![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 18 months ago
Closed 12 months ago
#15186 closed defect (fixed)
Crash changing Mac display configuration
| 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-14.4.1-x86_64-i386-64bit
ChimeraX Version: 1.8.dev202403271703 (2024-03-27 17:03:08 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 0x00007ff84e343100 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 280 in event_loop
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1069 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.surface._surface, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, chimerax.pdb_lib._load_libs, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, openmm._openmm, openmm.app.internal.compiled, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, PIL._imagingmath, chimerax.graphics._graphics (total: 51)
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{
"uptime" : 6100,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "iMac19,1",
"coalitionID" : 1282,
"osVersion" : {
"train" : "macOS 14.4.1",
"build" : "23E224",
"releaseType" : "User"
},
"captureTime" : "2024-05-13 20:47:39.6830 +0100",
"codeSigningMonitor" : 0,
"incident" : "EC520C6C-E48D-46D6-970F-15E73E7FCF5F",
"pid" : 3815,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-05-13 20:19:46.9910 +0100",
"procStartAbsTime" : 4454698726077,
"procExitAbsTime" : 6127289803439,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"12D9862C-C892-59F6-BF94-40ADD85044B2","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "D184F9A4-65DB-D022-6890-28A53A1C732F",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"sip" : "enabled",
"vmRegionInfo" : "0 is not in any region. Bytes before following region: 4295294976\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 100050000-100054000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x000000000000000d, 0x0000000000000000","rawCodes":[13,0],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"UNKNOWN_0xD at 0x0000000000000000"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":3815},
"vmregioninfo" : "0 is not in any region. Bytes before following region: 4295294976\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 100050000-100054000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
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"faultingThread" : 0,
"threads" : 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"path" : "\/usr\/lib\/system\/libsystem_kernel.dylib",
"name" : "libsystem_kernel.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703311118336,
"size" : 49144,
"uuid" : "5a006814-83f4-3c80-ab1f-528cdd08c0ff",
"path" : "\/usr\/lib\/system\/libsystem_pthread.dylib",
"name" : "libsystem_pthread.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703309725696,
"size" : 557048,
"uuid" : "6d02e870-f215-36ed-bf7d-435f66996bfe",
"path" : "\/usr\/lib\/system\/libsystem_c.dylib",
"name" : "libsystem_c.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703311319040,
"size" : 45048,
"uuid" : "56a3704c-42f6-3fb2-b45c-5371848c9400",
"path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
"name" : "libsystem_platform.dylib"
},
{
"size" : 0,
"source" : "A",
"base" : 0,
"uuid" : "00000000-0000-0000-0000-000000000000"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703368830976,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.AppKit",
"size" : 21159926,
"uuid" : "4905ef83-f061-3c82-bc30-70a4def63eee",
"path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
"name" : "AppKit",
"CFBundleVersion" : "2487.50.124"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703402176512,
"CFBundleShortVersionString" : "1.600.0",
"CFBundleIdentifier" : "com.apple.SkyLight",
"size" : 4591609,
"uuid" : "d0094308-9053-3411-906d-4a914a79a432",
"path" : "\/System\/Library\/PrivateFrameworks\/SkyLight.framework\/Versions\/A\/SkyLight",
"name" : "SkyLight"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703309422592,
"size" : 290802,
"uuid" : "85907582-b9ae-3a02-baca-2da374c6fbac",
"path" : "\/usr\/lib\/system\/libdispatch.dylib",
"name" : "libdispatch.dylib"
},
{
"source" : "P",
"arch" : "x86_64h",
"base" : 140703311540224,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.CoreFoundation",
"size" : 4829165,
"uuid" : "2780e326-c5fd-3a12-b906-b9449288005c",
"path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
"name" : "CoreFoundation",
"CFBundleVersion" : "2420"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703490179072,
"CFBundleShortVersionString" : "2.1.1",
"CFBundleIdentifier" : "com.apple.HIToolbox",
"size" : 2732028,
"uuid" : "5d06c99c-ac78-3bc4-8908-45a394e8180b",
"path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
"name" : "HIToolbox"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703307399168,
"size" : 592736,
"uuid" : "899f1e34-b624-3162-8003-04daa6829461",
"path" : "\/usr\/lib\/dyld",
"name" : "dyld"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703310282752,
"size" : 503796,
"uuid" : "1ada3159-e0b9-3850-9d06-ed79891009e8",
"path" : "\/usr\/lib\/libc++.1.dylib",
"name" : "libc++.1.dylib"
}
],
"sharedCache" : {
"base" : 140703306702848,
"size" : 25769803776,
"uuid" : "59b61d18-2d12-3a06-a536-f0b08e953ca2"
},
"vmSummary" : "ReadOnly portion of Libraries: Total=1.2G resident=0K(0%) swapped_out_or_unallocated=1.2G(100%)\nWritable regions: Total=2.5G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=2.5G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 128K 1 \nActivity Tracing 256K 1 \nCG image 380K 26 \nColorSync 248K 30 \nCoreAnimation 1076K 118 \nCoreGraphics 12K 2 \nCoreUI image data 5312K 42 \nFoundation 16K 1 \nIOKit 7940K 1 \nKernel Alloc Once 8K 1 \nMALLOC 2.0G 106 \nMALLOC guard page 96K 24 \nMach message 16K 2 \nOpenGL GLSL 384K 4 \nSTACK GUARD 172K 43 \nStack 187.3M 44 \nStack Guard 56.0M 1 \nVM_ALLOCATE 250.6M 181 \nVM_ALLOCATE (reserved) 96.0M 1 reserved VM address space (unallocated)\n__CTF 824 1 \n__DATA 44.1M 768 \n__DATA_CONST 60.2M 435 \n__DATA_DIRTY 1690K 220 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__LINKEDIT 216.5M 173 \n__OBJC_RO 71.7M 1 \n__OBJC_RW 2196K 2 \n__TEXT 1.0G 779 \ndyld private memory 648K 7 \nmapped file 207.9M 55 \nshared memory 3004K 33 \n=========== ======= ======= \nTOTAL 4.2G 3105 \nTOTAL, minus reserved VM space 4.1G 3105 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"logWritingSignature" : "35e8ca1c662d327cc0ca4f3315d81a42553c5e23",
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "63508950b3714d3622fc77f7",
"factorPackIds" : {
"SIRI_MEMORY_SYNC_CONFIG" : "6526e111d0c9ce2f459b54a8"
},
"deploymentId" : 240000015
},
{
"rolloutId" : "652eff3d1bce5442b8d753c9",
"factorPackIds" : {
},
"deploymentId" : 240000009
}
],
"experiments" : [
{
"treatmentId" : "2dffbe18-a39a-4f33-ada9-2cce30af39ca",
"experimentId" : "6384d56b96e8d228551ec182",
"deploymentId" : 400000032
}
]
}
}
===== Log before crash start =====
> set bgColor white
> alias cylinders cartoon style protein modeh tube rad 2 sides 24
> camera ortho
> cofr centerOfView
> volume defaultvalues limitVoxelCount false initialColors dark grey
> saveSettings true
Saved volume settings
> mousemode rightMode "translate selected models"
> mousemode alt rightMode "contour level"
> mousemode alt leftMode "move picked models"
> alias cofron cofr centerofview showpivot true
> alias cofroff cofr centerofview showpivot false
> alias symclip cofr centerofview; clip near -$1 far $1 position cofr
> alias cootmode set bgColor black; surface cap false; surface style solid;
> lighting flat; graphics silhouettes false; style stick; ~rib; color
> ##num_residues gold; color byhet ; disp; ~disp @H*; style solvent ball; size
> ballscale 0.1; size stickradius 0.07; transparency 70; cofr centerofview;
> clip near -10 far 10 position cofr; color ##~num_residues cornflower blue;
> cofron;
> alias cootmode_mesh surface cap false; surface style mesh; lighting flat;
> graphics silhouettes false; style stick; ~rib; color ##num_residues gold;
> color byhet ; disp; ~disp @H*; style solvent ball; size ballscale 0.1; size
> stickradius 0.07; cofr centerofview; clip near -10 far 10 position cofr;
> color ##~num_residues #3d60ffff; transparency 50
> alias ca_and_sidechains ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1;
> disp @P&nucleic&$1; style $1 stick; disp sidechain&$1; disp
> ~backbone&nucleic&$1; size stickradius 0.1; size pseudobondradius 0.1
> alias ca_trace ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1; disp
> @P&nucleic&$1; style $1 stick; size stickradius 0.1; size pseudobondradius
> 0.1
> alias map_sphere_15 surface unzone ##~num_residues; sel; close #10000;
> marker #10000 position cofr; sel ~sel; surface zone ##~num_residues
> nearAtoms sel distance 15; close #10000
> alias map_unsphere surface unzone ##~num_residues
> alias default_mol_display ~disp; rib; rainbow chain palette RdYlBu-5;
> lighting soft; style nucleic stick; display nucleic; clip off; set bgColor
> white; size ballscale 0.3 stickradius 0.2; cofroff; color ##~num_residues
> dark grey
> alias hidemaps surface unzone ##~num_residues; sel; close #10000; marker
> #10000 position cofr; sel ~sel; surface zone ##~num_residues nearAtoms sel
> distance 0; close #10000
> alias showmaps surface unzone ##~num_residues
> alias caps_off surface cap false
> alias caps_on surface cap true
> alias selbetween ks ri
> buttonpanel Shortcuts rows 3 columns 4
> buttonpanel Shortcuts add "Vol. Viewer" command "tool show 'Volume Viewer'"
> buttonpanel Shortcuts add "Model Panel" command "tool show Models"
> buttonpanel Shortcuts add Log command "tool show Log"
> buttonpanel Shortcuts add "Default Disp." command default_mol_display
> buttonpanel Shortcuts add "Map Sphere" command map_sphere_15
> buttonpanel Shortcuts add "Map Unsphere" command map_unsphere
> buttonpanel Shortcuts add "Center On" command cofron
> buttonpanel Shortcuts add "Center Off" command cofroff
> buttonpanel Shortcuts add "Coot Mode" command cootmode
> buttonpanel Shortcuts add "Mark Center" command "marker #10000 position
> cofr"
> buttonpanel Shortcuts add "Hide Dust" command "surface dust all"
> buttonpanel Shortcuts add "Show Dust" command "surface undust all"
> buttonpanel Shortcuts add "Color Grey" command "sel; sel sel-residues; sel
> ~sel; color sel dark grey target s; ~sel"
> buttonpanel Shortcuts add "Morph Maps" command "color all cornflower
> blue;material dull;volume morph #1-20 playStep 0.08 frames 200
> constantVolume true"
> alias reset ~tile; view initial; view orient
UCSF ChimeraX version: 1.8.dev202403271703 (2024-03-27)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /private/var/folders/dr/jc5bl8rs3656nl3tzhw2_pxm0000gn/T/ch.sudo.cyberduck/editor-848955a2-438d-46ed-b1df-
> ded02d1f3301/cephfs/hfagarasan/050424_P37-3_P36-63_Cyc1d/Class3D/job130/1782138036/run_it050_class004.mrc
Opened run_it050_class004.mrc as #1, grid size 120,120,120, pixel 2.52, shown
at level 0.0129, step 1, values float32
> open
> /private/var/folders/dr/jc5bl8rs3656nl3tzhw2_pxm0000gn/T/ch.sudo.cyberduck/editor-848955a2-438d-46ed-b1df-
> ded02d1f3301/cephfs/hfagarasan/050424_P37-3_P36-63_Cyc1d/Class3D/job130/1782138036/run_it050_class001.mrc
Opened run_it050_class001.mrc as #2, grid size 120,120,120, pixel 2.52, shown
at level 0.0146, step 1, values float32
> open
> /private/var/folders/dr/jc5bl8rs3656nl3tzhw2_pxm0000gn/T/ch.sudo.cyberduck/editor-848955a2-438d-46ed-b1df-
> ded02d1f3301/cephfs/hfagarasan/050424_P37-3_P36-63_Cyc1d/Class3D/job130/1782138036/run_it050_class003.mrc
Opened run_it050_class003.mrc as #3, grid size 120,120,120, pixel 2.52, shown
at level 0.0165, step 1, values float32
> open
> /private/var/folders/dr/jc5bl8rs3656nl3tzhw2_pxm0000gn/T/ch.sudo.cyberduck/editor-848955a2-438d-46ed-b1df-
> ded02d1f3301/cephfs/hfagarasan/050424_P37-3_P36-63_Cyc1d/Class3D/job130/1782138036/run_it050_class002.mrc
Opened run_it050_class002.mrc as #4, grid size 120,120,120, pixel 2.52, shown
at level 0.0126, step 1, values float32
> tile
4 models tiled
> select clear
> volume #1 level 0.01978
> volume #2 level 0.02196
> volume #3 level 0.02507
> volume #4 level 0.01991
> close #1-4
> open /Users/gghanim/Library/Containers/me.damir.dropover-
> mac/Data/tmp/Promises/134217728/run_it050_class001.mrc
Opened run_it050_class001.mrc as #1, grid size 120,120,120, pixel 2.52, shown
at level 0.0146, step 1, values float32
> open /Users/gghanim/Library/Containers/me.damir.dropover-
> mac/Data/tmp/Promises/134217728/run_it050_class002.mrc
Opened run_it050_class002.mrc as #2, grid size 120,120,120, pixel 2.52, shown
at level 0.0126, step 1, values float32
> open /Users/gghanim/Library/Containers/me.damir.dropover-
> mac/Data/tmp/Promises/134217728/run_it050_class003.mrc
Opened run_it050_class003.mrc as #3, grid size 120,120,120, pixel 2.52, shown
at level 0.0165, step 1, values float32
> open /Users/gghanim/Library/Containers/me.damir.dropover-
> mac/Data/tmp/Promises/134217728/run_it050_class004.mrc
Opened run_it050_class004.mrc as #4, grid size 120,120,120, pixel 2.52, shown
at level 0.0129, step 1, values float32
> tile
4 models tiled
> select clear
> volume #1 level 0.01694
> volume #2 level 0.01494
> volume #3 level 0.01923
> volume #4 level 0.01509
> ui tool show "Side View"
> select #3
2 models selected
> volume #3 level 0.01647
> select clear
> volume #1 level 0.004423
> volume #2 level 0.002564
> volume #3 level 0.001921
> volume #4 level 0.003399
> select clear
> volume #1 level 0.008454
> volume #2 level 0.006551
> volume #3 level 0.006606
> volume #4 level 0.007163
> volume #1 level 0.01876
> volume #2 level 0.01675
> volume #3 level 0.01858
> volume #4 level 0.01679
> volume #1 level 0.009168
> volume #2 level 0.007258
> volume #3 level 0.007436
> volume #4 level 0.00783
> volume #1 level 0.02086
> volume #2 level 0.01882
> volume #3 level 0.02102
> volume #4 level 0.01875
> open /Users/gghanim/Desktop/run_class001.mrc
Opened run_class001.mrc as #5, grid size 360,360,360, pixel 0.84, shown at
level 0.00191, step 1, values float32
> open /Users/gghanim/Desktop/lp20.mrc
Opened lp20.mrc as #6, grid size 360,360,360, pixel 0.84, shown at level
0.00243, step 1, values float32
> open /Users/gghanim/Desktop/run_class001.mrc
Failed opening file /Users/gghanim/Desktop/run_class001.mrc:
MRC file is truncated. Failed reading 1 values, type int32
> hide #!1-4 target m
> tile
2 models tiled
> select #5
2 models selected
> reset
> volume #6 color #a9a9a98a
> volume #6 level 0.001035
> volume #5 level 0.002753
> open
> /private/var/folders/dr/jc5bl8rs3656nl3tzhw2_pxm0000gn/T/ch.sudo.cyberduck/editor-848955a2-438d-46ed-b1df-
> ded02d1f3301/cephfs/hfagarasan/050424_P37-3_P36-63_Cyc1d/MaskCreate/job144/-138629580/mask.mrc
Opened mask.mrc as #7, grid size 120,120,120, pixel 2.52, shown at level 1,
step 1, values float32
> close #1-4
===== Log before crash end =====
Log:
> set bgColor white
> alias cylinders cartoon style protein modeh tube rad 2 sides 24
> camera ortho
> cofr centerOfView
> volume defaultvalues limitVoxelCount false initialColors dark grey
> saveSettings true
Saved volume settings
> mousemode rightMode "translate selected models"
> mousemode alt rightMode "contour level"
> mousemode alt leftMode "move picked models"
> alias cofron cofr centerofview showpivot true
> alias cofroff cofr centerofview showpivot false
> alias symclip cofr centerofview; clip near -$1 far $1 position cofr
> alias cootmode set bgColor black; surface cap false; surface style solid;
> lighting flat; graphics silhouettes false; style stick; ~rib; color
> ##num_residues gold; color byhet ; disp; ~disp @H*; style solvent ball; size
> ballscale 0.1; size stickradius 0.07; transparency 70; cofr centerofview;
> clip near -10 far 10 position cofr; color ##~num_residues cornflower blue;
> cofron;
> alias cootmode_mesh surface cap false; surface style mesh; lighting flat;
> graphics silhouettes false; style stick; ~rib; color ##num_residues gold;
> color byhet ; disp; ~disp @H*; style solvent ball; size ballscale 0.1; size
> stickradius 0.07; cofr centerofview; clip near -10 far 10 position cofr;
> color ##~num_residues #3d60ffff; transparency 50
> alias ca_and_sidechains ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1;
> disp @P&nucleic&$1; style $1 stick; disp sidechain&$1; disp
> ~backbone&nucleic&$1; size stickradius 0.1; size pseudobondradius 0.1
> alias ca_trace ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1; disp
> @P&nucleic&$1; style $1 stick; size stickradius 0.1; size pseudobondradius
> 0.1
> alias map_sphere_15 surface unzone ##~num_residues; sel; close #10000;
> marker #10000 position cofr; sel ~sel; surface zone ##~num_residues
> nearAtoms sel distance 15; close #10000
> alias map_unsphere surface unzone ##~num_residues
> alias default_mol_display ~disp; rib; rainbow chain palette RdYlBu-5;
> lighting soft; style nucleic stick; display nucleic; clip off; set bgColor
> white; size ballscale 0.3 stickradius 0.2; cofroff; color ##~num_residues
> dark grey
> alias hidemaps surface unzone ##~num_residues; sel; close #10000; marker
> #10000 position cofr; sel ~sel; surface zone ##~num_residues nearAtoms sel
> distance 0; close #10000
> alias showmaps surface unzone ##~num_residues
> alias caps_off surface cap false
> alias caps_on surface cap true
> alias selbetween ks ri
> buttonpanel Shortcuts rows 3 columns 4
> buttonpanel Shortcuts add "Vol. Viewer" command "tool show 'Volume Viewer'"
> buttonpanel Shortcuts add "Model Panel" command "tool show Models"
> buttonpanel Shortcuts add Log command "tool show Log"
> buttonpanel Shortcuts add "Default Disp." command default_mol_display
> buttonpanel Shortcuts add "Map Sphere" command map_sphere_15
> buttonpanel Shortcuts add "Map Unsphere" command map_unsphere
> buttonpanel Shortcuts add "Center On" command cofron
> buttonpanel Shortcuts add "Center Off" command cofroff
> buttonpanel Shortcuts add "Coot Mode" command cootmode
> buttonpanel Shortcuts add "Mark Center" command "marker #10000 position
> cofr"
> buttonpanel Shortcuts add "Hide Dust" command "surface dust all"
> buttonpanel Shortcuts add "Show Dust" command "surface undust all"
> buttonpanel Shortcuts add "Color Grey" command "sel; sel sel-residues; sel
> ~sel; color sel dark grey target s; ~sel"
> buttonpanel Shortcuts add "Morph Maps" command "color all cornflower
> blue;material dull;volume morph #1-20 playStep 0.08 frames 200
> constantVolume true"
> alias reset ~tile; view initial; view orient
UCSF ChimeraX version: 1.8.dev202403271703 (2024-03-27)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 ATI-5.5.17
OpenGL renderer: AMD Radeon Pro 570X 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: 6.6.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: iMac
Model Identifier: iMac19,1
Processor Name: 6-Core Intel Core i5
Processor Speed: 3 GHz
Number of Processors: 1
Total Number of Cores: 6
L2 Cache (per Core): 256 KB
L3 Cache: 9 MB
Memory: 64 GB
System Firmware Version: 2020.80.5.0.0
OS Loader Version: 580~1678
SMC Version (system): 2.46f13
Software:
System Software Overview:
System Version: macOS 14.4.1 (23E224)
Kernel Version: Darwin 23.4.0
Time since boot: 1 hour, 42 minutes
Graphics/Displays:
Radeon Pro 570X:
Chipset Model: Radeon Pro 570X
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 4 GB
Vendor: AMD (0x1002)
Device ID: 0x67df
Revision ID: 0x00c5
ROM Revision: 113-D0008A-042
VBIOS Version: 113-D0008A14GL-003
EFI Driver Version: 01.B1.042
Metal Support: Metal 2
Displays:
iMac:
Display Type: Built-In Retina LCD
Resolution: Retina 5K (5120 x 2880)
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.14.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.1.1
certifi: 2023.11.17
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.16
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.3
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.5
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.56
ChimeraX-AtomicLibrary: 14.0.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
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-Clipper: 0.23.0
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8.dev202403271703
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
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-ISOLDE: 1.8.dev0
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.9
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.1.4
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
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.15
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: 1.1
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.3
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: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.3
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: 1.0
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: 1.16.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2
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: 1.37.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
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: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.9
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.1
fonttools: 4.50.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.10.0
html2text: 2024.2.26
idna: 3.6
ihm: 0.43
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: 3.1.3
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: 5.1.0
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.3
matplotlib-inline: 0.1.6
msgpack: 1.0.8
ndindex: 1.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.2.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.9.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.3
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.2.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.0
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: 2.3.0
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3302
pyparsing: 3.1.2
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.2
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.2
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 25.1.2
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.12.0
setuptools: 69.2.0
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: 2.0.0
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: 0.6.1
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4
traitlets: 5.14.1
typing-extensions: 4.10.0
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 (4)
comment:1 by , 18 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash changing Mac display configuration |
comment:2 by , 18 months ago
Hi George,
Thanks for reporting this ChimeraX crash. We've seen several reports that look like yours and it appears from the C++ it might happen when you disconnect or connect an external display while running ChimeraX. Do you recall if you disconnected or connected an external display when ChimeraX was running before this crash? If not, is there anything else related to the display, like did you wake the display and then ChimeraX crashed?
This is a bug in the Qt 6.6 window toolkit that ChimeraX is hitting and we would like to figure out how to reproduce it so we can have the Qt project fix it.
Thanks,
Tom
comment:3 by , 17 months ago
I put an improved fix into the June 5 ChimeraX builds now on the download page for crashes related to connecting or disconnecting an external display.
comment:4 by , 12 months ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
This crash appears to be fixed by Qt 6.7 which has been in the ChimeraX daily builds for about 4 months.
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Reported by George Ghanim