![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 6 months ago
Closed 6 months ago
#17562 closed defect (duplicate)
Crash on Mac waking from sleep
| 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-15.1-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.
Fatal Python error: Segmentation fault
Current thread 0x00000001e963bac0 (most recent call first):
File "/Applications/ChimeraX-1.9.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.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.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, openmm._openmm, openmm.app.internal.compiled, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, chimerax.pdb_lib._load_libs, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, psutil._psutil_osx, psutil._psutil_posix, chimerax.graphics._graphics, PIL._imagingmath, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif (total: 54)
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"version" : 2,
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"modelCode" : "Mac16,1",
"coalitionID" : 2493,
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"captureTime" : "2025-05-05 17:44:07.9911 -0700",
"codeSigningMonitor" : 2,
"incident" : "FFFD1344-B254-4B6C-A3EE-486B71015770",
"pid" : 2123,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-05-05 10:45:54.3253 -0700",
"procStartAbsTime" : 39423792719,
"procExitAbsTime" : 627048984619,
"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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"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "D97943DC-6DFD-31A3-C756-1C3DDF53D08C",
"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=="},
"bootSessionUUID" : "24A54747-9966-4A08-9D08-6022CE9EDC9C",
"wakeTime" : 2116,
"sleepWakeUUID" : "30A39F3C-5D87-4F7A-A6A3-83CD3BDA26FD",
"sip" : "enabled",
"vmRegionInfo" : "0x8f0000081c0 is not in any region. Bytes after previous region: 9345848869313 Bytes before following region: 95726231060032\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL reserved VM address space (unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000001, 0x000088f0000081c0","rawCodes":[1,150564373561792],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x000088f0000081c0 -> 0x000008f0000081c0 (possible pointer authentication failure)"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":2123},
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===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/mariarafiq/Downloads/cryosparc_P410_J166_002_volume_map.mrc
Opened cryosparc_P410_J166_002_volume_map.mrc as #1, grid size 300,300,300,
pixel 0.74, shown at level 0.0391, step 2, values float32
> volume #1 step 1
> ui tool show "Side View"
> open
> /Users/mariarafiq/Downloads/cryosparc_P410_J163_011_volume_map_sharp.mrc
Opened cryosparc_P410_J163_011_volume_map_sharp.mrc as #2, grid size
300,300,300, pixel 0.74, shown at level 0.0504, step 2, values float32
> surface dust #2 size 7.4
> volume #2 step 1
> volume #2 level 0.1195
> open
> /Users/mariarafiq/Downloads/cryosparc_P410_J162_008_volume_map_sharp.mrc
Opened cryosparc_P410_J162_008_volume_map_sharp.mrc as #3, grid size
300,300,300, pixel 0.74, shown at level 0.0499, step 2, values float32
> surface dust #3 size 7.4
> volume #3 step 1
> volume #3 level 0.08332
> volume #3 level 0.07706
> show #!3 models
> close #3
> ui mousemode right "map eraser"
> volume erase #1 center 107.79,108.08,112.06 radius 22.205 outside true
Opened cryosparc_P410_J166_002_volume_map.mrc copy as #4, grid size
300,300,300, pixel 0.74, shown at step 1, values float32
> volume erase #4 center 107.34,107.65,111.9 radius 19.869 outside true
> vop resample #4 ingrid #1
> volume resample #4 ingrid #1
Expected a keyword
> vop resample #4 on grid #1
> volume resample #4 onGrid grid #1
Invalid "onGrid" argument: invalid density maps specifier
> vop resample #1 on grid #4
> volume resample #1 onGrid grid #4
Invalid "onGrid" argument: invalid density maps specifier
> vop resample #1 onGrid #4
Opened cryosparc_P410_J166_002_volume_map.mrc resampled as #3, grid size
300,300,300, pixel 0.74, shown at step 1, values float32
> vop resample #4 onGrid #1
Opened cryosparc_P410_J166_002_volume_map.mrc copy resampled as #5, grid size
300,300,300, pixel 0.74, shown at step 1, values float32
> save /Users/mariarafiq/Desktop/masks/J166_spherical_ligand_mask.mrc models
> #5
> volume #5 level 0.0391
> volume #5 level 0.0309
> volume #5 level 0.01835
> volume #5 level 0.03186
> volume #5 level 0.0391
> open /Users/mariarafiq/Downloads/cryosparc_P410_J169_mask.mrc
Opened cryosparc_P410_J169_mask.mrc as #6, grid size 300,300,300, pixel 0.74,
shown at level 5e-05, step 2, values float32
> view
> volume #6 step 1
> volume #6 color #b2ffb280
> open /Users/mariarafiq/Downloads/cryosparc_P410_J170_mask.mrc
Opened cryosparc_P410_J170_mask.mrc as #7, grid size 300,300,300, pixel 0.74,
shown at level 5e-05, step 2, values float32
> volume #7 step 1
> volume #7 color #e5bf9980
> close #7
> open "/Users/mariarafiq/Downloads/cryosparc_P410_J169_mask (1).mrc"
Opened cryosparc_P410_J169_mask (1).mrc as #7, grid size 300,300,300, pixel
0.74, shown at level 0.107, step 2, values float32
> volume #7 color #99bfe580
> open /Users/mariarafiq/Downloads/tclcactvs000vGnyIC.pdb
Summary of feedback from opening
/Users/mariarafiq/Downloads/tclcactvs000vGnyIC.pdb
---
warning | Ignored bad PDB record found on line 4
REVDAT 1 05-May-25 0 NONE 4
tclcactvs000vGnyIC.pdb title:
None 2 [more info...]
Non-standard residues in tclcactvs000vGnyIC.pdb #8
---
— ()
> select add #8
118 atoms, 120 bonds, 1 residue, 1 model selected
> hide #!7 models
> hide #!5 models
> view
> volume #6 level 0.009292
> select add #6
118 atoms, 120 bonds, 1 residue, 3 models selected
> select subtract #8
2 models selected
> hide #8 models
> volume #6 level 0.01853
> view
> show #8 models
> show #!6 models
> select subtract #6
Nothing selected
> hide #8 models
> show #8 models
> view
> select add #8
118 atoms, 120 bonds, 1 residue, 1 model selected
> close #9
> ui mousemode right "move picked models"
> view matrix models #8,1,0,0,54.671,0,1,0,132.98,0,0,1,97.532
> view
> ui mousemode right "move picked models"
> view matrix models #5,1,0,0,0.22889,0,1,0,0.052426,0,0,1,-1.4698
> view matrix models #8,1,0,0,51.679,0,1,0,126.7,0,0,1,101.74
> view matrix models #8,1,0,0,55.705,0,1,0,128.7,0,0,1,117
> view matrix models #8,1,0,0,58.488,0,1,0,125.44,0,0,1,126.17
> view matrix models #8,1,0,0,68.554,0,1,0,123.96,0,0,1,137.81
> view matrix models #8,1,0,0,82.06,0,1,0,118.75,0,0,1,145.55
> view matrix models #8,1,0,0,74.231,0,1,0,126.54,0,0,1,127.73
> view matrix models #5,1,0,0,-0.015338,0,1,0,-0.214,0,0,1,-1.5916
> view matrix models #8,1,0,0,81.408,0,1,0,133.64,0,0,1,110.1
> view matrix models #5,1,0,0,0.26401,0,1,0,0.0043148,0,0,1,-0.25077
> view matrix models #8,1,0,0,80.497,0,1,0,119.67,0,0,1,123.29
> view matrix models #5,1,0,0,-0.45483,0,1,0,-1.066,0,0,1,-2.9394
> view matrix models #5,1,0,0,-0.90885,0,1,0,-0.31307,0,0,1,-4.2423
> view matrix models #5,1,0,0,-0.9664,0,1,0,0.83912,0,0,1,-5.0047
> view matrix models #5,1,0,0,2.5697,0,1,0,9.5885,0,0,1,4.4216
> view matrix models #8,1,0,0,90.799,0,1,0,132.58,0,0,1,121.39
> view matrix models #5,1,0,0,2.9362,0,1,0,9.4391,0,0,1,6.2495
> view matrix models #8,1,0,0,100.23,0,1,0,131.38,0,0,1,129.09
> view matrix models #8,1,0,0,99.056,0,1,0,131.66,0,0,1,127.95
> view matrix models #8,1,0,0,94.951,0,1,0,129.34,0,0,1,119.72
> view matrix models #5,1,0,0,1.4376,0,1,0,8.0803,0,0,1,6.7663
> view matrix models #8,1,0,0,91.657,0,1,0,121.11,0,0,1,113.18
> view matrix models #5,1,0,0,0.30451,0,1,0,16.084,0,0,1,5.6172
> view matrix models #8,1,0,0,94.369,0,1,0,127.67,0,0,1,112.33
> view matrix models #8,1,0,0,101.66,0,1,0,117.02,0,0,1,113.71
> view matrix models #8,1,0,0,104.61,0,1,0,123.32,0,0,1,117.92
> view matrix models #5,1,0,0,0.25472,0,1,0,16.822,0,0,1,5.6805
> view matrix models #8,1,0,0,105.63,0,1,0,124.65,0,0,1,116.22
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.63263,-0.75887,-0.15461,106.24,-0.59422,-0.60366,0.53151,126.04,-0.49668,-0.24437,-0.83282,116.2
> view matrix models
> #8,0.32572,-0.85511,-0.40336,106.49,-0.82539,-0.46525,0.31981,126.14,-0.46113,0.22876,-0.85734,115.96
> view matrix models
> #8,0.40627,-0.76926,-0.49314,106.35,-0.77799,-0.57426,0.25486,126.12,-0.47924,0.28012,-0.83178,115.97
> view matrix models
> #8,0.40627,-0.76926,-0.49314,106.93,-0.77799,-0.57426,0.25486,122.79,-0.47924,0.28012,-0.83178,116.99
> fitmap #8 inMap #5
Fit molecule tclcactvs000vGnyIC.pdb (#8) to map J166_spherical_ligand_mask.mrc
(#5) using 118 atoms
average map value = 0.05728, steps = 204
shifted from previous position = 8.42
rotated from previous position = 140 degrees
atoms outside contour = 45, contour level = 0.039102
Position of tclcactvs000vGnyIC.pdb (#8) relative to
J166_spherical_ligand_mask.mrc (#5) coordinates:
Matrix rotation and translation
0.86649934 -0.35783110 -0.34804568 105.41098033
0.49879745 0.59344021 0.63168807 104.36742346
-0.01949334 -0.72096159 0.69270080 119.58449344
Axis -0.82758807 -0.20101731 0.52410879
Axis point 0.00000000 206.55586579 -17.78652635
Rotation angle (degrees) 54.80786246
Shift along axis -45.54124458
> view matrix models
> #8,0.82574,0.40439,-0.39323,105.38,0.09049,0.59314,0.79999,121.63,0.55675,-0.69617,0.45319,124.63
> view matrix models
> #8,-0.48976,0.65598,-0.5743,106.47,-0.16575,0.57664,0.8,121.88,0.85595,0.48701,-0.17369,123.66
> view matrix models
> #8,-0.68129,0.67655,-0.2795,106.74,0.10239,0.46614,0.87877,121.7,0.72482,0.57008,-0.38685,123.68
> view matrix models
> #8,-0.68129,0.67655,-0.2795,108.66,0.10239,0.46614,0.87877,124.32,0.72482,0.57008,-0.38685,118.2
> volume #5 level 0.0309
> view matrix models
> #8,-0.91949,-0.35935,-0.15938,109.35,-0.385,0.90514,0.18029,124.37,0.079475,0.22713,-0.97062,118.76
> view matrix models
> #8,-0.90195,-0.42203,0.091545,109.44,-0.40905,0.90289,0.13219,124.38,-0.13844,0.081781,-0.98699,119.02
> view matrix models
> #8,-0.90263,-0.41806,0.10239,109.44,-0.40435,0.90516,0.13113,124.38,-0.1475,0.076957,-0.98606,119.03
> view matrix models
> #8,-0.97784,-0.20173,0.055965,109.41,-0.20002,0.97918,0.034754,124.12,-0.061811,0.02279,-0.99783,118.97
> fitmap #8 inMap #5
Fit molecule tclcactvs000vGnyIC.pdb (#8) to map J166_spherical_ligand_mask.mrc
(#5) using 118 atoms
average map value = 0.06161, steps = 160
shifted from previous position = 7.36
rotated from previous position = 59.8 degrees
atoms outside contour = 28, contour level = 0.030897
Position of tclcactvs000vGnyIC.pdb (#8) relative to
J166_spherical_ligand_mask.mrc (#5) coordinates:
Matrix rotation and translation
-0.72109758 0.67896016 -0.13795427 109.22034280
0.56884491 0.69386474 0.44155089 102.39646608
0.39551707 0.23992670 -0.88656722 118.75775265
Axis -0.34712815 -0.91845583 -0.18958094
Axis point 28.03131271 0.00000000 53.30275691
Rotation angle (degrees) 163.11704593
Shift along axis -154.47429317
> view matrix models
> #8,-0.46485,0.85438,0.23227,109.28,0.85311,0.36203,0.37568,119.06,0.23688,0.37278,-0.89717,124.53
> view matrix models
> #8,-0.23168,0.89712,0.37616,109.09,0.94822,0.1219,0.29329,119.04,0.21726,0.42463,-0.87891,124.53
> ui mousemode right "move picked models"
> view matrix models
> #8,-0.23168,0.89712,0.37616,110,0.94822,0.1219,0.29329,121.08,0.21726,0.42463,-0.87891,116.96
> volume #5 color #ffb2b27b
> volume #5 color #ffb2b27a
> view matrix models #5,1,0,0,0.17269,0,1,0,16.676,0,0,1,5.947
> open "/Users/mariarafiq/Downloads/cryosparc_P410_J169_mask (2).mrc"
Opened cryosparc_P410_J169_mask (2).mrc as #9, grid size 300,300,300, pixel
0.74, shown at level 0.107, step 2, values float32
> open "/Users/mariarafiq/Downloads/cryosparc_P410_J169_mask (2).mrc"
Opened cryosparc_P410_J169_mask (2).mrc as #10, grid size 300,300,300, pixel
0.74, shown at level 0.107, step 2, values float32
> show #!1 models
> close #10
> close #9
> close #7
> close #6
> open "/Users/mariarafiq/Downloads/cryosparc_P410_J169_mask (3).mrc"
Opened cryosparc_P410_J169_mask (3).mrc as #6, grid size 300,300,300, pixel
0.74, shown at level 5e-05, step 2, values float32
> hide #!6 models
> open "/Users/mariarafiq/Downloads/cryosparc_P410_J169_mask (4).mrc"
Opened cryosparc_P410_J169_mask (4).mrc as #7, grid size 300,300,300, pixel
0.74, shown at level 5e-05, step 2, values float32
> ui tool show "Side View"
> open /Users/mariarafiq/Downloads/cryosparc_P410_J166_002_volume_map.mrc
Opened cryosparc_P410_J166_002_volume_map.mrc as #9, grid size 300,300,300,
pixel 0.74, shown at level 0.0391, step 2, values float32
> volume #7 color #b2ffff71
> volume #7 color #b2ffff70
> open "/Users/mariarafiq/Downloads/cryosparc_P410_J154_003_volume_map_sharp
> (1).mrc"
Opened cryosparc_P410_J154_003_volume_map_sharp (1).mrc as #10, grid size
300,300,300, pixel 0.74, shown at level 0.0452, step 2, values float32
> view
> volume #3 level 0.0778
> volume #10 step 1
> volume #10 level 0.1883
> select subtract #8
Nothing selected
> hide #8 models
> view matrix models #10,1,0,0,-0.8494,0,1,0,-5.9843,0,0,1,13.907
> view matrix models #10,1,0,0,7.5991,0,1,0,-3.967,0,0,1,13.994
> view matrix models #10,1,0,0,-1.8173,0,1,0,-4.3576,0,0,1,7.3998
> view matrix models #10,1,0,0,-3.0719,0,1,0,-5.0734,0,0,1,8.3111
> view matrix models #10,1,0,0,0.087856,0,1,0,-2.077,0,0,1,9.3492
> view matrix models #10,1,0,0,-2.6907,0,1,0,-10.023,0,0,1,27.875
> view matrix models #10,1,0,0,-5.199,0,1,0,-8.7637,0,0,1,17.923
> view matrix models #10,1,0,0,-10.83,0,1,0,-11.547,0,0,1,18.154
> show #!2 models
> open
> /Users/mariarafiq/Downloads/cryosparc_P410_J164_008_volume_map_sharp.mrc
Opened cryosparc_P410_J164_008_volume_map_sharp.mrc as #11, grid size
300,300,300, pixel 0.74, shown at level 0.047, step 2, values float32
> volume #11 step 1
> volume #11 level 0.06637
> ui tool show "Side View"
> volume #11 level 0.1156
> volume #11 level 0.09978
> open "/Users/mariarafiq/Downloads/cryosparc_P410_J158_002_volume_map_sharp
> (2).mrc"
Opened cryosparc_P410_J158_002_volume_map_sharp (2).mrc as #12, grid size
300,300,300, pixel 0.74, shown at level 0.0657, step 2, values float32
> volume #12 step 1
> volume #12 level 0.1269
> view
> volume #12 level 0.2799
> view matrix models #12,1,0,0,-15.965,0,1,0,-6.1341,0,0,1,-1.6828
> view matrix models #12,1,0,0,-12.202,0,1,0,-15.317,0,0,1,-13.363
> view matrix models #12,1,0,0,-16.987,0,1,0,-9.2493,0,0,1,3.7086
> vop gaussian #11 sdev 2.22
Opened cryosparc_P410_J164_008_volume_map_sharp.mrc gaussian as #13, grid size
300,300,300, pixel 0.74, shown at step 1, values float32
> vop gaussian #11 sdev 1.5
Opened cryosparc_P410_J164_008_volume_map_sharp.mrc gaussian as #14, grid size
300,300,300, pixel 0.74, shown at step 1, values float32
> volume #14 level 0.04706
> vop gaussian #11 sdev 1.1
Opened cryosparc_P410_J164_008_volume_map_sharp.mrc gaussian as #15, grid size
300,300,300, pixel 0.74, shown at step 1, values float32
> volume #15 level 0.04962
> volume #15 level 0.05445
> surface dust #15 size 7.4
> volume #15 level 0.04882
> view matrix models #15,1,0,0,-12.671,0,1,0,2.8251,0,0,1,-9.018
> volume #15 level 0.06249
> volume #15 level 0.08019
> volume #15 level 0.09145
> volume #15 level 0.07134
> volume #15 level 0.06812
> volume #15 level 0.06893
> open
> /Users/mariarafiq/Downloads/cryosparc_P410_J173_011_volume_map_sharp.mrc
Opened cryosparc_P410_J173_011_volume_map_sharp.mrc as #16, grid size
300,300,300, pixel 0.74, shown at level 0.0521, step 2, values float32
> volume #16 step 1
> volume #16 level 0.1042
> surface dust #16 size 7.4
> view matrix models #16,1,0,0,0.584,0,1,0,-3.1171,0,0,1,-2.3379
> volume #16 level 0.1766
> volume #16 level 0.1178
> volume #16 level 0.1359
> undust
Unknown command: undust
> ~dust
Unknown command: ~dust
> surface undust
Missing or invalid "surfaces" argument: empty atom specifier
> surface undust #16
> view matrix models #16,1,0,0,-12.552,0,1,0,-7.5084,0,0,1,-3.0238
> view matrix models #16,1,0,0,-8.7068,0,1,0,-3.671,0,0,1,-4.2909
> view matrix models #16,1,0,0,-2.04,0,1,0,2.6041,0,0,1,-4.1299
> volume #16 level 0.163
> volume #16 level 0.1155
> volume #16 level 0.1744
> volume #16 level 0.2151
> volume #16 level 0.197
> view matrix models #16,1,0,0,-2.2407,0,1,0,2.5442,0,0,1,-3.6562
> volume #16 level 0.1359
> volume #16 level 0.09288
> surface dust #16 size 7.4
> volume #16 level 0.07704
> volume #16 level 0.08156
> volume #16 level 0.09288
> volume #16 level 0.0793
> ui tool show "Side View"
> view
> view matrix models #16,1,0,0,-3.889,0,1,0,-0.76364,0,0,1,0.13671
> surface dust #16 size 7.4
> volume #16 level 0.1065
> view
> open
> /Users/mariarafiq/Downloads/cryosparc_P410_J174_010_volume_map_sharp.mrc
Opened cryosparc_P410_J174_010_volume_map_sharp.mrc as #17, grid size
300,300,300, pixel 0.74, shown at level 0.0513, step 2, values float32
> volume #17 step 1
> volume #17 level 0.0975
> volume #17 level 0.1364
> ui tool show "Side View"
> view
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/mariarafiq/Downloads/cryosparc_P410_J176_010_volume_map_sharp.mrc
Opened cryosparc_P410_J176_010_volume_map_sharp.mrc as #1, grid size
300,300,300, pixel 0.74, shown at level 0.0504, step 2, values float32
OpenGL version: 4.1 Metal - 89.3
OpenGL renderer: Apple M4
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: Mac16,1
Model Number: MW2V3LL/A
Chip: Apple M4
Total Number of Cores: 10 (4 performance and 6 efficiency)
Memory: 16 GB
System Firmware Version: 11881.41.5
OS Loader Version: 11881.41.5
Software:
System Software Overview:
System Version: macOS 15.1 (24B2083)
Kernel Version: Darwin 24.1.0
Time since boot: 23 hours, 42 minutes
Graphics/Displays:
Apple M4:
Chipset Model: Apple M4
Type: GPU
Bus: Built-In
Total Number of Cores: 10
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: Yes
Connection Type: Internal
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
autocommand: 2.2.2
babel: 2.16.0
backports.tarfile: 1.2.0
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-Clipper: 0.24.0
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: 1.9
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-ISOLDE: 1.9
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
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: 2.10.2
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
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
tomli: 2.0.1
tornado: 6.4.2
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 (2)
comment:1 by , 6 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 , 6 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
The ChimeraX bug report panel explained what we know about this crash
"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."
The ChimeraX daily build uses a newer Qt version and we have not seen these multi-monitor Mac crashes with it. You may want to try it.
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Reported by Maria Rafiq