377823],[6,26960],[6,9339]]},{""id"":549615,""frames"":[[0,140731418618552],[1,14562],[12,3377823],[6,26960],[6,9339]]},{""id"":549616,""frames"":[[0,140731418618552],[1,14562],[12,3377823],[6,26960],[6,9339]]},{""id"":549617,""frames"":[[0,140731418618552],[1,14562],[12,3377823],[6,26960],[6,9339]]},{""id"":549618,""frames"":[[0,140731418618552],[1,14562],[12,3377823],[6,26960],[6,9339]]},{""id"":549619,""frames"":[[0,140731418618552],[1,14562],[12,3377823],[6,26960],[6,9339]]},{""id"":552398,""frames"":[[7,371100]]},{""id"":552475,""name"":""ThreadPoolForegroundWorker"",""frames"":[[0,140731418618552],[1,3710],[5,45229202],[5,44869496],[5,44872016],[5,44870868],[5,45211143],[6,26960],[6,9339]]},{""id"":553768,""frames"":[[7,371100]]},{""id"":554189,""frames"":[[7,371100]]},{""id"":554265,""frames"":[[7,371100]]},{""id"":554444,""frames"":[[7,371100]]},{""id"":555007,""frames"":[[7,371100]]},{""id"":558574,""frames"":[[7,371100]]},{""id"":559276,""frames"":[[7,371100]]},{""id"":559537,""frames"":[[7,371100]]},{""id"":559538,""frames"":[[7,371100]]},{""id"":559944,""frames"":[[7,371100]]},{""id"":559945,""frames"":[[7,371100]]}], ""threadState"" : { ""x"" : [ 0, 0, 0, 8674029056, 4523012232, 6185681780258298123, 4523012232, 6185681780258298123, 11, 6185681780258298123, 8674029056, 140733732621193, 515, 0, 11, 22, 328, 0, 9223372041366928272, 6031286272, 131071, 4512173456, 18446744073709551615, 140731418618508, 140733733602392, 18446603339975949224, 0, 0, 140733733602402 ], ""flavor"" : ""ARM_THREAD_STATE64"", ""lr"" : 140731422263120, ""cpsr"" : 2147483648, ""fp"" : 1677721600, ""sp"" : 4512152464, ""esr"" : 1442840704, ""esr_description"" : "" Address size fault"", ""pc"" : 140731418618552 }, ""usedImages"" : [ [ ""00000000-0000-0000-0000-000000000000"", 0, ""A"" ], [ ""ab413518-ecde-3f04-a61c-278d3cf43076"", 140733733572608, ""P"" ], [ ""4af71812-4099-3e96-b271-1f259491a2b2"", 140733732556800, ""P"" ], [ ""1c3e1a0a-92a8-3cde-b622-8940b43a5df2"", 140733734055936, ""P"" ], [ ""04d8759b-1119-3e37-b922-32bdecb7c5d2"", 140733845823488, ""P"" ], [ ""86651daf-3bff-3a6f-b313-e84d303e55eb"", 5034074112, ""P"" ], [ ""b989df6c-adfe-3af9-9c91-07d2521f9e47"", 140733733765120, ""P"" ], [ ""c98e75a6-bdc8-3d5c-b95b-6422005e96d8"", 140728896413696, ""P"" ], [ ""7fdc4a6b-e70b-3c9e-a72e-cd15ddf0d90f"", 4514938880, ""P"" ], [ ""d6125191-ebf8-3e9e-aa83-52e897d6ea11"", 6058250240, ""P"" ], [ ""46680730-f553-3297-b602-7a4372447f83"", 140733734277120, ""P"" ], [ ""ea4b3536-a5af-3e5d-a8e3-a3f795f34f05"", 140733775785984, ""P"" ], [ ""9112000d-375c-34f0-9a66-9d68f91a12cd"", 4536655872, ""P"" ] ], ""legacyInfo"" : { ""imageExtraInfo"" : [ { ""size"" : 0 }, { ""size"" : 192512, ""arch"" : ""x86_64"", ""path"" : ""\/usr\/lib\/system\/libsystem_kernel.dylib"", ""name"" : ""libsystem_kernel.dylib"" }, { ""size"" : 561152, ""arch"" : ""x86_64"", ""path"" : ""\/usr\/lib\/system\/libsystem_c.dylib"", ""name"" : ""libsystem_c.dylib"" }, { ""size"" : 40960, ""arch"" : ""x86_64"", ""path"" : ""\/usr\/lib\/system\/libsystem_platform.dylib"", ""name"" : ""libsystem_platform.dylib"" }, { ""size"" : 2928640, ""arch"" : ""x86_64"", ""path"" : ""\/System\/Library\/Frameworks\/QuartzCore.framework\/Versions\/A\/QuartzCore"", ""name"" : ""QuartzCore"" }, { ""size"" : 131002368, ""arch"" : ""x86_64"", ""path"" : ""\/Applications\/ChimeraX-1.3.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt5\/Qt\/lib\/QtWebEngineCore.framework\/Versions\/5\/QtWebEngineCore"", ""name"" : ""QtWebEngineCore"" }, { ""size"" : 49152, ""arch"" : ""x86_64"", ""path"" : ""\/usr\/lib\/system\/libsystem_pthread.dylib"", ""name"" : ""libsystem_pthread.dylib"" }, { ""size"" : 475136, ""arch"" : ""arm64e"", ""path"" : ""\/Library\/Apple\/*\/runtime"", ""name"" : ""runtime"" }, { ""size"" : 2510848, ""arch"" : ""x86_64"", ""path"" : ""\/Applications\/ChimeraX-1.3.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/Python"", ""name"" : ""Python"" }, { ""size"" : 8192, ""arch"" : ""x86_64"", ""path"" : ""\/Applications\/ChimeraX-1.3.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/lib-dynload\/_queue.cpython-39-darwin.so"", ""name"" : ""_queue.cpython-39-darwin.so"" }, { ""size"" : 4833280, ""arch"" : ""x86_64"", ""path"" : ""\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation"", ""name"" : ""CoreFoundation"" }, { ""size"" : 14036992, ""arch"" : ""x86_64"", ""path"" : ""\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit"", ""name"" : ""AppKit"" }, { ""size"" : 62603264, ""arch"" : ""x86_64"", ""path"" : ""\/Applications\/ChimeraX-1.3.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/numpy\/.dylibs\/libopenblas.0.dylib"", ""name"" : ""libopenblas.0.dylib"" } ], ""threadTriggered"" : { ""index"" : 0, ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } } } ===== Log before crash start ===== UCSF ChimeraX version: 1.3 (2021-12-08) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/joanneboysen/Documents/SeniorBioEn/FinalProject/ighr_substratecolor.pdb > format pdb ighr_substratecolor.pdb title: The three-dimensional structures of two plant β-glucan endohydrolases with distinct substrate specificities [more info...] Chain information for ighr_substratecolor.pdb #1 --- Chain | Description | UniProt A | 1,3-1,4-β-glucanase | GUB2_HORVU > preset ""overall look"" publication Preset expands to these ChimeraX commands: set bg white graphics silhouettes t > select :232, 288 20 atoms, 18 bonds, 2 residues, 1 model selected > color sel red > select :33, 170, 92, 93, 168,170, 173, 291,275, 33, 283, 280, 34, 129, 135, > 210 159 atoms, 153 bonds, 14 residues, 1 model selected > select :33, 170, 92, 93, 168,170, 173, 291,275, 33, 283, 280, 34, 129, 135, > 210 159 atoms, 153 bonds, 14 residues, 1 model selected > color sel red > select :239 5 atoms, 4 bonds, 1 residue, 1 model selected > ui tool show Rotamers > swapaa interactive sel CYS rotLib Dynameomics /A GLY 239: phi 106.4, psi -0.1 trans Changed 9 bond radii > clashes #!1 & ~#1/A:239 & ~solvent radius 0.075 reveal true restrict #1.1 & > ~@c,ca,n 32 clashes > select :286 5 atoms, 4 bonds, 1 residue, 1 model selected > ui tool show Rotamers > swapaa interactive sel CYS rotLib Dynameomics /A GLY 286: phi 127.0, psi -147.6 trans Changed 9 bond radii > clashes #!1 & ~#1/A:286 & ~solvent radius 0.075 reveal true restrict #1.1 & > ~@c,ca,n 13 clashes No rotamers selected > swapaa #1/A:286 CYS criteria 2 rotLib Dynameomics Using Dynameomics library ighr_substratecolor.pdb #1/A GLY 286: phi 127.0, psi -147.6 trans Applying CYS rotamer (chi angles: -176.5) to ighr_substratecolor.pdb #1/A CYS 286 > select :240 5 atoms, 4 bonds, 1 residue, 1 model selected > ui tool show Rotamers > swapaa interactive sel CYS rotLib Dynameomics /A GLY 240: phi -173.9, psi 174.4 trans Changed 9 bond radii > clashes #!1 & ~#1/A:240 & ~solvent radius 0.075 reveal true restrict #1.1 & > ~@c,ca,n 5 clashes > swapaa #1/A:240 CYS criteria 1 rotLib Dynameomics Using Dynameomics library ighr_substratecolor.pdb #1/A GLY 240: phi -173.9, psi 174.4 trans Applying CYS rotamer (chi angles: -61.0) to ighr_substratecolor.pdb #1/A CYS 240 > show sel atoms > hide sel atoms > show sel atoms > save /Users/joanneboysen/Desktop/1ghr_mutA.pdb relModel #1 > ~select Nothing selected > show atoms > select :281 11 atoms, 10 bonds, 1 residue, 1 model selected > ui tool show Rotamers > swapaa interactive sel ASP rotLib Dynameomics /A ASN 281: phi -80.7, psi -3.8 trans Changed 45 bond radii > hbonds #!1 & ~#1/A:281 & ~solvent saltOnly true reveal true restrict #1.1 & > ~@c,ca,n 0 hydrogen bonds found > clashes #!1 & ~#1/A:281 & ~solvent radius 0.075 reveal true restrict #1.1 & > ~@c,ca,n No clashes > swapaa #1/A:281 ASP criteria 5 rotLib Dynameomics Using Dynameomics library ighr_substratecolor.pdb #1/A ASN 281: phi -80.7, psi -3.8 trans Applying ASP rotamer (chi angles: 74.7 109.8) to ighr_substratecolor.pdb #1/A ASP 281 > select :10 11 atoms, 10 bonds, 1 residue, 1 model selected > ui tool show Rotamers ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.3 (2021-12-08) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 71.0.7 OpenGL renderer: Apple M1 OpenGL vendor: AppleHardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro17,1 Processor Name: Unknown Processor Speed: 2.4 GHz Number of Processors: 1 Total Number of Cores: 8 L2 Cache (per Core): 4 MB Memory: 16 GB Software: System Software Overview: System Version: macOS 11.2.3 (20D91) Kernel Version: Darwin 20.3.0 Time since boot: 1 day 2:52 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 Locale: (None, 'UTF-8') PyQt5 5.15.2, Qt 5.15.2 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.2 Babel: 2.9.1 backcall: 0.2.0 blockdiag: 2.0.1 certifi: 2021.5.30 cftime: 1.5.1.1 charset-normalizer: 2.0.9 ChimeraX-AddCharge: 1.2.2 ChimeraX-AddH: 2.1.11 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.2.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.31 ChimeraX-AtomicLibrary: 4.2 ChimeraX-AtomSearch: 2.0 ChimeraX-AtomSearchLibrary: 1.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.0 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.6.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.2 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.2 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5 ChimeraX-CommandLine: 1.1.5 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.3 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1.5 ChimeraX-DistUI: 1.0 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0 ChimeraX-FunctionKey: 1.0 ChimeraX-Geometry: 1.1 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1 ChimeraX-Hbonds: 2.1.2 ChimeraX-Help: 1.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0 ChimeraX-Label: 1.1 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.4 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.1 ChimeraX-Map: 1.1 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 2.0.4 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.4 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.2.6 ChimeraX-ModelPanel: 1.2.1 ChimeraX-ModelSeries: 1.0 ChimeraX-Mol2: 2.0 ChimeraX-Morph: 1.0 ChimeraX-MouseModes: 1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.2 ChimeraX-OpenCommand: 1.7 ChimeraX-PDB: 2.6.5 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 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 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.4.6 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.1 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.6.1 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-Struts: 1.0 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1 ChimeraX-ToolshedUtils: 1.2 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.13.7 ChimeraX-uniprot: 2.2 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.0.1 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0 ChimeraX-WebServices: 1.0 ChimeraX-Zone: 1.0 colorama: 0.4.4 cxservices: 1.1 cycler: 0.11.0 Cython: 0.29.24 decorator: 5.1.0 docutils: 0.17.1 filelock: 3.0.12 funcparserlib: 0.3.6 grako: 3.16.5 h5py: 3.6.0 html2text: 2020.1.16 idna: 3.3 ihm: 0.21 imagecodecs: 2021.4.28 imagesize: 1.3.0 ipykernel: 5.5.5 ipython: 7.23.1 ipython-genutils: 0.2.0 jedi: 0.18.0 Jinja2: 3.0.1 jupyter-client: 6.1.12 jupyter-core: 4.9.1 kiwisolver: 1.3.2 lxml: 4.6.3 lz4: 3.1.3 MarkupSafe: 2.0.1 matplotlib: 3.4.3 matplotlib-inline: 0.1.3 msgpack: 1.0.2 netCDF4: 1.5.7 networkx: 2.6.3 numexpr: 2.8.0 numpy: 1.21.2 openvr: 1.16.801 packaging: 21.0 ParmEd: 3.2.0 parso: 0.8.3 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 8.3.2 pip: 21.2.4 pkginfo: 1.7.1 prompt-toolkit: 3.0.23 psutil: 5.8.0 ptyprocess: 0.7.0 pycollada: 0.7.1 pydicom: 2.1.2 Pygments: 2.10.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.6 PyQt5-commercial: 5.15.2 PyQt5-sip: 12.8.1 PyQtWebEngine-commercial: 5.15.2 python-dateutil: 2.8.2 pytz: 2021.3 pyzmq: 22.3.0 qtconsole: 5.1.1 QtPy: 1.11.3 RandomWords: 0.3.0 requests: 2.26.0 scipy: 1.7.1 setuptools: 57.5.0 sfftk-rw: 0.7.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 4.2.0 sphinx-autodoc-typehints: 1.12.0 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 2.0.0 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 suds-jurko: 0.6 tifffile: 2021.4.8 tinyarray: 1.2.3 tornado: 6.1 traitlets: 5.1.1 urllib3: 1.26.7 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.37.0 wheel-filename: 1.3.0 }}} " defect closed normal Core can't reproduce Tom Goddard all ChimeraX