Crash in event loop

[chimerax-bug-report@…]

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" : [
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  "flavor" : "ARM_THREAD_STATE64",
  "lr" : 140731422263120,
  "cpsr" : 2147483648,
  "fp" : 1677721600,
  "sp" : 4512152464,
  "esr" : 1442840704,
  "esr_description" : " Address size fault",
  "pc" : 140731418618552
},
  "usedImages" : [
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    "00000000-0000-0000-0000-000000000000",
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  [
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    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" : [
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      "arch" : "x86_64",
      "path" : "\/usr\/lib\/system\/libsystem_kernel.dylib",
      "name" : "libsystem_kernel.dylib"
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      "path" : "\/usr\/lib\/system\/libsystem_c.dylib",
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      "arch" : "x86_64",
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      "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"
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      "name" : "runtime"
    },
    {
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      "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"
    },
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      "size" : 4833280,
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      "path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
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      "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"
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  ],
  "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

[Eric Pettersen]

Possibly while doing something with rotamers