![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 6 months ago
Closed 6 months ago
#17764 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-15.4.1-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 0x0000000206334c80 (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, 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, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, psutil._psutil_osx, psutil._psutil_posix, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, PIL._imagingmath (total: 60)
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{
"uptime" : 74000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "Mac14,7",
"coalitionID" : 5596,
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"build" : "24E263",
"releaseType" : "User"
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"captureTime" : "2025-05-22 13:31:31.9858 +0200",
"codeSigningMonitor" : 1,
"incident" : "193FFDE4-6264-4971-8094-979B1CF50531",
"pid" : 57736,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-05-22 11:40:09.2715 +0200",
"procStartAbsTime" : 1630182202960,
"procExitAbsTime" : 1790560477496,
"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"},
"storeInfo" : {"deviceIdentifierForVendor":"3C872541-A155-53DA-AD75-6829CECF2FF6","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "B362EAEC-D592-0B8A-05EB-D3BB388A7463",
"appleIntelligenceStatus" : {"state":"available"},
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRm+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkZDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"bootSessionUUID" : "F19891BA-BDE1-4F38-A101-1E1A474A4E31",
"wakeTime" : 11322,
"sleepWakeUUID" : "A35868A0-8B24-42DD-B040-08933A4BEE5F",
"sip" : "enabled",
"vmRegionInfo" : "0x5fc16a790a58 is not in any region. Bytes after previous region: 104803283307097 Bytes before following region: 268796622248\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, 0x0000dfc16a790a58","rawCodes":[1,246021807999576],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000dfc16a790a58 -> 0x00005fc16a790a58 (possible pointer authentication failure)"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":57736},
"ktriageinfo" : "VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n",
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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/annguyen/Downloads/cryosparc_P8_J23_001_volume_map_sharp.mrc
> format mrc
Opened cryosparc_P8_J23_001_volume_map_sharp.mrc as #1, grid size 100,100,100,
pixel 5.73, shown at level 0.899, step 1, values float32
> open "/Users/annguyen/ownCloud - Anh Nguyen@oc.biophys.mpg.de/Chimera
> sessions/18-05-25-scSec72-scRibo-10xbin.cxs" format session
Opened cryosparc_P8_J16_class_02_00042_volume.mrc as #2, grid size
128,128,128, pixel 4.48, shown at level 0.159, step 1, values float32
Opened cryosparc_P8_J16_class_03_00042_volume.mrc z flip as #3, grid size
128,128,128, pixel 4.48, shown at level 0.27, step 1, values float32
Opened cryosparc_P8_J16_class_00_00042_volume.mrc z flip as #5, grid size
128,128,128, pixel 4.48, shown at level 0.0367, step 1, values float32
Opened cryosparc_P5_J26_class_04_00042_volume.mrc as #1, grid size
128,128,128, pixel 4.48, shown at level 0.0781, step 1, values float32
opened ChimeraX session
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.59086,0.31345,-0.7434,445.8,-0.73919,0.57952,-0.34316,385.12,0.32325,0.75227,0.57411,145.25
> view matrix models
> #7,0.76007,-0.059048,-0.64715,446.99,-0.19225,0.93085,-0.31073,382.03,0.62075,0.3606,0.69616,146.16
> view matrix models
> #7,0.90861,-0.16405,-0.38408,446.59,-0.073446,0.84253,-0.53362,382.62,0.41114,0.51306,0.75348,145.82
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.90861,-0.16405,-0.38408,431.19,-0.073446,0.84253,-0.53362,390.63,0.41114,0.51306,0.75348,167.57
> view matrix models
> #7,0.90861,-0.16405,-0.38408,411.79,-0.073446,0.84253,-0.53362,400.21,0.41114,0.51306,0.75348,153.94
> view matrix models
> #7,0.90861,-0.16405,-0.38408,413.1,-0.073446,0.84253,-0.53362,403.03,0.41114,0.51306,0.75348,157.73
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.48394,-0.26866,-0.83284,415.56,-0.097394,0.92926,-0.35636,402.31,0.86967,0.25357,0.42354,158.54
> view matrix models
> #7,0.58009,-0.3196,-0.74923,415.4,0.23887,0.94612,-0.21864,401.12,0.77874,-0.052136,0.62518,159.82
> ui tool show "Side View"
> hide #!2 models
> show #!1 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!5 models
> show #4 models
> show #!3 models
> hide #!1 models
> color #5 #b2b2ffd6 models
> hide #!3 models
> volume #5 level 0.1274
> show #!3 models
> hide #4 models
> show #4 models
> hide #!3 models
> ui tool show "Side View"
> select #6/AR
1169 atoms, 1200 bonds, 148 residues, 1 model selected
> select clear
> select #6/BT
1075 atoms, 1074 bonds, 217 residues, 1 model selected
Cell requested for row 4 is out of bounds for table with 10 rows! Resizing
table model.
> hide #4 models
> show #!3 models
> hide #!3 models
> show #!2 models
> hide #!5 models
> hide #!2 models
> show #!1 models
> color #1 #b2b2b2b8 models
> hide #!6 models
> hide #!7 models
> select add #6
205800 atoms, 220962 bonds, 5151 pseudobonds, 17074 residues, 4 models
selected
> open /Users/annguyen/Downloads/cryosparc_P9_J33_class_02_00062_volume.mrc
Opened cryosparc_P9_J33_class_02_00062_volume.mrc as #8, grid size
128,128,128, pixel 4.48, shown at level 0.722, step 1, values float32
> open /Users/annguyen/Downloads/cryosparc_P9_J33_class_01_00062_volume.mrc
Opened cryosparc_P9_J33_class_01_00062_volume.mrc as #9, grid size
128,128,128, pixel 4.48, shown at level 0.769, step 1, values float32
> select up
205800 atoms, 220962 bonds, 5151 pseudobonds, 17074 residues, 4 models
selected
> select up
205800 atoms, 220962 bonds, 5151 pseudobonds, 17074 residues, 4 models
selected
> select down
5151 pseudobonds, 3 models selected
> select down
11 pseudobonds, 1 model selected
> select down
11 pseudobonds, 1 model selected
> volflip #8
Unknown command: volflip #8
> volume flip #8
Opened cryosparc_P9_J33_class_02_00062_volume.mrc z flip as #10, grid size
128,128,128, pixel 4.48, shown at step 1, values float32
> volume flip #9
Opened cryosparc_P9_J33_class_01_00062_volume.mrc z flip as #11, grid size
128,128,128, pixel 4.48, shown at step 1, values float32
> close #8
> close #9
> select add #10
11 pseudobonds, 3 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #6.3,1,0,0,0,0,1,0,0,0,0,1,0,#10,1,0,0,-97.549,0,1,0,189.6,0,0,1,187.32
> select subtract #10
11 pseudobonds, 1 model selected
> select add #11
11 pseudobonds, 3 models selected
> view matrix models
> #6.3,1,0,0,0,0,1,0,0,0,0,1,0,#11,1,0,0,175.96,0,1,0,87.497,0,0,1,197.3
> volume #10 level 0.1687
> volume #11 level 0.1388
> ui mousemode right "rotate selected models"
> view matrix models
> #6.3,1,0,0,0,0,1,0,0,0,0,1,0,#11,0.31459,-0.010276,-0.94917,679.84,-0.82378,0.49386,-0.27838,569.47,0.47162,0.86948,0.1469,66.506
> ui mousemode right "translate selected models"
> view matrix models
> #6.3,1,0,0,0,0,1,0,0,0,0,1,0,#11,0.31459,-0.010276,-0.94917,678.55,-0.82378,0.49386,-0.27838,745.36,0.47162,0.86948,0.1469,-166.12
> view matrix models
> #6.3,1,0,0,0,0,1,0,0,0,0,1,0,#11,0.31459,-0.010276,-0.94917,470.37,-0.82378,0.49386,-0.27838,709.18,0.47162,0.86948,0.1469,-204.6
> view matrix models
> #6.3,1,0,0,0,0,1,0,0,0,0,1,0,#11,0.31459,-0.010276,-0.94917,528.12,-0.82378,0.49386,-0.27838,578.04,0.47162,0.86948,0.1469,-356.41
> select add #10
11 pseudobonds, 6 models selected
> view matrix models
> #6.3,1,0,0,0,0,1,0,0,0,0,1,0,#10,1,0,0,-93.64,0,1,0,185.75,0,0,1,191.28,#11,0.31459,-0.010276,-0.94917,532.03,-0.82378,0.49386,-0.27838,574.18,0.47162,0.86948,0.1469,-352.46
> select subtract #10
11 pseudobonds, 3 models selected
> select add #11
11 pseudobonds, 4 models selected
> select add #10
11 pseudobonds, 7 models selected
> select subtract #11
11 pseudobonds, 4 models selected
> select add #6
205800 atoms, 220962 bonds, 5151 pseudobonds, 17074 residues, 7 models
selected
> select subtract #6
3 models selected
> view matrix models #10,1,0,0,-88.387,0,1,0,188.61,0,0,1,178.22
> ui mousemode right "rotate selected models"
> view matrix models
> #10,-0.12223,0.25178,0.96003,-110.96,0.84315,0.53664,-0.033395,111.22,-0.5236,0.80537,-0.27789,404.39
> ui mousemode right "translate selected models"
> view matrix models
> #10,-0.12223,0.25178,0.96003,81.966,0.84315,0.53664,-0.033395,123.77,-0.5236,0.80537,-0.27789,136.3
> view matrix models
> #10,-0.12223,0.25178,0.96003,-0.3004,0.84315,0.53664,-0.033395,67,-0.5236,0.80537,-0.27789,115.25
> view matrix models
> #10,-0.12223,0.25178,0.96003,29.25,0.84315,0.53664,-0.033395,17.117,-0.5236,0.80537,-0.27789,74.259
> ui tool show "Fit in Map"
> fitmap #10 inMap #1
Fit map cryosparc_P9_J33_class_02_00062_volume.mrc z flip in map
cryosparc_P5_J26_class_04_00042_volume.mrc using 57547 points
correlation = 0.9668, correlation about mean = 0.8479, overlap = 3.447e+04
steps = 120, shift = 24.1, angle = 19.7 degrees
Position of cryosparc_P9_J33_class_02_00062_volume.mrc z flip (#10) relative
to cryosparc_P5_J26_class_04_00042_volume.mrc (#1) coordinates:
Matrix rotation and translation
-0.97873340 0.20508082 0.00476722 507.04152323
0.20458240 0.97753392 -0.05072883 -42.12606142
-0.01506363 -0.04867470 -0.99870106 587.46965762
Axis 0.10299879 0.99436746 -0.02499214
Axis point 257.17507857 0.00000000 291.93312044
Rotation angle (degrees) 179.42866054
Shift along axis -4.34624666
> fitmap #11 inMap #1
Fit map cryosparc_P9_J33_class_01_00062_volume.mrc z flip in map
cryosparc_P5_J26_class_04_00042_volume.mrc using 59683 points
correlation = 0.9783, correlation about mean = 0.9062, overlap = 3.718e+04
steps = 172, shift = 33.4, angle = 31.8 degrees
Position of cryosparc_P9_J33_class_01_00062_volume.mrc z flip (#11) relative
to cryosparc_P5_J26_class_04_00042_volume.mrc (#1) coordinates:
Matrix rotation and translation
0.98177103 0.18847476 -0.02455321 -41.60356428
-0.18726559 0.98129273 0.04467788 43.23556195
0.03251454 -0.03926548 0.99869964 8.32189739
Axis -0.21567656 -0.14662475 -0.96539360
Axis point 202.02954915 246.45786347 0.00000000
Rotation angle (degrees) 11.22163528
Shift along axis -5.40039656
> hide #!1 models
> show #!2 models
> hide #!11 models
> select subtract #10
Nothing selected
> color #10 #ddc7ffff models
> color #10 #b8aaffff models
> show #!6 models
> color #10 #b8aaffc7 models
> hide #!2 models
> ui tool show "Side View"
> show #!2 models
> hide #!2 models
> hide #!10 models
> show #!2 models
> save "/Users/annguyen/ownCloud - Anh Nguyen@oc.biophys.mpg.de/Chimera
> sessions/18-05-25-scSec72-scRibo-10xbin.cxs"
> hide #!2 models
> show #!5 models
> ui mousemode right "mark surface"
> show #4 models
> marker #4 position 306.3,293.8,24.08 color yellow radius 1
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.96283,0.22772,0.14524,-63.914,-0.26757,0.87757,0.39784,106.67,-0.036866,-0.42192,0.90589,144.78
> view matrix models
> #4,0.96283,0.22772,0.14524,-57.964,-0.26757,0.87757,0.39784,114.93,-0.036866,-0.42192,0.90589,152.16
> view matrix models
> #4,0.96283,0.22772,0.14524,-57.872,-0.26757,0.87757,0.39784,114.83,-0.036866,-0.42192,0.90589,152.14
> view matrix models
> #4,0.96283,0.22772,0.14524,-58.067,-0.26757,0.87757,0.39784,115.54,-0.036866,-0.42192,0.90589,152.47
> select add #4
2 atoms, 2 residues, 1 model selected
> select subtract #4
Nothing selected
> hide #4 models
> show #4 models
> hide #4 models
> show #!2 models
> hide #!5 models
> show #4 models
> show #!5 models
> show #!11 models
> volume #11 level 0.01184
> hide #!11 models
> volume #5 level 0.01202
> hide #!5 models
> show #!3 models
> volume #3 level 0.1426
> color #3 #9a6021ff models
> volume #3 level 0.2556
> color #2 #ffffb2c4 models
> hide #!3 models
> show #!1 models
> hide #!6 models
> hide #!2 models
> hide #4 models
> show #!10 models
> color #10 #b8aaffff models
> color #1 #b2b2b297 models
> color #1 #b2b2b296 models
> hide #!10 models
> show #!11 models
> color #1 #b2b2b2ff models
> color #11 #b2ffffb6 models
> color #11 #b2ffffb5 models
> color #11 #b2ffff00 models
> color #11 #b2ffff49 models
> show #4 models
> hide #!1 models
> show #!2 models
> hide #!11 models
> show #!6 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!5 models
> volume #5 level 0.06039
> show #!2 models
> hide #!5 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> hide #!6 models
> show #!5 models
> volume #5 color #b2b2ff
> color #10 #966bffff models
> color #10 #7ab6ffff models
> color #10 #5179a9ff models
> color #11 #ffaa3f49 models
> color #11 #bc7d2e49 models
> color #11 #bc60bc49 models
> color #11 #bc60bc4a models
> volume #5 color #b2b2ffa6
> color #2 #ffffb2ff models
> rename #1 cryosparc_P5_J26_class_04_00042_
> rename #1 cryosparc_P5_J26_class_04_00042_pulloutSec63
> rename #2 cryosparc_P8_J16_class_02_00042_60s
> rename #3 "cryosparc_P8_J16_class_03_00042_80s class3"
> rename #5 "cryosparc_P8_J16_class_00_00042_80s claas 0 flip"
> rename #5 "cryosparc_P8_J16_class_00_00042_80s class 0 flip"
> rename #10 "cryosparc_P9_J33_class_02_00062_Apoclass2 flip"
> rename #11 "cryosparc_P9_J33_class_01_00062_Apoclass1 flip"
> save "/Users/annguyen/ownCloud - Anh Nguyen@oc.biophys.mpg.de/Chimera
> sessions/18-05-25-scSec72-scRibo-10xbin.cxs"
> show #!7 models
> open /Users/annguyen/Downloads/cryosparc_P8_J151_class_03_00042_volume.mrc
Opened cryosparc_P8_J151_class_03_00042_volume.mrc as #8, grid size
128,128,128, pixel 4.48, shown at level 0.593, step 1, values float32
> open /Users/annguyen/Downloads/cryosparc_P9_J33_class_02_00062_volume.mrc
Opened cryosparc_P9_J33_class_02_00062_volume.mrc as #9, grid size
128,128,128, pixel 4.48, shown at level 0.722, step 1, values float32
> close #9
> volume #8 level 0.2279
> volume #8 level 0.1648
> select add #8
3 models selected
> view matrix models #8,1,0,0,25.515,0,1,0,-14.045,0,0,1,102.61
> view matrix models #8,1,0,0,18.355,0,1,0,-19.838,0,0,1,91.88
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.37938,0.91695,-0.12361,-29.995,0.39689,-0.0406,0.91697,-98.949,0.83579,-0.39694,-0.37933,359.98
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.37938,0.91695,-0.12361,-61.442,0.39689,-0.0406,0.91697,14.989,0.83579,-0.39694,-0.37933,54.171
> view matrix models
> #8,0.37938,0.91695,-0.12361,-36.197,0.39689,-0.0406,0.91697,2.5165,0.83579,-0.39694,-0.37933,31.453
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.036868,0.99921,-0.014898,7.9919,0.67085,-0.013697,0.74147,-34.03,0.74068,-0.03733,-0.67082,39.355
> view matrix models
> #8,-0.94882,0.27311,0.15857,451.5,0.31516,0.85098,0.42014,-87.218,-0.020202,0.44861,-0.8935,183.67
> fitmap #8 inMap #1
Fit map cryosparc_P8_J151_class_03_00042_volume.mrc in map
cryosparc_P5_J26_class_04_00042_pulloutSec63 using 57110 points
correlation = 0.9075, correlation about mean = 0.7521, overlap = 2.553e+04
steps = 276, shift = 40.5, angle = 46.5 degrees
Position of cryosparc_P8_J151_class_03_00042_volume.mrc (#8) relative to
cryosparc_P5_J26_class_04_00042_pulloutSec63 (#1) coordinates:
Matrix rotation and translation
0.20479148 -0.69460954 -0.68962161 623.70351191
-0.66458163 0.41858321 -0.61896630 538.62548865
0.71860394 0.58506890 -0.37590248 -0.07139224
Axis 0.64976738 -0.75996036 0.01620481
Axis point 542.11699057 0.00000000 283.13200142
Rotation angle (degrees) 112.10245175
Shift along axis -4.07298061
> hide #!2 models
> hide #4 models
> hide #!5 models
> hide #!7 models
> show #!7 models
> show #!7 cartoons
> hide #!7 surfaces
> hide #!8 models
> select subtract #8
Nothing selected
> show #!8 models
> show #!1 models
> hide #!8 models
> hide #!7 models
> hide #!1 models
> show #!8 models
> show #!7 models
> hide #!8 models
> hide #!7 models
> show #!2 models
> hide #!2 models
> show #!3 models
> color #3 #ab9e40ff models
> color #3 #9fab3cff models
> color #3 #c5d54bff models
> color #3 #50da57ff models
> color #3 #7fda72ff models
> color #3 #69b45fff models
> volume #3 level 0.2145
> show #!2 models
> hide #!2 models
> volume #3 level 0.2332
> hide #!3 models
> show #!5 models
> hide #!5 models
> show #!1 models
> show #!7 models
> hide #!7 models
> show #!8 models
> hide #!1 models
> volume #8 color #ffb2b2cb
> volume #8 color #ffb2b2cc
> show #!7 models
> select add #7
1514 atoms, 1534 bonds, 193 residues, 1 model selected
> view matrix models
> #7,0.67543,-0.5091,-0.53349,415.55,0.72529,0.58932,0.35588,400.3,0.13322,-0.62731,0.76729,163.64
> view matrix models
> #7,0.97754,-0.20092,0.063604,411.87,0.14958,0.87407,0.4622,399.91,-0.14846,-0.4423,0.88449,163.06
> view matrix models
> #7,0.99023,0.020832,-0.13785,411.29,0.066064,0.80059,0.59556,400.11,0.12277,-0.59885,0.7914,163.47
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.99023,0.020832,-0.13785,422.09,0.066064,0.80059,0.59556,400.38,0.12277,-0.59885,0.7914,163.36
> show #!6 models
> hide #!6 models
> show #!6 models
> view matrix models
> #7,0.99023,0.020832,-0.13785,425.37,0.066064,0.80059,0.59556,403.44,0.12277,-0.59885,0.7914,163.61
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.95885,-0.033813,-0.28188,426.07,-0.17264,0.71878,-0.67346,407.62,0.22539,0.69441,0.68337,157.43
> view matrix models
> #7,0.9866,-0.14932,-0.065793,426.01,0.044391,0.63361,-0.77238,407.81,0.15702,0.75911,0.63174,157.4
> view matrix models
> #7,0.39768,-0.2338,-0.88724,429.82,0.24593,0.95877,-0.14242,404.18,0.88395,-0.16156,0.43878,160.74
> view matrix models
> #7,0.89093,-0.42166,0.16868,426.93,-0.11881,-0.57489,-0.80956,414.09,0.43833,0.70122,-0.56228,160.13
> view matrix models
> #7,0.59256,-0.78428,-0.18379,430.24,-0.15962,0.10931,-0.98111,411.32,0.78956,0.6107,-0.060414,158.51
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.59256,-0.78428,-0.18379,432.41,-0.15962,0.10931,-0.98111,408.16,0.78956,0.6107,-0.060414,166.71
> view matrix models
> #7,0.59256,-0.78428,-0.18379,430.41,-0.15962,0.10931,-0.98111,405.52,0.78956,0.6107,-0.060414,164.49
> view matrix models
> #7,0.59256,-0.78428,-0.18379,428.3,-0.15962,0.10931,-0.98111,411.77,0.78956,0.6107,-0.060414,160.95
> hide #!8 models
> show #!1 models
> hide #!6 models
> hide #!7 models
===== 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
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M2
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac14,7
Model Number: Z16U000NJD/A
Chip: Apple M2
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 11881.101.1
OS Loader Version: 11881.101.1
Software:
System Software Overview:
System Version: macOS 15.4.1 (24E263)
Kernel Version: Darwin 24.4.0
Time since boot: 1 day, 19 hours, 53 minutes
Graphics/Displays:
Apple M2:
Chipset Model: Apple M2
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
DELL P3223QE:
Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus)
UI Looks like: 2560 x 1440 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMalign: 0.1.1
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
finufft: 2.3.1
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
Change History (2)
comment:1 by , 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 |
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