![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 18 months ago
Closed 17 months ago
#15239 closed defect (duplicate)
Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device returned engine == 0
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | 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: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x00000002048af240 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 892 in init
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1043 in
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main
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{
"uptime" : 180000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac14,2",
"coalitionID" : 1464,
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"build" : "23E224",
"releaseType" : "User"
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"captureTime" : "2024-05-17 08:47:17.3779 +0200",
"codeSigningMonitor" : 1,
"incident" : "1FB3BFDC-F1D6-47CC-84A1-5A83B61EDCD7",
"pid" : 3590,
"translated" : true,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-05-14 14:35:16.2569 +0200",
"procStartAbsTime" : 2623362463632,
"procExitAbsTime" : 4470309020738,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.6.1","CFBundleVersion":"1.6.1.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
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"parentProc" : "launchd",
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"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "D34F8069-E1C1-FE0D-96BE-91B1F96E2FD2",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"wakeTime" : 1,
"sleepWakeUUID" : "85F3721F-3792-41D2-806D-1ED4E0B57F72",
"sip" : "enabled",
"vmRegionInfo" : "0x18 is not in any region. Bytes before following region: 4369735656\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10474e000-10474f000 [ 4K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.6.1.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000018","rawCodes":[1,24],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000018"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":3590},
"vmregioninfo" : "0x18 is not in any region. Bytes before following region: 4369735656\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10474e000-10474f000 [ 4K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.6.1.app\/Contents\/MacOS\/ChimeraX",
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"uuid" : "85907582-b9ae-3a02-baca-2da374c6fbac",
"path" : "\/usr\/lib\/system\/libdispatch.dylib",
"name" : "libdispatch.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703393087488,
"CFBundleShortVersionString" : "2.1.1",
"CFBundleIdentifier" : "com.apple.HIToolbox",
"size" : 2732028,
"uuid" : "5d06c99c-ac78-3bc4-8908-45a394e8180b",
"path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
"name" : "HIToolbox"
}
],
"sharedCache" : {
"base" : 140703204524032,
"size" : 21474836480,
"uuid" : "b8d5ff9b-b3b6-327c-a409-07449b1e60da"
},
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"logWritingSignature" : "4e41ebdd1149326d80d1646a7ef67ab0003113ba",
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "645c2d2f9e69a025b0a37e29",
"factorPackIds" : {
},
"deploymentId" : 240000003
},
{
"rolloutId" : "6112d17137f5d11121dcd4e2",
"factorPackIds" : {
},
"deploymentId" : 240000550
}
],
"experiments" : [
{
"treatmentId" : "a34d22a1-a1a5-4126-a477-0c499e502c6a",
"experimentId" : "65835bc103dc58766bab2d27",
"deploymentId" : 400000011
}
]
},
"reportNotes" : [
"PC register does not match crashing frame (0x0 vs 0x7FF894EF6A78)"
]
}
===== Log before crash start =====
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/kgr849/Downloads/cryosparc_P48_J259_009_volume_map.mrc format
> mrc
Opened cryosparc_P48_J259_009_volume_map.mrc as #1, grid size 224,224,224,
pixel 1.5, shown at level 0.103, step 1, values float32
> open /Users/kgr849/Downloads/cryosparc_P48_J271_002_volume_map.mrc
Opened cryosparc_P48_J271_002_volume_map.mrc as #2, grid size 224,224,224,
pixel 1.5, shown at level 0.0843, step 1, values float32
> volume #2 level 0.08862
> volume #2 level 0.2237
> volume #1 level 0.2715
> volume #2 level 0.2044
> volume #2 level 0.1937
> volume #2 level 0.1765
> open /Users/kgr849/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/hTRPM4/Chimera/cryosparc_P48_J179_mask.mrc
Opened cryosparc_P48_J179_mask.mrc as #3, grid size 224,224,224, pixel 1.5,
shown at level 0.986, step 1, values float32
> volume #1 level 0.08974
> ui mousemode right select
> select #3
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.87861,-0.31195,-0.36157,130.48,0.25825,0.94727,-0.18972,-4.1365,0.40168,0.073313,0.91284,-65.724
> ui tool show "Fit in Map"
> fitmap #3 inMap #1
Fit map cryosparc_P48_J179_mask.mrc in map
cryosparc_P48_J259_009_volume_map.mrc using 112393 points
correlation = 0.6834, correlation about mean = 0, overlap = 8855
steps = 112, shift = 17.2, angle = 11.3 degrees
Position of cryosparc_P48_J179_mask.mrc (#3) relative to
cryosparc_P48_J259_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.79903807 -0.47329137 -0.37085502 175.89742421
0.43851937 0.88069010 -0.17912485 -13.61410817
0.41138659 -0.01949953 0.91125235 -60.81880048
Axis 0.13171137 -0.64544969 0.75236083
Axis point 137.62362742 317.05268061 0.00000000
Rotation angle (degrees) 37.29841378
Shift along axis -13.80277069
> open /Users/kgr849/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/hTRPM4/Chimera/hTRPM4_full_mask.mrc
Opened hTRPM4_full_mask.mrc as #4, grid size 224,224,224, pixel 1.5, shown at
level 1, step 1, values float32
> volume #4 level 0.2413
> ui mousemode right select
> select #4
2 models selected
Drag select of 1 cryosparc_P48_J259_009_volume_map.mrc , 4
hTRPM4_full_mask.mrc
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.96447,0.24519,0.09843,-53.314,-0.23383,0.96557,-0.11405,66.18,-0.123,0.086979,0.98859,8.2529,#4,0.96447,0.24519,0.09843,-53.314,-0.23383,0.96557,-0.11405,66.18,-0.123,0.086979,0.98859,8.2529
> undo
> ui mousemode right select
> ui mousemode right translate
> ui mousemode right select
> select clear
> select #4
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.89595,0.43138,-0.10575,-34.28,0.39768,-0.88517,-0.24149,296.77,-0.19778,0.17431,-0.96462,387.57
> view matrix models
> #4,0.99762,-0.012445,0.067875,-10.765,-0.012722,-0.99991,0.003651,337.03,0.067824,-0.0045058,-0.99769,379.46
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.99762,-0.012445,0.067875,-11.401,-0.012722,-0.99991,0.003651,335.47,0.067824,-0.0045058,-0.99769,351.28
> fitmap #4 inMap #1
Fit map hTRPM4_full_mask.mrc in map cryosparc_P48_J259_009_volume_map.mrc
using 670986 points
correlation = 0.6806, correlation about mean = 0.1795, overlap = 3.352e+04
steps = 112, shift = 22.7, angle = 5.13 degrees
Position of hTRPM4_full_mask.mrc (#4) relative to
cryosparc_P48_J259_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.99747325 -0.07104231 0.00031359 12.23312623
-0.07104235 -0.99747329 0.00011280 347.06375723
0.00030478 -0.00013480 -0.99999994 339.69726431
Axis -0.99936808 0.03554456 -0.00015450
Axis point 0.00000000 173.75995356 169.83693139
Rotation angle (degrees) 179.99290231
Shift along axis 0.05834901
> hide #!3 models
> hide #!2 models
> transparency sel 50
> view matrix models
> #4,0.99747,-0.071042,0.00031359,12.265,-0.071042,-0.99747,0.0001128,345.2,0.00030478,-0.0001348,-1,348.04
> undo
> open /Users/kgr849/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/hTRPM4/Chimera/hTRPM4_MSP_Science_box224_resampled.mrc
Opened hTRPM4_MSP_Science_box224_resampled.mrc as #5, grid size 224,224,224,
pixel 1.5, shown at level 2.61, step 1, values float32
> ui mousemode right select
> select clear
> select #5
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.32496,-0.45287,-0.83025,454.06,-0.52063,0.81855,-0.24271,163.85,0.78952,0.35338,-0.50177,77.787
> hide #!4 models
> view matrix models
> #5,-0.19102,-0.97362,-0.1248,384.03,-0.98016,0.19605,-0.029213,303.16,0.05291,0.11675,-0.99175,333
> fitmap #5 inMap #1
Fit map hTRPM4_MSP_Science_box224_resampled.mrc in map
cryosparc_P48_J259_009_volume_map.mrc using 112310 points
correlation = 0.6009, correlation about mean = 0.09451, overlap = 5.21e+04
steps = 108, shift = 1.57, angle = 9.19 degrees
Position of hTRPM4_MSP_Science_box224_resampled.mrc (#5) relative to
cryosparc_P48_J259_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
-0.28810148 -0.95759984 -0.00030465 376.29035526
-0.95759971 0.28810161 -0.00051745 279.93026482
0.00058328 0.00014265 -0.99999982 362.98598409
Axis 0.59661478 -0.80252775 0.00011681
Axis point 292.13543335 0.00000000 181.57822196
Rotation angle (degrees) 179.96830352
Shift along axis -0.10901681
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.2881,-0.9576,-0.00030465,375.44,-0.9576,0.2881,-0.00051745,280.09,0.00058328,0.00014265,-1,349.26
> fitmap #5 inMap #1
Fit map hTRPM4_MSP_Science_box224_resampled.mrc in map
cryosparc_P48_J259_009_volume_map.mrc using 112310 points
correlation = 0.8253, correlation about mean = 0.5199, overlap = 9.551e+04
steps = 188, shift = 11.8, angle = 15.8 degrees
Position of hTRPM4_MSP_Science_box224_resampled.mrc (#5) relative to
cryosparc_P48_J259_009_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
-0.53750734 -0.84325907 0.00000317 398.86260680
-0.84325907 0.53750734 0.00002190 218.94669812
-0.00002017 0.00000909 -1.00000000 337.60277907
Axis -0.48088104 0.87678585 0.00001077
Axis point 259.47422198 0.00000000 168.79853010
Rotation angle (degrees) 179.99923719
Shift along axis 0.16753917
> volume #5 level 2.606
> volume #5 level 4.704
> volume #1 level 0.1593
> hide #!5 models
> show #!4 models
> show #!5 models
> fitmap #4 inMap #5
Fit map hTRPM4_full_mask.mrc in map hTRPM4_MSP_Science_box224_resampled.mrc
using 670986 points
correlation = 0.1639, correlation about mean = 0.2324, overlap = 3.156e+05
steps = 260, shift = 2.86, angle = 50.1 degrees
Position of hTRPM4_full_mask.mrc (#4) relative to
hTRPM4_MSP_Science_box224_resampled.mrc (#5) coordinates:
Matrix rotation and translation
0.36907779 0.92939850 0.00012167 -50.54210027
-0.92939848 0.36907781 -0.00016570 261.39451417
-0.00019891 -0.00005192 0.99999998 -4.93882849
Axis 0.00006121 0.00017246 -0.99999998
Axis point 167.25560519 167.92331954 0.00000000
Rotation angle (degrees) 68.34124665
Shift along axis 4.98081580
> ui mousemode right select
> select clear
Drag select of 1 cryosparc_P48_J259_009_volume_map.mrc , 4
hTRPM4_full_mask.mrc , 5 hTRPM4_MSP_Science_box224_resampled.mrc
> select clear
> ui mousemode right translate
> show #!3 models
> volume resample
Missing or invalid "volumes" argument: empty atom specifier
> fitmap #3 inMap #4
Fit map cryosparc_P48_J179_mask.mrc in map hTRPM4_full_mask.mrc using 112393
points
correlation = 0.9896, correlation about mean = 0, overlap = 1.055e+05
steps = 468, shift = 29.9, angle = 55 degrees
Position of cryosparc_P48_J179_mask.mrc (#3) relative to hTRPM4_full_mask.mrc
(#4) coordinates:
Matrix rotation and translation
0.79698469 -0.52792236 -0.29345085 165.66765932
-0.58103135 -0.80281637 -0.13374770 398.48505234
-0.16497874 0.27709901 -0.94657179 357.68136780
Axis 0.94724334 -0.29620377 -0.12244747
Axis point 0.00000000 204.46084006 212.54648036
Rotation angle (degrees) 167.47506942
Shift along axis -4.90236667
> ui mousemode right select
> select #3
2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.93759,0.34192,-0.063402,-53.161,-0.30605,0.89791,0.31637,-83.698,0.1651,-0.27722,0.94651,-12.954
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.80011,0.36692,-0.47455,328.32,-0.38371,0.29502,0.87506,-89.321,0.46108,0.88223,-0.095254,-34.249
> view matrix models
> #3,-0.70084,0.64239,-0.31009,242.81,-0.15493,0.28725,0.94524,-141.87,0.69629,0.71051,-0.10179,-51.446
> view matrix models
> #3,-0.6639,0.69423,-0.27798,223.25,-0.11368,0.27371,0.95507,-149.16,0.73913,0.66567,-0.1028,-52.753
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.9193,-0.36679,0.14268,9.5783,-0.39309,-0.87352,0.28713,179.97,0.01932,-0.32004,-0.94721,364.99
> view matrix models
> #3,0.91603,-0.39944,0.036538,34.032,-0.39573,-0.88513,0.24484,189.76,-0.065457,-0.23874,-0.96887,372.92
> view matrix models
> #3,0.89585,-0.42947,-0.11405,69.269,-0.40554,-0.89511,0.18523,203.77,-0.18164,-0.11968,-0.97606,378.62
> view matrix models
> #3,0.89504,-0.43125,-0.11365,69.582,-0.40724,-0.8942,0.1859,203.82,-0.18179,-0.12011,-0.97597,378.69
> view matrix models
> #3,0.89694,-0.42872,-0.10818,67.9,-0.40398,-0.89403,0.19367,201.8,-0.17975,-0.13001,-0.97508,379.53
> view matrix models
> #3,0.89101,-0.43642,-0.12506,73.096,-0.41417,-0.89423,0.16976,208.01,-0.18592,-0.099464,-0.97752,376.88
> view matrix models
> #3,0.87874,-0.45,-0.15907,83.36,-0.43471,-0.89219,0.12254,220.03,-0.19707,-0.03853,-0.97963,370.9
> view matrix models
> #3,0.86209,-0.46408,-0.20355,96.388,-0.46158,-0.88489,0.062579,234.77,-0.20916,0.040007,-0.97706,361.83
> view matrix models
> #3,0.8347,-0.47056,-0.28608,117.24,-0.49613,-0.86802,-0.019813,253.68,-0.239,0.15847,-0.958,347.42
> view matrix models
> #3,0.86316,-0.46303,-0.20139,95.658,-0.46575,-0.88416,0.036657,240.15,-0.19503,0.062155,-0.97883,356.59
> view matrix models
> #3,0.88435,-0.44865,-0.12898,76.674,-0.44068,-0.8935,0.086393,227.87,-0.154,-0.019562,-0.98788,362.14
> view matrix models
> #3,0.87458,-0.25119,0.41473,-48.016,-0.38412,-0.88091,0.27649,181.33,0.29589,-0.40112,-0.86692,312.13
> view matrix models
> #3,0.91509,-0.39972,0.053217,31.192,-0.40325,-0.90765,0.11649,217.64,0.0017391,-0.12806,-0.99177,349.95
> view matrix models
> #3,0.80651,-0.56978,0.15777,54.748,0.06778,-0.17599,-0.98206,234.15,0.58732,0.80273,-0.10332,-44.383
> view matrix models
> #3,0.82253,-0.56742,0.038358,73.392,-0.55645,-0.81689,-0.15185,281.55,0.1175,0.10356,-0.98766,296.82
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.82253,-0.56742,0.038358,225.68,-0.55645,-0.81689,-0.15185,426.54,0.1175,0.10356,-0.98766,301.06
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.81869,-0.56525,0.1012,214.59,-0.55796,-0.82469,-0.092563,417.04,0.13578,0.019314,-0.99055,309.87
> view matrix models
> #3,0.82466,-0.54626,0.14675,202.6,-0.54883,-0.83553,-0.025978,404.73,0.1368,-0.059115,-0.98883,320.13
> view matrix models
> #3,0.82116,-0.55803,0.11957,209.8,-0.5542,-0.82974,-0.066359,412.28,0.13624,-0.011774,-0.99061,314.06
> view matrix models
> #3,-0.23974,-0.94973,0.20136,437.66,-0.97081,0.23608,-0.042345,336.06,-0.0073208,-0.20563,-0.9786,364.03
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.23974,-0.94973,0.20136,340.33,-0.97081,0.23608,-0.042345,260.56,-0.0073208,-0.20563,-0.9786,366.8
> fitmap #3 inMap #4
Fit map cryosparc_P48_J179_mask.mrc in map hTRPM4_full_mask.mrc using 112393
points
correlation = 0.9894, correlation about mean = 0, overlap = 1.065e+05
steps = 332, shift = 33.4, angle = 43.4 degrees
Position of cryosparc_P48_J179_mask.mrc (#3) relative to hTRPM4_full_mask.mrc
(#4) coordinates:
Matrix rotation and translation
-0.03485747 -0.99835373 0.04555035 331.92163209
0.99888090 -0.03334550 0.03354219 -1.74823673
-0.03196807 0.04666857 0.99839878 2.77069575
Axis 0.00656719 0.03878284 0.99922608
Axis point 166.88795301 159.44683403 0.00000000
Rotation angle (degrees) 92.00014878
Shift along axis 4.88054225
> hide #!4 models
> transparency sel 50
> ui mousemode right select
> select clear
> volume resample #3 onGrid #1
Opened cryosparc_P48_J179_mask.mrc resampled as #6, grid size 224,224,224,
pixel 1.5, shown at step 1, values float32
> save /Users/kgr849/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/hTRPM4/Chimera/hTRPM4_proteomer_box224_J259fit.mrc
> models #6
> volume #6 level 0.9667
> open /Users/kgr849/Downloads/cryosparc_P48_J273_mask.mrc
Opened cryosparc_P48_J273_mask.mrc as #7, grid size 224,224,224, pixel 1.5,
shown at level 1, step 1, values float32
> volume #7 level 0.939
Unsupported scale factor (0.000000) detected on Display1
Drag select of 1 cryosparc_P48_J259_009_volume_map.mrc , 5
hTRPM4_MSP_Science_box224_resampled.mrc , 6
hTRPM4_proteomer_box224_J259fit.mrc , 7 cryosparc_P48_J273_mask.mrc
> select clear
Drag select of 1 cryosparc_P48_J259_009_volume_map.mrc , 5
hTRPM4_MSP_Science_box224_resampled.mrc , 6
hTRPM4_proteomer_box224_J259fit.mrc , 7 cryosparc_P48_J273_mask.mrc
> select clear
> ui mousemode right translate
> open /Users/kgr849/Downloads/cryosparc_P48_J274_002_volume_map.mrc
Opened cryosparc_P48_J274_002_volume_map.mrc as #8, grid size 224,224,224,
pixel 1.5, shown at level 0.089, step 1, values float32
> hide #!7 models
> hide #!6 models
> volume #8 level 0.1788
> hide #!5 models
> open /Users/kgr849/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/hTRPM4/Chimera/cryosparc_P48_J182_mask.mrc
Opened cryosparc_P48_J182_mask.mrc as #9, grid size 224,224,224, pixel 1.5,
shown at level 0.734, step 1, values float32
> close #9
> open /Users/kgr849/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/hTRPM4/Chimera/hTRPM4_cyto_mask_C4_box224_resampled.mrc
Opened hTRPM4_cyto_mask_C4_box224_resampled.mrc as #9, grid size 224,224,224,
pixel 1.5, shown at level 0.000529, step 1, values float32
> close #9
> open /Users/kgr849/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/hTRPM4/Chimera/hTPRM4_flexdomain_smooth_box224.mrc
Opened hTPRM4_flexdomain_smooth_box224.mrc as #9, grid size 224,224,224, pixel
1.5, shown at level 0.000334, step 1, values float32
> show #!7 models
> ui mousemode right select
> select #9
2 models selected
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #9,0.96614,0.0054378,-0.25797,59.977,-0.25765,-0.0337,-0.96565,427.11,-0.013945,0.99942,-0.031158,51.819
> view matrix models
> #9,-0.26269,0.60719,0.74988,2.2035,0.93009,0.36615,0.029353,-92.089,-0.25674,0.70517,-0.66092,282.46
> view matrix models
> #9,-0.26621,0.60518,0.75026,3.1819,0.93195,0.36039,0.039974,-93.731,-0.24619,0.70984,-0.65994,279.31
> view matrix models
> #9,0.77787,-0.27802,-0.56357,209.85,-0.49432,-0.82445,-0.27556,463.42,-0.38803,0.49294,-0.77875,369.49
> view matrix models
> #9,0.59651,-0.79153,-0.13287,242.77,-0.80179,-0.59514,-0.054198,442.28,-0.036177,0.13886,-0.98965,400.09
> ui mousemode right "translate selected models"
> view matrix models
> #9,0.59651,-0.79153,-0.13287,257.04,-0.80179,-0.59514,-0.054198,447.71,-0.036177,0.13886,-0.98965,328.93
> view matrix models
> #9,0.59651,-0.79153,-0.13287,252.68,-0.80179,-0.59514,-0.054198,410.46,-0.036177,0.13886,-0.98965,319.91
> view matrix models
> #9,0.59651,-0.79153,-0.13287,226.91,-0.80179,-0.59514,-0.054198,410.78,-0.036177,0.13886,-0.98965,321.01
Window position QRect(1577,869 338x98) outside any known screen, using primary
screen
> fitmap #9 inMap #7
Fit map hTPRM4_flexdomain_smooth_box224.mrc in map cryosparc_P48_J273_mask.mrc
using 39705 points
correlation = 0.7896, correlation about mean = 0.008853, overlap = 6.424e+04
steps = 132, shift = 3.33, angle = 9.68 degrees
Position of hTPRM4_flexdomain_smooth_box224.mrc (#9) relative to
cryosparc_P48_J273_mask.mrc (#7) coordinates:
Matrix rotation and translation
0.54298402 -0.83953438 0.01871854 213.37390235
-0.83700958 -0.54287917 -0.06853588 415.49039157
0.06770013 0.02154629 -0.99747303 321.62577465
Axis 0.87826053 -0.47754844 0.02461558
Axis point 0.00000000 261.05613664 163.87050845
Rotation angle (degrees) 177.06032957
Shift along axis -3.10190996
> color #7 #b2ffb24e models
> hide #!7 models
> show #!5 models
> hide #!8 models
> hide #!5 models
> volume resample #9 onGrid #1
Opened hTPRM4_flexdomain_smooth_box224.mrc resampled as #10, grid size
224,224,224, pixel 1.5, shown at step 1, values float32
> volume #10 level 0.02137
> volume gaussian #9 sDev 2
Opened hTPRM4_flexdomain_smooth_box224.mrc gaussian as #11, grid size
224,224,224, pixel 1.5, shown at step 1, values float32
> volume #11 level 0.0279
> save /Users/kgr849/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/hTRPM4/Chimera/hTRPM4_flex_box224_J259.mrc models #11
> open /Users/kgr849/Downloads/cryosparc_P48_J276_mask.mrc
Opened cryosparc_P48_J276_mask.mrc as #12, grid size 224,224,224, pixel 1.5,
shown at level 0.794, step 1, values float32
> hide #!10 models
> select subtract #9
Nothing selected
> hide #!11 models
> hide #!12 models
> show #!3 models
> show #!2 models
> hide #!2 models
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!6 models
> volume #6 level 0.9903
> ui tool show "Segment Map"
Segmenting hTRPM4_proteomer_box224_J259fit.mrc, density threshold 0.990260
Showing 5 region surfaces
97910 watershed regions, grouped to 5 regions
Showing hTRPM4_proteomer_box224_J259fit.seg - 5 regions, 5 surfaces
Segmenting hTRPM4_proteomer_box224_J259fit.mrc, density threshold 0.990260
Showing 17 region surfaces
97910 watershed regions, grouped to 17 regions
Showing hTRPM4_proteomer_box224_J259fit.seg - 17 regions, 17 surfaces
Segmenting hTRPM4_proteomer_box224_J259fit.mrc, density threshold 0.990260
Only showing 60 of 5180 regions.
Showing 60 of 5180 region surfaces
97910 watershed regions, grouped to 5180 regions
Showing hTRPM4_proteomer_box224_J259fit.seg - 5180 regions, 60 surfaces
Segmenting hTRPM4_proteomer_box224_J259fit.mrc, density threshold 0.990260
Showing 5 region surfaces
97910 watershed regions, grouped to 5 regions
Showing hTRPM4_proteomer_box224_J259fit.seg - 5 regions, 5 surfaces
Segmenting hTRPM4_proteomer_box224_J259fit.mrc, density threshold 0.990260
Showing 3 region surfaces
97910 watershed regions, grouped to 3 regions
Showing hTRPM4_proteomer_box224_J259fit.seg - 3 regions, 3 surfaces
Segmenting hTRPM4_proteomer_box224_J259fit.mrc, density threshold 0.990260
Only showing 2000 of 5180 regions.
Showing 2000 of 5180 region surfaces
97910 watershed regions, grouped to 5180 regions
Showing hTRPM4_proteomer_box224_J259fit.seg - 5180 regions, 2000 surfaces
Segmenting hTRPM4_proteomer_box224_J259fit.mrc, density threshold 0.990260
Only showing 2000 of 5180 regions.
Showing 2000 of 5180 region surfaces
97910 watershed regions, grouped to 5180 regions
Showing hTRPM4_proteomer_box224_J259fit.seg - 5180 regions, 2000 surfaces
> select #13.5
1 model selected
> show #!12 models
> hide #!12 models
> show #!11 models
> hide #!13 models
> hide #!6 models
> view matrix models #13.5,1,0,0,-1.2286,0,1,0,-0.85805,0,0,1,-9.2414
> show #!12 models
> view matrix models #13.5,1,0,0,-6.181,0,1,0,0.076582,0,0,1,-23.628
> show #!2 models
> hide #!2 models
Unsupported scale factor (0.000000) detected on Display0
QPainter::begin: Paint device returned engine == 0, type: 3
===== Log before crash end =====
Log:
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M2
OpenGL vendor: Apple
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: Mac
Model Identifier: Mac14,2
Model Number: Z15S000HZDK/A
Chip: Unknown
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 10151.101.3
OS Loader Version: 10151.101.3
Software:
System Software Overview:
System Version: macOS 14.4.1 (23E224)
Kernel Version: Darwin 23.4.0
Time since boot: 9 days, 1 hour, 24 minutes
Graphics/Displays:
Apple M2:
Chipset Model: Apple M2
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina Display
Resolution: 2560 x 1664 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
HP E24 G4:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
build: 0.10.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 3.1.0
ChimeraX-AddCharge: 1.5.9.1
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.43.10
ChimeraX-AtomicLibrary: 10.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
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: 2.8
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.6.1
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.1
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
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: 1.8.2
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.0.12
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.9
ChimeraX-ModelPanel: 1.3.7
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.0
ChimeraX-NRRD: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.1
ChimeraX-PDB: 2.7.2
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-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.8.3
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: 1.10.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.28.4
ChimeraX-uniprot: 2.2.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
contourpy: 1.0.7
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7
decorator: 5.1.1
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.39.3
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.9.26
imagesize: 1.4.1
importlib-metadata: 6.6.0
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.6
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.3.0
jupyterlab-widgets: 3.0.7
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.2
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
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: 9.3.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.5.0
prompt-toolkit: 3.0.38
psutil: 5.9.4
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
python-dateutil: 2.8.2
pytz: 2023.3
pyzmq: 25.0.2
qtconsole: 5.4.0
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.28.2
scipy: 1.9.3
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4.1
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tcia-utils: 1.2.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.1
traitlets: 5.9.0
typing-extensions: 4.5.0
tzdata: 2023.3
urllib3: 1.26.15
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.7
zipp: 3.15.0
Change History (2)
comment:1 by , 17 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device returned engine == 0 |
comment:2 by , 17 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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