Opened 21 months ago
Closed 21 months ago
#14682 closed defect (can't reproduce)
Crash setting active window
| Reported by: | 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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"SIRI_MORPHUN_ASSETS" : "6103050cbfe6dc472e1c982a"
},
"deploymentId" : 240000066
},
{
"rolloutId" : "601d9415f79519000ccd4b69",
"factorPackIds" : {
"SIRI_TEXT_TO_SPEECH" : "622657ce37186c771d5404ad"
},
"deploymentId" : 240000416
},
{
"rolloutId" : "63582c5f8a53461413999550",
"factorPackIds" : {
},
"deploymentId" : 240000002
},
{
"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" : {
},
"deploymentId" : 240000069
},
{
"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 , 21 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Window Toolkit |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash setting active window |
comment:2 by , 21 months ago
| Status: | accepted → feedback |
|---|
comment:3 by , 21 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 , 21 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | feedback → closed |
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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Hi Huping,
--Eric