![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 4 years ago
Closed 4 years ago
#6468 closed defect (can't reproduce)
Crash in Qt event loop after saving sessions with maps
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sessions | Version: | |
| Keywords: | Cc: | ||
| 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: 1.3 (2021-12-08 23:08:33 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x00007000075ed000 (most recent call first):
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 316 in wait
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 574 in wait
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 1284 in run
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Current thread 0x00000001106b8600 (most recent call first):
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 301 in event_loop
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py", line 867 in init
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py", line 1018 in
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main
{"app_name":"ChimeraX","timestamp":"2022-03-25 21:46:23.00 -0400","app_version":"1.3.0","slice_uuid":"9596eff5-d2be-396c-9c4e-6177235c3dae","build_version":"1.3.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":1,"is_first_party":0,"bug_type":"309","os_version":"macOS 12.2.1 (21D62)","incident_id":"E762CDE2-18D6-419B-9643-01360E6DEE38","name":"ChimeraX"}
{
"uptime" : 630000,
"procLaunch" : "2022-03-25 20:45:30.0594 -0400",
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro16,1",
"procStartAbsTime" : 627203471819743,
"coalitionID" : 41917,
"osVersion" : {
"train" : "macOS 12.2.1",
"build" : "21D62",
"releaseType" : "User"
},
"captureTime" : "2022-03-25 21:46:14.5340 -0400",
"incident" : "E762CDE2-18D6-419B-9643-01360E6DEE38",
"bug_type" : "309",
"pid" : 48042,
"procExitAbsTime" : 630847951425409,
"cpuType" : "X86-64",
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.3.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.3.0","CFBundleVersion":"1.3.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"D925C038-417C-5232-8E26-B18684AC4B44","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "67FBC4A0-8B5F-1AB5-AADA-75EAE622406F",
"wakeTime" : 5885,
"bridgeVersion" : {"build":"19P744","train":"6.2"},
"sleepWakeUUID" : "F40FE598-E502-4EE8-A029-208F07F02700",
"sip" : "enabled",
"vmRegionInfo" : "0 is not in any region. Bytes before following region: 4481150976\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10b18f000-10b190000 [ 4K] r-x\/r-x SM=COW ...acOS\/ChimeraX",
"isCorpse" : 1,
"exception" : {"codes":"0x000000000000000d, 0x0000000000000000","rawCodes":[13,0],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"UNKNOWN_0xD at 0x0000000000000000"},
"ktriageinfo" : "VM - 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\nVM - Compressor failed a blocking pager_get\n",
"vmregioninfo" : "0 is not in any region. Bytes before following region: 4481150976\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10b18f000-10b190000 [ 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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"rolloutId" : "602ad4dac86151000cf27e46",
"factorPackIds" : {
"SIRI_DICTATION_ASSETS" : "6193d03f2171a2330e561dfc"
},
"deploymentId" : 240000305
},
{
"rolloutId" : "601d9415f79519000ccd4b69",
"factorPackIds" : {
"SIRI_TEXT_TO_SPEECH" : "622657ce37186c771d5404ad"
},
"deploymentId" : 240000416
},
{
"rolloutId" : "5ffde50ce2aacd000d47a95f",
"factorPackIds" : {
},
"deploymentId" : 240000123
},
{
"rolloutId" : "5fc94383418129005b4e9ae0",
"factorPackIds" : {
},
"deploymentId" : 240000295
}
],
"experiments" : [
]
}
}
===== Log before crash start =====
UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/kate/Desktop/Modelling/cryosparc_J207.cxs
Opened cryosparc_P18_J203_class_02_00142_volume.mrc z flip as #4, grid size
128,128,128, pixel 2.59, shown at level 0.322, step 1, values float32
Opened cryosparc_P18_J203_class_01_00142_volume.mrc z flip as #5, grid size
128,128,128, pixel 2.59, shown at level 0.514, step 1, values float32
Opened cryosparc_P18_J203_class_00_00142_volume.mrc z flip as #6, grid size
128,128,128, pixel 2.59, shown at level 0.315, step 1, values float32
Opened cryosparc_P18_J185_class_00_00162_volume.mrc as #2, grid size
128,128,128, pixel 2.59, shown at level 0.221, step 1, values float32
Opened cryosparc_P18_J185_class_01_00162_volume.mrc as #3, grid size
128,128,128, pixel 2.59, shown at level 0.381, step 1, values float32
Opened cryosparc_P18_J185_class_02_00162_volume.mrc as #7, grid size
128,128,128, pixel 2.59, shown at level 0.222, step 1, values float32
Opened cryosparc_P18_J185_class_00_00162_volume.mrc z flip as #8, grid size
128,128,128, pixel 2.59, shown at level 0.28, step 1, values float32
Opened cryosparc_P18_J185_class_01_00162_volume.mrc z flip as #9, grid size
128,128,128, pixel 2.59, shown at level 0.325, step 1, values float32
Opened cryosparc_P18_J185_class_02_00162_volume.mrc z flip as #10, grid size
128,128,128, pixel 2.59, shown at level 0.225, step 1, values float32
Opened cryosparc_P18_J207_class_02_00102_volume.mrc z flip as #14, grid size
128,128,128, pixel 2.59, shown at level 0.464, step 1, values float32
Opened cryosparc_P18_J207_class_00_00102_volume.mrc z flip as #13, grid size
128,128,128, pixel 2.59, shown at level 0.282, step 1, values float32
Opened cryosparc_P18_J207_class_01_00102_volume.mrc z flip as #16, grid size
128,128,128, pixel 2.59, shown at level 0.282, step 1, values float32
Opened cryosparc_P18_J207_class_03_00102_volume.mrc z flip as #12, grid size
128,128,128, pixel 2.59, shown at level 0.282, step 1, values float32
Opened cryosparc_P18_J209_005_volume_map.mrc z flip as #17, grid size
400,400,400, pixel 0.83, shown at level 0.0773, step 1, values float32
opened ChimeraX session
> select #17
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #17,0.99982,0.017549,0.0076871,-3.913,-0.018067,0.99713,0.073491,-8.432,-0.0063754,-0.073616,0.99727,11.472
> ui tool show "Fit in Map"
Fit molecule 3lz0 (#15) to map cryosparc_P18_J209_005_volume_map.mrc z flip
(#17) using 11908 atoms
average map value = 0.09375, steps = 64
shifted from previous position = 1.11
rotated from previous position = 3.95 degrees
atoms outside contour = 3912, contour level = 0.077264
Position of 3lz0 (#15) relative to cryosparc_P18_J209_005_volume_map.mrc z
flip (#17) coordinates:
Matrix rotation and translation
-0.01066791 -0.98142446 0.19155217 145.42854530
-0.92976680 -0.06076261 -0.36309998 163.03020845
0.36799441 -0.18197237 -0.91184767 218.58520600
Axis 0.70181525 -0.68366085 0.20015793
Axis point 0.00000000 142.57591251 97.16426346
Rotation angle (degrees) 172.58574997
Shift along axis 34.35816382
> open /Users/kate/Desktop/Modelling/cryosparc_J207.cxs
Opened cryosparc_P18_J203_class_02_00142_volume.mrc z flip as #4, grid size
128,128,128, pixel 2.59, shown at level 0.322, step 1, values float32
Opened cryosparc_P18_J203_class_01_00142_volume.mrc z flip as #5, grid size
128,128,128, pixel 2.59, shown at level 0.514, step 1, values float32
Opened cryosparc_P18_J203_class_00_00142_volume.mrc z flip as #6, grid size
128,128,128, pixel 2.59, shown at level 0.315, step 1, values float32
Opened cryosparc_P18_J185_class_00_00162_volume.mrc as #2, grid size
128,128,128, pixel 2.59, shown at level 0.221, step 1, values float32
Opened cryosparc_P18_J185_class_01_00162_volume.mrc as #3, grid size
128,128,128, pixel 2.59, shown at level 0.381, step 1, values float32
Opened cryosparc_P18_J185_class_02_00162_volume.mrc as #7, grid size
128,128,128, pixel 2.59, shown at level 0.222, step 1, values float32
Opened cryosparc_P18_J185_class_00_00162_volume.mrc z flip as #8, grid size
128,128,128, pixel 2.59, shown at level 0.28, step 1, values float32
Opened cryosparc_P18_J185_class_01_00162_volume.mrc z flip as #9, grid size
128,128,128, pixel 2.59, shown at level 0.325, step 1, values float32
Opened cryosparc_P18_J185_class_02_00162_volume.mrc z flip as #10, grid size
128,128,128, pixel 2.59, shown at level 0.225, step 1, values float32
Opened cryosparc_P18_J207_class_02_00102_volume.mrc z flip as #14, grid size
128,128,128, pixel 2.59, shown at level 0.464, step 1, values float32
Opened cryosparc_P18_J207_class_00_00102_volume.mrc z flip as #13, grid size
128,128,128, pixel 2.59, shown at level 0.282, step 1, values float32
Opened cryosparc_P18_J207_class_01_00102_volume.mrc z flip as #16, grid size
128,128,128, pixel 2.59, shown at level 0.282, step 1, values float32
Opened cryosparc_P18_J207_class_03_00102_volume.mrc z flip as #12, grid size
128,128,128, pixel 2.59, shown at level 0.282, step 1, values float32
Opened cryosparc_P18_J209_005_volume_map.mrc z flip as #17, grid size
400,400,400, pixel 0.83, shown at level 0.0773, step 1, values float32
opened ChimeraX session
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /Users/kate/Desktop/Modelling/cryosparc_J207.cxs
Opened cryosparc_P18_J203_class_02_00142_volume.mrc z flip as #4, grid size
128,128,128, pixel 2.59, shown at level 0.322, step 1, values float32
Opened cryosparc_P18_J203_class_01_00142_volume.mrc z flip as #5, grid size
128,128,128, pixel 2.59, shown at level 0.514, step 1, values float32
Opened cryosparc_P18_J203_class_00_00142_volume.mrc z flip as #6, grid size
128,128,128, pixel 2.59, shown at level 0.315, step 1, values float32
Opened cryosparc_P18_J185_class_00_00162_volume.mrc as #2, grid size
128,128,128, pixel 2.59, shown at level 0.221, step 1, values float32
Opened cryosparc_P18_J185_class_01_00162_volume.mrc as #3, grid size
128,128,128, pixel 2.59, shown at level 0.381, step 1, values float32
Opened cryosparc_P18_J185_class_02_00162_volume.mrc as #7, grid size
128,128,128, pixel 2.59, shown at level 0.222, step 1, values float32
Opened cryosparc_P18_J185_class_00_00162_volume.mrc z flip as #8, grid size
128,128,128, pixel 2.59, shown at level 0.28, step 1, values float32
Opened cryosparc_P18_J185_class_01_00162_volume.mrc z flip as #9, grid size
128,128,128, pixel 2.59, shown at level 0.325, step 1, values float32
Opened cryosparc_P18_J185_class_02_00162_volume.mrc z flip as #10, grid size
128,128,128, pixel 2.59, shown at level 0.225, step 1, values float32
Opened cryosparc_P18_J207_class_02_00102_volume.mrc z flip as #14, grid size
128,128,128, pixel 2.59, shown at level 0.464, step 1, values float32
Opened cryosparc_P18_J207_class_00_00102_volume.mrc z flip as #13, grid size
128,128,128, pixel 2.59, shown at level 0.282, step 1, values float32
Opened cryosparc_P18_J207_class_01_00102_volume.mrc z flip as #16, grid size
128,128,128, pixel 2.59, shown at level 0.282, step 1, values float32
Opened cryosparc_P18_J207_class_03_00102_volume.mrc z flip as #12, grid size
128,128,128, pixel 2.59, shown at level 0.282, step 1, values float32
Opened cryosparc_P18_J209_005_volume_map.mrc z flip as #17, grid size
400,400,400, pixel 0.83, shown at level 0.0773, step 1, values float32
Log from Fri Mar 25 20:46:34 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /home/behrouzi/Downloads/cryosparc_P18_J203_class_02_00142_volume.mrc
Opened cryosparc_P18_J203_class_02_00142_volume.mrc as #1, grid size
128,128,128, pixel 2.59, shown at level 0.292, step 1, values float32
> open /home/behrouzi/Downloads/cryosparc_P18_J203_class_01_00142_volume.mrc
Opened cryosparc_P18_J203_class_01_00142_volume.mrc as #2, grid size
128,128,128, pixel 2.59, shown at level 0.266, step 1, values float32
> open /home/behrouzi/Downloads/cryosparc_P18_J203_class_00_00142_volume.mrc
Opened cryosparc_P18_J203_class_00_00142_volume.mrc as #3, grid size
128,128,128, pixel 2.59, shown at level 0.276, step 1, values float32
> hide #!2 models
> hide #!3 models
> volume #1 level 0.4142
> volume #1 level 0.3302
> vop flip #1-3
Opened cryosparc_P18_J203_class_02_00142_volume.mrc z flip as #4, grid size
128,128,128, pixel 2.59, shown at step 1, values float32
Opened cryosparc_P18_J203_class_01_00142_volume.mrc z flip as #5, grid size
128,128,128, pixel 2.59, shown at step 1, values float32
Opened cryosparc_P18_J203_class_00_00142_volume.mrc z flip as #6, grid size
128,128,128, pixel 2.59, shown at step 1, values float32
> close #1
> close #2
> close #3
> volume #4 level 0.2507
> volume #4 level 0.2601
> volume #4 level 0.3864
> volume #4 level 0.4121
> 1ubq
Unknown command: 1ubq
> open 1ubq
1ubq title:
Structure of ubiquitin refined At 1.8 angstroms resolution [more info...]
Chain information for 1ubq #1
---
Chain | Description | UniProt
A | ubiquitin | UBIQ_HUMAN
> select #1
660 atoms, 608 bonds, 134 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #1,1,0,0,123.07,0,1,0,71.882,0,0,1,128.61
> view matrix models #1,1,0,0,124.38,0,1,0,127.68,0,0,1,105.11
> ui tool show "Fit in Map"
Fit molecule 1ubq (#1) to map cryosparc_P18_J203_class_02_00142_volume.mrc z
flip (#4) using 660 atoms
average map value = 0.3686, steps = 160
shifted from previous position = 7.72
rotated from previous position = 85.3 degrees
atoms outside contour = 492, contour level = 0.41212
Position of 1ubq (#1) relative to cryosparc_P18_J203_class_02_00142_volume.mrc
z flip (#4) coordinates:
Matrix rotation and translation
0.97144537 -0.18611259 -0.14715975 136.19150881
-0.12832275 0.10956376 -0.98566174 165.28304353
0.19956743 0.97640047 0.08255273 83.48543591
Axis 0.98432828 -0.17394625 0.02899204
Axis point 0.00000000 50.36749314 141.19726907
Rotation angle (degrees) 85.30905899
Shift along axis 107.72720008
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.87175,-0.46961,-0.13971,200.65,0.36294,-0.42739,-0.82802,164.15,0.32913,-0.77253,0.54302,125.29
> view matrix models
> #1,-0.92246,-0.37312,-0.099221,198.49,0.29136,-0.50415,-0.81298,168.41,0.25332,-0.77886,0.57377,127.23
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.92246,-0.37312,-0.099221,201.04,0.29136,-0.50415,-0.81298,173.4,0.25332,-0.77886,0.57377,122.67
> volume #4 level 0.3706
> hide #1 models
> volume #5 level 0.2151
> volume #5 level 0.2887
> volume #5 level 0.2726
> volume #6 level 0.2491
> volume #6 level 0.3154
> volume #5 level 0.5694
> volume #4 level 0.2576
> open
> /home/behrouzi/cryosparc/cryosparc_220307_Clr4/cryosparc_P18_J185_class_00_00162_volume.mrc
Opened cryosparc_P18_J185_class_00_00162_volume.mrc as #2, grid size
128,128,128, pixel 2.59, shown at level 0.221, step 1, values float32
> open
> /home/behrouzi/cryosparc/cryosparc_220307_Clr4/cryosparc_P18_J185_class_01_00162_volume.mrc
Opened cryosparc_P18_J185_class_01_00162_volume.mrc as #3, grid size
128,128,128, pixel 2.59, shown at level 0.269, step 1, values float32
> open
> /home/behrouzi/cryosparc/cryosparc_220307_Clr4/cryosparc_P18_J185_class_02_00162_volume.mrc
Opened cryosparc_P18_J185_class_02_00162_volume.mrc as #7, grid size
128,128,128, pixel 2.59, shown at level 0.25, step 1, values float32
> hide #!4 models
> hide #!2 models
> hide #!3 models
> hide #!7 models
> show #!7 models
> vop flip #3
Opened cryosparc_P18_J185_class_01_00162_volume.mrc z flip as #8, grid size
128,128,128, pixel 2.59, shown at step 1, values float32
> vop flip #2
Opened cryosparc_P18_J185_class_00_00162_volume.mrc z flip as #9, grid size
128,128,128, pixel 2.59, shown at step 1, values float32
> vop flip #7
Opened cryosparc_P18_J185_class_02_00162_volume.mrc z flip as #10, grid size
128,128,128, pixel 2.59, shown at step 1, values float32
> ~select #1
Nothing selected
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!9 models
> hide #!10 models
> hide #!8 models
> volume #3 level 0.3807
> volume #7 level 0.2219
> close #10
> close #9
> close #8
> vop flip #2,3,7
Opened cryosparc_P18_J185_class_00_00162_volume.mrc z flip as #8, grid size
128,128,128, pixel 2.59, shown at step 1, values float32
Opened cryosparc_P18_J185_class_01_00162_volume.mrc z flip as #9, grid size
128,128,128, pixel 2.59, shown at step 1, values float32
Opened cryosparc_P18_J185_class_02_00162_volume.mrc z flip as #10, grid size
128,128,128, pixel 2.59, shown at step 1, values float32
> volume #10 level 0.2247
> volume #9 level 0.239
> volume #8 level 0.1833
> volume #8 level 0.2797
> volume #9 level 0.325
> show #!4 models
> hide #!9 models
> show #!5 models
> hide #!4 models
> hide #!5 models
> show #!4 models
> show #!5 models
> show #!6 models
> volume #5 level 0.2887
> hide #!6 models
> hide #!4 models
> volume #5 level 0.2358
> hide #!5 models
> show #!6 models
> open
> /home/behrouzi/cryosparc/cryosparc_220307_Clr4/cryosparc_P18_J207_class_00_00102_volume.mrc
Opened cryosparc_P18_J207_class_00_00102_volume.mrc as #11, grid size
128,128,128, pixel 2.59, shown at level 0.292, step 1, values float32
> open
> /home/behrouzi/cryosparc/cryosparc_220307_Clr4/cryosparc_P18_J207_class_01_00102_volume.mrc
Opened cryosparc_P18_J207_class_01_00102_volume.mrc as #12, grid size
128,128,128, pixel 2.59, shown at level 0.262, step 1, values float32
> open
> /home/behrouzi/cryosparc/cryosparc_220307_Clr4/cryosparc_P18_J207_class_02_00102_volume.mrc
Opened cryosparc_P18_J207_class_02_00102_volume.mrc as #13, grid size
128,128,128, pixel 2.59, shown at level 0.306, step 1, values float32
> hide #!6 models
> hide #!12 models
> hide #!13 models
> volume #11 level 0.4088
> volume #11 level 0.2873
> hide #!11 models
> show #!12 models
> hide #!12 models
> show #!13 models
> vop flip #13
Opened cryosparc_P18_J207_class_02_00102_volume.mrc z flip as #14, grid size
128,128,128, pixel 2.59, shown at step 1, values float32
> volume #13 level 0.4081
> hide #!13 models
> show #!4 models
> volume #4 level 0.3222
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> hide #!4 models
> show #!5 models
> show #!14 models
> open 3lz0
3lz0 title:
Crystal Structure of Nucleosome Core Particle Composed of the Widom 601 DNA
Sequence (orientation 1) [more info...]
Chain information for 3lz0 #15
---
Chain | Description | UniProt
A E | Histone H3.2 | H32_XENLA
B F | Histone H4 | H4_XENLA
C G | Histone H2A | Q6AZJ8_XENLA
D H | Histone H2B 1.1 | H2B11_XENLA
I | DNA (145-mer) |
J | DNA (145-mer) |
Non-standard residues in 3lz0 #15
---
CL — chloride ion
MN — manganese (II) ion
> select #15
11908 atoms, 12700 bonds, 334 pseudobonds, 1051 residues, 3 models selected
> view matrix models #15,1,0,0,225.86,0,1,0,44.811,0,0,1,16.474
> view matrix models #15,1,0,0,173,0,1,0,128.83,0,0,1,143.44
> view matrix models #15,1,0,0,187.87,0,1,0,188.43,0,0,1,113.43
> ui mousemode right "rotate selected models"
> view matrix models
> #15,0.087514,-0.98792,-0.12789,153.13,0.9308,0.035359,0.36381,171.17,-0.35489,-0.15088,0.92265,106.15
> hide #!14 models
> volume #5 level 0.5142
> hide sel atoms
> show sel cartoons
> view matrix models
> #15,0.4357,-0.82483,-0.3603,173.92,0.87658,0.29795,0.37793,175.04,-0.20438,-0.4805,0.85285,105.27
> view matrix models
> #15,0.37177,-0.91265,0.16986,147.74,-0.89372,-0.40136,-0.20044,148.38,0.25111,-0.077286,-0.96487,202.08
> view matrix models
> #15,-0.043627,-0.87192,0.4877,126.21,-0.93044,-0.14232,-0.33769,159.1,0.36385,-0.4685,-0.80506,189.15
> view matrix models
> #15,-0.065002,-0.88689,0.45739,126.76,-0.9292,-0.11332,-0.35178,160.35,0.36381,-0.44787,-0.81673,190.1
> view matrix models
> #15,-0.19304,-0.94641,0.25891,131.43,-0.90688,0.071369,-0.4153,167.51,0.37456,-0.31497,-0.87206,195.56
> ui mousemode right "translate selected models"
> view matrix models
> #15,-0.19304,-0.94641,0.25891,141.27,-0.90688,0.071369,-0.4153,164.53,0.37456,-0.31497,-0.87206,199.89
Fit molecule 3lz0 (#15) to map cryosparc_P18_J203_class_02_00142_volume.mrc z
flip (#4) using 11908 atoms
average map value = 0.5527, steps = 80
shifted from previous position = 12.4
rotated from previous position = 10.5 degrees
atoms outside contour = 1025, contour level = 0.32218
Position of 3lz0 (#15) relative to
cryosparc_P18_J203_class_02_00142_volume.mrc z flip (#4) coordinates:
Matrix rotation and translation
-0.02418109 -0.97986826 0.19817536 145.21368009
-0.92678755 -0.05234851 -0.37191997 163.55384603
0.37480676 -0.19265989 -0.90686386 215.74768192
Axis 0.69697531 -0.68675480 0.20638136
Axis point 0.00000000 143.64511866 95.01294070
Rotation angle (degrees) 172.61138207
Shift along axis 33.41526061
> hide #!5 models
> color sel bychain
> show #!14 models
> close #13
> close #12
> close #11
> open
> /home/behrouzi/cryosparc/cryosparc_220307_Clr4/cryosparc_P18_J207_class_00_00102_volume.mrc
Opened cryosparc_P18_J207_class_00_00102_volume.mrc as #11, grid size
128,128,128, pixel 2.59, shown at level 0.292, step 1, values float32
> open
> /home/behrouzi/cryosparc/cryosparc_220307_Clr4/cryosparc_P18_J207_class_01_00102_volume.mrc
Opened cryosparc_P18_J207_class_01_00102_volume.mrc as #12, grid size
128,128,128, pixel 2.59, shown at level 0.262, step 1, values float32
> select up
12568 atoms, 13308 bonds, 334 pseudobonds, 1185 residues, 28 models selected
> select up
12568 atoms, 13308 bonds, 334 pseudobonds, 1185 residues, 28 models selected
> vop flip #11,12
Opened cryosparc_P18_J207_class_00_00102_volume.mrc z flip as #13, grid size
128,128,128, pixel 2.59, shown at step 1, values float32
Opened cryosparc_P18_J207_class_01_00102_volume.mrc z flip as #16, grid size
128,128,128, pixel 2.59, shown at step 1, values float32
> ~select #1
11908 atoms, 12700 bonds, 334 pseudobonds, 1051 residues, 27 models selected
> show #1 models
> hide #1 models
> ~select #2
11908 atoms, 12700 bonds, 334 pseudobonds, 1051 residues, 25 models selected
> ~select #3
11908 atoms, 12700 bonds, 334 pseudobonds, 1051 residues, 23 models selected
> ~select #4
11908 atoms, 12700 bonds, 334 pseudobonds, 1051 residues, 21 models selected
> ~select #5
11908 atoms, 12700 bonds, 334 pseudobonds, 1051 residues, 19 models selected
> ~select #6
11908 atoms, 12700 bonds, 334 pseudobonds, 1051 residues, 17 models selected
> ~select #7
11908 atoms, 12700 bonds, 334 pseudobonds, 1051 residues, 15 models selected
> ~select #8
11908 atoms, 12700 bonds, 334 pseudobonds, 1051 residues, 13 models selected
> ~select #15
10 models selected
> ~select #14
8 models selected
> ~select #12
6 models selected
> ~select #11
4 models selected
> ~select #10
2 models selected
> ~select #9
Nothing selected
> hide #!13 models
> hide #!14 models
> volume #16 level 0.5822
> volume #16 level 0.1861
> hide #!16 models
> show #!14 models
Fit molecule 3lz0 (#15) to map cryosparc_P18_J207_class_02_00102_volume.mrc z
flip (#14) using 11908 atoms
average map value = 0.5131, steps = 36
shifted from previous position = 0.0965
rotated from previous position = 0.148 degrees
atoms outside contour = 996, contour level = 0.30581
Position of 3lz0 (#15) relative to
cryosparc_P18_J207_class_02_00102_volume.mrc z flip (#14) coordinates:
Matrix rotation and translation
-0.02279591 -0.97949752 0.20016232 145.20081148
-0.92652134 -0.05451162 -0.37227232 163.51565359
0.37555099 -0.19394095 -0.90628272 215.79936649
Axis 0.69749224 -0.68598269 0.20720118
Axis point -0.00000000 143.55390536 94.92324854
Rotation angle (degrees) 172.65535069
Shift along axis 33.82141608
> volume #14 level 0.5607
> volume #14 level 0.4751
> volume #14 level 0.278
> volume #14 level 0.4472
> volume #14 level 0.3829
> show #!13 models
> hide #!14 models
> close #11
> close #12
> volume #13 level 0.4971
> volume #13 level 0.337
> volume #13 level 0.6234
> volume #13 level 0.2603
> volume #13 level 0.2378
> volume #13 level 0.3167
> show #!16 models
> volume #16 level 0.2875
> open
> /home/behrouzi/cryosparc/cryosparc_220307_Clr4/cryosparc_P18_J207_class_03_00102_volume.mrc
Opened cryosparc_P18_J207_class_03_00102_volume.mrc as #11, grid size
128,128,128, pixel 2.59, shown at level 0.297, step 1, values float32
> hide #!11 models
> hide #!13 models
> show #!11 models
> hide #!16 models
> vop flip #11
Opened cryosparc_P18_J207_class_03_00102_volume.mrc z flip as #12, grid size
128,128,128, pixel 2.59, shown at step 1, values float32
> close #11
> show #!16 models
> hide #!16 models
> volume #12 level 0.4054
> volume #12 level 0.2819
> hide #!15 models
> show #!13 models
> volume #13 level 0.2829
> show #!14 models
> show #!16 models
> hide #!16 models
> hide #!13 models
> hide #!12 models
> volume #14 level 0.2437
> show #!15 models
> volume #14 level 0.2115
> hide #!15 models
> show #!16 models
> volume #16 level 0.282
> volume #13 level 0.282
> volume #14 level 0.282
> hide #!16 models
> hide #!14 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!12 models
> hide #!13 models
> show #!14 models
> show #!13 models
> hide #!14 models
> hide #!13 models
> show #!14 models
> hide #!14 models
> show #!16 models
> hide #!16 models
> show #!14 models
> show #1 models
> color #1 #a40000 transparency 0
> volume #14 level 0.4641
> volume #14 level 0.5069
> show #!15 models
> volume #14 level 0.4812
> volume #14 level 0.4512
> select #1
660 atoms, 608 bonds, 134 residues, 1 model selected
> view matrix models
> #1,-0.92246,-0.37312,-0.099221,203.04,0.29136,-0.50415,-0.81298,170.03,0.25332,-0.77886,0.57377,120.14
> view matrix models
> #1,-0.92246,-0.37312,-0.099221,198.97,0.29136,-0.50415,-0.81298,202.36,0.25332,-0.77886,0.57377,127.84
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.94635,-0.23064,-0.22632,197.56,0.12458,-0.90665,0.40307,198.23,-0.29816,0.35325,0.88674,104.1
> view matrix models
> #1,-0.91358,-0.3343,-0.23156,199.85,0.20275,-0.86802,0.45324,193.78,-0.35252,0.36712,0.86078,105.78
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.91358,-0.3343,-0.23156,201.93,0.20275,-0.86802,0.45324,178.94,-0.35252,0.36712,0.86078,94.219
> view matrix models
> #1,-0.91358,-0.3343,-0.23156,189.86,0.20275,-0.86802,0.45324,235.61,-0.35252,0.36712,0.86078,83.543
> view matrix models
> #1,-0.91358,-0.3343,-0.23156,211.69,0.20275,-0.86802,0.45324,174.44,-0.35252,0.36712,0.86078,98.339
> view matrix models
> #1,-0.91358,-0.3343,-0.23156,206.95,0.20275,-0.86802,0.45324,172.73,-0.35252,0.36712,0.86078,99.432
> view matrix models
> #1,-0.91358,-0.3343,-0.23156,229.89,0.20275,-0.86802,0.45324,152.59,-0.35252,0.36712,0.86078,107.72
> volume #14 level 0.4255
> view matrix models
> #1,-0.91358,-0.3343,-0.23156,192.78,0.20275,-0.86802,0.45324,112.64,-0.35252,0.36712,0.86078,119.18
> view matrix models
> #1,-0.91358,-0.3343,-0.23156,134.98,0.20275,-0.86802,0.45324,148.14,-0.35252,0.36712,0.86078,83.719
> view matrix models
> #1,-0.91358,-0.3343,-0.23156,137.97,0.20275,-0.86802,0.45324,171.15,-0.35252,0.36712,0.86078,138.9
> view matrix models
> #1,-0.91358,-0.3343,-0.23156,169.05,0.20275,-0.86802,0.45324,184.36,-0.35252,0.36712,0.86078,125.81
> view matrix models
> #1,-0.91358,-0.3343,-0.23156,169.58,0.20275,-0.86802,0.45324,175.53,-0.35252,0.36712,0.86078,135.52
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.44579,-0.03476,-0.89446,157.95,0.091297,0.99227,-0.084063,131.12,0.89047,-0.11914,-0.43917,135.93
> view matrix models
> #1,-0.75265,-0.2316,-0.61635,168.37,-0.15504,0.97211,-0.17595,140.83,0.63991,-0.036865,-0.76757,146.82
> view matrix models
> #1,-0.81251,-0.50783,-0.28625,172.84,-0.39309,0.83989,-0.37425,155.64,0.43048,-0.19155,-0.88204,159.96
> view matrix models
> #1,-0.1411,-0.68594,-0.71384,165.58,-0.97557,0.21898,-0.017587,186.1,0.16838,0.69392,-0.70009,137.38
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.1411,-0.68594,-0.71384,165.3,-0.97557,0.21898,-0.017587,187.87,0.16838,0.69392,-0.70009,131.8
> view matrix models
> #1,-0.1411,-0.68594,-0.71384,166.4,-0.97557,0.21898,-0.017587,186.54,0.16838,0.69392,-0.70009,135.08
> view matrix models
> #1,-0.1411,-0.68594,-0.71384,164.23,-0.97557,0.21898,-0.017587,187.69,0.16838,0.69392,-0.70009,132.54
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.025945,-0.46002,-0.88753,155.29,-0.98681,0.13011,-0.096284,192.16,0.15977,0.87833,-0.45058,122.69
> view matrix models
> #1,-0.24119,0.50465,-0.82895,132.61,-0.13084,0.82946,0.54303,133.32,0.96162,0.23943,-0.13403,112.46
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.24119,0.50465,-0.82895,77.704,-0.13084,0.82946,0.54303,156.48,0.96162,0.23943,-0.13403,177.24
> view matrix models
> #1,-0.24119,0.50465,-0.82895,150.97,-0.13084,0.82946,0.54303,139.34,0.96162,0.23943,-0.13403,137.09
> view matrix models
> #1,-0.24119,0.50465,-0.82895,155.5,-0.13084,0.82946,0.54303,133.79,0.96162,0.23943,-0.13403,125.53
> view matrix models
> #1,-0.24119,0.50465,-0.82895,150.77,-0.13084,0.82946,0.54303,129.54,0.96162,0.23943,-0.13403,111.28
> view matrix models
> #1,-0.24119,0.50465,-0.82895,137.26,-0.13084,0.82946,0.54303,135.08,0.96162,0.23943,-0.13403,118.23
> volume #14 level 0.2413
> volume #14 level 0.4362
Fit molecule 1ubq (#1) to map cryosparc_P18_J207_class_02_00102_volume.mrc z
flip (#14) using 660 atoms
average map value = 0.4132, steps = 76
shifted from previous position = 10.6
rotated from previous position = 34 degrees
atoms outside contour = 422, contour level = 0.43624
Position of 1ubq (#1) relative to cryosparc_P18_J207_class_02_00102_volume.mrc
z flip (#14) coordinates:
Matrix rotation and translation
0.04614331 0.73031158 -0.68155395 118.39545684
-0.52465781 0.59831732 0.60559934 158.31374099
0.85006175 0.32963824 0.41077202 101.90968678
Axis -0.13803319 -0.76610004 -0.62772411
Axis point 61.46613916 0.00000000 46.86111250
Rotation angle (degrees) 88.41749967
Shift along axis -201.59783434
> view matrix models
> #1,0.046143,0.73031,-0.68155,124.18,-0.52466,0.59832,0.6056,154.92,0.85006,0.32964,0.41077,99.561
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.13443,-0.36502,0.92124,126.8,-0.85717,0.42361,0.29293,175.94,-0.49717,-0.82904,-0.25594,187.94
> view matrix models
> #1,0.48172,-0.30197,-0.82266,145.3,0.25998,-0.84725,0.46323,178.23,-0.83688,-0.43702,-0.32963,187.46
> view matrix models
> #1,-0.28143,0.90719,-0.31272,122.1,0.35997,-0.20228,-0.91077,179.72,-0.8895,-0.36889,-0.26964,185.89
> view matrix models
> #1,-0.17293,0.89292,0.41568,106.32,0.046398,0.42895,-0.90213,169.62,-0.98384,-0.13672,-0.11561,178.85
> view matrix models
> #1,-0.23774,0.9641,0.11826,111.37,0.21833,0.17167,-0.96066,173.38,-0.94647,-0.20256,-0.25131,182.16
> view matrix models
> #1,-0.1952,0.97781,0.076099,110.41,0.13299,0.10326,-0.98572,178.52,-0.97171,-0.18229,-0.15019,180.51
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.1952,0.97781,0.076099,106.6,0.13299,0.10326,-0.98572,178.15,-0.97171,-0.18229,-0.15019,188.32
> view matrix models
> #1,-0.1952,0.97781,0.076099,109.95,0.13299,0.10326,-0.98572,171.27,-0.97171,-0.18229,-0.15019,174.94
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.76479,-0.64398,0.019477,131.85,-0.27485,-0.29878,0.91389,162.28,-0.5827,-0.70429,-0.4055,183.78
> view matrix models
> #1,0.47248,-0.078137,0.87787,108.03,-0.88061,-0.082248,0.46664,181.91,0.035742,-0.99354,-0.10767,168.66
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.47248,-0.078137,0.87787,105.78,-0.88061,-0.082248,0.46664,184.73,0.035742,-0.99354,-0.10767,166.73
> view matrix models
> #1,0.47248,-0.078137,0.87787,106.32,-0.88061,-0.082248,0.46664,189.27,0.035742,-0.99354,-0.10767,166.01
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.50961,-0.083959,0.8563,105.76,-0.8568,-0.14055,0.49613,189.82,0.078696,-0.98651,-0.14356,165.13
> view matrix models
> #1,0.57307,-0.35122,0.74043,114.13,-0.79908,-0.039035,0.59995,183.1,-0.18181,-0.93548,-0.30302,174.28
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.57307,-0.35122,0.74043,120.2,-0.79908,-0.039035,0.59995,180.62,-0.18181,-0.93548,-0.30302,173.65
> volume #14 level 0.387
> open
> /home/behrouzi/cryosparc/cryosparc_220307_Clr4/cryosparc_P18_J209_005_volume_map.mrc
Opened cryosparc_P18_J209_005_volume_map.mrc as #11, grid size 400,400,400,
pixel 0.83, shown at level 0.0549, step 2, values float32
> hide #!14 models
> vop flip #11
Opened cryosparc_P18_J209_005_volume_map.mrc z flip as #17, grid size
400,400,400, pixel 0.83, shown at step 1, values float32
Fit map cryosparc_P18_J209_005_volume_map.mrc z flip in map
cryosparc_P18_J207_class_02_00102_volume.mrc z flip using 639858 points
correlation = 0.9935, correlation about mean = 0.9268, overlap = 2.568e+04
steps = 52, shift = 2.23, angle = 0.523 degrees
Position of cryosparc_P18_J209_005_volume_map.mrc z flip (#17) relative to
cryosparc_P18_J207_class_02_00102_volume.mrc z flip (#14) coordinates:
Matrix rotation and translation
0.99995836 0.00469834 -0.00782269 0.71936693
-0.00469611 0.99998893 0.00030346 0.75861923
0.00782403 -0.00026671 0.99996936 -3.50246066
Axis -0.03122682 -0.85691938 -0.51450371
Axis point 373.74992925 0.00000000 94.47855415
Rotation angle (degrees) 0.52309649
Shift along axis 1.12948994
Fit map cryosparc_P18_J209_005_volume_map.mrc z flip in map
cryosparc_P18_J207_class_02_00102_volume.mrc z flip using 639858 points
correlation = 0.9935, correlation about mean = 0.9268, overlap = 2.568e+04
steps = 24, shift = 0.00305, angle = 0.0232 degrees
Position of cryosparc_P18_J209_005_volume_map.mrc z flip (#17) relative to
cryosparc_P18_J207_class_02_00102_volume.mrc z flip (#14) coordinates:
Matrix rotation and translation
0.99996159 0.00464670 -0.00743210 0.65975411
-0.00464525 0.99998919 0.00021226 0.76603634
0.00743300 -0.00017773 0.99997236 -3.44947842
Axis -0.02224140 -0.84775622 -0.52991953
Axis point 381.43699002 0.00000000 90.28237028
Rotation angle (degrees) 0.50233677
Shift along axis 1.16386004
> volume #14 level 0.4641
> close #11
> volume #17 level 0.07726
> transparency #17 60
> save /home/behrouzi/cryosparc/cryosparc_220307_Clr4/cryosparc_J207.cxs
> includeMaps true
——— End of log from Fri Mar 25 20:46:34 2022 ———
opened ChimeraX session
OpenGL version: 4.1 ATI-4.7.103
OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro16,1
Processor Name: 8-Core Intel Core i9
Processor Speed: 2.3 GHz
Number of Processors: 1
Total Number of Cores: 8
L2 Cache (per Core): 256 KB
L3 Cache: 16 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: 34 days 10:24
Graphics/Displays:
Intel UHD Graphics 630:
Chipset Model: Intel UHD Graphics 630
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3e9b
Revision ID: 0x0002
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Family: Supported, Metal GPUFamily macOS 2
AMD Radeon Pro 5500M:
Chipset Model: AMD Radeon Pro 5500M
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 4 GB
Vendor: AMD (0x1002)
Device ID: 0x7340
Revision ID: 0x0040
ROM Revision: 113-D3220E-190
VBIOS Version: 113-D32206U1-019
Option ROM Version: 113-D32206U1-019
EFI Driver Version: 01.A1.190
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Family: Supported, Metal GPUFamily macOS 2
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 3072 x 1920 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.2
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2021.5.30
cftime: 1.5.1.1
charset-normalizer: 2.0.9
ChimeraX-AddCharge: 1.2.2
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.2.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.31
ChimeraX-AtomicLibrary: 4.2
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.0
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.6.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.2
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5
ChimeraX-CommandLine: 1.1.5
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.3
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.5
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.1.2
ChimeraX-Help: 1.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0
ChimeraX-Label: 1.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.4
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.4
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.4
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.2.6
ChimeraX-ModelPanel: 1.2.1
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.2
ChimeraX-OpenCommand: 1.7
ChimeraX-PDB: 2.6.5
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.4.6
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.6.1
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.13.7
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.0.1
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
cxservices: 1.1
cycler: 0.11.0
Cython: 0.29.24
decorator: 5.1.0
docutils: 0.17.1
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 3.6.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.21
imagecodecs: 2021.4.28
imagesize: 1.3.0
ipykernel: 5.5.5
ipython: 7.23.1
ipython-genutils: 0.2.0
jedi: 0.18.0
Jinja2: 3.0.1
jupyter-client: 6.1.12
jupyter-core: 4.9.1
kiwisolver: 1.3.2
lxml: 4.6.3
lz4: 3.1.3
MarkupSafe: 2.0.1
matplotlib: 3.4.3
matplotlib-inline: 0.1.3
msgpack: 1.0.2
netCDF4: 1.5.7
networkx: 2.6.3
numexpr: 2.8.0
numpy: 1.21.2
openvr: 1.16.801
packaging: 21.0
ParmEd: 3.2.0
parso: 0.8.3
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 8.3.2
pip: 21.2.4
pkginfo: 1.7.1
prompt-toolkit: 3.0.23
psutil: 5.8.0
ptyprocess: 0.7.0
pycollada: 0.7.1
pydicom: 2.1.2
Pygments: 2.10.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.6
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.2
pytz: 2021.3
pyzmq: 22.3.0
qtconsole: 5.1.1
QtPy: 1.11.3
RandomWords: 0.3.0
requests: 2.26.0
scipy: 1.7.1
setuptools: 57.5.0
sfftk-rw: 0.7.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.2.0
sphinx-autodoc-typehints: 1.12.0
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
suds-jurko: 0.6
tifffile: 2021.4.8
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.7
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.0
wheel-filename: 1.3.0
Change History (2)
comment:1 by , 4 years ago
| Component: | Unassigned → Sessions |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash saving sessions with maps |
comment:2 by , 4 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | assigned → closed |
| Summary: | Crash saving sessions with maps → Crash in Qt event loop after saving sessions with maps |
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Crash was in _PyObject_Call apparently Qt calling a callback function we registered. We have received many reports of this kind of crash. I suspect it is a PyQt reference counting bug where a Python callback function object is deleted because its reference count drops to zero, and yet it is still referenced by being connected to some PyQt signal. When that signal fires it crashes calling the deleted function.
We should probably investigate this crash mechanism, file a PyQt bug report if we can figure it out, and work around it in our code making sure Qt callbacks are kept alive or disconnected.