Opened 20 months ago
Closed 20 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" : [{"queue":"com.apple.main-thread","instructionState":{"instructionStream":{"bytes":[46,15,31,132,0,0,0,0,0,15,31,68,0,0,85,72,137,229,72,137,248,72,139,78,48,72,137,15,72,139,86,56,72,137,87,8,72,139,86,64,72,137,87,16,72,133,201,116,4,240,131,1,1,93,195,15,31,128,0,0,0,0,85,72,137,229,65,87,65,86,65,85,65,84,83,72,131,236,40,73,137,254,15,87,192,15,17,7,72,199,71,16,0,0,0,0,76,139,102,64,77,133,228,15,132,213,1,0,0,72,139,70,56,72,137,69,184,73,193,228,3,69,49,255,72,141,93,192,235,39,102,46,15,31,132,0,0,0,0,0,102,144,76,137,247,49,246,49,210,49,201,232,114,4,0,0,73,131,199,8,77,57,252,15,132,153,1,0,0,72,139,69,184,74,139,4,56,72,139,72,88,72,133,201,116,100,139,81,4,133,210,116],"offset":96}},"frames":[{"imageOffset":28946,"symbol":"__pthread_kill","symbolLocation":10,"imageIndex":0},{"imageOffset":25108,"symbol":"pthread_kill","symbolLocation":263,"imageIndex":1},{"imageOffset":278980,"symbol":"raise","symbolLocation":26,"imageIndex":2},{"imageOffset":15917,"symbol":"_sigtramp","symbolLocation":29,"imageIndex":3},{"imageOffset":0,"imageIndex":4},{"imageOffset":176619,"imageIndex":5},{"imageOffset":170109,"imageIndex":5},{"imageOffset":782706,"imageIndex":6},{"imageOffset":548878,"symbol":"QGuiApplicationPrivate::processActivatedEvent(QWindowSystemInterfacePrivate::ActivatedWindowEvent*)","symbolLocation":942,"imageIndex":7},{"imageOffset":910876,"imageIndex":7},{"imageOffset":395111,"imageIndex":5},{"imageOffset":1478141,"symbol":"-[NSWindow 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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 , 20 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 , 20 months ago
Status: | accepted → feedback |
---|
comment:3 by , 20 months ago
Dear Eric, I saved a session then went to a talk for 1h. After came back I was intended to erase a small part of the map. This was when it crashed. All the best, Huping
comment:4 by , 20 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
Note:
See TracTickets
for help on using tickets.
Hi Huping,
--Eric