![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 5 months ago
Closed 5 months ago
#17878 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-15.5-x86_64-i386-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 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 0x0000000201286200 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 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, scipy._lib._ccallback_c, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.linalg._propack._spropack, scipy.sparse.linalg._propack._dpropack, scipy.sparse.linalg._propack._cpropack, scipy.sparse.linalg._propack._zpropack, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, scipy.spatial._ckdtree, scipy._lib.messagestream, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.special._ufuncs_cxx, scipy.special._cdflib, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, markupsafe._speedups, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, psutil._psutil_osx, psutil._psutil_posix, PIL._imagingmath, 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, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets (total: 100)
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{
"uptime" : 320000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 504,
"deployVersion" : 210,
"modelCode" : "Mac15,3",
"coalitionID" : 43497,
"osVersion" : {
"train" : "macOS 15.5",
"build" : "24F74",
"releaseType" : "User"
},
"captureTime" : "2025-06-03 11:56:44.3861 +0100",
"codeSigningMonitor" : 1,
"incident" : "ACABB4D0-C7A0-445D-9ADB-6ECFF34EEBF7",
"pid" : 41042,
"translated" : true,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-06-03 10:07:29.7101 +0100",
"procStartAbsTime" : 7740896047296,
"procExitAbsTime" : 7898195612396,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"1471129C-D77B-5A9E-8DC6-7F9ABAB8E310","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "6A59DD4E-FB92-DFCC-0F73-D34E1FCE92E1",
"appleIntelligenceStatus" : {"state":"available"},
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
"bootSessionUUID" : "222EB217-5473-49B4-8766-8645265148E5",
"wakeTime" : 12143,
"sleepWakeUUID" : "584C971E-9540-4D0C-8BA2-59B261FA2C52",
"sip" : "enabled",
"vmRegionInfo" : "0x499000024af7 is not in any region. Bytes after previous region: 80401787931384 Bytes before following region: 24670291997961\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, 0x0002499000024af7","rawCodes":[1,643832777689847],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0002499000024af7 -> 0x0000499000024af7 (possible pointer authentication failure)"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":41042},
"vmregioninfo" : "0x499000024af7 is not in any region. Bytes after previous region: 80401787931384 Bytes before following region: 24670291997961\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 ",
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"faultingThread" : 0,
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},
"reportNotes" : [
"RIP register does not match crashing frame (0x0 vs 0x7FF895B12AE0)"
]
}
===== Log before crash start =====
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 /Users/bs18klrh/Downloads/cryosparc_P216_J41_013_volume_map_sharp.mrc
Opened cryosparc_P216_J41_013_volume_map_sharp.mrc as #1, grid size
448,448,448, pixel 0.74, shown at level 0.0751, step 2, values float32
> volume #1 step 1
> volume #1 level 0.1377
> open "/Users/bs18klrh/Desktop/BTD_nano/Reprocessed correct pixel
> size/BTDNano_Map_1.mrc"
Opened BTDNano_Map_1.mrc as #2, grid size 512,512,512, pixel 0.74, shown at
level 0.0772, step 2, values float32
> open "/Users/bs18klrh/Desktop/BTD_nano/Reprocessed correct pixel
> size/BTDNano_Model_1_CaBLAM1.03.pdb"
Summary of feedback from opening /Users/bs18klrh/Desktop/BTD_nano/Reprocessed
correct pixel size/BTDNano_Model_1_CaBLAM1.03.pdb
---
warnings | Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
16624 messages similar to the above omitted
Chain information for BTDNano_Model_1_CaBLAM1.03.pdb #3
---
Chain | Description
A B C D | No description available
> select add #1
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.034506,-0.99233,-0.11873,354.64,-0.99844,0.029023,0.047601,318.97,-0.043789,0.12019,-0.99178,300.55
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.034506,-0.99233,-0.11873,355.53,-0.99844,0.029023,0.047601,318.72,-0.043789,0.12019,-0.99178,350.77
> view matrix models
> #1,-0.034506,-0.99233,-0.11873,381.55,-0.99844,0.029023,0.047601,348.69,-0.043789,0.12019,-0.99178,356.24
> view matrix models
> #1,-0.034506,-0.99233,-0.11873,382.8,-0.99844,0.029023,0.047601,345.29,-0.043789,0.12019,-0.99178,354.16
> view matrix models
> #1,-0.034506,-0.99233,-0.11873,381.66,-0.99844,0.029023,0.047601,340.04,-0.043789,0.12019,-0.99178,354.15
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.049104,-0.99036,-0.12952,385.45,-0.99871,0.047021,0.019088,341.59,-0.012814,0.13029,-0.99139,347.28
> view matrix models
> #1,0.86219,-0.50033,-0.079368,145.28,-0.50619,-0.85707,-0.095976,427.9,-0.020004,0.12292,-0.99221,349.82
> view matrix models
> #1,0.74049,-0.66486,-0.098118,195.67,-0.67178,-0.73646,-0.079591,432.78,-0.019343,0.12485,-0.99199,349.36
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.74049,-0.66486,-0.098118,193.97,-0.67178,-0.73646,-0.079591,438.24,-0.019343,0.12485,-0.99199,349.39
> volume #2 step 1
> volume #2 level 0.2006
> view matrix models
> #1,0.74049,-0.66486,-0.098118,195.97,-0.67178,-0.73646,-0.079591,437.8,-0.019343,0.12485,-0.99199,349.05
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.63496,-0.76675,-0.094446,229.78,-0.77254,-0.63068,-0.073625,436.03,-0.0031129,0.11971,-0.9928,347.34
> view matrix models
> #1,0.71883,-0.69215,-0.064974,198.88,-0.695,-0.71766,-0.04407,432.95,-0.016126,0.076836,-0.99691,357.26
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.71883,-0.69215,-0.064974,199.54,-0.695,-0.71766,-0.04407,432.61,-0.016126,0.076836,-0.99691,358.26
> view matrix models
> #1,0.71883,-0.69215,-0.064974,194.36,-0.695,-0.71766,-0.04407,428.34,-0.016126,0.076836,-0.99691,357.8
> view matrix models
> #1,0.71883,-0.69215,-0.064974,197.24,-0.695,-0.71766,-0.04407,430.58,-0.016126,0.076836,-0.99691,358.04
> ui tool show "Fit in Map"
> fitmap #1 inMap #2
Fit map cryosparc_P216_J41_013_volume_map_sharp.mrc in map BTDNano_Map_1.mrc
using 328048 points
correlation = 0.9582, correlation about mean = 0.8501, overlap = 3.798e+04
steps = 136, shift = 1.22, angle = 7.39 degrees
Position of cryosparc_P216_J41_013_volume_map_sharp.mrc (#1) relative to
BTDNano_Map_1.mrc (#2) coordinates:
Matrix rotation and translation
0.64472097 -0.76441799 0.00004202 209.27333899
-0.76441799 -0.64472097 -0.00000041 423.01853679
0.00002740 -0.00003186 -1.00000000 368.87866670
Axis -0.90683113 0.42149412 -0.00001183
Axis point 0.00000000 260.14604205 184.43592284
Rotation angle (degrees) 179.99900632
Shift along axis -11.48011537
> volume #1 level 0.1885
> select subtract #1
Nothing selected
> volume #2 level 0.23
> volume #1 level 0.2103
> hide #!3 models
> volume #2 level 0.1875
> volume #1 level 0.1921
> ui tool show "Hide Dust"
> surface dust #1 size 4.44
> surface dust #2 size 4.44
> lighting soft
> volume #1 level 0.1776
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> show #!3 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!3 models
> show #!2 models
> show #!3 models
> hide #!2 models
> hide #!1 models
> hide #!3 models
> show #!2 models
> show #!1 models
> volume subtract #1 #2
Opened volume difference as #4, grid size 448,448,448, pixel 0.74, shown at
step 1, values float32
> volume #4 level 0.2622
> show #!3 models
> volume subtract #2 #1
Opened volume difference as #5, grid size 512,512,512, pixel 0.74, shown at
step 1, values float32
> close #4
> volume #5 level 0.257
> volume #5 level 0.2053
> show atoms
> ui tool show "Side View"
> set bgColor white
> hide atoms
> volume #5 level 0.1732
> surface dust #5 size 4.44
> show #!1 models
> hide #!1 models
> save "/Users/bs18klrh/OneDrive - University of
> Leeds/Research_Postgrad/Thesis
> Bits/Nanodiscs/BTD_Amph_Nano_volumesubtractsession.cxs"
> close
> open "/Users/bs18klrh/Library/CloudStorage/OneDrive-
> UniversityofLeeds/Research_Postgrad/EM/Model_Building/300323 AM237/Final(_)
> July'24/TRPC5_AM237_allribbons_all_lig_2lip_refined_024.pdb"
Summary of feedback from opening
/Users/bs18klrh/Library/CloudStorage/OneDrive-
UniversityofLeeds/Research_Postgrad/EM/Model_Building/300323 AM237/Final(_)
July'24/TRPC5_AM237_allribbons_all_lig_2lip_refined_024.pdb
---
warnings | Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
16930 messages similar to the above omitted
Chain information for TRPC5_AM237_allribbons_all_lig_2lip_refined_024.pdb #1
---
Chain | Description
A B C D | No description available
> open "/Users/bs18klrh/Library/CloudStorage/OneDrive-
> UniversityofLeeds/Research_Postgrad/EM/Model_Building/300323 AM237/Final(_)
> July'24/J155_ResolveMap.mrc"
Opened J155_ResolveMap.mrc as #2, grid size 143,143,172, pixel 0.74,0.74,0.74,
shown at level 4.55, step 1, values float32
> open "/Users/bs18klrh/Downloads/cryosparc_P18_J28_011_volume_map_sharp
> (2).mrc"
Opened cryosparc_P18_J28_011_volume_map_sharp (2).mrc as #3, grid size
512,512,512, pixel 0.74, shown at level 0.0686, step 2, values float32
> volume #2 level 1.308
> volume #3 step 1
> volume #3 level 0.1326
> select add #3
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.9686,0.23082,-0.092334,347.21,0.21322,0.9623,0.16887,-66.171,0.12783,0.14388,-0.9813,334.78
> view matrix models
> #3,-0.97023,0.21441,-0.11261,354.58,0.209,0.9762,0.057974,-46.386,0.12236,0.032713,-0.99195,358.95
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.97023,0.21441,-0.11261,340.65,0.209,0.9762,0.057974,-76.42,0.12236,0.032713,-0.99195,305.98
> view matrix models
> #3,-0.97023,0.21441,-0.11261,332.59,0.209,0.9762,0.057974,-77.363,0.12236,0.032713,-0.99195,307.95
> view matrix models
> #3,-0.97023,0.21441,-0.11261,331.53,0.209,0.9762,0.057974,-75.632,0.12236,0.032713,-0.99195,308.31
> view matrix models
> #3,-0.97023,0.21441,-0.11261,331.36,0.209,0.9762,0.057974,-76.955,0.12236,0.032713,-0.99195,304.59
> view matrix models
> #3,-0.97023,0.21441,-0.11261,329.38,0.209,0.9762,0.057974,-76.165,0.12236,0.032713,-0.99195,304.47
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.97363,0.2243,0.041623,298.08,0.2256,0.97376,0.029771,-73.351,-0.033853,0.038377,-0.99869,334.3
> fitmap #3 inMap #2
Fit map cryosparc_P18_J28_011_volume_map_sharp (2).mrc in map
J155_ResolveMap.mrc using 368476 points
correlation = 0.9203, correlation about mean = 0.8371, overlap = 2.783e+05
steps = 196, shift = 3.94, angle = 10.4 degrees
Position of cryosparc_P18_J28_011_volume_map_sharp (2).mrc (#3) relative to
J155_ResolveMap.mrc (#2) coordinates:
Matrix rotation and translation
-0.99864561 0.05202828 0.00005358 339.15808821
0.05202828 0.99864561 0.00003529 -39.20548979
-0.00005167 0.00003803 -1.00000000 335.57479560
Axis 0.02602575 0.99966127 0.00001715
Axis point 170.09381094 0.00000000 167.78325877
Rotation angle (degrees) 179.99698390
Shift along axis -30.35960997
> select subtract #3
Nothing selected
> surface dust #3 size 4.44
> volume #3 level 0.1228
> surface dust #3 size 4.44
> surface dust #3 size 4.29
> surface dust #3 size 6.59
> volume subtract #3 #2
Opened volume difference as #4, grid size 512,512,512, pixel 0.74, shown at
step 1, values float32
> volume #4 level 1.57
> volume subtract #2 #3
Opened volume difference as #5, grid size 143,143,172, pixel 0.74,0.74,0.74,
shown at step 1, values float32
> close #5
> close #4
> volume #2 level 0.3073
> close #2
> open "/Users/bs18klrh/Library/CloudStorage/OneDrive-
> UniversityofLeeds/Research_Postgrad/EM/Model_Building/300323
> AM237/J51_finalmap.mrc"
Opened J51_finalmap.mrc as #2, grid size 432,432,432, pixel 0.731, shown at
level 0.086, step 2, values float32
> close #2
> open "/Users/bs18klrh/Downloads/cryosparc_P35_J163_013_volume_map_sharp
> (5).mrc"
Opened cryosparc_P35_J163_013_volume_map_sharp (5).mrc as #2, grid size
432,432,432, pixel 0.74, shown at level 0.0854, step 2, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #2 step 1
> volume #2 level 0.1798
> volume #2 level 0.1204
> volume #2 level 0.1588
> surface dust #3 size 6.59
> surface dust #2 size 4.44
> volume subtract #2 #3
Opened volume difference as #4, grid size 432,432,432, pixel 0.74, shown at
step 1, values float32
> surface dust #4 size 4.44
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume subtract #3 #2
Opened volume difference as #5, grid size 512,512,512, pixel 0.74, shown at
step 1, values float32
> volume #5 level 0.1765
> surface dust #5 size 4.44
> volume #5 level 0.1429
> volume #5 color #ff85ff
> show #!2 models
> show #!3 models
> hide #!1 models
> show #!5 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!5 models
> show #!4 models
> show #!5 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> show #!3 models
> show #!2 models
> volume #2 level 0.198
> volume #3 level 0.2239
> volume #2 level 0.3014
> volume #3 level 0.2836
> show #!5 models
> volume #5 level 0.1671
> hide #!3 models
> show #!4 models
> hide #!5 models
> show #!1 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> show #!3 models
> hide #!4 models
> hide #!3 models
> volume #2 level 0.2372
> show #!3 models
> volume #3 level 0.2317
> show #!4 models
> show #!5 models
> hide #!2 models
> hide #!4 models
> show #!4 models
> hide #!3 models
> volume #4 level 0.2147
> show #!2 models
> volume #2 level 0.2907
> volume #3 level 0.1928
> select add #5
3 models selected
> select subtract #5
Nothing selected
> select add #5
3 models selected
> close #5
> select add #4
3 models selected
> close #4
> volume #2 level 0.1618
> ui tool show "Fit in Map"
> fitmap #2 inMap #3
Fit map cryosparc_P35_J163_013_volume_map_sharp (5).mrc in map
cryosparc_P18_J28_011_volume_map_sharp (2).mrc using 284760 points
correlation = 0.96, correlation about mean = 0.8512, overlap = 3.923e+04
steps = 48, shift = 0.0945, angle = 0.0519 degrees
Position of cryosparc_P35_J163_013_volume_map_sharp (5).mrc (#2) relative to
cryosparc_P18_J28_011_volume_map_sharp (2).mrc (#3) coordinates:
Matrix rotation and translation
-0.99859895 0.05291629 0.00008081 340.58660877
0.05291629 0.99859895 -0.00007073 21.37572228
-0.00008444 -0.00006636 -0.99999999 335.50177297
Axis 0.02646920 0.99964963 -0.00003503
Axis point 170.01724085 0.00000000 167.74423779
Rotation angle (degrees) 179.99526449
Shift along axis 30.37153548
> volume #3 level 0.2228
> volume #2 level 0.2201
> volume #2 color #ffb2b280
> volume #3 color #ffffb282
> ui tool show "Side View"
> volume subtract #3 #2
Opened volume difference as #4, grid size 512,512,512, pixel 0.74, shown at
step 1, values float32
> volume #4 level 0.1698
> ui tool show "Hide Dust"
> surface dust #4 size 4.44
> volume #4 level 0.1288
> volume #4 level 0.08379
> volume #4 level 0.1142
> volume #4 level 0.1526
> hide #!1 models
> show #!1 models
> select add #1
22580 atoms, 23112 bonds, 28 pseudobonds, 2696 residues, 3 models selected
> ui mousemode right "translate selected models"
> view matrix models #1,1,0,0,0.068897,0,1,0,-0.094972,0,0,1,1.7756
> view matrix models #1,1,0,0,0.80147,0,1,0,-0.52854,0,0,1,2.2016
> view matrix models #1,1,0,0,0.35242,0,1,0,-1.9022,0,0,1,2.2569
> view matrix models #1,1,0,0,0.091042,0,1,0,-2.0422,0,0,1,4.3565
> view matrix models #1,1,0,0,0.28916,0,1,0,-0.34771,0,0,1,1.6703
> view matrix models #1,1,0,0,-0.23796,0,1,0,-0.29813,0,0,1,1.0237
> select subtract #1
Nothing selected
> undo
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M3
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: Mac
Model Identifier: Mac15,3
Model Number: Z1C8000FDB/A
Chip: Unknown
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 11881.121.1
OS Loader Version: 11881.121.1
Software:
System Software Overview:
System Version: macOS 15.5 (24F74)
Kernel Version: Darwin 24.5.0
Time since boot: 18 days, 3 hours, 2 minutes
Graphics/Displays:
Apple M3:
Chipset Model: Apple M3
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
PLX2283H-DP:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4
charset-normalizer: 3.3.2
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: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
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: 2.2.4
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: 1.8
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
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: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
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: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
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-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.5
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PhenixUI: 1.3.7
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
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: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StarMap: 1.2.15
ChimeraX-StdCommands: 1.16.5
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: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
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: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
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: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
pyqtgraph: 0.13.7
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
Send2Trash: 1.8.3
SEQCROW: 1.8.14
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
Change History (2)
comment:1 by , 5 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 , 5 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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