![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 8 months ago
Closed 8 months ago
#17095 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-14.7.3-x86_64-i386-64bit
ChimeraX Version: 1.8.dev202404140648 (2024-04-14 06:48:11 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 0x00007ff851f41fc0 (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 283 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 1006 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 1169 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, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, 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, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imagingmath (total: 53)
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{
"uptime" : 190000,
"procRole" : "Background",
"version" : 2,
"userID" : 503,
"deployVersion" : 210,
"modelCode" : "MacBookPro16,2",
"coalitionID" : 5148,
"osVersion" : {
"train" : "macOS 14.7.3",
"build" : "23H417",
"releaseType" : "User"
},
"captureTime" : "2025-03-13 22:23:41.0943 +0000",
"codeSigningMonitor" : 0,
"incident" : "7D27E50C-7FFE-4156-9CDD-1DAE81B10616",
"pid" : 7355,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-03-13 14:14:09.1544 +0000",
"procStartAbsTime" : 185126265281979,
"procExitAbsTime" : 196441457629992,
"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":"7FF298D8-9CAA-50B0-B14E-B75862530066","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "29B489BC-839B-868D-A960-82E747B97847",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"wakeTime" : 2536,
"bridgeVersion" : {"build":"22P3051","train":"9.3"},
"sleepWakeUUID" : "741B8EB3-03A2-4A61-89EE-64F990F95457",
"sip" : "enabled",
"vmRegionInfo" : "0 is not in any region. Bytes before following region: 4557934592\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10fac9000-10facd000 [ 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":7355},
"ktriageinfo" : "VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n",
"vmregioninfo" : "0 is not in any region. Bytes before following region: 4557934592\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10fac9000-10facd000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
"threads" : 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"arch" : "x86_64",
"base" : 140703373131776,
"size" : 503796,
"uuid" : "acdb3afe-f896-313c-8d5b-2b2810639d29",
"path" : "\/usr\/lib\/libc++.1.dylib",
"name" : "libc++.1.dylib"
}
],
"sharedCache" : {
"base" : 140703369551872,
"size" : 25769803776,
"uuid" : "591fd48a-5a0e-30ca-8302-8813b921751d"
},
"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 384K 3 \nActivity Tracing 256K 1 \nCG image 896K 49 \nCG raster data 8K 1 \nColorSync 268K 34 \nCoreAnimation 1852K 212 \nCoreGraphics 20K 4 \nCoreImage 12K 1 \nCoreUI image data 5292K 60 \nFoundation 36K 2 \nIOKit 15.5M 2 \nKernel Alloc Once 8K 1 \nMALLOC 1.9G 7252 \nMALLOC guard page 32K 8 \nMALLOC_LARGE (reserved) 256K 1 reserved VM address space (unallocated)\nMach message 16K 2 \nOpenGL GLSL 384K 4 \nSTACK GUARD 140K 35 \nStack 160.8M 36 \nStack Guard 56.0M 1 \nVM_ALLOCATE 344.6M 258 \nVM_ALLOCATE (reserved) 32.0M 1 reserved VM address space (unallocated)\n__CTF 824 1 \n__DATA 44.8M 784 \n__DATA_CONST 53.2M 458 \n__DATA_DIRTY 1841K 229 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 210.8M 148 \n__OBJC_RO 71.9M 1 \n__OBJC_RW 2201K 2 \n__TEXT 1.0G 792 \ndyld private memory 32K 2 \nmapped file 254.2M 80 \nshared memory 3516K 32 \n=========== ======= ======= \nTOTAL 4.2G 10500 \nTOTAL, minus reserved VM space 4.2G 10500 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"logWritingSignature" : "5bf87bef3faa28f255cd783d56a19b3ea480104d",
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "6297d96be2c9387df974efa4",
"factorPackIds" : {
},
"deploymentId" : 240000032
},
{
"rolloutId" : "61675b89201f677a9a4cbd65",
"factorPackIds" : {
"HEALTH_FEATURE_AVAILABILITY" : "65a855f5f087695cfac03d1f"
},
"deploymentId" : 240000170
}
],
"experiments" : [
]
}
}
===== Log before crash start =====
UCSF ChimeraX version: 1.8.dev202404140648 (2024-04-14)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/chitrajoshi/Desktop/SLCO2A1/structure/Publication/Refined
> structures/Zafirlukast/RealSpaceRefine_30/ZLK_real_space_refined_030.pdb"
Chain information for ZLK_real_space_refined_030.pdb #1
---
Chain | Description
A | No description available
4 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> open /Users/chitrajoshi/Downloads/cryosparc_P79_J77_008_volume_map.mrc
Opened cryosparc_P79_J77_008_volume_map.mrc as #2, grid size 300,300,300,
pixel 0.832, shown at level 0.126, step 2, values float32
> open /Users/chitrajoshi/Downloads/cryosparc_P79_J77_008_volume_map_sharp.mrc
Opened cryosparc_P79_J77_008_volume_map_sharp.mrc as #3, grid size
300,300,300, pixel 0.832, shown at level 0.179, step 2, values float32
> hide #!2 models
> hide #!1 models
> volume #2 step 1
> volume #3 step 1
> volume flip #2
Opened cryosparc_P79_J77_008_volume_map.mrc z flip as #4, grid size
300,300,300, pixel 0.832, shown at step 1, values float32
> volume flip #3
Opened cryosparc_P79_J77_008_volume_map_sharp.mrc z flip as #5, grid size
300,300,300, pixel 0.832, shown at step 1, values float32
> hide #!5 models
> hide #!4 models
> show #!1 models
> show #!4 models
> fitmap #1 inMap #4
Fit molecule ZLK_real_space_refined_030.pdb (#1) to map
cryosparc_P79_J77_008_volume_map.mrc z flip (#4) using 4423 atoms
average map value = 0.4756, steps = 48
shifted from previous position = 0.0369
rotated from previous position = 0.0899 degrees
atoms outside contour = 246, contour level = 0.12556
Position of ZLK_real_space_refined_030.pdb (#1) relative to
cryosparc_P79_J77_008_volume_map.mrc z flip (#4) coordinates:
Matrix rotation and translation
0.99999927 0.00025238 -0.00118398 0.10273886
-0.00025120 0.99999947 0.00099888 -0.12661938
0.00118423 -0.00099858 0.99999880 -0.00509267
Axis -0.63638415 -0.75450343 -0.16043621
Axis point 0.20939609 -0.00000000 103.42033301
Rotation angle (degrees) 0.08991926
Shift along axis 0.03097042
> volume #4 level 0.2721
> volume #4 level 0.1842
> hide #!4 models
> show #!5 models
> fitmap #1 inMap #5
Fit molecule ZLK_real_space_refined_030.pdb (#1) to map
cryosparc_P79_J77_008_volume_map_sharp.mrc z flip (#5) using 4423 atoms
average map value = 1.349, steps = 36
shifted from previous position = 0.0218
rotated from previous position = 0.029 degrees
atoms outside contour = 378, contour level = 0.17926
Position of ZLK_real_space_refined_030.pdb (#1) relative to
cryosparc_P79_J77_008_volume_map_sharp.mrc z flip (#5) coordinates:
Matrix rotation and translation
0.99999920 0.00067357 -0.00107213 0.03793616
-0.00067278 0.99999950 0.00074320 -0.02353566
0.00107264 -0.00074248 0.99999915 -0.01543709
Axis -0.50602529 -0.73051414 -0.45857116
Axis point 12.25185238 0.00000000 37.77011672
Rotation angle (degrees) 0.08410947
Shift along axis 0.00507548
> volume #5 level 0.5874
> color #5 #4ba1a7ff models
> color #5 #4ca4aeff models
> surface dust #5 size 8.32
> volume #5 level 0.4304
> open "/Users/chitrajoshi/Desktop/SLCO2A1/structure/Publication/Refined
> structures/Zafirlukast/cryosparc_P79_J69_flipped.mrc"
Opened cryosparc_P79_J69_flipped.mrc as #6, grid size 300,300,300, pixel
0.832, shown at level 0.126, step 2, values float32
> open "/Users/chitrajoshi/Desktop/SLCO2A1/structure/Publication/Refined
> structures/Zafirlukast/cryosparc_P79_J69_flipped_sharp.mrc"
Opened cryosparc_P79_J69_flipped_sharp.mrc as #7, grid size 300,300,300, pixel
0.832, shown at level 0.171, step 2, values float32
> open /Users/chitrajoshi/Downloads/cryosparc_P79_J79_008_volume_map_sharp.mrc
Opened cryosparc_P79_J79_008_volume_map_sharp.mrc as #8, grid size
300,300,300, pixel 0.832, shown at level 0.178, step 2, values float32
> open /Users/chitrajoshi/Downloads/cryosparc_P79_J79_008_volume_map.mrc
Opened cryosparc_P79_J79_008_volume_map.mrc as #9, grid size 300,300,300,
pixel 0.832, shown at level 0.126, step 2, values float32
> hide #!5 models
> hide #!6 models
> hide #!7 models
> hide #!8 models
> hide #!9 models
> volume flip #8
Opened cryosparc_P79_J79_008_volume_map_sharp.mrc z flip as #10, grid size
300,300,300, pixel 0.832, shown at step 1, values float32
> volume flip #9
Opened cryosparc_P79_J79_008_volume_map.mrc z flip as #11, grid size
300,300,300, pixel 0.832, shown at step 1, values float32
> hide #!10 models
> hide #!11 models
> open /Users/chitrajoshi/Downloads/cryosparc_P79_J83_map_sharp.mrc
Opened cryosparc_P79_J83_map_sharp.mrc as #12, grid size 300,300,300, pixel
0.832, shown at level 0.177, step 2, values float32
> volume flip #12
Opened cryosparc_P79_J83_map_sharp.mrc z flip as #13, grid size 300,300,300,
pixel 0.832, shown at step 1, values float32
> volume #12 step 1
> volume #13 level 0.4443
> surface dust #13 size 8.32
> volume #13 level 0.7446
> show #!7 models
> hide #!13 models
> close #2
> close #3
> close #8
> close #9
> close #12
> volume #7 step 1
> volume #7 level 0.3514
> surface dust #7 size 8.32
> volume #7 level 0.4568
> surface dust #7 size 8.32
> volume #7 level 0.4869
> show #!13 models
> volume #13 level 0.487
> transparency #7.1#13.1 50
> volume #!7,13 style surface
> transparency #7.1#13.1 0
> show #!5 models
> volume #5 level 0.487
> hide #!7 models
> hide #!13 models
> hide #!5 models
> show #!7 models
> hide #!7 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!1 models
> show #!5 models
> hide #!13 models
> show #!13 models
> hide #!5 models
> show #!5 models
> hide #!13 models
> show #!13 models
> hide #!5 models
> show #!5 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> hide #!5 models
> show #!5 models
> show #!13 models
> hide #!5 models
> show #!7 models
> hide #!13 models
> show #!13 models
> hide #!7 models
> show #!7 models
> hide #!13 models
> show #!13 models
> hide #!7 models
> show #!7 models
> hide #!13 models
> show #!5 models
> hide #!7 models
> hide #!5 models
> show #!5 models
> show #!7 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> show #!1 models
> volume #5 level 0.7382
> hide #!7 models
> select add #1
4423 atoms, 4545 bonds, 2 pseudobonds, 566 residues, 2 models selected
> show sel atoms
> select subtract #1
Nothing selected
> select add #5
2 models selected
> transparency sel 50
> select subtract #5
Nothing selected
> set bgColor white
> show #!7 models
> hide #!5 models
> transparency #7.1 50
> volume #7 level 0.738
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!13 models
> volume #13 level 0.738
> volume #!5,13 showOutlineBox true
> volume #!5,13 showOutlineBox false
> transparency #5.1#13.1 0
> hide #!5 models
> transparency #13.1 50
> show #!5 models
> hide #!13 models
> transparency #5.1 50
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> hide #!5 models
> show #!11 models
> volume #11 level 0.738
> volume #11 level 0.17
> show #!10 models
> hide #!11 models
> volume #10 level 0.738
> transparency #10.1 50
> surface dust #10 size 8.32
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> hide #!10 models
> show #!4 models
> hide #!1 models
> hide #!4 models
> show #!6 models
> volume #6 step 1
> volume #6 level 0.1579
> hide #!6 models
> show #!4 models
> save "/Users/chitrajoshi/Desktop/SLCO2A1/structure/Publication/Refined
> structures/Zafirlukast/cryosparc_P79_J77_flipped.mrc" models #4
> save "/Users/chitrajoshi/Desktop/SLCO2A1/structure/Publication/Refined
> structures/Zafirlukast/cryosparc_P79_J77_flipped_sharp.mrc" models #5
> open
> /Users/chitrajoshi/Downloads/J77_viewing_direction_distribution_iteration_008.bild.bild
Opened BILD data containing 3072 objects
> hide #!4 models
> hide #2 models
> show #2 models
> save "/Users/chitrajoshi/Desktop/SLCO2A1/structure/Publication/Refined
> structures/Zafirlukast/Viewing direction .png" width 875 height 670
> supersample 4 transparentBackground true
> open /Users/chitrajoshi/Downloads/cryosparc_P79_J53_005_volume_map.mrc
Opened cryosparc_P79_J53_005_volume_map.mrc as #3, grid size 300,300,300,
pixel 0.832, shown at level 0.124, step 2, values float32
> hide #2 models
> volume flip #3
Opened cryosparc_P79_J53_005_volume_map.mrc z flip as #8, grid size
300,300,300, pixel 0.832, shown at step 1, values float32
> show #!4 models
> volume #4 level 0.124
> hide #!8 models
> hide #!4 models
> show #!8 models
> open /Users/chitrajoshi/Downloads/cryosparc_P79_J54_005_volume_map.mrc
Opened cryosparc_P79_J54_005_volume_map.mrc as #9, grid size 300,300,300,
pixel 0.832, shown at level 0.125, step 2, values float32
> open /Users/chitrajoshi/Downloads/cryosparc_P79_J55_005_volume_map.mrc
Opened cryosparc_P79_J55_005_volume_map.mrc as #12, grid size 300,300,300,
pixel 0.832, shown at level 0.128, step 2, values float32
> hide #!8 models
> hide #!9 models
> volume flip #9
Opened cryosparc_P79_J54_005_volume_map.mrc z flip as #14, grid size
300,300,300, pixel 0.832, shown at step 1, values float32
> volume flip #12
Opened cryosparc_P79_J55_005_volume_map.mrc z flip as #15, grid size
300,300,300, pixel 0.832, shown at step 1, values float32
> hide #!14 models
> hide #!15 models
> show #!14 models
> volume #14 level 0.1911
> show #!15 models
> hide #!14 models
> volume #15 level 0.2165
> volume #15 level 0.191
> show #!14 models
> hide #!15 models
> show #!15 models
> hide #!14 models
> show #!8 models
> hide #!15 models
> volume #8 level 0.191
> color #8 #bb94e4ff models
> show #!14 models
> hide #!8 models
> show #!8 models
> hide #!14 models
> ui tool show "Side View"
> show #!1 models
> fitmap #1 inMap #8
Fit molecule ZLK_real_space_refined_030.pdb (#1) to map
cryosparc_P79_J53_005_volume_map.mrc z flip (#8) using 4423 atoms
average map value = 0.4629, steps = 56
shifted from previous position = 0.0871
rotated from previous position = 0.262 degrees
atoms outside contour = 676, contour level = 0.191
Position of ZLK_real_space_refined_030.pdb (#1) relative to
cryosparc_P79_J53_005_volume_map.mrc z flip (#8) coordinates:
Matrix rotation and translation
0.99999660 -0.00155001 0.00209632 -0.00703026
0.00155355 0.99999736 -0.00169207 -0.03126690
-0.00209369 0.00169532 0.99999637 0.01623145
Axis 0.54477779 0.67385937 0.49912995
Axis point 11.75880681 0.00000000 -0.99262390
Rotation angle (degrees) 0.17813112
Shift along axis -0.01679782
> volume #8 level 0.147
> volume #8 level 0.191
> show #!14 models
> hide #!8 models
> transparency #14.1 50
> transparency #14.1 0
> transparency #14.1 50
> show #!15 models
> hide #!14 models
> hide #!15 models
> view
> open /Users/chitrajoshi/Downloads/cryosparc_P79_J86_009_volume_map.mrc
Opened cryosparc_P79_J86_009_volume_map.mrc as #16, grid size 300,300,300,
pixel 0.832, shown at level 0.125, step 2, values float32
> fitmap #1 inMap #16
Fit molecule ZLK_real_space_refined_030.pdb (#1) to map
cryosparc_P79_J86_009_volume_map.mrc (#16) using 4423 atoms
average map value = 0.1465, steps = 112
shifted from previous position = 4.44
rotated from previous position = 5.64 degrees
atoms outside contour = 2548, contour level = 0.12542
Position of ZLK_real_space_refined_030.pdb (#1) relative to
cryosparc_P79_J86_009_volume_map.mrc (#16) coordinates:
Matrix rotation and translation
0.99918952 -0.00977414 0.03904841 -3.31706085
0.00625660 0.99599333 0.08920838 -11.15167491
-0.03976389 -0.08889177 0.99524725 21.27474748
Axis -0.91138249 0.40330200 0.08203325
Axis point 0.00000000 231.77742478 136.64149053
Rotation angle (degrees) 5.60724729
Shift along axis 0.27085505
> volume flip #16
Opened cryosparc_P79_J86_009_volume_map.mrc z flip as #17, grid size
300,300,300, pixel 0.832, shown at step 1, values float32
> fitmap #1 inMap #17
Fit molecule ZLK_real_space_refined_030.pdb (#1) to map
cryosparc_P79_J86_009_volume_map.mrc z flip (#17) using 4423 atoms
average map value = 0.4833, steps = 84
shifted from previous position = 4.45
rotated from previous position = 5.66 degrees
atoms outside contour = 239, contour level = 0.12542
Position of ZLK_real_space_refined_030.pdb (#1) relative to
cryosparc_P79_J86_009_volume_map.mrc z flip (#17) coordinates:
Matrix rotation and translation
0.99999274 -0.00369430 0.00093440 0.39428453
0.00369592 0.99999166 -0.00174015 -0.27641056
-0.00092796 0.00174359 0.99999805 -0.14486100
Axis 0.41573313 0.22224517 0.88191442
Axis point 73.51562359 109.42701444 0.00000000
Rotation angle (degrees) 0.24006262
Shift along axis -0.02526878
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #16 step 1
> close #16
> volume #17 level 0.2421
> surface dust #17 size 8.32
> volume #17 level 0.197
> hide #!17 models
> show #!5 models
> volume #5 level 0.197
> show #!6 models
> hide #!5 models
> volume #6 level 0.197
> hide #!6 models
> show #!17 models
> hide #!17 models
> show #!6 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> open
> /Users/chitrajoshi/Downloads/J86_viewing_direction_distribution_iteration_009.bild.bild
Opened BILD data containing 3072 objects
> hide #!6 models
> hide #!1 models
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.8.dev202404140648 (2024-04-14)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
Compositor returned null texture
OpenGL version: 4.1 INTEL-22.5.12
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine
OpenGL vendor: Intel 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: MacBookPro16,2
Processor Name: Quad-Core Intel Core i5
Processor Speed: 2 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 512 KB
L3 Cache: 6 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 2069.80.3.0.0 (iBridge: 22.16.13051.0.0,0)
OS Loader Version: 580.140.1~51
Software:
System Software Overview:
System Version: macOS 14.7.3 (23H417)
Kernel Version: Darwin 23.6.0
Time since boot: 11 days, 1 hour, 35 minutes
Graphics/Displays:
Intel Iris Plus Graphics:
Chipset Model: Intel Iris Plus Graphics
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x8a53
Revision ID: 0x0007
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
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: 1.2.1
certifi: 2023.11.17
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.16
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
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: 1.56.1
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-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.dev202404140648
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-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: 1.2
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
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: 1.5.15
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: 1.13.4
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: 2.1
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: 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: 1.37.2
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4
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: 1.1.3
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: 3.13.3
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: 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: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.6
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.0.1
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: 4.2.0
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: 6.6.3
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: 25.1.2
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
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: 0.6.3
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 , 8 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 , 8 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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