![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 4 months ago
Closed 4 months ago
#18008 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-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 0x00000001f154df00 (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, 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.surface._surface, 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, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets (total: 54)
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{
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"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro18,3",
"coalitionID" : 2530,
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"build" : "24F74",
"releaseType" : "User"
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"captureTime" : "2025-06-16 19:30:39.4339 -0400",
"codeSigningMonitor" : 1,
"incident" : "C552D606-0828-4890-B617-7E59EAB48D03",
"pid" : 11590,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-06-16 14:18:16.6059 -0400",
"procStartAbsTime" : 1899052796154,
"procExitAbsTime" : 2240329521934,
"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":"1F210A2C-AA23-5746-A995-64425BC5C84B","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "DB21C13B-D80C-314E-D035-48708297B8A8",
"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" : "1CDFE94F-25B9-4191-BDA7-5C6374DEC289",
"wakeTime" : 9,
"sleepWakeUUID" : "85364A0E-B2B1-4D85-B2F6-27008A5F80AE",
"sip" : "enabled",
"vmRegionInfo" : "0x169 is not in any region. Bytes before following region: 4306026135\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 100a8c000-100a90000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"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":11590},
"vmregioninfo" : "0x169 is not in any region. Bytes before following region: 4306026135\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 100a8c000-100a90000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
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"faultingThread" : 0,
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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/yoojoong/Downloads/cryosparc_P18_J521_class_00_00006_volume.mrc
Opened cryosparc_P18_J521_class_00_00006_volume.mrc as #1, grid size
192,192,192, pixel 1.46, shown at level 0.0398, step 1, values float32
> open /Users/yoojoong/Downloads/cryosparc_P18_J521_class_01_00006_volume.mrc
Opened cryosparc_P18_J521_class_01_00006_volume.mrc as #2, grid size
192,192,192, pixel 1.46, shown at level 0.0395, step 1, values float32
> open /Users/yoojoong/Downloads/cryosparc_P18_J521_class_02_00006_volume.mrc
Opened cryosparc_P18_J521_class_02_00006_volume.mrc as #3, grid size
192,192,192, pixel 1.46, shown at level 0.0397, step 1, values float32
> open /Users/yoojoong/Downloads/cryosparc_P18_J521_class_03_00006_volume.mrc
Opened cryosparc_P18_J521_class_03_00006_volume.mrc as #4, grid size
192,192,192, pixel 1.46, shown at level 0.0398, step 1, values float32
> open /Users/yoojoong/Downloads/cryosparc_P18_J521_class_04_00006_volume.mrc
Opened cryosparc_P18_J521_class_04_00006_volume.mrc as #5, grid size
192,192,192, pixel 1.46, shown at level 0.04, step 1, values float32
> open /Users/yoojoong/Downloads/cryosparc_P18_J521_class_05_00006_volume.mrc
Opened cryosparc_P18_J521_class_05_00006_volume.mrc as #6, grid size
192,192,192, pixel 1.46, shown at level 0.0399, step 1, values float32
> open /Users/yoojoong/Downloads/cryosparc_P18_J521_class_06_00006_volume.mrc
Opened cryosparc_P18_J521_class_06_00006_volume.mrc as #7, grid size
192,192,192, pixel 1.46, shown at level 0.0396, step 1, values float32
> open /Users/yoojoong/Downloads/cryosparc_P18_J521_class_07_00006_volume.mrc
Opened cryosparc_P18_J521_class_07_00006_volume.mrc as #8, grid size
192,192,192, pixel 1.46, shown at level 0.0399, step 1, values float32
> open /Users/yoojoong/Downloads/cryosparc_P18_J521_class_08_00006_volume.mrc
Opened cryosparc_P18_J521_class_08_00006_volume.mrc as #9, grid size
192,192,192, pixel 1.46, shown at level 0.0397, step 1, values float32
> open /Users/yoojoong/Downloads/cryosparc_P18_J521_class_09_00006_volume.mrc
Opened cryosparc_P18_J521_class_09_00006_volume.mrc as #10, grid size
192,192,192, pixel 1.46, shown at level 0.0397, step 1, values float32
> open
> /Users/yoojoong/Library/CloudStorage/Dropbox/1_RothLab/Experiments/Projects/Tas2Rs/TAS2R14/2025/Prog-
> TAS2R14/Structure_work/WorkingModels&Maps_SetB-2_J318(best)/WorkingModels/TwoProg-
> TAS2R14_J318_J302-0612-2200noLig.pdb
Chain information for TwoProg-TAS2R14_J318_J302-0612-2200noLig.pdb #11
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
R | No description available
> set bgColor white
> graphics silhouettes true
> fitmap #11 inMap #1
Fit molecule TwoProg-TAS2R14_J318_J302-0612-2200noLig.pdb (#11) to map
cryosparc_P18_J521_class_00_00006_volume.mrc (#1) using 8655 atoms
average map value = 0.07383, steps = 232
shifted from previous position = 1.04
rotated from previous position = 2.26 degrees
atoms outside contour = 1799, contour level = 0.039753
Position of TwoProg-TAS2R14_J318_J302-0612-2200noLig.pdb (#11) relative to
cryosparc_P18_J521_class_00_00006_volume.mrc (#1) coordinates:
Matrix rotation and translation
0.99937872 0.02123089 -0.02813207 0.56966415
-0.02172968 0.99960993 -0.01754463 5.06877401
0.02774861 0.01814503 0.99945024 -6.09632622
Axis 0.45173112 -0.70729301 -0.54376059
Axis point 220.25876810 0.00000000 15.59142798
Rotation angle (degrees) 2.26395615
Shift along axis -0.01283145
> lighting soft
> molmap #11 /R/B/C/D/A 3
Opened TwoProg-TAS2R14_J318_J302-0612-2200noLig.pdb map 3 as #12, grid size
100,128,137, pixel 1, shown at level 0.11, step 1, values float32
> volume subtract #1 #12
Opened volume difference as #13, grid size 192,192,192, pixel 1.46, shown at
step 1, values float32
> volume subtract #2 #12
Opened volume difference as #14, grid size 192,192,192, pixel 1.46, shown at
step 1, values float32
> volume subtract #3 #12
Opened volume difference as #15, grid size 192,192,192, pixel 1.46, shown at
step 1, values float32
> volume subtract #4 #12
Opened volume difference as #16, grid size 192,192,192, pixel 1.46, shown at
step 1, values float32
> volume subtract #5 #12
Opened volume difference as #17, grid size 192,192,192, pixel 1.46, shown at
step 1, values float32
> volume subtract #6 #12
Opened volume difference as #18, grid size 192,192,192, pixel 1.46, shown at
step 1, values float32
> volume subtract #7 #12
Opened volume difference as #19, grid size 192,192,192, pixel 1.46, shown at
step 1, values float32
> volume subtract #8 #12
Opened volume difference as #20, grid size 192,192,192, pixel 1.46, shown at
step 1, values float32
> volume subtract #9 #12
Opened volume difference as #21, grid size 192,192,192, pixel 1.46, shown at
step 1, values float32
> volume subtract #10 #12
Opened volume difference as #22, grid size 192,192,192, pixel 1.46, shown at
step 1, values float32
> surface dust #13 #14 #15 #16 #17 #18 #19 #20 #21 #22 size 5
> volume level 0.09
> hide #!11 models
> open
> /Users/yoojoong/Library/CloudStorage/Dropbox/1_RothLab/Experiments/Projects/Tas2Rs/TAS2R14/2025/Prog-
> TAS2R14/Structure_work/WorkingModels/STR_OBP_2.cif
Summary of feedback from opening
/Users/yoojoong/Library/CloudStorage/Dropbox/1_RothLab/Experiments/Projects/Tas2Rs/TAS2R14/2025/Prog-
TAS2R14/Structure_work/WorkingModels/STR_OBP_2.cif
---
warning | Atom C22 is not in the residue template for STR /R:403
> open
> /Users/yoojoong/Library/CloudStorage/Dropbox/1_RothLab/Experiments/Projects/Tas2Rs/TAS2R14/2025/Prog-
> TAS2R14/Structure_work/WorkingModels&Maps_SetA-combined/cmpd28p1-TAS2R14.pdb
Summary of feedback from opening
/Users/yoojoong/Library/CloudStorage/Dropbox/1_RothLab/Experiments/Projects/Tas2Rs/TAS2R14/2025/Prog-
TAS2R14/Structure_work/WorkingModels&Maps_SetA-combined/cmpd28p1-TAS2R14.pdb
---
warning | Start residue of secondary structure not found: HELIX 23 23 ALA R 226 THR R 253 1 28
Chain information for cmpd28p1-TAS2R14.pdb #24
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
R | No description available
> hide #23#!24 atoms
> select ::name="LIG"::name="STR"
92 atoms, 103 bonds, 4 residues, 3 models selected
> show sel & #23#!24 atoms
> hide #!13-22 target m
> show #!13 models
> ui tool show "Side View"
> volume #13 level 0.0719
> volume level 0.07
> volume #14 color #b2ffff81
> volume #14 level 0.0835
> volume #14 level 0.07
> volume #15 color #b2b2ff7d
> volume #15 level 0.0655
> volume #16 color #ffb2ff7f
> volume #16 level 0.06552
> volume #17 color #ffb2b281
> volume #17 level 0.05195
> volume #17 level 0.07451
> volume #18 color #b2ffb27f
> volume #18 level 0.1155
> volume #19 color #e5bf9980
> volume #19 level 0.09699
> volume #20 color #99bfe57d
> volume #20 level 0.06093
> volume #21 level 0.08353
> volume #21 color #cccc9982
> close #1-10
> close #13-22
> close #12
> open /Users/yoojoong/Downloads/cryosparc_P18_J523_class_00_00006_volume.mrc
Opened cryosparc_P18_J523_class_00_00006_volume.mrc as #1, grid size
168,168,168, pixel 1.66, shown at level 0.0498, step 1, values float32
> open /Users/yoojoong/Downloads/cryosparc_P18_J523_class_01_00006_volume.mrc
Opened cryosparc_P18_J523_class_01_00006_volume.mrc as #2, grid size
168,168,168, pixel 1.66, shown at level 0.0499, step 1, values float32
> open /Users/yoojoong/Downloads/cryosparc_P18_J523_class_02_00006_volume.mrc
Opened cryosparc_P18_J523_class_02_00006_volume.mrc as #3, grid size
168,168,168, pixel 1.66, shown at level 0.0501, step 1, values float32
> open /Users/yoojoong/Downloads/cryosparc_P18_J523_class_03_00006_volume.mrc
Opened cryosparc_P18_J523_class_03_00006_volume.mrc as #4, grid size
168,168,168, pixel 1.66, shown at level 0.0499, step 1, values float32
> open /Users/yoojoong/Downloads/cryosparc_P18_J523_class_04_00006_volume.mrc
Opened cryosparc_P18_J523_class_04_00006_volume.mrc as #5, grid size
168,168,168, pixel 1.66, shown at level 0.0501, step 1, values float32
> open /Users/yoojoong/Downloads/cryosparc_P18_J523_class_05_00006_volume.mrc
Opened cryosparc_P18_J523_class_05_00006_volume.mrc as #6, grid size
168,168,168, pixel 1.66, shown at level 0.05, step 1, values float32
> open /Users/yoojoong/Downloads/cryosparc_P18_J523_class_06_00006_volume.mrc
Opened cryosparc_P18_J523_class_06_00006_volume.mrc as #7, grid size
168,168,168, pixel 1.66, shown at level 0.0499, step 1, values float32
> open /Users/yoojoong/Downloads/cryosparc_P18_J523_class_07_00006_volume.mrc
Opened cryosparc_P18_J523_class_07_00006_volume.mrc as #8, grid size
168,168,168, pixel 1.66, shown at level 0.05, step 1, values float32
> open /Users/yoojoong/Downloads/cryosparc_P18_J523_class_08_00006_volume.mrc
Opened cryosparc_P18_J523_class_08_00006_volume.mrc as #9, grid size
168,168,168, pixel 1.66, shown at level 0.0499, step 1, values float32
> open /Users/yoojoong/Downloads/cryosparc_P18_J523_class_09_00006_volume.mrc
Opened cryosparc_P18_J523_class_09_00006_volume.mrc as #10, grid size
168,168,168, pixel 1.66, shown at level 0.0501, step 1, values float32
> volume level 0.07
> hide #!2-10 target m
> ui mousemode right zoom
> volume #1 level 0.12
> volume level 0.12
> show #!2 models
> hide #!1 models
> show #!3 models
> hide #!2 models
> show #!4 models
> hide #!3 models
> show #!5 models
> hide #!4 models
> show #!6 models
> hide #!5 models
> show #!7 models
> hide #!6 models
> select clear
> show #!8 models
> hide #!7 models
> select clear
> show #!9 models
> hide #!8 models
> show #!10 models
> hide #!9 models
> show #!11 models
> hide #!10 models
> show #!10 models
> show #!9 models
> hide #!11 models
> hide #!9 models
> hide #!10 models
> show #!1 models
> volume #1 level 0.09855
> show #!2 models
> hide #!1 models
> volume level 0.09
> volume #2 level 0.108
> volume level 0.1
> show #!1 models
> hide #!2 models
> show #!3 models
> hide #!1 models
> volume #3 level 0.09344
> show #!4 models
> hide #!3 models
> volume #4 level 0.1
> show #!5 models
> hide #!4 models
> volume #5 level 0.1108
> volume #6 level 0.101
> volume #7 level 0.09482
> open /Users/yoojoong/Downloads/cryosparc_P18_J524_class_00_00005_volume.mrc
Opened cryosparc_P18_J524_class_00_00005_volume.mrc as #12, grid size
120,120,120, pixel 2.33, shown at level 0.0832, step 1, values float32
> open /Users/yoojoong/Downloads/cryosparc_P18_J524_class_01_00005_volume.mrc
Opened cryosparc_P18_J524_class_01_00005_volume.mrc as #13, grid size
120,120,120, pixel 2.33, shown at level 0.083, step 1, values float32
> open /Users/yoojoong/Downloads/cryosparc_P18_J524_class_02_00005_volume.mrc
Opened cryosparc_P18_J524_class_02_00005_volume.mrc as #14, grid size
120,120,120, pixel 2.33, shown at level 0.0829, step 1, values float32
> open /Users/yoojoong/Downloads/cryosparc_P18_J524_class_03_00005_volume.mrc
Opened cryosparc_P18_J524_class_03_00005_volume.mrc as #15, grid size
120,120,120, pixel 2.33, shown at level 0.0831, step 1, values float32
> open /Users/yoojoong/Downloads/cryosparc_P18_J524_class_04_00005_volume.mrc
Opened cryosparc_P18_J524_class_04_00005_volume.mrc as #16, grid size
120,120,120, pixel 2.33, shown at level 0.0831, step 1, values float32
> open /Users/yoojoong/Downloads/cryosparc_P18_J524_class_05_00005_volume.mrc
Opened cryosparc_P18_J524_class_05_00005_volume.mrc as #17, grid size
120,120,120, pixel 2.33, shown at level 0.083, step 1, values float32
> open /Users/yoojoong/Downloads/cryosparc_P18_J524_class_06_00005_volume.mrc
Opened cryosparc_P18_J524_class_06_00005_volume.mrc as #18, grid size
120,120,120, pixel 2.33, shown at level 0.0828, step 1, values float32
> open /Users/yoojoong/Downloads/cryosparc_P18_J524_class_07_00005_volume.mrc
Opened cryosparc_P18_J524_class_07_00005_volume.mrc as #19, grid size
120,120,120, pixel 2.33, shown at level 0.0832, step 1, values float32
> open /Users/yoojoong/Downloads/cryosparc_P18_J524_class_08_00005_volume.mrc
Opened cryosparc_P18_J524_class_08_00005_volume.mrc as #20, grid size
120,120,120, pixel 2.33, shown at level 0.0832, step 1, values float32
> open /Users/yoojoong/Downloads/cryosparc_P18_J524_class_09_00005_volume.mrc
Opened cryosparc_P18_J524_class_09_00005_volume.mrc as #21, grid size
120,120,120, pixel 2.33, shown at level 0.0829, step 1, values float32
> volume level 0.1
> hide #!13-21 target m
> show #!13 models
> hide #!12 models
> show #!14 models
> hide #!13 models
> show #!15 models
> hide #!14 models
> show #!16 models
> hide #!15 models
> show #!17 models
> hide #!16 models
> show #!18 models
> hide #!17 models
> volume level 0.12
> show #!19 models
> hide #!18 models
> show #!20 models
> hide #!19 models
> show #!21 models
> hide #!20 models
> volume level 0.13
> volume level 0.15
> hide #!21 models
> show #!12 models
> volume #12 step 2
> volume #12 step 1
> show #!13 models
> hide #!12 models
> show #!14 models
> hide #!13 models
> volume #14 level 0.1524
> show #!15 models
> hide #!14 models
> volume #15 level 0.1399
> show #!16 models
> hide #!15 models
> volume #16 level 0.1239
> volume #16 level 0.1273
> show #!17 models
> hide #!16 models
> volume #17 level 0.1523
> show #!18 models
> hide #!17 models
> volume #18 level 0.1477
> show #!19 models
> hide #!18 models
> volume #19 level 0.1478
> show #!20 models
> hide #!19 models
> volume #20 level 0.139
> open /Users/yoojoong/Downloads/cryosparc_P18_J525_class_00_00010_volume.mrc
Opened cryosparc_P18_J525_class_00_00010_volume.mrc as #22, grid size
168,168,168, pixel 1.66, shown at level 0.0499, step 1, values float32
> open /Users/yoojoong/Downloads/cryosparc_P18_J525_class_01_00010_volume.mrc
Opened cryosparc_P18_J525_class_01_00010_volume.mrc as #25, grid size
168,168,168, pixel 1.66, shown at level 0.05, step 1, values float32
> open /Users/yoojoong/Downloads/cryosparc_P18_J525_class_02_00010_volume.mrc
Opened cryosparc_P18_J525_class_02_00010_volume.mrc as #26, grid size
168,168,168, pixel 1.66, shown at level 0.0497, step 1, values float32
> open /Users/yoojoong/Downloads/cryosparc_P18_J525_class_03_00010_volume.mrc
Opened cryosparc_P18_J525_class_03_00010_volume.mrc as #27, grid size
168,168,168, pixel 1.66, shown at level 0.0499, step 1, values float32
> open /Users/yoojoong/Downloads/cryosparc_P18_J525_class_04_00010_volume.mrc
Opened cryosparc_P18_J525_class_04_00010_volume.mrc as #28, grid size
168,168,168, pixel 1.66, shown at level 0.0498, step 1, values float32
> hide #23#!20-22,24-28 target m
> show #!22 models
> volume level 0.15
> volume level 0.12
> show #!25 models
> hide #!22 models
> show #!26 models
> hide #!25 models
> show #!27 models
> hide #!26 models
> show #!28 models
> hide #!27 models
> volume level 0.11
> volume level 0.1
> hide #!27 models
> hide #!28 models
> show #!22 models
> show #!25 models
> hide #!22 models
> show #!26 models
> hide #!25 models
> show #!27 models
> hide #!26 models
> show #!28 models
> hide #!27 models
> volume #28 level 0.119
> volume #27 level 0.1202
> hide #!28 models
> hide #!27 models
> show #!25 models
> show #!22 models
> hide #!25 models
> volume #22 level 0.123
> show #!25 models
> hide #!22 models
> volume #25 level 0.1208
> volume level 0.12
> show #!26 models
> hide #!25 models
> show #!25 models
> hide #!25 models
> show #!27 models
> hide #!26 models
> show #!28 models
> hide #!27 models
> show #!25 models
> hide #!28 models
> show #!22 models
> hide #!25 models
> show #!25 models
> hide #!22 models
> show #!26 models
> hide #!25 models
> volume #26 level 0.1088
> show #!27 models
> hide #!26 models
> volume #27 level 0.09343
> volume #28 level 0.09254
> hide #!27 models
> volume #28 level 0.08831
> open /Users/yoojoong/Downloads/cryosparc_P18_J526_class_00_00010_volume.mrc
Opened cryosparc_P18_J526_class_00_00010_volume.mrc as #29, grid size
120,120,120, pixel 2.33, shown at level 0.0828, step 1, values float32
> open /Users/yoojoong/Downloads/cryosparc_P18_J526_class_01_00010_volume.mrc
Opened cryosparc_P18_J526_class_01_00010_volume.mrc as #30, grid size
120,120,120, pixel 2.33, shown at level 0.0833, step 1, values float32
> open /Users/yoojoong/Downloads/cryosparc_P18_J526_class_02_00010_volume.mrc
Opened cryosparc_P18_J526_class_02_00010_volume.mrc as #31, grid size
120,120,120, pixel 2.33, shown at level 0.083, step 1, values float32
> open /Users/yoojoong/Downloads/cryosparc_P18_J526_class_03_00010_volume.mrc
Opened cryosparc_P18_J526_class_03_00010_volume.mrc as #32, grid size
120,120,120, pixel 2.33, shown at level 0.0829, step 1, values float32
> open /Users/yoojoong/Downloads/cryosparc_P18_J526_class_04_00010_volume.mrc
Opened cryosparc_P18_J526_class_04_00010_volume.mrc as #33, grid size
120,120,120, pixel 2.33, shown at level 0.0829, step 1, values float32
> hide #!28-33 target m
> show #!28 models
> hide #!28 models
> show #!29 models
> volume level 0.1
> volume level 0.13
> show #!30 models
> hide #!29 models
> show #!31 models
> hide #!30 models
> show #!32 models
> hide #!31 models
> show #!33 models
> hide #!32 models
> show #!32 models
> hide #!33 models
> volume #32 level 0.1359
> show #!31 models
> hide #!32 models
> volume #31 level 0.1524
> show #!30 models
> hide #!31 models
> volume #30 level 0.1384
> volume #30 level 0.1324
> show #!29 models
> hide #!30 models
> volume #29 level 0.1278
> volume #30 level 0.1372
> hide #!29 models
> volume #30 level 0.1396
> volume #31 level 0.1578
> volume #32 level 0.1561
> volume #33 level 0.1233
> volume #32 level 0.1359
> show #23 models
> show #!24 models
> volume #32 level 0.1288
> hide #!32 models
> show #!29 models
> volume #29 level 0.1201
> show #!30 models
> hide #!29 models
> volume #30 level 0.1324
> show #!31 models
> hide #!30 models
> volume #31 level 0.145
> volume #32 level 0.1347
> hide #!31 models
> volume #32 level 0.1371
> volume #33 level 0.1132
> volume #30 level 0.1061
> volume #29 level 0.09597
> volume #29 level 0.09
> volume level 0.09
> volume level 0.1
> volume level 0.11
> hide #!33 models
> volume #32 level 0.1159
> volume #33 level 0.11
> show #!31 models
> show #!32 models
> hide #!33 models
> hide #!32 models
> show #!32 models
> hide #!31 models
> show #!31 models
> show #!30 models
> show #!29 models
> hide #!32 models
> hide #!31 models
> show #!31 models
> hide #!31 models
> hide #!30 models
> show #!30 models
> hide #!29 models
> show #!29 models
> hide #!30 models
> volume level 0.13
> volume level 0.14
> show #!30 models
> hide #!29 models
> show #!33 models
> hide #!30 models
> show #!29 models
> hide #!29 models
> show #!29 models
> hide #!33 models
> show #!33 models
> hide #!29 models
> show #!29 models
> hide #!33 models
> show #!33 models
> hide #!29 models
> show #!31 models
> show #!32 models
> hide #!32 models
> hide #!33 models
> show #!32 models
> hide #!31 models
> show #!30 models
> hide #!32 models
> show #!32 models
> hide #!30 models
> show #!31 models
> hide #!32 models
> open /Users/yoojoong/Downloads/cryosparc_P18_J533_004_volume_map_sharp.mrc
Opened cryosparc_P18_J533_004_volume_map_sharp.mrc as #34, grid size
320,320,320, pixel 0.874, shown at level 0.0226, step 2, values float32
> hide #!31 models
> surface dust #34
> volume #34 step 1
> volume #34 level 0.08992
> ui mousemode right translate
> ui tool show "Side View"
> hide #!24 models
> volume #34 color #b2b2b27a
> volume #34 level 0.1112
> volume #34 level 0.1006
> volume #34 level 0.08637
> volume #34 color #b2b2b2
> volume #34 level 0.1254
> volume #34 level 0.09346
> show #!32 models
> show #!31 models
> hide #!34 models
> hide #!32 models
> hide #!31 models
> show #!30 models
> show #!32 models
> hide #!32 models
> show #!33 models
> hide #!33 models
> hide #!30 models
> open /Users/yoojoong/Downloads/cryosparc_P18_J534_004_volume_map_sharp.mrc
Opened cryosparc_P18_J534_004_volume_map_sharp.mrc as #35, grid size
320,320,320, pixel 0.874, shown at level 0.021, step 2, values float32
> volume #35 step 1
> volume #35 level 0.1312
> volume #35 level 0.1178
> show #!24 models
> hide #23 models
> volume #35 level 0.07776
> surface dust #35
> volume #35 level 0.1011
===== 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/yoojoong/Downloads/cryosparc_P18_J534_004_volume_map_sharp.mrc
Opened cryosparc_P18_J534_004_volume_map_sharp.mrc as #1, grid size
320,320,320, pixel 0.874, shown at level 0.021, step 2, values float32
> open /Users/yoojoong/Downloads/cryosparc_P18_J533_004_volume_map_sharp.mrc
Opened cryosparc_P18_J533_004_volume_map_sharp.mrc as #2, grid size
320,320,320, pixel 0.874, shown at level 0.0226, step 2, values float32
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M1 Pro
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: MacBookPro18,3
Model Number: MKGR3LL/A
Chip: Apple M1 Pro
Total Number of Cores: 8 (6 performance and 2 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: 1 day, 4 hours, 29 minutes
Graphics/Displays:
Apple M1 Pro:
Chipset Model: Apple M1 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 14
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
LG ULTRAFINE:
Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus)
UI Looks like: 2560 x 1440 @ 60.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
T24i-10:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 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-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
Change History (2)
comment:1 by , 4 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 , 4 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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