![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 9 months ago
Closed 9 months ago
#16831 closed defect (duplicate)
Crash moving window between screens
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| 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-15.3-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX.
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{
"uptime" : 490000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac14,9",
"coalitionID" : 5514,
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"build" : "24D60",
"releaseType" : "User"
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"captureTime" : "2025-02-10 14:51:08.4732 -0600",
"codeSigningMonitor" : 1,
"incident" : "0C879639-DC0D-49C2-97EA-0459B9F44751",
"pid" : 4043,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-02-04 12:20:36.1758 -0600",
"procStartAbsTime" : 22082626121,
"procExitAbsTime" : 11859739845813,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.9.0","CFBundleVersion":"1.9.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
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"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "5B00E8DA-FAA8-5A75-2BE6-92DDC3DE9D18",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
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Log:
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/jamesfleckenstein/Library/CloudStorage/Box-Box/Grant
> Applications/Grant Applications (1)/NIH/R01AI089894_2025/EatA-Fab40_SepA-
> Fab40_sesh.cxs"
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
Log from Mon Feb 10 12:01:26 2025 Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "C:/Users/David/Documents/lab/Berndsen/EatA/maps/EatA-Fab40/EatA-
> Fab40_cryosparc_P7_J140_008_volume_map_sharp (1).mrc"
Opened EatA-Fab40_cryosparc_P7_J140_008_volume_map_sharp (1).mrc as #1, grid
size 270,270,270, pixel 0.928, shown at level 0.214, step 2, values float32
> rename #1 EatA-Fab40.mrc
> open "C:/Users/David/Downloads/cryosparc_P7_J219_008_volume_map_sharp
> (2).mrc"
Opened cryosparc_P7_J219_008_volume_map_sharp (2).mrc as #2, grid size
256,256,256, pixel 0.968, shown at level 0.0847, step 1, values float32
> rename #2 SepA-Fab40.mrc
> volume #1 level 0.2915
> volume #1 step 1
> volume #2 level 0.1229
> volume #1 level 0.4495
> volume #1 level 0.4811
> volume #2 level 0.1515
> select #2
2 models selected
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.99528,-0.022128,0.094458,-9.1091,-0.0084167,0.95027,0.3113,-33.664,-0.09665,-0.31063,0.94561,56.038
> view matrix models
> #2,0.99609,-0.034942,0.081192,-5.8956,0.0072106,0.94761,0.31935,-36.15,-0.088097,-0.31752,0.94415,56.109
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.99609,-0.034942,0.081192,-1.0656,0.0072106,0.94761,0.31935,-31.438,-0.088097,-0.31752,0.94415,60.654
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.97477,-0.1541,0.16147,5.4315,0.093157,0.93829,0.33307,-41.768,-0.20283,-0.30963,0.92897,74.591
> view matrix models
> #2,0.98523,-0.10953,0.13165,2.6943,0.061126,0.94301,0.3271,-37.958,-0.15997,-0.31422,0.93578,69.439
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.98523,-0.10953,0.13165,0.47414,0.061126,0.94301,0.3271,-35.954,-0.15997,-0.31422,0.93578,72.327
> view matrix models
> #2,0.98523,-0.10953,0.13165,1.3651,0.061126,0.94301,0.3271,-35.84,-0.15997,-0.31422,0.93578,73.673
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.98432,-0.094426,0.14901,-2.6515,0.043303,0.94817,0.3148,-32.857,-0.17101,-0.30341,0.93739,73.381
> view matrix models
> #2,0.97775,-0.11906,0.17269,-1.9918,0.05862,0.94559,0.32002,-34.949,-0.20139,-0.30278,0.93154,77.49
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.97775,-0.11906,0.17269,-1.6744,0.05862,0.94559,0.32002,-35.568,-0.20139,-0.30278,0.93154,79.539
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.97611,-0.085052,0.19996,-9.2188,0.025827,0.9591,0.28188,-28.543,-0.21575,-0.26998,0.93838,76.244
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.97611,-0.085052,0.19996,-9.2609,0.025827,0.9591,0.28188,-26.13,-0.21575,-0.26998,0.93838,73.45
> view matrix models
> #2,0.97611,-0.085052,0.19996,-8.5345,0.025827,0.9591,0.28188,-26.691,-0.21575,-0.26998,0.93838,74.811
> ui tool show "Fit in Map"
> fitmap #1 inMap #2
Fit map EatA-Fab40.mrc in map SepA-Fab40.mrc using 79465 points
correlation = 0.613, correlation about mean = 0.388, overlap = 1.719e+04
steps = 76, shift = 1.52, angle = 2.29 degrees
Position of EatA-Fab40.mrc (#1) relative to SepA-Fab40.mrc (#2) coordinates:
Matrix rotation and translation
0.97901752 0.00979199 -0.20354068 25.01550111
-0.07312106 0.94920549 -0.30604290 50.79338471
0.19020516 0.31450447 0.93000480 -62.04307872
Axis 0.83904544 -0.53238588 -0.11210718
Axis point 0.00000000 225.89349653 130.04694651
Rotation angle (degrees) 21.70289236
Shift along axis 0.90293609
> select clear
> lighting soft
> graphics silhouettes true
> volume #1 level 0.5463
> volume #2 level 0.1614
> volume #2 level 0.1909
> select #2
2 models selected
> view matrix models
> #2,0.97611,-0.085052,0.19996,-9.9333,0.025827,0.9591,0.28188,-27.903,-0.21575,-0.26998,0.93838,72.054
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.97204,-0.0847,0.21903,-11.921,0.013409,0.95119,0.30833,-28.867,-0.23445,-0.29677,0.92572,79.033
> view matrix models
> #2,0.97434,-0.074834,0.21228,-12.498,0.014437,0.96195,0.27284,-25.744,-0.22462,-0.26278,0.93835,72.257
> fitmap #1 inMap #2
Fit map EatA-Fab40.mrc in map SepA-Fab40.mrc using 70546 points
correlation = 0.6223, correlation about mean = 0.3837, overlap = 1.689e+04
steps = 80, shift = 3.39, angle = 0.997 degrees
Position of EatA-Fab40.mrc (#1) relative to SepA-Fab40.mrc (#2) coordinates:
Matrix rotation and translation
0.97902917 0.00963153 -0.20349233 25.02757104
-0.07296714 0.94918971 -0.30612855 50.78822609
0.19020433 0.31455704 0.92998719 -62.05035725
Axis 0.83917035 -0.53228006 -0.11167387
Axis point 0.00000000 225.87349042 129.97690901
Rotation angle (degrees) 21.70457647
Shift along axis 0.89823864
> select clear
> close session
> open "C:/Users/David/Documents/lab/Berndsen/EatA/maps/EatA-Fab40/EatA-
> Fab40_cryosparc_P7_J140_008_volume_map_sharp (1).mrc"
Opened EatA-Fab40_cryosparc_P7_J140_008_volume_map_sharp (1).mrc as #1, grid
size 270,270,270, pixel 0.928, shown at level 0.214, step 2, values float32
> volume #1 step 1
> volume #1 level 0.3407
> volume #1 level 0.7358
> open "C:/Users/David/Downloads/cryosparc_P7_J219_008_volume_map_sharp
> (2).mrc"
Opened cryosparc_P7_J219_008_volume_map_sharp (2).mrc as #2, grid size
256,256,256, pixel 0.968, shown at level 0.0847, step 1, values float32
> volume #2 level 0.1706
> volume #2 level 0.2136
> select #2
2 models selected
> view matrix models
> #2,0.96149,-0.27437,-0.015941,39.003,0.25813,0.88165,0.39505,-67.972,-0.094334,-0.38395,0.91852,67.065
> view matrix models
> #2,0.98091,-0.13986,0.13514,1.3738,0.086076,0.93532,0.34318,-46.916,-0.1744,-0.325,0.9295,68.34
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.98091,-0.13986,0.13514,2.0191,0.086076,0.93532,0.34318,-42.195,-0.1744,-0.325,0.9295,73.577
> view matrix models
> #2,0.98091,-0.13986,0.13514,6.2278,0.086076,0.93532,0.34318,-41.778,-0.1744,-0.325,0.9295,73.343
> view matrix models
> #2,0.98091,-0.13986,0.13514,4.5362,0.086076,0.93532,0.34318,-39.647,-0.1744,-0.325,0.9295,74.574
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.97966,-0.1068,0.16986,-3.6769,0.046741,0.94474,0.32446,-33.615,-0.19513,-0.30992,0.93052,75.16
> view matrix models
> #2,0.97717,-0.091769,0.19164,-7.9511,0.036077,0.96048,0.27599,-27.946,-0.20939,-0.26277,0.94186,69.863
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.97717,-0.091769,0.19164,-7.8314,0.036077,0.96048,0.27599,-29.151,-0.20939,-0.26277,0.94186,71.895
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.97786,-0.092647,0.18764,-7.2966,0.035208,0.95671,0.2889,-30.264,-0.20628,-0.27589,0.93879,73.461
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.97786,-0.092647,0.18764,-6.5336,0.035208,0.95671,0.2889,-28.672,-0.20628,-0.27589,0.93879,72.867
> view matrix models
> #2,0.97786,-0.092647,0.18764,-6.7199,0.035208,0.95671,0.2889,-29.317,-0.20628,-0.27589,0.93879,73.835
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.97754,-0.1067,0.18172,-4.2648,0.042277,0.9441,0.32692,-33.578,-0.20645,-0.3119,0.92741,79.561
> view matrix models
> #2,0.97808,-0.099571,0.1829,-5.3205,0.036697,0.94695,0.31928,-32.258,-0.20499,-0.30557,0.92984,78.327
> ui tool show "Fit in Map"
> fitmap #2 inMap #1
Fit map cryosparc_P7_J219_008_volume_map_sharp (2).mrc in map EatA-
Fab40_cryosparc_P7_J140_008_volume_map_sharp (1).mrc using 48767 points
correlation = 0.6415, correlation about mean = 0.3984, overlap = 1.422e+04
steps = 52, shift = 0.547, angle = 1.48 degrees
Position of cryosparc_P7_J219_008_volume_map_sharp (2).mrc (#2) relative to
EatA-Fab40_cryosparc_P7_J140_008_volume_map_sharp (1).mrc (#1) coordinates:
Matrix rotation and translation
0.97966507 -0.07409755 0.18645614 -8.52475550
0.01191349 0.94915063 0.31459679 -29.20509180
-0.20028582 -0.30597815 0.93073249 77.85667149
Axis -0.84287339 0.52527822 0.11682136
Axis point 0.00000000 224.50713487 130.69046301
Rotation angle (degrees) 21.60037158
Shift along axis 0.93981335
> rename #1 EatA-Fab40.mrc
> rename #2 SepA-Fab40.mrc
> view matrix models
> #2,0.98069,-0.081497,0.17781,-6.6622,0.01937,0.94506,0.32633,-31.131,-0.19463,-0.31659,0.92838,78.729
> ui tool show "Fit in Map"
> fitmap #2 inMap #1
Fit map SepA-Fab40.mrc in map EatA-Fab40.mrc using 48767 points
correlation = 0.6416, correlation about mean = 0.3977, overlap = 1.423e+04
steps = 56, shift = 0.0571, angle = 0.898 degrees
Position of SepA-Fab40.mrc (#2) relative to EatA-Fab40.mrc (#1) coordinates:
Matrix rotation and translation
0.97965863 -0.07392983 0.18655656 -8.54984305
0.01168718 0.94910442 0.31474467 -29.21120086
-0.20033067 -0.30616201 0.93066237 77.88857404
Axis -0.84296901 0.52525437 0.11623725
Axis point 0.00000000 224.46875115 130.63791218
Rotation angle (degrees) 21.60992390
Shift along axis 0.91749541
> select clear
> open C:/Users/David/Documents/lab/Berndsen/Phenix/RealSpaceRefine_18/EatA-
> Fab40mod-IN-Fab15map-RSR_real_space_refined_018.pdb
Chain information for EatA-Fab40mod-IN-Fab15map-RSR_real_space_refined_018.pdb
#3
---
Chain | Description
A | No description available
B | No description available
C | No description available
> select /C:666
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
40 atoms, 39 bonds, 6 residues, 1 model selected
> select up
7821 atoms, 7968 bonds, 1031 residues, 1 model selected
> select up
11083 atoms, 11312 bonds, 1461 residues, 1 model selected
> view matrix models
> #3,-0.99103,0.086581,-0.10177,265.07,0.10515,0.035518,-0.99382,221.56,-0.082431,-0.99561,-0.044304,256.17
> view matrix models
> #3,0.84904,0.40271,0.34198,-68.925,0.41718,-0.9082,0.033719,149.47,0.32417,0.11404,-0.9391,198.48
> view matrix models
> #3,0.9691,0.24336,-0.040373,-17.273,0.24543,-0.96764,0.058598,175.25,-0.024807,-0.066696,-0.99746,271.66
> view matrix models
> #3,0.93683,0.31665,-0.14862,-6.9025,0.34734,-0.89231,0.28833,123.62,-0.041311,-0.32174,-0.94593,294.97
> view matrix models
> #3,0.99776,0.029839,-0.059857,4.8563,0.035633,-0.99453,0.098193,200.54,-0.0566,-0.10011,-0.99337,278.95
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.99776,0.029839,-0.059857,-9.0141,0.035633,-0.99453,0.098193,211.2,-0.0566,-0.10011,-0.99337,266.96
> view matrix models
> #3,0.99776,0.029839,-0.059857,-9.4409,0.035633,-0.99453,0.098193,227.85,-0.0566,-0.10011,-0.99337,268.92
> view matrix models
> #3,0.99776,0.029839,-0.059857,-2.6804,0.035633,-0.99453,0.098193,228.29,-0.0566,-0.10011,-0.99337,268.38
> view matrix models
> #3,0.99776,0.029839,-0.059857,1.462,0.035633,-0.99453,0.098193,227.55,-0.0566,-0.10011,-0.99337,266.56
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.98877,0.13323,0.067713,-25.338,0.12139,-0.98025,0.15615,207.16,0.08718,-0.14618,-0.98541,251.69
> view matrix models
> #3,0.99845,0.051907,0.019865,-11.463,0.048113,-0.98617,0.1586,217.1,0.027823,-0.1574,-0.98714,260.93
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.99845,0.051907,0.019865,-10.574,0.048113,-0.98617,0.1586,217.07,0.027823,-0.1574,-0.98714,260.97
> fitmap #3 inMap #1
Fit molecule EatA-Fab40mod-IN-Fab15map-RSR_real_space_refined_018.pdb (#3) to
map EatA-Fab40.mrc (#1) using 11083 atoms
average map value = 0.3358, steps = 196
shifted from previous position = 3.03
rotated from previous position = 5.69 degrees
atoms outside contour = 8608, contour level = 0.73576
Position of EatA-Fab40mod-IN-Fab15map-RSR_real_space_refined_018.pdb (#3)
relative to EatA-Fab40.mrc (#1) coordinates:
Matrix rotation and translation
0.99547704 0.09109883 -0.02695313 -6.32677284
0.09300268 -0.99238446 0.08076870 221.07084642
-0.01938994 -0.08291010 -0.99636838 259.90892236
Axis -0.99886671 -0.04615516 0.01161845
Axis point 0.00000000 116.02054766 125.37750571
Rotation angle (degrees) 175.30035947
Shift along axis -0.86422088
> show sel atoms
> volume #1 color #b2b2b2dc
> volume #1 color #b2b2b2b4
> volume #1 color #b2b2b278
> view matrix models
> #3,0.99548,0.091099,-0.026953,-4.7336,0.093003,-0.99238,0.080769,224.29,-0.01939,-0.08291,-0.99637,260.55
> close session
> open C:/Users/David/Documents/lab/Berndsen/EatA/maps/EatA-Fab40/EatA-
> Fab40_cryosparc_P7_J140_008_volume_map_sharp_ALIGNED-TO-FAB15.mrc
Opened EatA-Fab40_cryosparc_P7_J140_008_volume_map_sharp_ALIGNED-TO-FAB15.mrc
as #1, grid size 270,270,270, pixel 0.928, shown at level 0.173, step 2,
values float32
> volume #1 step 1
> volume #1 level 0.3883
> open C:/Users/David/Documents/lab/Berndsen/Phenix/RealSpaceRefine_18/EatA-
> Fab40mod-IN-Fab15map-RSR_real_space_refined_018.pdb
Chain information for EatA-Fab40mod-IN-Fab15map-RSR_real_space_refined_018.pdb
#2
---
Chain | Description
A | No description available
B | No description available
C | No description available
> open "C:/Users/David/Downloads/cryosparc_P7_J219_008_volume_map_sharp
> (2).mrc"
Opened cryosparc_P7_J219_008_volume_map_sharp (2).mrc as #3, grid size
256,256,256, pixel 0.968, shown at level 0.0847, step 1, values float32
> volume #3 level 0.1945
> rename #1 EatA-Fab40.mrc
> rename #2 EatA-Fab40_model.pdb
> rename #1 EatA-Fab40_map.mrc
> rename #3 SepA-Fab40_map.mrc
> select #3
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.45329,0.66248,0.59637,17.62,-0.56074,0.30815,-0.76851,245.6,-0.69289,-0.68277,0.2318,260.09
> view matrix models
> #3,-0.79552,-0.24086,-0.55599,311.2,0.59228,-0.11548,-0.79741,163.05,0.12786,-0.96366,0.23452,195.94
> view matrix models
> #3,0.77248,-0.62924,-0.08555,111.94,-0.62428,-0.72779,-0.2839,313.56,0.11638,0.27271,-0.95503,202.91
> view matrix models
> #3,0.83831,-0.54515,-0.0069855,84.257,-0.50347,-0.76917,-0.39356,318.13,0.20918,0.33344,-0.91927,180.24
> view matrix models
> #3,0.73626,-0.67181,0.081185,100.02,-0.53405,-0.65054,-0.53999,326.39,0.41558,0.35421,-0.83775,143.05
> view matrix models
> #3,0.9568,-0.12711,0.26149,-13.192,-0.035768,-0.944,-0.32799,275.16,0.28854,0.30447,-0.90777,172.82
> lighting soft
[Repeated 2 time(s)]
> graphics silhouettes false
> graphics silhouettes true
> view matrix models
> #3,0.9995,-0.00083852,0.031678,-3.8733,0.0081219,-0.95948,-0.28166,265.91,0.03063,0.28178,-0.95899,212.48
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.9995,-0.00083852,0.031678,-2.4206,0.0081219,-0.95948,-0.28166,269.75,0.03063,0.28178,-0.95899,200.92
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.90585,-0.33819,0.25505,19.984,-0.21623,-0.88695,-0.40812,303.79,0.36424,0.31455,-0.87658,147.17
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.90585,-0.33819,0.25505,20.426,-0.21623,-0.88695,-0.40812,305.1,0.36424,0.31455,-0.87658,144.01
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.97204,-0.032205,0.23258,-20.607,0.060804,-0.92224,-0.38181,273.2,0.22679,0.38528,-0.8945,154.18
> view matrix models
> #3,0.97451,-0.091953,0.20462,-10.295,-0.015075,-0.93691,-0.34924,279.75,0.22382,0.33726,-0.91442,162.73
> view matrix models
> #3,0.9768,-0.071379,0.20191,-12.646,0.013307,-0.92077,-0.38989,279.66,0.21374,0.38353,-0.89845,156.44
> view matrix models
> #3,0.97016,-0.075357,0.23045,-15.025,0.014217,-0.93116,-0.36434,277.53,0.24204,0.35675,-0.9023,156.74
> view matrix models
> #3,0.96732,-0.080419,0.24047,-15.368,0.019657,-0.92173,-0.38732,278.7,0.2528,0.37939,-0.89003,151.24
> view matrix models
> #3,0.96488,-0.092955,0.2457,-14.267,0.0099377,-0.92171,-0.38774,279.9,0.2625,0.37657,-0.88842,150.22
> view matrix models
> #3,0.97804,-0.010113,0.20816,-20.811,0.082921,-0.89747,-0.43321,274.21,0.1912,0.44096,-0.87693,149.59
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.97804,-0.010113,0.20816,-19.462,0.082921,-0.89747,-0.43321,274.67,0.1912,0.44096,-0.87693,152.21
> view matrix models
> #3,0.97804,-0.010113,0.20816,-19.696,0.082921,-0.89747,-0.43321,274.84,0.1912,0.44096,-0.87693,151.61
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.98557,0.0033362,0.16925,-17.219,0.07628,-0.90131,-0.42642,275.21,0.15113,0.43317,-0.88855,158.74
> view matrix models
> #3,0.98538,-0.0069629,0.17022,-16.105,0.06106,-0.91835,-0.39104,274.51,0.15904,0.39572,-0.9045,164.25
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.98538,-0.0069629,0.17022,-16.068,0.06106,-0.91835,-0.39104,274.38,0.15904,0.39572,-0.9045,164.32
> ui tool show "Fit in Map"
> fitmap #3 inMap #1
Fit map SepA-Fab40_map.mrc in map EatA-Fab40_map.mrc using 54583 points
correlation = 0.656, correlation about mean = 0.4087, overlap = 1.324e+04
steps = 80, shift = 1.61, angle = 2.98 degrees
Position of SepA-Fab40_map.mrc (#3) relative to EatA-Fab40_map.mrc (#1)
coordinates:
Matrix rotation and translation
0.97640136 -0.02971384 0.21390999 -17.63771279
0.06075407 -0.91269692 -0.40409565 274.78897101
0.20724222 0.40755544 -0.88935327 153.61603109
Axis 0.99381232 0.00816424 0.11077190
Axis point 0.00000000 120.98836134 107.30324009
Rotation angle (degrees) 155.89862954
Shift along axis 1.73120477
> select clear
> volume #1 color #b2b2b2dc
> volume #3 color #ffffb2dc
> show atoms
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> volume #1 color #b2b2b278
> volume #3 color #ffffb278
> volume #3 color #ffffb2
> volume #1 color #b2b2b2
> hide #!3 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> save C:/Users/David/Documents/lab/Berndsen/EatA/sessions/EatA-Fab40_SepA-
> Fab40_sesh.cxs
——— End of log from Mon Feb 10 12:01:26 2025 ———
opened ChimeraX session
> hide #2 models
> show #2 models
OpenGL version: 4.1 Metal - 89.3
OpenGL renderer: Apple M2 Pro
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac14,9
Model Number: Z17H000CGLL/A
Chip: Apple M2 Pro
Total Number of Cores: 12 (8 performance and 4 efficiency)
Memory: 32 GB
System Firmware Version: 11881.81.2
OS Loader Version: 11881.81.2
Software:
System Software Overview:
System Version: macOS 15.3 (24D60)
Kernel Version: Darwin 24.3.0
Time since boot: 6 days, 2 hours, 48 minutes
Graphics/Displays:
Apple M2 Pro:
Chipset Model: Apple M2 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 19
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Studio Display:
Display Type: Retina LCD
Resolution: 5120 x 2880 Retina
Display Serial Number: PCQ1PYK7Q2
Display Firmware Version: Version 17.0 (Build 21A329)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Studio Display:
Display Type: Retina LCD
Resolution: 5120 x 2880 Retina
Display Serial Number: Y97G6YP3MV
Display Firmware Version: Version 17.0 (Build 21A329)
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
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: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
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: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
Change History (2)
comment:1 by , 9 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash moving window between screens |
comment:2 by , 9 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
This crash is due to Qt window toolkit bug on Mac with multiple displays. The ChimeraX bug reporter panel you used had an explanation of what we know about it:
"This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX."
We just started putting a newer Qt version 6.8.2 instead of 6.7 into the ChimeraX daily build a few days ago and you may want to try that. Possibly the newer Qt has fixed the problem.
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Reported by James Fleckenstein