#14682 closed defect (can't reproduce)

Crash setting active window

Reported by: hwang@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Window Toolkit Version:
Keywords: Cc: Tom Goddard
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.5.dev202209130706 (2022-09-13 07:06:45 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Thread 0x00007000286ab000 (most recent call first):
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 576 in _handle_results
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007000276a8000 (most recent call first):
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 528 in _handle_tasks
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007000266a5000 (most recent call first):
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/selectors.py", line 416 in select
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/connection.py", line 936 in wait
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 499 in _wait_for_updates
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 519 in _handle_workers
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007000256a2000 (most recent call first):
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x000070002469f000 (most recent call first):
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x000070002369c000 (most recent call first):
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x0000700022699000 (most recent call first):
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x0000700021696000 (most recent call first):
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x0000700020693000 (most recent call first):
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x000070001f690000 (most recent call first):
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x000070001e68d000 (most recent call first):
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x000070001d68a000 (most recent call first):
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x000070001c687000 (most recent call first):
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x000070001b684000 (most recent call first):
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x000070001a681000 (most recent call first):
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x000070001967e000 (most recent call first):
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x000070001867b000 (most recent call first):
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x0000700017678000 (most recent call first):
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x0000700016675000 (most recent call first):
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x0000700015672000 (most recent call first):
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x000070001466f000 (most recent call first):
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x000070001366c000 (most recent call first):
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x0000700012669000 (most recent call first):
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Current thread 0x0000000110d42600 (most recent call first):
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 283 in event_loop
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 884 in init
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1035 in 
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
  File "/Applications/ChimeraX_Daily.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":"2024-03-01 15:07:11.00 +0000","app_version":"1.5.0","slice_uuid":"5df621ee-554e-36a8-b448-93b2334e5480","build_version":"1.5.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 12.2.1 (21D62)","incident_id":"7DE633C1-C169-438B-8E46-2144FDC6402F","name":"ChimeraX"}
{
  "uptime" : 1000000,
  "procLaunch" : "2024-01-24 16:30:43.1629 +0000",
  "procRole" : "Foreground",
  "version" : 2,
  "userID" : 502,
  "deployVersion" : 210,
  "modelCode" : "iMac20,2",
  "procStartAbsTime" : 121178618053802,
  "coalitionID" : 7934,
  "osVersion" : {
    "train" : "macOS 12.2.1",
    "build" : "21D62",
    "releaseType" : "User"
  },
  "captureTime" : "2024-03-01 15:07:00.7810 +0000",
  "incident" : "7DE633C1-C169-438B-8E46-2144FDC6402F",
  "bug_type" : "309",
  "pid" : 54641,
  "procExitAbsTime" : 1009509997110247,
  "cpuType" : "X86-64",
  "procName" : "ChimeraX",
  "procPath" : "\/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
  "bundleInfo" : {"CFBundleShortVersionString":"1.5.0","CFBundleVersion":"1.5.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
  "storeInfo" : {"deviceIdentifierForVendor":"4E4C9BE7-2F4F-5D0C-9412-C86B35F148C2","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "39F2E734-1901-8474-980B-C5A1E7B85EEE",
  "wakeTime" : 15,
  "bridgeVersion" : {"build":"19P744","train":"6.2"},
  "sleepWakeUUID" : "41B3CA96-E8E2-44EC-8C08-2A8F37823543",
  "sip" : "enabled",
  "vmRegionInfo" : "0x40 is not in any region.  Bytes before following region: 4450586560\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      __TEXT                      109469000-10946a000    [    4K] r-x\/r-x SM=COW  ...acOS\/ChimeraX",
  "isCorpse" : 1,
  "exception" : {"codes":"0x0000000000000001, 0x0000000000000040","rawCodes":[1,64],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000040"},
  "ktriageinfo" : "VM - Fault hit memory shortage\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\n",
  "vmregioninfo" : "0x40 is not in any region.  Bytes before following region: 4450586560\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      __TEXT                      109469000-10946a000    [    4K] 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" : 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  "vmSummary" : "ReadOnly portion of Libraries: Total=1.4G resident=0K(0%) swapped_out_or_unallocated=1.4G(100%)\nWritable regions: Total=11.1G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=11.1G(100%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nAccelerate framework              1152K        9 \nActivity Tracing                   256K        1 \nCG backing stores                 3840K        4 \nCG image                          4712K       78 \nColorSync                          248K       29 \nCoreAnimation                     21.3M      147 \nCoreGraphics                        12K        2 \nCoreImage                           60K        5 \nCoreServices                       624K        2 \nCoreUI image data                 5148K       43 \nFoundation                          36K        2 \nKernel Alloc Once                    8K        1 \nMALLOC                            10.0G     2349 \nMALLOC guard page                   32K        8 \nMALLOC_LARGE (reserved)            384K        1         reserved VM address space (unallocated)\nMALLOC_NANO (reserved)           128.0M        1         reserved VM address space (unallocated)\nMach message                        16K        3 \nOpenGL GLSL                        384K        4 \nSTACK GUARD                        212K       53 \nStack                            511.4M       54 \nStack Guard                       56.0M        1 \nVM_ALLOCATE                      332.1M      251 \nVM_ALLOCATE (reserved)           192.0M        1         reserved VM address space (unallocated)\n__DATA                            56.3M      682 \n__DATA_CONST                      30.4M      347 \n__DATA_DIRTY                      1639K      219 \n__FONT_DATA                          4K        1 \n__GLSLBUILTINS                    5176K        1 \n__LINKEDIT                       672.5M      156 \n__OBJC_RO                         81.8M        1 \n__OBJC_RW                         3136K        2 \n__TEXT                           781.1M      683 \n__UNICODE                          588K        1 \ndyld private memory               1184K        3 \nmapped file                      229.8M       57 \nshared memory                     3492K       23 \n===========                     =======  ======= \nTOTAL                             13.0G     5225 \nTOTAL, minus reserved VM space    12.7G     5225 \n",
  "legacyInfo" : {
  "threadTriggered" : {
    "name" : "CrBrowserMain",
    "queue" : "com.apple.main-thread"
  }
},
  "trialInfo" : {
  "rollouts" : [
    {
      "rolloutId" : "602ad4dac86151000cf27e46",
      "factorPackIds" : {
        "SIRI_DICTATION_ASSETS" : "6193d03f2171a2330e561dfc"
      },
      "deploymentId" : 240000305
    },
    {
      "rolloutId" : "60da5e84ab0ca017dace9abf",
      "factorPackIds" : {

      },
      "deploymentId" : 240000008
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    {
      "rolloutId" : "607844aa04477260f58a8077",
      "factorPackIds" : {
        "SIRI_MORPHUN_ASSETS" : "6103050cbfe6dc472e1c982a"
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      "deploymentId" : 240000066
    },
    {
      "rolloutId" : "601d9415f79519000ccd4b69",
      "factorPackIds" : {
        "SIRI_TEXT_TO_SPEECH" : "622657ce37186c771d5404ad"
      },
      "deploymentId" : 240000416
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    {
      "rolloutId" : "63582c5f8a53461413999550",
      "factorPackIds" : {

      },
      "deploymentId" : 240000002
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      "rolloutId" : "5fb4245a1bbfe8005e33a1e1",
      "factorPackIds" : {

      },
      "deploymentId" : 240000021
    },
    {
      "rolloutId" : "5f72dc58705eff005a46b3a9",
      "factorPackIds" : {

      },
      "deploymentId" : 240000015
    },
    {
      "rolloutId" : "60f8ddccefea4203d95cbeef",
      "factorPackIds" : {
        "NETWORK_SERVICE_PROXY_CONFIG_UPDATE" : "6401414cc679dd6bc5828183"
      },
      "deploymentId" : 240000025
    },
    {
      "rolloutId" : "5fc94383418129005b4e9ae0",
      "factorPackIds" : {

      },
      "deploymentId" : 240000614
    },
    {
      "rolloutId" : "60186475825c62000ccf5450",
      "factorPackIds" : {

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      "deploymentId" : 240000069
    },
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      "rolloutId" : "5ffde50ce2aacd000d47a95f",
      "factorPackIds" : {

      },
      "deploymentId" : 240000364
    }
  ],
  "experiments" : [

  ]
}
}
===== Log before crash start =====
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.5.dev202209130706 (2022-09-13)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Volumes/hwang/TMEM208/M_Psite.pdb format pdb

No such file/path: /Volumes/hwang/TMEM208/M_Psite.pdb  

> open /Users/hwang/Desktop/Fig5modelmembraneMaps.cxs format session

Opened 41205_lp20.mrc as #5, grid size 256,256,256, pixel 2.62, shown at level
1.03, step 1, values float32  
Opened tmem208dHelix.mrc as #3, grid size 80,80,80, pixel 1, shown at level
0.0883, step 1, values float32  
Opened SRPrest.mrc as #13, grid size 200,200,200, pixel 1, shown at level
0.145, step 1, values float32  
Opened M.mrc as #14, grid size 72,72,72, pixel 1, shown at level 0.137, step
1, values float32  
Opened NC.mrc as #15, grid size 40,40,40, pixel 1, shown at level 0.12, step
1, values float32  
Opened SRP54NG.mrc as #16, grid size 104,104,104, pixel 1, shown at level
0.142, step 1, values float32  
Opened SRaNG.mrc as #17, grid size 104,104,104, pixel 1, shown at level 0.147,
step 1, values float32  
opened ChimeraX session  

> hide #!17 models

> hide #!16 models

> hide #!15 models

> hide #!14 models

> hide #!13 models

> hide #!9 models

> show #!7 models

> hide #!5 models

> hide #!3 models

> select #7/x:349

8 atoms, 7 bonds, 1 residue, 1 model selected  
Alignment identifier is 7/x  

> select #7/x:337

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #7/x:337,338,341,366,367,371,373

64 atoms, 59 bonds, 7 residues, 1 model selected  

> color sel blue

> select #7/x:342,345,349,469

27 atoms, 25 bonds, 3 residues, 1 model selected  

> color sel lime

> hide #!7 models

> show #!2 models

> show #!1 models

> hide #!1 models

> close session

> open /Volumes/hwang/TMEM208/M.pdb format pdb

Summary of feedback from opening /Volumes/hwang/TMEM208/M.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 TYR q 19
ASN q 24 1 6  
Start residue of secondary structure not found: HELIX 2 2 THR q 45 ALA q 55 1
11  
Start residue of secondary structure not found: HELIX 3 3 SER q 100 THR q 117
1 18  
Start residue of secondary structure not found: HELIX 4 4 GLU u 58 GLN u 68 1
11  
Start residue of secondary structure not found: HELIX 5 5 PHE u 77 ASN u 96 1
20  
82 messages similar to the above omitted  
Cannot find LINK/SSBOND residue MG (300 )  
Cannot find LINK/SSBOND residue MG (300 )  
Cannot find LINK/SSBOND residue GTP (301 )  
Cannot find LINK/SSBOND residue GTP (301 )  
Cannot find LINK/SSBOND residue GTP (301 )  
7 messages similar to the above omitted  
  
Chain information for M.pdb #1  
---  
Chain | Description  
x | No description available  
  

> close session

> open /Volumes/hwang/TMEM208/M.pdb format pdb

Summary of feedback from opening /Volumes/hwang/TMEM208/M.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 TYR q 19
ASN q 24 1 6  
Start residue of secondary structure not found: HELIX 2 2 THR q 45 ALA q 55 1
11  
Start residue of secondary structure not found: HELIX 3 3 SER q 100 THR q 117
1 18  
Start residue of secondary structure not found: HELIX 4 4 GLU u 58 GLN u 68 1
11  
Start residue of secondary structure not found: HELIX 5 5 PHE u 77 ASN u 96 1
20  
82 messages similar to the above omitted  
Cannot find LINK/SSBOND residue MG (300 )  
Cannot find LINK/SSBOND residue MG (300 )  
Cannot find LINK/SSBOND residue GTP (301 )  
Cannot find LINK/SSBOND residue GTP (301 )  
Cannot find LINK/SSBOND residue GTP (301 )  
7 messages similar to the above omitted  
  
Chain information for M.pdb #1  
---  
Chain | Description  
x | No description available  
  

> close session

> open /Users/hwang/Downloads/SRP54M_cf187_0_weblogo.pdb format pdb

Chain information for SRP54M_cf187_0_weblogo.pdb #1  
---  
Chain | Description  
A | No description available  
  

> select /A:39

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select #A:342,345,349,469

Expected an objects specifier or a keyword  

> close session

> open /Users/hwang/Desktop/Fig5modelmembraneMaps.cxs format session

Opened 41205_lp20.mrc as #5, grid size 256,256,256, pixel 2.62, shown at level
1.03, step 1, values float32  
Opened tmem208dHelix.mrc as #3, grid size 80,80,80, pixel 1, shown at level
0.0883, step 1, values float32  
Opened SRPrest.mrc as #13, grid size 200,200,200, pixel 1, shown at level
0.145, step 1, values float32  
Opened M.mrc as #14, grid size 72,72,72, pixel 1, shown at level 0.137, step
1, values float32  
Opened NC.mrc as #15, grid size 40,40,40, pixel 1, shown at level 0.12, step
1, values float32  
Opened SRP54NG.mrc as #16, grid size 104,104,104, pixel 1, shown at level
0.142, step 1, values float32  
Opened SRaNG.mrc as #17, grid size 104,104,104, pixel 1, shown at level 0.147,
step 1, values float32  
opened ChimeraX session  

> hide #!3 models

> hide #!5 models

> hide #!9 models

> hide #!13 models

> hide #!14 models

> hide #!15 models

> hide #!16 models

> hide #!17 models

> show #!2 models

> open 7obq

7obq title:  
SRP-SR at the distal site conformation [more info...]  
  
Chain information for 7obq #18  
---  
Chain | Description | UniProt  
1 | SRP RNA |  
q | Signal recognition particle 19 | J9PAS6_CANLF  
s | EM14S01-3B_G0054400.mRNA.1.CDS.1 | A0A7I9EWR8_YEASX  
u | Signal recognition particle subunit SRP68,Signal recognition particle
subunit SRP68 | SRP68_CANLF  
v | Signal recognition particle receptor subunit β | G1STG2_RABIT  
x | Signal recognition particle 54 kDa protein | SRP54_CANLF  
y | SRP receptor subunit α | A0A5F9CI80_RABIT  
z | Signal recognition particle subunit SRP72 | SRP72_CANLF  
  
Non-standard residues in 7obq #18  
---  
GNP — phosphoaminophosphonic acid-guanylate ester  
GTP — guanosine-5'-triphosphate  
MG — magnesium ion  
  

> hide #!2 models

> select add #18

27739 atoms, 28877 bonds, 167 pseudobonds, 2965 residues, 6 models selected  

> hide sel & #!18 atoms

> show sel & #!18 cartoons

> hide #!18 models

> show #!1 models

> select #1/x:317

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #1/x:342,345,349,469

38 atoms, 35 bonds, 4 residues, 1 model selected  

> color sel red

> select add #1/s:39

52 atoms, 50 bonds, 5 residues, 1 model selected  

> select up

394 atoms, 397 bonds, 48 residues, 1 model selected  

> select up

4275 atoms, 4339 bonds, 555 residues, 1 model selected  

> select ~sel

321917 atoms, 345252 bonds, 4469 pseudobonds, 26432 residues, 42 models
selected  

> hide sel & #!1 cartoons

> select #1/x:245

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #1/x:312

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/x:3-312

2384 atoms, 2418 bonds, 310 residues, 1 model selected  

> hide sel cartoons

> select #1/x:342,345,349,369

35 atoms, 32 bonds, 4 residues, 1 model selected  

> color sel red

> show sel atoms

> style sel stick

Changed 35 atom styles  

> select up

351 atoms, 352 bonds, 43 residues, 1 model selected  

> select #7/x:337,338,341,366,367,371,373

64 atoms, 59 bonds, 7 residues, 1 model selected  

> select #1/x:366

9 atoms, 8 bonds, 1 residue, 1 model selected  

> color sel red

> show sel atoms

> style sel stick

Changed 9 atom styles  

> select #1/x:337,338,341,367,371,373

55 atoms, 50 bonds, 6 residues, 1 model selected  

> color sel lime

> show sel atoms

> style sel stick

Changed 55 atom styles  

> select #1/x:351,355,359

30 atoms, 29 bonds, 3 residues, 1 model selected  

> color sel lime

> show sel atoms

> style sel stick

Changed 30 atom styles  

> select #1/s:35

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select up

158 atoms, 159 bonds, 20 residues, 1 model selected  

> mlp sel

Map values for surface "7obr_s SES surface": minimum -23.7, mean -2.044,
maximum 22.5  
To also show corresponding color key, enter the above mlp command and add key
true  

> coulombic sel

The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:  
7obr #1/s ASP 56  
7obr #1/s TYR 57  
7obr #1/s GLN 58  
7obr #1/s GLU 59  
7obr #1/s PRO 60  
7obr #1/s ASN 61  
7obr #1/s SER 62  
7obr #1/s ASN 63  
7obr #1/s TYR 64  
7obr #1/s THR 65  
7obr #1/s ASN 66  
7obr #1/s ASP 67  
7obr #1/s LYS 69  
7obr #1/s HIS 90  

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for 7obr_s SES surface #1.4: minimum, -11.44, mean 0.64,
maximum 10.89  
To also show corresponding color key, enter the above coulombic command and
add key true  

> close session

> open /Users/hwang/Desktop/amberM_7obr.cxs format session

opened ChimeraX session  

> shape sphere center #18/x:337 @CA radius 1.5

> shape sphere center #18/x:338 @CA radius 1.5

> shape sphere center #18/x:341 @CA radius 1.5

> select add #23

1 model selected  

> color #23 orange

> shape sphere center #18/x:366 @CA radius 1.5

> select subtract #23

Nothing selected  

> select add #24

1 model selected  

> color #24 orange

> shape sphere center #18/x:367 @CA radius 1.5

> shape sphere center #18/x:371 @CA radius 1.5

> shape sphere center #18/x:373 @CA radius 1.5

> select clear

> view

> ui tool show "Side View"

> save /Users/hwang/Desktop/amberM_7obr.cxs includeMaps true

> save /Users/hwang/Desktop/M_amber_new.png width 1272 height 1129 supersample
> 3 transparentBackground true

> close session

> open 4i4t

Summary of feedback from opening 4i4t fetched from pdb  
---  
warnings | Unknown polymer entity '10' near line 38867  
Unknown polymer entity '11' near line 38935  
Atom H1 is not in the residue template for MET /A:1  
Atom H1 is not in the residue template for MET /B:1  
Atom H1 is not in the residue template for MET /C:1  
Atom H1 is not in the residue template for MET /D:1  
Atom H1 is not in the residue template for MET /F:1  
1 messages similar to the above omitted  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
notes | Fetching compressed mmCIF 4i4t from
http://files.rcsb.org/download/4i4t.cif  
Fetching CCD CL from http://ligand-expo.rcsb.org/reports/C/CL/CL.cif  
Fetching CCD GOL from http://ligand-expo.rcsb.org/reports/G/GOL/GOL.cif  
Fetching CCD MES from http://ligand-expo.rcsb.org/reports/M/MES/MES.cif  
Fetching CCD ZPN from http://ligand-expo.rcsb.org/reports/Z/ZPN/ZPN.cif  
Fetching CCD ACP from http://ligand-expo.rcsb.org/reports/A/ACP/ACP.cif  
  
4i4t title:  
Crystal structure of tubulin-RB3-TTL-Zampanolide complex [more info...]  
  
Chain information for 4i4t #1  
---  
Chain | Description | UniProt  
A C | Tubulin alpha-1B chain | TBA1B_BOVIN  
B D | Tubulin beta-2B chain | TBB2B_BOVIN  
E | Stathmin-4 | STMN4_RAT  
F | Tubulin Tyrosine ligase, TTL | E1BQ43_CHICK  
  
Non-standard residues in 4i4t #1  
---  
ACP — phosphomethylphosphonic acid adenylate ester (adenosine-5'-[β,
γ-methylene]triphosphate)  
CA — calcium ion  
CL — chloride ion  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
GTP — guanosine-5'-triphosphate  
MES — 2-(N-morpholino)-ethanesulfonic acid  
MG — magnesium ion  
ZPN —
(2Z,4E)-N-[(S)-[(1S,2E,5S,8E,10Z,17S)-3,11-dimethyl-19-methylidene-7,13-dioxo-6,21-dioxabicyclo[15.3.1]henicosa-2,8,10-trien-5-yl](hydroxy)methyl]hexa-2,4-dienamide
((-)-ZAMPANOLIDE (Bound form))  
  

> hide atoms

> show cartoons

> sequence chain #1/A#1/C

Alignment identifier is 1  

> select /A,C:1

38 atoms, 36 bonds, 2 residues, 1 model selected  

> select /A,C:1-104

3114 atoms, 3150 bonds, 208 residues, 1 model selected  

> select /A,C:1

38 atoms, 36 bonds, 2 residues, 1 model selected  

> select /A,C:1-440

13596 atoms, 13752 bonds, 880 residues, 1 model selected  

> rainbow sel

> close session

> open /Users/hwang/Desktop/Fig5modelmembraneMaps.cxs format session

Opened 41205_lp20.mrc as #5, grid size 256,256,256, pixel 2.62, shown at level
1.03, step 1, values float32  
Opened tmem208dHelix.mrc as #3, grid size 80,80,80, pixel 1, shown at level
0.0883, step 1, values float32  
Opened SRPrest.mrc as #13, grid size 200,200,200, pixel 1, shown at level
0.145, step 1, values float32  
Opened M.mrc as #14, grid size 72,72,72, pixel 1, shown at level 0.137, step
1, values float32  
Opened NC.mrc as #15, grid size 40,40,40, pixel 1, shown at level 0.12, step
1, values float32  
Opened SRP54NG.mrc as #16, grid size 104,104,104, pixel 1, shown at level
0.142, step 1, values float32  
Opened SRaNG.mrc as #17, grid size 104,104,104, pixel 1, shown at level 0.147,
step 1, values float32  
opened ChimeraX session  

> hide #!3 models

> show #!3 models

> show #!2 models

> hide #!2 models

> close #10-11#12

> close #7

> close #6

> show #4 models

> hide #4 models

> close #4

> show #!8 models

> hide #!8 models

> color #3 #fffb00ff models

> color #3 #ffd479ff models

> hide #!9 models

> color #13 #005493ff models

> color #14 #00fdffff models

> color #14 #76d6ffff models

> hide #!16 models

> show #!16 models

> color #16 #0096ffff models

> color #16 #005493ff models

> color #16 #0096ffff models

> color #16 #676767ff models

> color #16 #777777ff models

> color #16 #7f7f7fff models

> color #16 grey models

> color #16 #005493ff models

> color #16 #0096ffff models

> color #14 #73fdffff models

> color #16 #76d6ffff models

> color #16 #7a81ffff models

> color #16 #0096ffff models

> color #17 #7a81ffff models

> color #13 #193e6dff models

> hide #!3 models

> hide #!5 models

> hide #!13 models

> hide #!14 models

> hide #!15 models

> hide #!16 models

> hide #!17 models

> show #!9 models

> hide #!9 models

> show #!8 models

> hide #!8 models

> show #!2 models

> hide #!2 models

> show #!1 models

> hide #!1 models

> show #!8 models

> close #8

> show #!1 models

> select #1/x:82

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/x:312

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/x:3-312

2384 atoms, 2418 bonds, 310 residues, 1 model selected  

> save /Users/hwang/Desktop/SRP54NG_psite.pdb selectedOnly true relModel #3

> hide #!1 models

> open /Users/hwang/Desktop/SRP54NG_psite.pdb

Summary of feedback from opening /Users/hwang/Desktop/SRP54NG_psite.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 GLN A 8
GLY A 13 1 6  
Start residue of secondary structure not found: HELIX 2 2 ASP A 33 HIS A 38 1
6  
Start residue of secondary structure not found: HELIX 3 3 PRO A 141 THR A 143
1 3  
Start residue of secondary structure not found: HELIX 4 4 GLY A 173 LYS A 177
1 5  
Start residue of secondary structure not found: HELIX 5 5 LYS A 181 ALA A 191
1 11  
485 messages similar to the above omitted  
Cannot find LINK/SSBOND residue CYS (46 )  
Cannot find LINK/SSBOND residue CYS (83 )  
Cannot find LINK/SSBOND residue C (3632 )  
Cannot find LINK/SSBOND residue C (3636 )  
Cannot find LINK/SSBOND residue C (1678 )  
130 messages similar to the above omitted  
  
Chain information for SRP54NG_psite.pdb #4  
---  
Chain | Description  
x | No description available  
  

> open /Volumes/hwang/TMEM208/SRP54NG_Psite.mrc

Opened SRP54NG_Psite.mrc as #6, grid size 96,96,96, pixel 1, shown at level
0.358, step 1, values float32  

> volume #6 level 0.08514

> close #4

> select add #1

146701 atoms, 157882 bonds, 3992 pseudobonds, 11605 residues, 4 models
selected  

> select subtract #1

Nothing selected  

> show #!3 models

> hide #!3 models

> show #!13 models

> show #!14 models

> show #!15 models

> show #!16 models

> show #!17 models

> hide #!17 models

> hide #!16 models

> color #6 #0096ffff models

> show #!16 models

> hide #!16 models

> hide #!6 models

> show #!5 models

> show #!3 models

> show #!6 models

> hide #!6 models

> show #!16 models

> show #!17 models

> save /Users/hwang/Dropbox/Huping/draft/TMEM208/dock_preHO_maps.cxs
> includeMaps true

> show #!6 models

> hide #!16 models

> hide #!17 models

> hide #!3 models

> close session

> open /Users/hwang/Desktop/Fig5modelmembraneMaps.cxs format session

Opened 41205_lp20.mrc as #5, grid size 256,256,256, pixel 2.62, shown at level
1.03, step 1, values float32  
Opened tmem208dHelix.mrc as #3, grid size 80,80,80, pixel 1, shown at level
0.0883, step 1, values float32  
Opened SRPrest.mrc as #13, grid size 200,200,200, pixel 1, shown at level
0.145, step 1, values float32  
Opened M.mrc as #14, grid size 72,72,72, pixel 1, shown at level 0.137, step
1, values float32  
Opened NC.mrc as #15, grid size 40,40,40, pixel 1, shown at level 0.12, step
1, values float32  
Opened SRP54NG.mrc as #16, grid size 104,104,104, pixel 1, shown at level
0.142, step 1, values float32  
Opened SRaNG.mrc as #17, grid size 104,104,104, pixel 1, shown at level 0.147,
step 1, values float32  
opened ChimeraX session  

> close #13-17

> show #!12 models

> close #3

> show #!6 models

> hide #!9 models

> show #!1 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!1 models

> show #4 models

> hide #4 models

> show #4 models

> close #4

> close #7-8

> close #10-11#12

> show #!1 models

> hide #!6 models

> hide #!5 models

Drag select of 777 residues  

> select up

15961 atoms, 17121 bonds, 1305 residues, 5 models selected  

> select up

19167 atoms, 20380 bonds, 1719 residues, 5 models selected  

> select add #2/u:453

19175 atoms, 20387 bonds, 1720 residues, 5 models selected  

> select up

19359 atoms, 20576 bonds, 1742 residues, 6 models selected  

> select up

19767 atoms, 20989 bonds, 1800 residues, 6 models selected  

> select up

19776 atoms, 20997 bonds, 1801 residues, 6 models selected  

> select add #2/u:378

19782 atoms, 21002 bonds, 1802 residues, 6 models selected  
Drag select of 47 residues  

> select up

20077 atoms, 21294 bonds, 1841 residues, 6 models selected  

> select up

20878 atoms, 22113 bonds, 1940 residues, 6 models selected  
Drag select of 12 residues  

> select add #2/u:353

20947 atoms, 22121 bonds, 1953 residues, 6 models selected  

> select up

21222 atoms, 22459 bonds, 1986 residues, 6 models selected  

> select up

22663 atoms, 23923 bonds, 2160 residues, 6 models selected  

> select ~sel

136386 atoms, 146874 bonds, 3750 pseudobonds, 10722 residues, 13 models
selected  

> color (#!1-2 & sel) light gray

> select clear

> select #1/1:294

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select up

5341 atoms, 5972 bonds, 249 residues, 1 model selected  

> color sel light gray

> color sel medium blue

> select #1/s:39

14 atoms, 15 bonds, 1 residue, 1 model selected  

> select up

158 atoms, 159 bonds, 20 residues, 1 model selected  

> select up

502 atoms, 514 bonds, 67 residues, 1 model selected  

> color sel red

> select #1/x:55

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/x:312

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/x:3-312

2384 atoms, 2418 bonds, 310 residues, 1 model selected  

> color sel cornflower blue

> select #1/x:313

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/x:313-490

1389 atoms, 1406 bonds, 178 residues, 1 model selected  

> color sel cyan

> hide #!2 models

> select #1/u:180

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select add #1/q:14

18 atoms, 16 bonds, 2 residues, 1 model selected  

> select up

223 atoms, 226 bonds, 26 residues, 1 model selected  

> select up

2470 atoms, 2512 bonds, 299 residues, 1 model selected  

> color sel medium blue

> select clear

> show #!6 models

> hide #!6 models

> show #!6 models

> color #6 #ffd479ff

> hide #!6 models

> hide #!1 models

> show #!2 models

> show #!6 models

> show #!1 models

> hide #!1 models

> select #2/1:220

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select up

3542 atoms, 3964 bonds, 165 residues, 2 models selected  

> select up

11170 atoms, 11705 bonds, 1125 residues, 2 models selected  

> select down

3542 atoms, 3964 bonds, 165 residues, 6 models selected  

> open 7obq

7obq title:  
SRP-SR at the distal site conformation [more info...]  
  
Chain information for 7obq #3  
---  
Chain | Description | UniProt  
1 | SRP RNA |  
q | Signal recognition particle 19 | J9PAS6_CANLF  
s | EM14S01-3B_G0054400.mRNA.1.CDS.1 | A0A7I9EWR8_YEASX  
u | Signal recognition particle subunit SRP68,Signal recognition particle
subunit SRP68 | SRP68_CANLF  
v | Signal recognition particle receptor subunit β | G1STG2_RABIT  
x | Signal recognition particle 54 kDa protein | SRP54_CANLF  
y | SRP receptor subunit α | A0A5F9CI80_RABIT  
z | Signal recognition particle subunit SRP72 | SRP72_CANLF  
  
Non-standard residues in 7obq #3  
---  
GNP — phosphoaminophosphonic acid-guanylate ester  
GTP — guanosine-5'-triphosphate  
MG — magnesium ion  
  

> select add #2

11170 atoms, 11705 bonds, 159 pseudobonds, 1125 residues, 6 models selected  

> select subtract #2

5 models selected  

> select add #3

16668 atoms, 17274 bonds, 164 pseudobonds, 1846 residues, 4 models selected  

> hide sel atoms

> show sel cartoons

> ui tool show Matchmaker

> matchmaker #!3 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 7obq, chain u (#2) with 7obq, chain u (#3), sequence alignment
score = 2488.5  
RMSD between 441 pruned atom pairs is 0.000 angstroms; (across all 441 pairs:
0.000)  
  

> matchmaker #!3 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 7obq, chain u (#2) with 7obq, chain u (#3), sequence alignment
score = 2488.5  
RMSD between 441 pruned atom pairs is 0.000 angstroms; (across all 441 pairs:
0.000)  
  

> hide #!2 models

> close #2

> select clear

> select #3/s:20

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select up

95 atoms, 94 bonds, 19 residues, 1 model selected  

> select up

100 atoms, 99 bonds, 20 residues, 1 model selected  

> color sel red

> select #3/1:244

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select up

3542 atoms, 3964 bonds, 165 residues, 1 model selected  

> select up

16668 atoms, 17274 bonds, 1846 residues, 1 model selected  

> select down

3542 atoms, 3964 bonds, 165 residues, 1 model selected  

> color sel medium blue

> select clear

> select #3/x:320

9 atoms, 8 bonds, 1 residue, 1 model selected  
Alignment identifier is 3/x  

> select #3/x:316-437

865 atoms, 873 bonds, 1 pseudobond, 109 residues, 2 models selected  

> color (#!3 & sel) cyan

> select #3/x:20-303

2184 atoms, 2218 bonds, 284 residues, 1 model selected  

> color sel cornflower blue

> select #3/y:434

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select up

132 atoms, 134 bonds, 17 residues, 1 model selected  

> select up

2349 atoms, 2379 bonds, 308 residues, 1 model selected  

> select up

3516 atoms, 3566 bonds, 456 residues, 1 model selected  

> select down

2349 atoms, 2379 bonds, 308 residues, 1 model selected  
Alignment identifier is 3/y  

> select #3/y:147

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #3/y:2-147

1134 atoms, 1153 bonds, 146 residues, 1 model selected  

> color sel medium blue

> select clear

Drag select of 226 residues, 1 pseudobonds  

> select up

3375 atoms, 3414 bonds, 1 pseudobond, 440 residues, 2 models selected  

> select up

6193 atoms, 6280 bonds, 1 pseudobond, 788 residues, 2 models selected  

> color (#!3 & sel) medium blue

> select clear

> select #3/q:92

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select up

118 atoms, 119 bonds, 15 residues, 1 model selected  

> select up

842 atoms, 856 bonds, 104 residues, 1 model selected  

> color sel medium blue

> select clear

> show #!5 models

> hide #!5 models

> save /Users/hwang/Dropbox/Huping/draft/TMEM208/dock_preHO_pdb.cxs
> includeMaps true

> close session

> open /Users/hwang/Dropbox/Huping/draft/TMEM208/dock_preHO_maps.cxs format
> session

Opened 41205_lp20.mrc as #5, grid size 256,256,256, pixel 2.62, shown at level
1.03, step 1, values float32  
Opened tmem208dHelix.mrc as #3, grid size 80,80,80, pixel 1, shown at level
0.0883, step 1, values float32  
Opened SRPrest.mrc as #13, grid size 200,200,200, pixel 1, shown at level
0.145, step 1, values float32  
Opened M.mrc as #14, grid size 72,72,72, pixel 1, shown at level 0.137, step
1, values float32  
Opened NC.mrc as #15, grid size 40,40,40, pixel 1, shown at level 0.12, step
1, values float32  
Opened SRP54NG.mrc as #16, grid size 104,104,104, pixel 1, shown at level
0.142, step 1, values float32  
Opened SRaNG.mrc as #17, grid size 104,104,104, pixel 1, shown at level 0.147,
step 1, values float32  
Opened SRP54NG_Psite.mrc as #6, grid size 96,96,96, pixel 1, shown at level
0.0851, step 1, values float32  
opened ChimeraX session  

> show #!9 models

> lighting simple

> lighting full

> lighting soft

> lighting simple

> turn y 10

> turn y 170

> turn y 180

> hide #!5 models

> show #!1 models

> select #1/Y:40

9 atoms, 8 bonds, 1 residue, 1 model selected  
Alignment identifier is 1/Y  

> hide #!1 models

> show #!5 models

> turn y 180

> hide #!13 models

> show #!2 models

> hide #!16 models

> hide #!17 models

> select #2/q:91

4 atoms, 3 bonds, 1 residue, 1 model selected  
Alignment identifier is 2/q  

> show #!13 models

> hide #!13 models

> select clear

> select #2/u:437

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select add #2/q:90

17 atoms, 15 bonds, 2 residues, 2 models selected  

> select clear

> select #2/u:437

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select up

238 atoms, 241 bonds, 29 residues, 2 models selected  

> select up

600 atoms, 609 bonds, 81 residues, 2 models selected  

> molmap 8

Missing or invalid "atoms" argument: invalid atoms specifier  

> molmap #2/u 8

Opened 7obq map 8 as #4, grid size 41,38,60, pixel 2.67, shown at level
0.0618, step 1, values float32  

> color #4 silver models

> color #4 #929292ff models

> select #2/1:221

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select up

3542 atoms, 3964 bonds, 165 residues, 2 models selected  

> color (#!2 & sel) medium blue

> select clear

> select #2/1:138

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select up

3542 atoms, 3964 bonds, 165 residues, 2 models selected  

> ui tool show "Color Actions"

> color sel dark blue

> color sel dark slate blue

> color sel midnight blue

> select clear

> hide #!5 models

> show #!5 models

> hide #!4 models

> select #2/u:433

7 atoms, 6 bonds, 1 residue, 1 model selected  
Alignment identifier is 2/u  

> select #2/v:174

6 atoms, 5 bonds, 1 residue, 1 model selected  
Destroying pre-existing alignment with identifier 2/v  
Alignment identifier is 2/v  

> select #2/q:90

8 atoms, 7 bonds, 1 residue, 1 model selected  

> molmap #2/q 8

Opened 7obq map 8 as #7, grid size 32,33,32, pixel 2.67, shown at level
0.0603, step 1, values float32  

> color #17 #919191ff models

> color #7 #797979ff models

> show #!17 models

> hide #!17 models

> show #!4 models

> show #!16 models

> show #!17 models

> color #17 #d783ffff models

> color #17 #7a81ffff models

> select #2/z:582

9 atoms, 8 bonds, 1 residue, 1 model selected  
Alignment identifier is 2/z  

> select #2/v:68

8 atoms, 7 bonds, 1 residue, 1 model selected  

> molmap #2/v 8

Opened 7obq map 8 as #8, grid size 39,35,34, pixel 2.67, shown at level
0.0662, step 1, values float32  

> color #8 #797979ff models

> color #8 #919191ff models

> color #7 #929292ff models

> select #2/z:582

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select up

46 atoms, 46 bonds, 5 residues, 2 models selected  

> molmap #2/z 8

Opened 7obq map 8 as #10, grid size 35,34,37, pixel 2.67, shown at level
0.0313, step 1, values float32  

> color #10 #919191ff models

> show #!1 models

> hide #!1 models

> ui tool show "Color Actions"

> select add #16

46 atoms, 46 bonds, 5 residues, 4 models selected  

> color sel cornflower blue

> select subtract #16

46 atoms, 46 bonds, 5 residues, 2 models selected  

> select add #14

46 atoms, 46 bonds, 5 residues, 4 models selected  

> color sel cornflower blue

> select subtract #14

46 atoms, 46 bonds, 5 residues, 2 models selected  

> select add #16

46 atoms, 46 bonds, 5 residues, 4 models selected  

> color sel steel blue

> color sel light slate gray

> color sel steel blue

> select clear

> select add #4

2 models selected  

> select add #7

4 models selected  

> select add #8

6 models selected  

> select add #10

8 models selected  

> ui tool show "Color Actions"

> color sel light slate gray

> select clear

> select add #16

2 models selected  

> color #16 #6493bdff models

> color #16 #6b9cc9ff models

> color #16 #6694bfff models

> color #16 #5d88afff models

> color #16 #5982a8ff models

> color #16 #5c86adff models

> color #16 #577fa4ff models

> select clear

> select add #10

2 models selected  

> select subtract #10

Nothing selected  

> select add #16

2 models selected  

> ui tool show "Color Actions"

> color sel royal blue

> select clear

> close session

> open /Users/hwang/Dropbox/Huping/draft/TMEM208/dock_preHO_maps.cxs format
> session

Opened 41205_lp20.mrc as #5, grid size 256,256,256, pixel 2.62, shown at level
1.03, step 1, values float32  
Opened tmem208dHelix.mrc as #3, grid size 80,80,80, pixel 1, shown at level
0.0883, step 1, values float32  
Opened SRPrest.mrc as #13, grid size 200,200,200, pixel 1, shown at level
0.145, step 1, values float32  
Opened M.mrc as #14, grid size 72,72,72, pixel 1, shown at level 0.137, step
1, values float32  
Opened NC.mrc as #15, grid size 40,40,40, pixel 1, shown at level 0.12, step
1, values float32  
Opened SRP54NG.mrc as #16, grid size 104,104,104, pixel 1, shown at level
0.142, step 1, values float32  
Opened SRaNG.mrc as #17, grid size 104,104,104, pixel 1, shown at level 0.147,
step 1, values float32  
Opened SRP54NG_Psite.mrc as #6, grid size 96,96,96, pixel 1, shown at level
0.0851, step 1, values float32  
opened ChimeraX session  

> select add #16

2 models selected  

> ui tool show "Color Actions"

> color sel steel blue

> color sel cadet blue

> color sel cornflower blue

> color sel sky blue

> select clear

> select add #14

2 models selected  

> color sel powder blue

> color sel pale turquoise

> color sel aquamarine

> color sel light cyan

> color sel cornflower blue

> color sel light sky blue

> color sel sky blue

> color sel light sky blue

> color sel sky blue

> select #16

2 models selected  

> ui tool show "Color Actions"

> color sel cornflower blue

> select clear

> lighting simple

> show #!9 models

> hide #!9 models

> show #!9 models

> hide #!9 models

> hide #!3 models

> hide #!16 models

> hide #!17 models

> show #!6 models

> turn y 180

> hide #!14 models

> hide #!15 models

> hide #!13 models

> show #!1 models

> turn y 180

> select #6

2 models selected  

> hide #!6 models

> turn y 180

> select #1/s:36

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select up

158 atoms, 159 bonds, 20 residues, 1 model selected  

> select up

502 atoms, 514 bonds, 67 residues, 1 model selected  

> molmap #1/s 8

Opened 7obr map 8 as #4, grid size 37,52,43, pixel 2.67, shown at level
0.0279, step 1, values float32  

> color #4 #ff2600ff models

> select #1/x:332

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/x:312-313

16 atoms, 15 bonds, 2 residues, 1 model selected  

> select #1/x:313-490

1389 atoms, 1406 bonds, 178 residues, 1 model selected  

> molmap #1/x:313-490 8

Opened 7obr map 8 as #7, grid size 40,32,35, pixel 2.67, shown at level 0.052,
step 1, values float32  

> select add #1

146701 atoms, 157882 bonds, 3992 pseudobonds, 11605 residues, 4 models
selected  

> select subtract #1

Nothing selected  

> select add #7

2 models selected  

> ui tool show "Color Actions"

> color sel sky blue

> select #1/u:180

7 atoms, 6 bonds, 1 residue, 1 model selected  

> molmap #1/u 8

Opened 7obr map 8 as #8, grid size 34,42,37, pixel 2.67, shown at level
0.0617, step 1, values float32  

> select #1/1:134

20 atoms, 21 bonds, 1 residue, 1 model selected  

> molmap #1/1 8

Opened 7obr map 8 as #10, grid size 65,75,92, pixel 2.67, shown at level
0.0625, step 1, values float32  

> select clear

> select #1/q:90

8 atoms, 7 bonds, 1 residue, 1 model selected  

> molmap #1/q 8

Opened 7obr map 8 as #11, grid size 31,33,32, pixel 2.67, shown at level
0.0548, step 1, values float32  
Drag select of 221 residues, 29 7obr map 8  

> color (#!1 & sel) medium blue

> select add #1

146701 atoms, 157882 bonds, 3992 pseudobonds, 11605 residues, 10 models
selected  

> select subtract #1

6 models selected  

> select subtract #8

4 models selected  

> select add #8

6 models selected  

> color #8.1#10.1#11.1 medium blue

> ui tool show "Color Actions"

> color sel midnight blue

> show #!13 models

> hide #!13 models

> show #!13 models

> hide #!13 models

> ui tool show "Color Actions"

> color sel dark slate gray

> show #!13 models

> color sel navy

> color sel dark blue

> color sel navy

> color sel dark slate gray

> color sel midnight blue

> select add #13

8 models selected  

> select subtract #11

6 models selected  

> select subtract #10

4 models selected  

> select subtract #8

2 models selected  

> select subtract #13

Nothing selected  

> select add #8

2 models selected  

> select add #10

4 models selected  

> select add #11

6 models selected  

> select add #13

8 models selected  

> select subtract #13

6 models selected  

> color #10 #153560ff models

> color #10 #193e6dff models

> color #11 #193e6dff models

> hide #!13 models

> color #8 #193e6dff models

> show #!6 models

> hide #!1 models

> show #!9 models

> hide #!9 models

> save /Users/hwang/Dropbox/Huping/draft/TMEM208/dock_preHO_maps_2.cxs
> includeMaps true


===== Log before crash end =====

Log:
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.5.dev202209130706 (2022-09-13)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 ATI-4.7.103
OpenGL renderer: AMD Radeon Pro 5700 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.1
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: iMac
      Model Identifier: iMac20,2
      Processor Name: 10-Core Intel Core i9
      Processor Speed: 3.6 GHz
      Number of Processors: 1
      Total Number of Cores: 10
      L2 Cache (per Core): 256 KB
      L3 Cache: 20 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      System Firmware Version: 1715.81.2.0.0 (iBridge: 19.16.10744.0.0,0)
      OS Loader Version: 540.80.2~11

Software:

    System Software Overview:

      System Version: macOS 12.2.1 (21D62)
      Kernel Version: Darwin 21.3.0
      Time since boot: 39 days 5:04

Graphics/Displays:

    AMD Radeon Pro 5700:

      Chipset Model: AMD Radeon Pro 5700
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 8 GB
      Vendor: AMD (0x1002)
      Device ID: 0x731b
      Revision ID: 0x0040
      ROM Revision: 113-D1820Q-231
      VBIOS Version: 113-D182A2XG-013
      Option ROM Version: 113-D182A2XG-013
      EFI Driver Version: 01.01.231
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        iMac:
          Display Type: Built-In Retina LCD
          Resolution: Retina 5K (5120 x 2880)
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.0.8
    Babel: 2.10.3
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.8.0
    certifi: 2021.10.8
    cftime: 1.6.1
    charset-normalizer: 2.1.1
    ChimeraX-AddCharge: 1.4
    ChimeraX-AddH: 2.2
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.6
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.41.2
    ChimeraX-AtomicLibrary: 7.0.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.7.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.1
    ChimeraX-ChangeChains: 1.0
    ChimeraX-CheckWaters: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.2
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.2
    ChimeraX-CommandLine: 1.2.4
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.5.dev202209130706
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.3
    ChimeraX-DockPrep: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.1
    ChimeraX-MatchMaker: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.8
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.6
    ChimeraX-ModelPanel: 1.3.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.9.1
    ChimeraX-PDB: 2.6.7
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.7.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.1.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.24
    ChimeraX-uniprot: 2.2.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.1.3
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.1
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.5
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.32
    debugpy: 1.6.3
    decorator: 5.1.1
    docutils: 0.19
    entrypoints: 0.4
    executing: 1.0.0
    filelock: 3.7.1
    fonttools: 4.37.1
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.33
    imagecodecs: 2022.7.31
    imagesize: 1.4.1
    importlib-metadata: 4.12.0
    ipykernel: 6.15.1
    ipython: 8.4.0
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.1.2
    jupyter-client: 7.3.4
    jupyter-core: 4.11.1
    kiwisolver: 1.4.4
    line-profiler: 3.5.1
    lxml: 4.9.1
    lz4: 4.0.2
    MarkupSafe: 2.1.1
    matplotlib: 3.5.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.5
    netCDF4: 1.6.0
    networkx: 2.8.5
    numexpr: 2.8.3
    numpy: 1.23.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.2.0
    pip: 22.2.2
    pkginfo: 1.8.3
    prompt-toolkit: 3.0.31
    psutil: 5.9.1
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.12.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.1
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.1
    python-dateutil: 2.8.2
    pytz: 2022.2.1
    pyzmq: 23.2.1
    qtconsole: 5.3.1
    QtPy: 2.2.0
    RandomWords: 0.4.0
    requests: 2.28.1
    scipy: 1.9.0
    setuptools: 65.1.1
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 5.1.1
    sphinx-autodoc-typehints: 1.19.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.5.0
    tables: 3.7.0
    tifffile: 2022.7.31
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.3.0
    urllib3: 1.26.12
    wcwidth: 0.2.5
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    zipp: 3.8.1

Change History (4)

comment:1 by Eric Pettersen, 20 months ago

Cc: Tom Goddard added
Component: UnassignedWindow Toolkit
Owner: set to Eric Pettersen
Platform: all
Project: ChimeraX
Status: newaccepted
Summary: ChimeraX bug report submissionCrash setting active window

comment:2 by Eric Pettersen, 20 months ago

Status: acceptedfeedback

Hi Huping,

Thanks for reporting this problem. Do you remember if this crash occurred as you saving your session, or were you doing something after that when the crash occurred?

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

comment:3 by hwang@…, 20 months ago

Dear Eric,

I saved a session then went to a talk for 1h. After came back I was intended to erase a small part of the map. This was when it crashed. 

All the best,
Huping


comment:4 by Eric Pettersen, 20 months ago

Resolution: can't reproduce
Status: feedbackclosed

Hi Huping,

I would recommend upgrading to the ChimeraX 1.7.1 release. There was a bug in the 1.6.1 release related to waking from sleep that may or may not have also been in the 1.5 release that you are using. In any event, using the latest release will make it easier to debug the problem in the unlikely event that it's not fixed by the 1.7.1 release.

--Eric

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