![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
#16312 closed defect (duplicate)
Crash on Mac waking from sleep, Qt 6.7
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | chimerax-programmers | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-15.1-arm64-arm-64bit
ChimeraX Version: 1.9rc202411082121 (2024-11-08 21:21:14 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 0x00000001f7463ac0 (most recent call first):
File "/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
File "/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
File "/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, chimerax.surface._surface, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, openmm._openmm, openmm.app.internal.compiled, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, psutil._psutil_osx, psutil._psutil_posix, PIL._imagingmath, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize (total: 60)
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{
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"procRole" : "Foreground",
"version" : 2,
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"deployVersion" : 210,
"modelCode" : "Mac16,8",
"coalitionID" : 18033,
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"releaseType" : "User"
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"captureTime" : "2024-11-14 15:59:00.9401 -0600",
"codeSigningMonitor" : 2,
"incident" : "5D1834EE-38C8-4CE0-A2A8-6588221A8383",
"pid" : 17509,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-11-14 14:14:32.4345 -0600",
"procStartAbsTime" : 1242709889266,
"procExitAbsTime" : 1351143422012,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.9-rc2024.11.08.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.9.0","CFBundleVersion":"1.9.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
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"parentProc" : "launchd",
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"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "7FA5FDF8-8D67-28A2-72D7-B9E65B3FCACD",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRcuD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkWfg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
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"sleepWakeUUID" : "2F844393-7B8C-485E-9022-B24A8BA95B15",
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"exception" : {"codes":"0x0000000000000001, 0x0000000000000169","rawCodes":[1,361],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000169"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":17509},
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===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
> mousemode middleMode center
> cofr centerOfView
> alias cofron cofr centerofview showpivot true
> alias cofroff cofr centerofview showpivot false
> alias symclip cofr centerofview; clip near -$1 far $1 position cofr
> alias cootmode set bgColor black; surface cap false; surface style solid;
> lighting flat; graphics silhouettes false; style stick; ~rib; color
> ##num_residues gold; color byhet ; disp; ~disp @H*; style ions ball; style
> solvent ball; size ballscale 0.2; size stickradius 0.07; transparency 70;
> cofr centerofview; clip near -10 far 10 position cofr; color ##~num_residues
> cornflower blue
> alias cootmode_mesh set bgColor black; surface cap false; surface style
> mesh; lighting flat; graphics silhouettes false; style stick; ~rib; color
> ##num_residues gold; color byhet ; disp; ~disp @H*; style solvent ball;
> style ions ball; size ballscale 0.2; size stickradius 0.07; cofr
> centerofview; clip near -10 far 10 position cofr; color ##~num_residues
> #3d60ffff; transparency 50
> alias cootmode_off surface style solid; lighting soft; graphics silhouettes
> false; hide atoms; default_mol_display; transparency 0; symclip 40; color
> ##~num_residues grey; size stickradius 0.2;
> alias ca_and_sidechains ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1;
> disp @P&nucleic&$1; style $1 stick; disp sidechain&$1; disp
> ~backbone&nucleic&$1; size stickradius 0.1; size pseudobondradius 0.1
> alias ca_trace ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1; disp
> @P&nucleic&$1; style $1 stick; size stickradius 0.1; size pseudobondradius
> 0.1
> alias map_sphere_15 surface unzone ##~num_residues; sel; close #10000;
> marker #10000 position cofr; sel ~sel; surface zone ##~num_residues
> nearAtoms sel distance 15; close #10000
> alias map_unsphere surface unzone ##~num_residues
> alias default_mol_display ~disp; rib; rainbow chain palette Pastel1-5;
> lighting soft; color byhet
> alias hidemaps surface unzone ##~num_residues; sel; close #10000; marker
> #10000 position cofr; sel ~sel; surface zone ##~num_residues nearAtoms sel
> distance 0; close #10000
> alias showmaps surface unzone ##~num_residues
> alias licorice car style protein modeh default arrows f xsect oval width 1
> thick 1; style stick; size stickRadius 0.5; ~disp @H*; color byhet
> alias caps_off surface cap false
> alias caps_on surface cap true
> alias rock_movie cofr showpivot false; movie record supersample 3; rock y
> 40; wait 136; movie encode ~/Desktop/rock_movie.mp4 quality high; stop
> alias publication_figure save Figure.png format png supersample 3
> transparentBackground true width 3000 height 3000
> buttonpanel Shortcuts rows 3 columns 5
> buttonpanel Shortcuts add default_disp command default_mol_display
> buttonpanel Shortcuts add Hide_H command "~disp @H*"
> buttonpanel Shortcuts add Licorice command licorice
> buttonpanel Shortcuts add Ribbons command "preset ribbons"
> buttonpanel Shortcuts add RockMovie command rock_movie
> buttonpanel Shortcuts add SymClip10 command "symclip 10"
> buttonpanel Shortcuts add SymClip20 command "symclip 20"
> buttonpanel Shortcuts add map_sphere command map_sphere_15
> buttonpanel Shortcuts add map_unsphere command map_unsphere
> buttonpanel Shortcuts add PubFigure command publication_figure
> buttonpanel Shortcuts add coot_mode command cootmode
> buttonpanel Shortcuts add coot_mesh command cootmode_mesh
> buttonpanel Shortcuts add coot_off command cootmode_off
> buttonpanel Shortcuts add hidemaps command hidemaps
> buttonpanel Shortcuts add showmaps command showmaps
> ui tool show "Model Panel"
UCSF ChimeraX version: 1.9rc202411082121 (2024-11-08)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/zhouling95/Library/CloudStorage/Box-Box/McLellan
> Lab/Manuscripts/In Progress/S2 Antibodies/02
> Structure-N6-2/maps/cryosparc_P5_J162_map_sharp.mrc"
Opened cryosparc_P5_J162_map_sharp.mrc as #1, grid size 512,512,512, pixel
0.94, shown at level 0.00016, step 2, values float32
> open "/Users/zhouling95/Library/CloudStorage/Box-Box/McLellan
> Lab/Manuscripts/In Progress/S2 Antibodies/02
> Structure-N6-2/maps/cryosparc_P5_J161_013_volume_map_sharp.mrc"
Opened cryosparc_P5_J161_013_volume_map_sharp.mrc as #2, grid size
512,512,512, pixel 0.94, shown at level 0.0306, step 2, values float32
> surface dust #1 size 9.4
> surface dust #2 size 9.4
> volume #1 step 1
> volume #2 step 1
> volume #1 level 0.02475
> volume #2 level 0.06649
> close #2
> open "/Users/zhouling95/Library/CloudStorage/Box-Box/McLellan
> Lab/Manuscripts/In Progress/S2 Antibodies/02
> Structure-N6-2/maps/cryosparc_P5_J162_map_sharp.mrc"
Opened cryosparc_P5_J162_map_sharp.mrc as #2, grid size 512,512,512, pixel
0.94, shown at level 0.00016, step 2, values float32
> surface dust #1 size 9.4
> surface dust #2 size 9.4
> volume #2 level 0.02475
> volume #2 step 1
> volume #2 level 0.02475
> open "/Users/zhouling95/Library/CloudStorage/Box-Box/McLellan
> Lab/Manuscripts/In Progress/S2 Antibodies/02
> Structure-N6-2/maps/cryosparc_P5_J161_013_volume_map_sharp.mrc"
Opened cryosparc_P5_J161_013_volume_map_sharp.mrc as #3, grid size
512,512,512, pixel 0.94, shown at level 0.0306, step 2, values float32
> surface dust #1 size 9.4
> surface dust #2 size 9.4
> surface dust #3 size 9.4
> volume #3 level 0.06339
> close #1-3
> open "/Users/zhouling95/Library/CloudStorage/Box-Box/Personal Backup/2024/02
> SARS-CoV-2 S2/S2 antibodies/B3-1/B3-1
> maps/Local/cryosparc_P120_J185_006_volume_map_half_A_deepEMhancer-
> sharpened.mrc"
Opened cryosparc_P120_J185_006_volume_map_half_A_deepEMhancer-sharpened.mrc as
#1, grid size 384,384,384, pixel 0.81, shown at level 0.00079, step 2, values
float32
> surface dust #1 size 8.1
> volume #1 step 1
> volume #1 level 0.0482
> set bgColor white
> surface dust #1 size 8.1
> volume #1 level 0.0561
> volume #1 level 0.03635
> open "/Users/zhouling95/Library/CloudStorage/Box-Box/McLellan
> Lab/Manuscripts/In Progress/S2 Antibodies/03
> Structure-B3-1/RealSpaceRefine_51/B3-1_S2_045_isolde_real_space_refined_051.pdb"
Chain information for B3-1_S2_045_isolde_real_space_refined_051.pdb #2
---
Chain | Description
B | No description available
H | No description available
L | No description available
> hide #!1 models
> select #2/B
5448 atoms, 5501 bonds, 1 pseudobond, 353 residues, 2 models selected
> ui tool show "Color Actions"
> color sel royal blue
> color sel dodger blue
> color sel cornflower blue
> select #2/H
1808 atoms, 1830 bonds, 119 residues, 1 model selected
> ui tool show "Color Actions"
> color sel indian red
> color sel saddle brown
> color sel indian red
> select #2/L
1600 atoms, 1622 bonds, 106 residues, 1 model selected
> ui tool show "Color Actions"
> color sel light coral
> color sel light salmon
> color sel dark salmon
> color sel light salmon
> select add #2
8856 atoms, 8953 bonds, 1 pseudobond, 578 residues, 2 models selected
> select subtract #2
Nothing selected
> lighting soft
> select #2/B
5448 atoms, 5501 bonds, 1 pseudobond, 353 residues, 2 models selected
> select #2/B
5448 atoms, 5501 bonds, 1 pseudobond, 353 residues, 2 models selected
> ui tool show "Color Actions"
> color sel royal blue
> select add #2
8856 atoms, 8953 bonds, 1 pseudobond, 578 residues, 2 models selected
> select subtract #2
Nothing selected
> show #!1 models
> color #1 #fefefeff models
> color zone #1 near #2 distance 4.86
> hide #!1 models
> show #!1 models
> hide #!2 models
> surface dust #1 size 8.1
> graphics silhouettes true
> volume #1 level 0.05262
> volume #1 level 0.06076
> ui tool show "Side View"
> publication_figure
> save Figure.png format png supersample 3 transparentBackground true width
> 3000 height 3000
> publication_figure
> save Figure.png format png supersample 3 transparentBackground true width
> 3000 height 3000
> hide #!1 models
> show #!2 models
> select #2/H
1808 atoms, 1830 bonds, 119 residues, 1 model selected
> ui tool show "Color Actions"
> color sel fire brick
> select add #2
8856 atoms, 8953 bonds, 1 pseudobond, 578 residues, 2 models selected
> select subtract #2
Nothing selected
> publication_figure
> save Figure.png format png supersample 3 transparentBackground true width
> 3000 height 3000
> show #!1 models
> open "/Users/zhouling95/Library/CloudStorage/Box-Box/McLellan
> Lab/Manuscripts/In Progress/S2 Antibodies/03
> Structure-B3-1/maps/cryosparc_P120_J178_009_volume_map_sharp.mrc"
Opened cryosparc_P120_J178_009_volume_map_sharp.mrc as #3, grid size
384,384,384, pixel 0.81, shown at level 0.0131, step 2, values float32
> surface dust #1 size 8.1
> surface dust #3 size 8.1
> volume #3 step 1
> volume #3 level 0.04086
> volume #3 level 0.03019
> volume #3 color #fffdf8
> combined #2
Unknown command: combined #2
> combine #2
> select add #4
8856 atoms, 8953 bonds, 1 pseudobond, 578 residues, 2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.91808,-0.33716,-0.20844,431.91,0.36827,-0.92004,-0.13384,230.63,-0.14665,-0.19964,0.96883,60.489
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.91808,-0.33716,-0.20844,419.41,0.36827,-0.92004,-0.13384,275.41,-0.14665,-0.19964,0.96883,59.688
> fitmap #4 inMap #3
Fit molecule copy of B3-1_S2_045_isolde_real_space_refined_051.pdb (#4) to map
cryosparc_P120_J178_009_volume_map_sharp.mrc (#3) using 8856 atoms
average map value = 0.01518, steps = 2000
shifted from previous position = 5.29
rotated from previous position = 9.85 degrees
atoms outside contour = 6841, contour level = 0.030185
Position of copy of B3-1_S2_045_isolde_real_space_refined_051.pdb (#4)
relative to cryosparc_P120_J178_009_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
-0.88957154 -0.44644594 -0.09668758 406.36882755
0.45259202 -0.89006477 -0.05426944 240.26813012
-0.06182983 -0.09203658 0.99383416 25.32851927
Axis -0.04193991 -0.03870907 0.99837000
Axis point 175.09907464 169.02896030 0.00000000
Rotation angle (degrees) 153.24008934
Shift along axis -1.05639699
> view matrix models
> #4,-0.88957,-0.44645,-0.096688,397.8,0.45259,-0.89006,-0.054269,242.99,-0.06183,-0.092037,0.99383,14.562
> fitmap #4 inMap #3
Fit molecule copy of B3-1_S2_045_isolde_real_space_refined_051.pdb (#4) to map
cryosparc_P120_J178_009_volume_map_sharp.mrc (#3) using 8856 atoms
average map value = 0.0177, steps = 180
shifted from previous position = 4.73
rotated from previous position = 6.87 degrees
atoms outside contour = 6455, contour level = 0.030185
Position of copy of B3-1_S2_045_isolde_real_space_refined_051.pdb (#4)
relative to cryosparc_P120_J178_009_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
-0.85742548 -0.50185165 -0.11387041 402.13197889
0.51410097 -0.84516849 -0.14625460 236.22338926
-0.02284157 -0.18394331 0.98267142 22.88692973
Axis -0.03692370 -0.08918113 0.99533078
Axis point 169.09098000 174.49997184 0.00000000
Rotation angle (degrees) 149.31223513
Shift along axis -13.13480497
> view matrix models
> #4,-0.85743,-0.50185,-0.11387,396.17,0.5141,-0.84517,-0.14625,234.15,-0.022842,-0.18394,0.98267,22.391
> fitmap #4 inMap #3
Fit molecule copy of B3-1_S2_045_isolde_real_space_refined_051.pdb (#4) to map
cryosparc_P120_J178_009_volume_map_sharp.mrc (#3) using 8856 atoms
average map value = 0.01843, steps = 220
shifted from previous position = 4.06
rotated from previous position = 7.58 degrees
atoms outside contour = 6406, contour level = 0.030185
Position of copy of B3-1_S2_045_isolde_real_space_refined_051.pdb (#4)
relative to cryosparc_P120_J178_009_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
-0.78633202 -0.60600218 -0.12018032 402.18822573
0.61665709 -0.78172702 -0.09293486 198.86139143
-0.03762948 -0.14718770 0.98839253 16.29255147
Axis -0.04422871 -0.06729817 0.99675211
Axis point 167.44540745 169.00058962 0.00000000
Rotation angle (degrees) 142.16993186
Shift along axis -14.93163743
> view matrix models
> #4,-0.78633,-0.606,-0.12018,405.74,0.61666,-0.78173,-0.092935,200.17,-0.037629,-0.14719,0.98839,28.055
> view matrix models
> #4,-0.78633,-0.606,-0.12018,407,0.61666,-0.78173,-0.092935,200.96,-0.037629,-0.14719,0.98839,25.775
> volume #3 level 0.01951
> fitmap #4 inMap #3
Fit molecule copy of B3-1_S2_045_isolde_real_space_refined_051.pdb (#4) to map
cryosparc_P120_J178_009_volume_map_sharp.mrc (#3) using 8856 atoms
average map value = 0.01863, steps = 2000
shifted from previous position = 3.77
rotated from previous position = 3 degrees
atoms outside contour = 5449, contour level = 0.019514
Position of copy of B3-1_S2_045_isolde_real_space_refined_051.pdb (#4)
relative to cryosparc_P120_J178_009_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
-0.75716428 -0.63640118 -0.14729493 409.42926322
0.64990442 -0.75662030 -0.07176325 184.81023473
-0.06577612 -0.15006419 0.98648580 29.61780889
Axis -0.06063907 -0.06313110 0.99616132
Axis point 171.73945523 168.49580044 0.00000000
Rotation angle (degrees) 139.78698486
Shift along axis -6.99056693
> view matrix models
> #4,-0.75716,-0.6364,-0.14729,409.67,0.6499,-0.75662,-0.071763,185.78,-0.065776,-0.15006,0.98649,29.629
> view matrix models
> #4,-0.75716,-0.6364,-0.14729,409.45,0.6499,-0.75662,-0.071763,190.8,-0.065776,-0.15006,0.98649,30.066
> view matrix models
> #4,-0.75716,-0.6364,-0.14729,408.87,0.6499,-0.75662,-0.071763,190.38,-0.065776,-0.15006,0.98649,33.009
> fitmap #4 inMap #3
Fit molecule copy of B3-1_S2_045_isolde_real_space_refined_051.pdb (#4) to map
cryosparc_P120_J178_009_volume_map_sharp.mrc (#3) using 8856 atoms
average map value = 0.01874, steps = 2000
shifted from previous position = 4.32
rotated from previous position = 4.56 degrees
atoms outside contour = 5426, contour level = 0.019514
Position of copy of B3-1_S2_045_isolde_real_space_refined_051.pdb (#4)
relative to cryosparc_P120_J178_009_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
-0.75721404 -0.64951397 -0.06898188 401.45931323
0.65316248 -0.75335921 -0.07634572 188.42944412
-0.00238053 -0.10286643 0.99469233 14.36128609
Axis -0.02032787 -0.05104931 0.99848923
Axis point 165.89507038 169.16684644 0.00000000
Rotation angle (degrees) 139.28296855
Shift along axis -3.44041782
> view matrix models
> #4,-0.75721,-0.64951,-0.068982,400.14,0.65316,-0.75336,-0.076346,190.02,-0.0023805,-0.10287,0.99469,16.977
> view matrix models
> #4,-0.75721,-0.64951,-0.068982,401.18,0.65316,-0.75336,-0.076346,190.99,-0.0023805,-0.10287,0.99469,17.97
> view matrix models
> #4,-0.75721,-0.64951,-0.068982,401.06,0.65316,-0.75336,-0.076346,193.05,-0.0023805,-0.10287,0.99469,11.252
> view matrix models
> #4,-0.75721,-0.64951,-0.068982,402.88,0.65316,-0.75336,-0.076346,191.95,-0.0023805,-0.10287,0.99469,11.165
> view matrix models
> #4,-0.75721,-0.64951,-0.068982,400.39,0.65316,-0.75336,-0.076346,189.02,-0.0023805,-0.10287,0.99469,10.396
> view matrix models
> #4,-0.75721,-0.64951,-0.068982,397.6,0.65316,-0.75336,-0.076346,188.2,-0.0023805,-0.10287,0.99469,11.142
> fitmap #4 inMap #3
Fit molecule copy of B3-1_S2_045_isolde_real_space_refined_051.pdb (#4) to map
cryosparc_P120_J178_009_volume_map_sharp.mrc (#3) using 8856 atoms
average map value = 0.02053, steps = 364
shifted from previous position = 1.92
rotated from previous position = 12.9 degrees
atoms outside contour = 5183, contour level = 0.019514
Position of copy of B3-1_S2_045_isolde_real_space_refined_051.pdb (#4)
relative to cryosparc_P120_J178_009_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
-0.61092633 -0.77254908 -0.17302294 404.41158725
0.78385250 -0.62092890 0.00475032 131.90076010
-0.11110480 -0.13272237 0.98490634 36.37132472
Axis -0.08791571 -0.03959752 0.99534058
Axis point 171.94640459 164.41203078 0.00000000
Rotation angle (degrees) 128.57030320
Shift along axis -4.57521874
> view matrix models
> #4,-0.61093,-0.77255,-0.17302,404.35,0.78385,-0.62093,0.0047503,131.1,-0.1111,-0.13272,0.98491,39.786
> fitmap #4 inMap #3
Fit molecule copy of B3-1_S2_045_isolde_real_space_refined_051.pdb (#4) to map
cryosparc_P120_J178_009_volume_map_sharp.mrc (#3) using 8856 atoms
average map value = 0.02631, steps = 132
shifted from previous position = 1.23
rotated from previous position = 10.4 degrees
atoms outside contour = 4310, contour level = 0.019514
Position of copy of B3-1_S2_045_isolde_real_space_refined_051.pdb (#4)
relative to cryosparc_P120_J178_009_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
-0.48313036 -0.87030693 -0.09566035 383.18069357
0.87446721 -0.48507316 -0.00333603 95.90322257
-0.04349890 -0.08526357 0.99540844 19.43097500
Axis -0.04688338 -0.02984961 0.99845428
Axis point 163.82841830 161.01780461 0.00000000
Rotation angle (degrees) 119.10407620
Shift along axis -1.42653879
> select subtract #4
Nothing selected
> combine #4
> select add #5
8856 atoms, 8953 bonds, 1 pseudobond, 578 residues, 2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.41011,0.84572,0.34143,52.142,-0.89465,-0.30028,-0.33081,444.99,-0.17725,-0.44113,0.87977,113.76
> view matrix models
> #5,0.31189,0.90507,0.2891,-79.453,-0.94536,0.32603,-0.00078397,310.54,-0.094965,-0.27306,0.9573,62
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.31189,0.90507,0.2891,-91.342,-0.94536,0.32603,-0.00078397,266.26,-0.094965,-0.27306,0.9573,54.955
> view matrix models
> #5,0.31189,0.90507,0.2891,-104.16,-0.94536,0.32603,-0.00078397,265.35,-0.094965,-0.27306,0.9573,55.206
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.20507,0.96453,0.16621,1.4825,-0.9777,-0.19403,-0.080303,358.93,-0.045206,-0.17897,0.98282,28.464
> fitmap #5 inMap #3
Fit molecule copy of copy of B3-1_S2_045_isolde_real_space_refined_051.pdb
(#5) to map cryosparc_P120_J178_009_volume_map_sharp.mrc (#3) using 8856 atoms
average map value = 0.01839, steps = 128
shifted from previous position = 2.53
rotated from previous position = 2.12 degrees
atoms outside contour = 5476, contour level = 0.019514
Position of copy of copy of B3-1_S2_045_isolde_real_space_refined_051.pdb (#5)
relative to cryosparc_P120_J178_009_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
-0.20863332 0.96376562 0.16621663 0.97947404
-0.97795095 -0.20399545 -0.04469676 352.46132985
-0.00916976 -0.17187695 0.98507575 19.54496263
Axis -0.06509492 0.08976841 -0.99383313
Axis point 142.12362545 176.39647742 0.00000000
Rotation angle (degrees) 102.34375771
Shift along axis 12.15170344
> view matrix models
> #5,-0.21173,0.96199,0.17245,0.78514,-0.97564,-0.21841,0.020519,343.51,0.057403,-0.1639,0.98481,6.3107
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.21173,0.96199,0.17245,1.5856,-0.97564,-0.21841,0.020519,343.46,0.057403,-0.1639,0.98481,10.49
> fitmap #5 inMap #3
Fit molecule copy of copy of B3-1_S2_045_isolde_real_space_refined_051.pdb
(#5) to map cryosparc_P120_J178_009_volume_map_sharp.mrc (#3) using 8856 atoms
average map value = 0.02014, steps = 156
shifted from previous position = 1.84
rotated from previous position = 6.6 degrees
atoms outside contour = 5177, contour level = 0.019514
Position of copy of copy of B3-1_S2_045_isolde_real_space_refined_051.pdb (#5)
relative to cryosparc_P120_J178_009_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
-0.31616814 0.93622723 0.15335020 27.06863813
-0.94853892 -0.31496413 -0.03273414 359.77361060
0.01765322 -0.15580813 0.98762958 16.89798616
Axis -0.06499305 0.07165902 -0.99530944
Axis point 142.26436450 170.58576579 0.00000000
Rotation angle (degrees) 108.76887173
Shift along axis 7.20302526
> fitmap #5 inMap #3
Fit molecule copy of copy of B3-1_S2_045_isolde_real_space_refined_051.pdb
(#5) to map cryosparc_P120_J178_009_volume_map_sharp.mrc (#3) using 8856 atoms
average map value = 0.02014, steps = 76
shifted from previous position = 0.0257
rotated from previous position = 0.225 degrees
atoms outside contour = 5177, contour level = 0.019514
Position of copy of copy of B3-1_S2_045_isolde_real_space_refined_051.pdb (#5)
relative to cryosparc_P120_J178_009_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
-0.31971292 0.93516286 0.15249287 27.98634209
-0.94737172 -0.31829109 -0.03431617 360.31720560
0.01644592 -0.15543875 0.98770862 17.03977876
Axis -0.06404108 0.07193203 -0.99535146
Axis point 142.42699080 170.57725257 0.00000000
Rotation angle (degrees) 108.97452327
Shift along axis 7.16550327
> view matrix models
> #5,-0.31971,0.93516,0.15249,27.314,-0.94737,-0.31829,-0.034316,360.23,0.016446,-0.15544,0.98771,18.774
> view matrix models
> #5,-0.31971,0.93516,0.15249,26.819,-0.94737,-0.31829,-0.034316,361.7,0.016446,-0.15544,0.98771,21.138
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.44903,0.87675,0.1723,55.56,-0.87405,-0.47103,0.11901,345.36,0.1855,-0.097157,0.97783,-16.439
> fitmap #5 inMap #3
Fit molecule copy of copy of B3-1_S2_045_isolde_real_space_refined_051.pdb
(#5) to map cryosparc_P120_J178_009_volume_map_sharp.mrc (#3) using 8856 atoms
average map value = 0.02462, steps = 100
shifted from previous position = 2.76
rotated from previous position = 8.46 degrees
atoms outside contour = 4535, contour level = 0.019514
Position of copy of copy of B3-1_S2_045_isolde_real_space_refined_051.pdb (#5)
relative to cryosparc_P120_J178_009_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
-0.50188464 0.85458892 0.13337758 76.44830772
-0.86337208 -0.50425049 -0.01789140 371.74322613
0.05196592 -0.12413390 0.99090379 7.20692620
Axis -0.06165536 0.04724536 -0.99697868
Axis point 144.46982821 164.03144913 0.00000000
Rotation angle (degrees) 120.50514077
Shift along axis 5.66454420
> select subtract #5
Nothing selected
> select #4/B
5448 atoms, 5501 bonds, 1 pseudobond, 353 residues, 2 models selected
> ui tool show "Color Actions"
> color sel sky blue
> select #5/B
5448 atoms, 5501 bonds, 1 pseudobond, 353 residues, 2 models selected
> color sel steel blue
> select add #5
8856 atoms, 8953 bonds, 1 pseudobond, 578 residues, 2 models selected
> select subtract #5
Nothing selected
Color zone shortcut requires 1 displayed atomic model and 1 map, got 3 atomic
models, 1 maps.
> hide #!3 models
> show #!3 models
Color zone shortcut requires 1 displayed atomic model and 1 map, got 3 atomic
models, 1 maps.
> select add #2
8856 atoms, 8953 bonds, 1 pseudobond, 578 residues, 2 models selected
> select add #4
17712 atoms, 17906 bonds, 2 pseudobonds, 1156 residues, 4 models selected
> select add #5
26568 atoms, 26859 bonds, 3 pseudobonds, 1734 residues, 6 models selected
Color zone shortcut requires 1 displayed atomic model and 1 map, got 3 atomic
models, 1 maps.
> select subtract #4
17712 atoms, 17906 bonds, 2 pseudobonds, 1156 residues, 4 models selected
> select subtract #5
8856 atoms, 8953 bonds, 1 pseudobond, 578 residues, 2 models selected
> color zone #3 near sel & #2 distance 4.86
> combined #2, #4, #5
Unknown command: combined #2, #4, #5
> combined #2, 4,5
Unknown command: combined #2, 4,5
> combined #2, 4, 5
Unknown command: combined #2, 4, 5
> select subtract #2
Nothing selected
> volume #3 level 0.03659
> save "/Users/zhouling95/Documents/Academic/McLellan Lab/B3-1 global
> colored.cxs" includeMaps true
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
> mousemode middleMode center
> cofr centerOfView
> alias cofron cofr centerofview showpivot true
> alias cofroff cofr centerofview showpivot false
> alias symclip cofr centerofview; clip near -$1 far $1 position cofr
> alias cootmode set bgColor black; surface cap false; surface style solid;
> lighting flat; graphics silhouettes false; style stick; ~rib; color
> ##num_residues gold; color byhet ; disp; ~disp @H*; style ions ball; style
> solvent ball; size ballscale 0.2; size stickradius 0.07; transparency 70;
> cofr centerofview; clip near -10 far 10 position cofr; color ##~num_residues
> cornflower blue
> alias cootmode_mesh set bgColor black; surface cap false; surface style
> mesh; lighting flat; graphics silhouettes false; style stick; ~rib; color
> ##num_residues gold; color byhet ; disp; ~disp @H*; style solvent ball;
> style ions ball; size ballscale 0.2; size stickradius 0.07; cofr
> centerofview; clip near -10 far 10 position cofr; color ##~num_residues
> #3d60ffff; transparency 50
> alias cootmode_off surface style solid; lighting soft; graphics silhouettes
> false; hide atoms; default_mol_display; transparency 0; symclip 40; color
> ##~num_residues grey; size stickradius 0.2;
> alias ca_and_sidechains ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1;
> disp @P&nucleic&$1; style $1 stick; disp sidechain&$1; disp
> ~backbone&nucleic&$1; size stickradius 0.1; size pseudobondradius 0.1
> alias ca_trace ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1; disp
> @P&nucleic&$1; style $1 stick; size stickradius 0.1; size pseudobondradius
> 0.1
> alias map_sphere_15 surface unzone ##~num_residues; sel; close #10000;
> marker #10000 position cofr; sel ~sel; surface zone ##~num_residues
> nearAtoms sel distance 15; close #10000
> alias map_unsphere surface unzone ##~num_residues
> alias default_mol_display ~disp; rib; rainbow chain palette Pastel1-5;
> lighting soft; color byhet
> alias hidemaps surface unzone ##~num_residues; sel; close #10000; marker
> #10000 position cofr; sel ~sel; surface zone ##~num_residues nearAtoms sel
> distance 0; close #10000
> alias showmaps surface unzone ##~num_residues
> alias licorice car style protein modeh default arrows f xsect oval width 1
> thick 1; style stick; size stickRadius 0.5; ~disp @H*; color byhet
> alias caps_off surface cap false
> alias caps_on surface cap true
> alias rock_movie cofr showpivot false; movie record supersample 3; rock y
> 40; wait 136; movie encode ~/Desktop/rock_movie.mp4 quality high; stop
> alias publication_figure save Figure.png format png supersample 3
> transparentBackground true width 3000 height 3000
> buttonpanel Shortcuts rows 3 columns 5
> buttonpanel Shortcuts add default_disp command default_mol_display
> buttonpanel Shortcuts add Hide_H command "~disp @H*"
> buttonpanel Shortcuts add Licorice command licorice
> buttonpanel Shortcuts add Ribbons command "preset ribbons"
> buttonpanel Shortcuts add RockMovie command rock_movie
> buttonpanel Shortcuts add SymClip10 command "symclip 10"
> buttonpanel Shortcuts add SymClip20 command "symclip 20"
> buttonpanel Shortcuts add map_sphere command map_sphere_15
> buttonpanel Shortcuts add map_unsphere command map_unsphere
> buttonpanel Shortcuts add PubFigure command publication_figure
> buttonpanel Shortcuts add coot_mode command cootmode
> buttonpanel Shortcuts add coot_mesh command cootmode_mesh
> buttonpanel Shortcuts add coot_off command cootmode_off
> buttonpanel Shortcuts add hidemaps command hidemaps
> buttonpanel Shortcuts add showmaps command showmaps
> ui tool show "Model Panel"
UCSF ChimeraX version: 1.9rc202411082121 (2024-11-08)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 89.3
OpenGL renderer: Apple M4 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: Mac16,8
Model Number: MX2J3LL/A
Chip: Apple M4 Pro
Total Number of Cores: 14 (10 performance and 4 efficiency)
Memory: 24 GB
System Firmware Version: 11881.41.5
OS Loader Version: 11881.41.5
Software:
System Software Overview:
System Version: macOS 15.1 (24B2082)
Kernel Version: Darwin 24.1.0
Time since boot: 2 days, 2 hours, 2 minutes
Graphics/Displays:
Apple M4 Pro:
Chipset Model: Apple M4 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 20
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
LG ULTRAGEAR:
Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
UI Looks like: 2560 x 1440 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
auditwheel: 6.1.0
autocommand: 2.2.2
babel: 2.16.0
backports.tarfile: 1.2.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.7.1
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.17
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: 1.58.7
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: 2.4.7
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13
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-Clipper: 0.23.0
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: 1.9rc202411082121
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: 1.2.5
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-ISOLDE: 1.8.dev0
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.11
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: 1.5.17
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-QScore: 1.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.1
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: 3.2.6
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: 1.3.0
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.8
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.54.1
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.12.1
html2text: 2024.2.26
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
importlib_metadata: 8.0.0
importlib_resources: 6.4.0
inflect: 7.3.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jaraco.context: 5.3.0
jaraco.functools: 4.0.1
jaraco.text: 3.12.1
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
more-itertools: 10.3.0
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: 2.10.1
numpy: 1.26.4
openvr: 1.26.701
ordered-set: 4.1.0
packaging: 23.2
packaging: 24.1
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
platformdirs: 4.2.2
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
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
tomli: 2.0.1
tornado: 6.4.1
traitlets: 5.14.3
typeguard: 4.3.0
typing_extensions: 4.12.2
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: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
zipp: 3.19.2
Change History (6)
comment:1 by , 12 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash on Mac waking from sleep |
comment:2 by , 12 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
| Summary: | Crash on Mac waking from sleep → Crash on Mac waking from sleep, Qt 6.7 |
comment:3 by , 12 months ago
There have been 5 instances of this crash in Qt 6.7 reported including mine in my development build, and 4 in the release candidates in about 2 weeks.
comment:4 by , 12 months ago
| Cc: | added |
|---|
We got another report today. That makes 5 reports in 10 days. It appears the crash is as frequent as it was with Qt 6.6 in ChimeraX 1.8.
Anything we can do about this? Qt 6.8 is out but trying that would delay our ChimeraX 1.9 release into January, and I'd guess it is unlikely to fix the problem. I could add a one-time popup on Mac when ChimeraX starts with two displays that warns that connecting and disconnecting displays and possibly sleeping or moving ChimeraX between displays causes a crash due to bugs in the Qt window toolkit we are so far unable to fix. At least users would know what to avoid, and we might get fewer reports.
Note:
See TracTickets
for help on using tickets.
Crash in Qt 6.7 in _NSViewHierarchyDidChangeBackingProperties.
I'm perplexed that we had over a hundred tickets for ChimeraX daily builds with Qt 6.7 and no reports of this crash. We have far fewer total tickets for the 1.9 release candidates and yet we have many (6?) reports of this Mac external display crash. What explains this? The reporter of this ticket reported the same crash twice #16311.