id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
14682	Crash setting active window	hwang@…	Eric Pettersen	"{{{
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},
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}
===== 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

}}}
"	defect	closed	normal		Window Toolkit		can't reproduce		Tom Goddard				all	ChimeraX