![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 10 months ago
Closed 10 months ago
#16591 closed defect (duplicate)
Crash on Mac waking from sleep
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-15.1.1-x86_64-i386-64bit
ChimeraX Version: 1.8rc202405230136 (2024-05-23 01:36:41 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 0x00007ff852289b40 (most recent call first):
File "/Applications/ChimeraX-1.8-rc2024.05.23.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 302 in event_loop
File "/Applications/ChimeraX-1.8-rc2024.05.23.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-rc2024.05.23.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, 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, 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: 59)
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{
"uptime" : 67000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro16,1",
"coalitionID" : 9984,
"osVersion" : {
"train" : "macOS 15.1.1",
"build" : "24B91",
"releaseType" : "User"
},
"captureTime" : "2025-01-09 10:56:07.0908 -0500",
"codeSigningMonitor" : 0,
"incident" : "6735424E-3012-4D2A-87A8-871763EA64B6",
"pid" : 27310,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-01-09 07:29:25.9299 -0500",
"procStartAbsTime" : 57735280283630,
"procExitAbsTime" : 67659596024937,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.8-rc2024.05.23.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"FFF118B0-153B-5EE1-936A-C142B9AE2051","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "0C06254D-FB60-474E-DE2B-A6A751CDC42B",
"lowPowerMode" : 1,
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"bootSessionUUID" : "12105A9C-F56A-4FEA-BB8A-46A6BBE24B97",
"wakeTime" : 8,
"bridgeVersion" : {"build":"22P1072","train":"9.1"},
"sleepWakeUUID" : "1D4AB5BB-AA5D-4948-AD72-4A6B2AA47FE6",
"sip" : "enabled",
"vmRegionInfo" : "0 is not in any region. Bytes before following region: 4549517312\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10f2c2000-10f2c6000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.8-rc2024.05.23.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000000","rawCodes":[1,0],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000000"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":27310},
"vmregioninfo" : "0 is not in any region. Bytes before following region: 4549517312\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10f2c2000-10f2c6000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.8-rc2024.05.23.app\/Contents\/MacOS\/ChimeraX",
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"faultingThread" : 0,
"threads" : 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"rolloutId" : "5fb4245a1bbfe8005e33a1e1",
"factorPackIds" : {
},
"deploymentId" : 240000021
}
],
"experiments" : [
]
}
}
===== Log before crash start =====
Startup Messages
---
notes | available bundle cache has not been initialized yet
Database-fetch provider 'redo' in bundle Map specified unknown data format
'MTZ'
UCSF ChimeraX version: 1.8rc202405230136 (2024-05-23)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/olgakarlita2012/Desktop/PKG/PKG Manuscript Final Figures/PKG
> Chimera figures.cxs"
opened ChimeraX session
> set bgColor white
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting simple
> lighting full
> lighting flat
> color #1 #acacacff
> color #1 #cdcdcdff
> color #1 #e9e9e9ff
> color #1 #dededeff
> color #1 #cdcdcdff
> color #1 gainsboro
> color #1 #bfdaf1ff
> color #1 #a4bcd0ff
> color #1 #c9e6ffff
> color #1 #c9e6ff8c
> color #1 #c9e6ff1c
> color #1 #c9e6ff00
> color #1 #ebebebff
> color #1 #d6d6d6ff
> color #1 #ebebebff
> color #1 #d6d6d6ff
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> select /a: 226, 227, 234, 240, 243, 244, 246, 247, 248, 250, 252, 265, 268,
> 276, 278, 280, 296, 298, 302, 303, 311, 319, 321, 327,338, 341, 342, 347,
> 360, 366
238 atoms, 218 bonds, 30 residues, 1 model selected
> color sel cornflower blue
> color sel #bed9f0ff
> color sel #bdd9f0ff
> color sel #bdd8efff
> color sel #8ca0b1ff
> color sel #788998ff
> color sel #728290ff
> color sel #70808dff
> color sel #6e7e8bff
> color sel #6e7d8bff
> color sel #6d7d8aff
> color sel #6d7c8aff
> color sel #6c7c89ff
> color sel #6c7b89ff
> color sel #6b7b88ff
> color sel #6a7986ff
> color sel #697885ff
> color sel #697884ff
> color sel #687784ff
> color sel #677683ff
> color sel #677682ff
> color sel #677582ff
> color sel #667582ff
> color sel #667581ff
> color sel #667481ff
> color sel #697885ff
> color sel #6f7f8dff
> color sel #728290ff
> color sel #768695ff
> color sel #788998ff
> color sel #798a99ff
> color sel #7b8d9cff
> color sel #7e909fff
> color sel #8396a6ff
> color sel #889bacff
> color sel #8b9fb0ff
> color sel #8ea2b4ff
> color sel #8fa4b5ff
> color sel #91a6b8ff
> color sel #92a7b9ff
> color sel #93a8baff
> color sel #95aabdff
> color sel #96abbdff
> color sel #96abbeff
> color sel #96acbeff
> color sel #97adbfff
> color sel #99afc1ff
> color sel #9bb1c4ff
> color sel #9bb2c5ff
> color sel #9eb4c8ff
> color sel #a0b7cbff
> color sel #a1b8ccff
> color sel #a3bacfff
> color sel #a6bdd2ff
> color sel #a7bfd4ff
> color sel #a9c1d6ff
> color sel #aac2d7ff
> color sel #abc4d9ff
> color sel #abc3d8ff
> color sel #aac2d7ff
> color sel #a8c0d5ff
> color sel #a6bed2ff
> color sel #a3bbcfff
> color sel #a2b9cdff
> color sel #a1b8ccff
> color sel #a0b7cbff
> color sel #9fb6caff
> color sel #9fb5c9ff
> color sel #9eb5c9ff
> color sel #9eb4c8ff
> color sel #9eb4c8fa
> color sel #9eb4c8ed
> color sel #9eb4c8bd
> color sel #9eb4c8b6
> color sel #9eb4c8ad
> color sel #9eb4c8a7
> color sel #9eb4c8a3
> color sel #9eb4c8a0
> color sel #9eb4c89e
> color sel #9eb4c89d
> color sel #9eb4c89c
> color sel #9eb4c89b
> color sel #9eb4c89a
> color sel #9eb4c898
> color sel #9eb4c895
> color sel #9eb4c88f
> color sel #9eb4c88c
> color sel #9eb4c889
> color sel #9eb4c883
> color sel #9eb4c880
> color sel #9eb4c88a
> color sel #9eb4c88d
> color sel #9eb4c893
> color sel #9eb4c89c
> color sel #9eb4c8a0
> color sel #9eb4c8af
> color sel #9eb4c8ba
> color sel #9eb4c8bd
> color sel #9eb4c8c0
> color sel #9eb4c8c6
> color sel #9eb4c8cb
> color sel #9eb4c8ce
> color sel #9eb4c8d0
> color sel #9eb4c8d2
> color sel #9eb4c8d3
> color sel #9eb4c8d6
> color sel #9eb4c8d9
> color sel #9eb4c8dc
> color sel #9eb4c8de
> color sel #9eb4c8e1
> color sel #9eb4c8e3
> color sel #9eb4c8e8
> color sel #9eb4c8ea
> color sel #9eb4c8ec
> color sel #9eb4c8ed
> color sel #9eb4c8ef
> color sel #9eb4c8f0
> color sel #9eb4c8f1
> color sel #9eb4c8f2
> color sel #9eb4c8f3
> color sel #9eb4c8f6
> color sel #9eb4c8fa
> color sel #9eb4c8fb
> color sel #9eb4c8fc
> color sel #9eb4c8fe
> color sel #9eb4c8ff
> color sel #bcd7eeff
> color sel #bbd4eeff
> color sel #bad4edff
> color sel #b9d3ecff
> color sel #b8d2ebff
> color sel #b8d1ebff
> color sel #b8d1eaff
> color sel #b6cfe8ff
> color sel #b5cee7ff
> color sel #b4cde6ff
> color sel #b3cbe4ff
> color sel #b2cae2ff
> color sel #b1c9e1ff
> color sel #b0c8e1ff
> color sel #b0c8e0ff
> color sel #afc7dfff
> color sel #aec6deff
> color sel #aec5ddff
> color sel #adc5ddff
> color sel #adc4dcff
> color sel #acc3dbff
> color sel #abc3daff
> color sel #abc2daff
> color sel #abc2d9ff
> color sel #aac1d8ff
> color sel #a9c0d8ff
> color sel #a9c0d7ff
> color sel #a8bfd6ff
> color sel #a7bed5ff
> color sel #a7bed4ff
> color sel #a6bdd4ff
> color sel #a6bdd3ff
> color sel #a6bcd3ff
> color sel #a5bcd3ff
> color sel #a5bcd2ff
> color sel #6e87acff
> color sel #6e87acfa
> color sel #6e87aced
> color sel #6e87ace3
> color sel #6e87acdc
> color sel #6e87acd5
> color sel #6e87accb
> color sel #6e87acc7
> color sel #6e87acc4
> color sel #6e87acc1
> color sel #6e87acbe
> color sel #6e87acbc
> color sel #6e87acb9
> color sel #6e87acb3
> color sel #6e87acb2
> color sel #6e87acb0
> color sel #6e87acaf
> color sel #6e87acb0
> color sel #6e87acb2
> color sel #6e87acb3
> select clear
> select /a:234
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide sel cartoons
> hide sel atoms
> show sel atoms
> hide sel target a
> cartoon sel
> select clear
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting flat
> select /a: 226, 227, 234, 240, 243, 244, 246, 247, 248, 250, 252, 265, 268,
> 276, 278, 280, 296, 298, 302, 303, 311, 319, 321, 327,338, 341, 342, 347,
> 360, 366
238 atoms, 218 bonds, 30 residues, 1 model selected
> color sel #6e87acb3
> color sel #6e87acb4
> color sel #6e87acb8
> color sel #6e87acbf
> color sel #6e87acc9
> color sel #6e87accf
> color sel #6e87acd9
> color sel #6e87ace2
> color sel #6e87ace8
> color sel #6e87aceb
> color sel #6e87acf0
> color sel #6e87acff
> color sel #6e87acf5
> color sel #6e87ace9
> color sel #6e87acbb
> color sel #6e87aca4
> color sel #6e87ac99
> color sel #6e87ac95
> color sel #6e87ac92
> color sel #6e87ac8d
> color sel #6e87ac87
> color sel #6e87ac82
> color sel #6e87ac80
> color sel #6e87ac76
> color sel #6e87ac74
> color sel #6e87ac72
> color sel #6e87ac71
> color sel #6e87ac70
> color sel #6e87ac6e
> color sel #6e87ac6d
> color sel #6e87ac6c
> color sel #6e87ac6b
> color sel #6e87ac6a
> color sel #6e87ac69
> color sel #6e87ac68
> color sel #6e87ac67
> color sel #6e87ac68
> color sel #6e87ac77
> color sel #6e87ac80
> color sel #6e87ac8a
> color sel #6e87aca7
> color sel #6e87acc6
> color sel #6e87acea
> color sel #6e87acf8
> color sel #6e87acf9
> color sel #6e87acfb
> color sel #6e87acfe
> color sel #6e87acff
> color sel #6d86acff
> color sel #6f88afff
> color sel #7089b0ff
> color sel #728bb3ff
> color sel #738db5ff
> color sel #748eb6ff
> color sel #748fb7ff
> color sel #758fb8ff
> color sel #7690b9ff
> color sel #7691baff
> color sel #7792bbff
> color sel #7893bcff
> color sel #7894bdff
> color sel #7995bfff
> color sel #7a95c0ff
> color sel #7b96c1ff
> color sel #7b97c2ff
> color sel #7c98c2ff
> color sel #7d99c5ff
> color sel #7d9ac5ff
> color sel #7e9bc7ff
> color sel #7f9cc8ff
> color sel #829fccff
> color sel #84a2d0ff
> color sel #87a6d5ff
> color sel #89a9d8ff
> color sel #8aa9d9ff
> color sel #8aa9d8ff
> color sel #89a8d7ff
> color sel #88a7d6ff
> color sel #87a5d4ff
> color sel #85a4d2ff
> color sel #84a2d0ff
> color sel #82a0cdff
> color sel #829fcdff
> color sel #829fccff
> color sel #819fccff
> color sel #819fcbff
> color sel #819fccff
> color sel #82a0cdff
> color sel #84a2cfff
> color sel #85a3d1ff
> color sel #87a6d5ff
> color sel #88a6d6ff
> color sel #88a7d6ff
> color sel #88a8d7ff
> select clear
> save "/Users/olgakarlita2012/Desktop/PKG/PKG Manuscript Final Figures/T and
> Class CHESCA/T-CHESCA map chimera.png" width 713 height 715 supersample 3
> save "/Users/olgakarlita2012/Desktop/PKG/PKG Manuscript Final Figures/T and
> Class CHESCA/T-CHESCA map chimera.png" width 1600 height 1604 supersample 3
> color #1 #dededfff
> select /a: 227, 229, 233, 234, 243, 246, 247, 250, 251, 252, 265, 266, 276,
> 304, 337, 338, 339, 341, 345, 350, 360, 366
186 atoms, 177 bonds, 22 residues, 1 model selected
> color sel #cbdac9ff
> color sel #6b895bff
> color sel #6a895bff
> color sel #6b8a5bff
> color sel #6b8b5cff
> color sel #6d8d5dff
> color sel #6e8e5eff
> color sel #709160ff
> color sel #719160ff
> color sel #739462ff
> color sel #749663ff
> color sel #759764ff
> color sel #769965ff
> color sel #779965ff
> color sel #779a66ff
> color sel #789b67ff
> color sel #799c67ff
> color sel #7a9e68ff
> color sel #7b9f69ff
> color sel #7ca16aff
> color sel #7fa46dff
> color sel #80a56dff
> color sel #80a66eff
> color sel #81a66eff
> color sel #82a76fff
> color sel #82a86fff
> color sel #83aa70ff
> color sel #84aa70ff
> color sel #84aa71ff
> color sel #85ac72ff
> color sel #86ad73ff
> color sel #87af74ff
> color sel #88b075ff
> color sel #8ab276ff
> color sel #8bb376ff
> color sel #8cb578ff
> color sel #8db678ff
> color sel #8db678fe
> color sel #8db678fb
> color sel #8db678f6
> color sel #8db678f3
> color sel #8db678ef
> color sel #8db678ea
> color sel #8db678e8
> color sel #8db678e6
> color sel #8db678e5
> color sel #8db678e4
> color sel #8db678e1
> color sel #8db678e0
> color sel #8db678de
> color sel #8db678dc
> color sel #8db678db
> color sel #8db678d8
> color sel #8db678d2
> color sel #8db678d1
> color sel #8db678d2
> color sel #8db678d3
> color sel #8db678d5
> color sel #8db678d7
> color sel #8db678d8
> color sel #8db678d9
> color sel #8db678da
> color sel #8db678dc
> color sel #8db678dd
> color sel #8db678df
> color sel #8db678e0
> color sel #8db678e2
> color sel #8db678e4
> color sel #8db678e5
> color sel #8db678e6
> color sel #8db678e7
> color sel #8db678e9
> color sel #8db678ea
> color sel #8db678eb
> color sel #8db678ec
> color sel #8db678ed
> color sel #8db678ee
> color sel #8db678ef
> color sel #8db679ef
> color sel #8eb779ef
> color sel #8fb97aef
> color sel #8fb97bef
> color sel #90ba7bef
> color sel #90bb7bef
> color sel #91bb7cef
> color sel #91bb7cf0
> select clear
> select /a: 227, 229, 233, 234, 243, 246, 247, 250, 251, 252, 265, 266, 276,
> 304, 337, 338, 339, 341, 345, 350, 360, 366
186 atoms, 177 bonds, 22 residues, 1 model selected
> color sel #91bb7cf0
> color sel #8cb578f0
> color sel #81a76ef0
> color sel #7ea36cf0
> color sel #7ea26bf0
> color sel #7da26bf0
> color sel #7ea36cf0
> color sel #7fa46df0
> color sel #80a66ef0
> color sel #81a66ef0
> color sel #81a76ef0
> color sel #82a86ff0
> color sel #83a970f0
> color sel #83aa70f0
> color sel #84aa71f0
> color sel #85ac72f0
> color sel #86ad72f0
> color sel #86ad73f0
> color sel #86ae73f0
> color sel #87af74f0
> color sel #88b074f0
> color sel #89b175f0
> color sel #8ab376f0
> color sel #92bc7cf0
> color sel #97c481f0
> color sel #99c582f0
> color sel #9cca85f0
> color sel #9ecc87f0
> color sel #a0cf89f0
> color sel #a4d38cf0
> color sel #a5d68df0
> color sel #a3d38cf0
> color sel #a0cf89f0
> color sel #9dcb86f0
> color sel #9bc985f0
> color sel #9ac683f0
> color sel #98c482f0
> color sel #96c280f0
> color sel #96c180f0
> color sel #95c07ff0
> color sel #94bf7ff0
> color sel #93be7ef0
> color sel #92bd7df0
> color sel #92bc7cf0
> color sel #91bb7cf0
> color sel #90ba7bf0
> color sel #90b97bf0
> color sel #8fb97af0
> color sel #8fb87af0
> color sel #8eb87af0
> color sel #8eb879f0
> color sel #8eb779f0
> color sel #8db679f0
> color sel #8db678f0
> color sel #8db578f0
> color sel #8cb578f0
> color sel #8cb477f0
> color sel #8bb477f0
> color sel #8bb376f0
> color sel #8ab276f0
> color sel #89b175f0
> color sel #88b074f0
> color sel #87af73f0
> color sel #87ae73f0
> select clear
> save "/Users/olgakarlita2012/Desktop/PKG/PKG Manuscript Final Figures/T and
> Class CHESCA/Class-CHESCA/Class C map chimera.png" width 1600 height 1836
> supersample 3
> color #1 #e5e4e5ff
> select /a227, 234, 243, 246, 250, 252, 327, 360
Nothing selected
> select /a227, 234, 243, 246, 250, 252, 327, 360
Nothing selected
> select /a: 227, 234, 243, 246, 250, 252, 327, 360
69 atoms, 63 bonds, 8 residues, 1 model selected
> color sel #7c5da1ff
> color sel #7c5da1fb
> color sel #7c5da1f8
> color sel #7c5da1ef
> color sel #7c5da1eb
> color sel #7c5da1e7
> color sel #7c5da1e4
> color sel #7c5da1da
> color sel #7c5da1d5
> color sel #7c5da1d2
> color sel #7c5da1ce
> color sel #7c5da1c8
> color sel #7c5da1c5
> color sel #7c5da1c3
> color sel #7c5da1c1
> color sel #7c5da1c0
> color sel #7c5da1bf
> color sel #7c5da1be
> color sel #7c5da1bd
> color sel #7b5ba1bd
> color sel #7b5ca1bd
> color sel #7c5ca3bd
> color sel #7f5ea5bd
> color sel #8160a8bd
> color sel #8260aabd
> color sel #8462acbd
> color sel #8563aebd
> color sel #8664b0bd
> color sel #8865b1bd
> color sel #8966b3bd
> color sel #8a67b5bd
> color sel #8c68b7bd
> color sel #8d68b8bd
> color sel #8d69b8bd
> color sel #8e6ababd
> color sel #906bbcbd
> color sel #906bbdbd
> color sel #916bbdbd
> color sel #926cbebd
> color sel #936dc0bd
> color sel #946ec1bd
> color sel #946ec1bc
> color sel #946ec1bb
> color sel #946ec1b1
> color sel #946ec1aa
> color sel #946ec1a3
> color sel #946ec1a1
> color sel #946ec19f
> color sel #946ec19b
> color sel #946ec199
> color sel #946ec198
> color sel #946ec197
> color sel #946ec196
> color sel #946ec197
> color sel #946ec199
> color sel #946ec19a
> color sel #946ec19b
> color sel #946ec19c
> color sel #946ec19d
> color sel #946ec19f
> color sel #946ec19e
> select clear
> save "/Users/olgakarlita2012/Desktop/PKG/PKG Manuscript Final Figures/T C
> and DRMs map common DRMs.png" width 473 height 730 supersample 3
> select /a: 227, 234, 243, 246, 250, 252, 327, 360
69 atoms, 63 bonds, 8 residues, 1 model selected
> style sel stick
Changed 69 atom styles
> show sel atoms
> hide sel atoms
> show sel atoms
> select clear
> lighting flat
> lighting shadows true intensity 0.5
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows false
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting flat
> lighting soft
> lighting flat
> save "/Users/olgakarlita2012/Desktop/PKG/PKG Manuscript Final Figures/T C
> and DRMs map common DRMs.png" width 1600 height 1589 supersample 3
===== Log before crash end =====
Log:
Startup Messages
---
notes | available bundle cache has not been initialized yet
Database-fetch provider 'redo' in bundle Map specified unknown data format
'MTZ'
UCSF ChimeraX version: 1.8rc202405230136 (2024-05-23)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 ATI-6.1.13
OpenGL renderer: AMD Radeon Pro 5300M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
Python: 3.11.4
Locale: 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: MacBook Pro
Model Identifier: MacBookPro16,1
Processor Name: 6-Core Intel Core i7
Processor Speed: 2.6 GHz
Number of Processors: 1
Total Number of Cores: 6
L2 Cache (per Core): 256 KB
L3 Cache: 12 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 2069.40.2.0.0 (iBridge: 22.16.11072.0.0,0)
OS Loader Version: 582~2132
Software:
System Software Overview:
System Version: macOS 15.1.1 (24B91)
Kernel Version: Darwin 24.1.0
Time since boot: 3 days, 51 minutes
Graphics/Displays:
Intel UHD Graphics 630:
Chipset Model: Intel UHD Graphics 630
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3e9b
Revision ID: 0x0000
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Support: Metal 3
AMD Radeon Pro 5300M:
Chipset Model: AMD Radeon Pro 5300M
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 4 GB
Vendor: AMD (0x1002)
Device ID: 0x7340
Revision ID: 0x0043
ROM Revision: 113-D3220E-190
VBIOS Version: 113-D32207P1-019
Option ROM Version: 113-D32207P1-019
EFI Driver Version: 01.A1.190
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 3072 x 1920 Retina
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
LG IPS FULLHD:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number:
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Connection Type: DVI or HDMI
Adapter Firmware Version: 0.00
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: 1.6.3
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
ChimeraX-AtomicLibrary: 14.0.5
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: 1.2.4
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: 1.0.4
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: 1.8rc202405230136
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: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.16
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: 1.13.4
ChimeraX-PDB: 2.7.5
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: 1.1.1
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: 3.0.10
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-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: 1.4.2
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: 4.51.0
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: 8.1.2
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.10
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: 3.0.43
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
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
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
traitlets: 5.14.2
typing-extensions: 4.11.0
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.10
Change History (2)
comment:1 by , 10 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 , 10 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
This crash is caused by a bug in the Qt window toolkit used by ChimeraX and sometimes happens when an external display is unplugged or plugged in or when the computer wakes from sleep. The crash still happens in ChimeraX 1.9 (with newer Qt toolkit version) but maybe a bit less frequently. We have no solution for this and are hoping a newer Qt window toolkit version will fix it. We will be updating from Qt 6.7 to Qt 6.8 soon.
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Reported by Karla Martinez