![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 11 months ago
Closed 11 months ago
#16397 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-arm64-arm-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 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 0x00000001e698f840 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
File "/Applications/ChimeraX-1.8.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.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.surface._surface, chimerax.map._map, chimerax.pdb_lib._load_libs, 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, openmm._openmm, openmm.app.internal.compiled, 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, psutil._psutil_osx, psutil._psutil_posix, lxml._elementpath, lxml.etree, PIL._imagingmath (total: 63)
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{
"uptime" : 160000,
"procRole" : "Background",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "Mac14,14",
"coalitionID" : 37498,
"osVersion" : {
"train" : "macOS 15.1.1",
"build" : "24B91",
"releaseType" : "User"
},
"captureTime" : "2024-12-02 08:52:21.3262 -0500",
"codeSigningMonitor" : 1,
"incident" : "DFE7F041-2500-43F0-8CD7-90577CDAF0FC",
"pid" : 99507,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-12-01 23:51:20.2913 -0500",
"procStartAbsTime" : 3254336225762,
"procExitAbsTime" : 4033402048512,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"A4893B70-4CE1-5169-91F7-AB7D8DA1BBD0","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "8775FD83-8054-3B30-E02E-86F34B016EC7",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRcuD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkWfg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"bootSessionUUID" : "4B69F258-D8CA-4374-817A-D335A1DD3003",
"wakeTime" : 166832,
"sleepWakeUUID" : "3FEF8AF4-C7AA-43F3-AF35-49ED582A7AB8",
"sip" : "enabled",
"vmRegionInfo" : "0x6861a77fcbb8 is not in any region. Bytes after previous region: 9214978149305 \n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV \n---> \n UNUSED SPACE AT END",
"exception" : {"codes":"0x0000000000000001, 0x00006861a77fcbb8","rawCodes":[1,114768631286712],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00006861a77fcbb8"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":99507},
"vmregioninfo" : "0x6861a77fcbb8 is not in any region. Bytes after previous region: 9214978149305 \n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV \n---> \n UNUSED SPACE AT END",
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"faultingThread" : 0,
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"size" : 534452,
"uuid" : "6beafde4-b011-3e47-8aae-4d7b6e4bb7e8",
"path" : "\/usr\/lib\/dyld",
"name" : "dyld"
},
{
"size" : 0,
"source" : "A",
"base" : 0,
"uuid" : "00000000-0000-0000-0000-000000000000"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6467158016,
"size" : 581628,
"uuid" : "601f843f-71f1-30bb-88fb-55b131097d1d",
"path" : "\/usr\/lib\/libc++.1.dylib",
"name" : "libc++.1.dylib"
}
],
"sharedCache" : {
"base" : 6463602688,
"size" : 4753735680,
"uuid" : "f66bac4e-1e78-38af-b867-c1cf5daa0302"
},
"vmSummary" : "ReadOnly portion of Libraries: Total=1.7G resident=0K(0%) swapped_out_or_unallocated=1.7G(100%)\nWritable regions: Total=5.6G written=2682K(0%) resident=2682K(0%) swapped_out=0K(0%) unallocated=5.6G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 256K 2 \nActivity Tracing 256K 1 \nCG image 768K 40 \nColorSync 592K 31 \nCoreAnimation 2752K 160 \nCoreGraphics 48K 3 \nCoreServices 624K 2 \nCoreUI image data 5424K 41 \nFoundation 48K 2 \nKernel Alloc Once 32K 1 \nMALLOC 4.5G 207 \nMALLOC guard page 288K 18 \nMach message 64K 2 \nOpenGL GLSL 384K 4 \nSTACK GUARD 1168K 73 \nStack 174.0M 74 \nStack Guard 56.0M 1 \nVM_ALLOCATE 322.0M 224 \nVM_ALLOCATE (reserved) 608.0M 4 reserved VM address space (unallocated)\n__AUTH 3684K 489 \n__AUTH_CONST 53.6M 704 \n__CTF 824 1 \n__DATA 27.6M 879 \n__DATA_CONST 30.8M 893 \n__DATA_DIRTY 2000K 254 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__LINKEDIT 622.8M 185 \n__OBJC_RW 2354K 1 \n__TEXT 1.0G 910 \n__TPRO_CONST 272K 2 \ndyld private memory 48K 2 \nmapped file 592.2M 112 \nowned unmapped memory 82.8M 1 \npage table in kernel 2682K 1 \nshared memory 3744K 25 \n=========== ======= ======= \nTOTAL 8.0G 5351 \nTOTAL, minus reserved VM space 7.4G 5351 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"logWritingSignature" : "f0d2c1f9447108e388dab579e48f4e613728ce18",
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "6297d96be2c9387df974efa4",
"factorPackIds" : {
},
"deploymentId" : 240000032
},
{
"rolloutId" : "64c17a9925d75a7281053d4c",
"factorPackIds" : {
"SIRI_AUDIO_DISABLE_MEDIA_ENTITY_SYNC" : "64d29746ad29a465b3bbeace"
},
"deploymentId" : 240000001
}
],
"experiments" : [
{
"treatmentId" : "45f4e2a5-551b-4bc2-a2dc-19c244dda8f8",
"experimentId" : "6643969b3099cf28e049862f",
"deploymentId" : 400000007
}
]
}
}
===== Log before crash start =====
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/menmt0930/Downloads/aMSA_new_model.cxs
Opened postprocess_masked_sharpened.ccp4 as #2, grid size 320,320,320, pixel
1.03, shown at level 0.0117, step 1, values float32
Log from Sun Dec 1 18:10:16 2024 Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/menmt0930/Downloads/8-layers_strand.pdb
Chain information for 8-layers_strand.pdb #1
---
Chain | Description
A1 A2 A3 A4 A5 A6 A7 A8 | No description available
B1 B2 B3 B4 B5 B6 B7 B8 | No description available
C1 C2 C3 | No description available
C4 | No description available
C5 C6 C7 | No description available
C8 | No description available
> style stick
Changed 8396 atom styles
> hide cartoons
> show cartoons
> hide atoms
> argument: setattr res ss_type 0
Unknown command: argument: setattr res ss_type 0
> setattr res ss_type 0
Assigning ss_type attribute to 1245 items
> setattr /B1-B8:38-42, 44-46, 48-50, 52-55, 60-63, 69-71, 75-82, 90-92, 94-99
> res ss_type 2
Assigning ss_type attribute to 312 items
> setattr /A1-A8:15-17, 25-57, 32-34, 37-40, 43-45, 54-58, 62-65, 69-71,
> 76-79, 81-82, 87-92, 94-99 res ss_type 2
Assigning ss_type attribute to 496 items
> setattr /A1-A8 res ss_type 0
Assigning ss_type attribute to 696 items
> setattr /A1-A8:15-17, 25-27, 32-34, 37-40, 43-45, 54-58, 62-65, 69-71,
> 76-79, 81-82, 87-92, 94-99 res ss_type 2
Assigning ss_type attribute to 368 items
OpenType support missing for ".AppleSystemUIFont", script 10
> save /Users/menmt0930/Downloads/8-layers_strand.pdb relModel #1
> select /A1-A8
4664 atoms, 4680 bonds, 696 residues, 1 model selected
> color sel light sea green
> set bgColor white
> select clear
> select /B1-B8
3504 atoms, 3520 bonds, 504 residues, 1 model selected
> color sel hot pink
> select clear
> select /C1-C8
228 atoms, 220 bonds, 45 residues, 1 model selected
> color sel dim gray
> select clear
> save /Users/menmt0930/Downloads/8-layers_strand.pdb relModel #1
> close
> open /Users/menmt0930/Downloads/8-layers_strand.pdb format pdb
Chain information for 8-layers_strand.pdb #1
---
Chain | Description
A1 A2 A3 A4 A5 A6 A7 A8 | No description available
B1 B2 B3 B4 B5 B6 B7 B8 | No description available
C1 C2 C3 | No description available
C4 | No description available
C5 C6 C7 | No description available
C8 | No description available
> close
> open /Users/menmt0930/Downloads/8-layers_strand.pdb
Chain information for 8-layers_strand.pdb #1
---
Chain | Description
A1 A2 A3 A4 A5 A6 A7 A8 | No description available
B1 B2 B3 B4 B5 B6 B7 B8 | No description available
C1 C2 C3 | No description available
C4 | No description available
C5 C6 C7 | No description available
C8 | No description available
> style stick
Changed 8396 atom styles
> show cartoons
> hide atoms
> open
> /Volumes/masa6tb/phenix_Gabor/2/LocalAnisoSharpen_2/postprocess_masked_sharpened.ccp4
> format ccp4
Opened postprocess_masked_sharpened.ccp4 as #2, grid size 320,320,320, pixel
1.03, shown at level 0.000294, step 2, values float32
> volume #2 step 1
> volume #2 color #ffd479
> volume #2 color #ffd4791b
> volume #2 level 0.01368
> volume #2 color #ffd4794c
> volume #2 level 0.01166
> select /C1-C8
228 atoms, 220 bonds, 45 residues, 1 model selected
> color sel dim gray
> select /B1-B8
3504 atoms, 3520 bonds, 504 residues, 1 model selected
> color sel hot pink
> select /C1-C8
228 atoms, 220 bonds, 45 residues, 1 model selected
> select /C1-C8
228 atoms, 220 bonds, 45 residues, 1 model selected
> select /B1-B8
3504 atoms, 3520 bonds, 504 residues, 1 model selected
> select /A1-A8
4664 atoms, 4680 bonds, 696 residues, 1 model selected
> color sel cornflower blue
> select clear
> save /Users/menmt0930/Downloads/aMSA_new_model.cxs
——— End of log from Sun Dec 1 18:10:16 2024 ———
opened ChimeraX session
> hide #1 models
> set bgColor black
> view orient
> volume #2 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 164.8 tiltedSlabSpacing 1.03 tiltedSlabPlaneCount 10
> mousemode rightMode "rotate slab"
> volume #2 level -1.231e-05,0 level 0.0002941,0.8 level 0.06391,1
> volume #2 level -1.231e-05,0 level 0.01349,0.7559 level 0.06391,1
> volume #2 style surface
> volume #2 level 0.05
> volume #2 level 0.02
> volume #2 level 0.005
> volume #2 level 0.008
> volume #2 level 0.01
> volume #2 style image colorMode opaque8 orthoplanes xyz positionPlanes
> 159,159,159 imageMode orthoplanes
> volume #2 region 0,0,159,319,319,159 step 1 colorMode auto8 imageMode "full
> region"
> view orient
> volume #2 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 164.8 tiltedSlabSpacing 1.03 tiltedSlabPlaneCount 10
> mousemode rightMode "rotate slab"
> volume planes z style image imageMode "full region"
> mousemode rightMode "move planes"
> volume showOutlineBox false
> volume #2 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 164.8 tiltedSlabSpacing 1.03 tiltedSlabPlaneCount 10
> mousemode rightMode "rotate slab"
> ui mousemode right "move planes"
> volume #2 tiltedSlabOffset 139 tiltedSlabPlaneCount 10
> volume #2 tiltedSlabOffset 131.8 tiltedSlabPlaneCount 10
> volume #2 tiltedSlabOffset 140.1 tiltedSlabPlaneCount 10
> volume #2 tiltedSlabOffset 123.6 tiltedSlabPlaneCount 10
> volume #2 tiltedSlabOffset 152.4 tiltedSlabPlaneCount 10
> volume #2 level 0.002738,0.01471 level 0.01349,0.7559 level 0.06391,1
> volume #2 level 0.004,0.01471 level 0.01349,0.7559 level 0.06391,1
> volume #2 level 0.005,0.01471 level 0.01349,0.7559 level 0.06391,1
> volume #2 level 0.005,0.01471 level 0.01111,0.7706 level 0.06391,1
> volume #2 level 0.005,0.01471 level 0.05,0.7706 level 0.06391,1
> volume #2 style surface
> volume #2 style image tiltedSlabOffset 131.3 tiltedSlabSpacing 1.03
> tiltedSlabPlaneCount 64
> volume #2 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 164.8 tiltedSlabSpacing 1.03 tiltedSlabPlaneCount 10
> mousemode rightMode "rotate slab"
> ui mousemode right "move planes"
> volume planes z style image imageMode "full region"
> mousemode rightMode "move planes"
> volume #2 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 164.8 tiltedSlabSpacing 1.03 tiltedSlabPlaneCount 10
> mousemode rightMode "rotate slab"
> ui mousemode right "move planes"
> volume #2 tiltedSlabOffset 164.8 tiltedSlabPlaneCount 10
> volume #2 tiltedSlabOffset 150.4 tiltedSlabPlaneCount 10
> volume #2 level 0.005,0.01471 level 0.004,0.7706 level 0.06391,1
> volume #2 level 0.005,0.01471 level 0.003633,0.3882 level 0.06391,1
> volume #2 level 0.007383,0.8971 level 0.003633,0.3882 level 0.06391,1
> volume #2 level 0.007383,0.8971 level 0.00235,0.06471 level 0.06391,1
> volume #2 level 0.007383,0.8971 level 0.004,0.06471 level 0.06391,1
> volume #2 level 0.01,0.8971 level 0.004,0.06471 level 0.06391,1
> volume #2 level 0.015,0.8971 level 0.004,0.06471 level 0.06391,1
> volume #2 level 0.013,0.8971 level 0.004,0.06471 level 0.06391,1
> volume #2 level 0.012,0.8971 level 0.004,0.06471 level 0.06391,1
> volume #2 level 0.012,0.8971 level 0.003,0.06471 level 0.06391,1
> volume #2 level 0.012,0.8971 level 0.002,0.06471 level 0.06391,1
> volume #2 level 0.012,0.8971 level 0.004,0.06471 level 0.06391,1
> volume #2 level 0.012,0.8971 level 0.005,0.06471 level 0.06391,1
> turn x 90
> volume #2 tiltedSlabOffset 150.4 tiltedSlabPlaneCount 10
> ui mousemode right "move planes"
> view orient
> volume #2 tiltedSlabOffset 155.5 tiltedSlabPlaneCount 10
OpenType support missing for ".AppleSystemUIFont", script 10
> turn x 90
> volume #2 level 0.01,0.8971 level 0.005,0.06471 level 0.06391,1
> volume #2 level 0.015,0.8971 level 0.005,0.06471 level 0.06391,1
> volume #2 level 0.014,0.8971 level 0.005,0.06471 level 0.06391,1
> volume #2 level 0.013,0.8971 level 0.005,0.06471 level 0.06391,1
> volume #2 level 0.012,0.8971 level 0.005,0.06471 level 0.06391,1
> volume #2 level 0.01,0.8971 level 0.005,0.06471 level 0.06391,1
> volume #2 level 0.0125,0.8971 level 0.005,0.06471 level 0.06391,1
> save /Users/menmt0930/Downloads/cross-section.png width 1032 height 898
> supersample 3
> hide #!2 models
> show #1 models
> hide #1 models
> show #!2 models
> volume #2 style surface
> close #2
> open /Users/menmt0930/Downloads/3-2.mrc
Opened 3-2.mrc as #2, grid size 320,320,320, pixel 1.03, shown at level
6.71e-06, step 2, values float32
> volume #2 step 1
> volume #2 level 0.005908
> volume #2 level 0.006374
> show #1 models
> select /A3, B3, C3
1057 atoms, 1060 bonds, 157 residues, 1 model selected
> select ~sel & ##selected
7339 atoms, 7360 bonds, 1088 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> close #1
> open /Users/menmt0930/Downloads/8-layers_strand.pdb
Chain information for 8-layers_strand.pdb #1
---
Chain | Description
A1 A2 A3 A4 A5 A6 A7 A8 | No description available
B1 B2 B3 B4 B5 B6 B7 B8 | No description available
C1 C2 C3 | No description available
C4 | No description available
C5 C6 C7 | No description available
C8 | No description available
> select /A4, B4, C4
1051 atoms, 1054 bonds, 156 residues, 1 model selected
> select ~sel & ##selected
7345 atoms, 7366 bonds, 1089 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> style stick
Changed 1051 atom styles
> show atoms
> volume #2 color #b2b2b24f
> volume #2 level 0.005442
> volume #2 level 0.00715
> volume #2 level 0.005753
> close #2
> open /Users/menmt0930/Downloads/aMSA_new_model.cxs
Opened postprocess_masked_sharpened.ccp4 as #2, grid size 320,320,320, pixel
1.03, shown at level 0.0117, step 1, values float32
opened ChimeraX session
> ui tool show "Side View"
> hide #1 models
> volume #2 level 0.01038
> volume #2 level 0.01
> volume #2 level 0.01128
> open
> /Users/menmt0930/mnt/masa20tb4/Relion/atypical_msa_tcortex/LocalRes/job1225/relion_locres.mrc
> format mrc
Opened relion_locres.mrc as #3, grid size 320,320,320, pixel 1.03, shown at
level 23.5, step 2, values float32
> ui tool show "Surface Color"
> key red-white-blue :0.0 :0.5 :1.0 showTool true
> ui mousemode right "color key"
> key red-white-blue :0.0 :0.5 :1.0 white:
> key red:0.0 white:0.5 blue:1.0 white: white:
> key white: white: blue:1.0 white:0.5 red:0.0
> key red:0.0 white:0.5 blue:1.0 white: white:
> ui mousemode right "move planes"
> color sample #2.1 map #3 palette
> 3,#0000ff:3.2,#00ffff:3.4,#00ff00:3.6,#ffff00:3.8,#ff0000
Map values for surface "surface": minimum 3.082, mean 3.333, maximum 5.28
Map values for surface "cap far": minimum 3.133, mean 3.36, maximum 4.736
Map values for surface "cap near": minimum 3.133, mean 3.362, maximum 5.121
> color sample #2.1 map #3 palette
> 3,#0000ff:3.2,#00ffff:3.4,#00ff00:3.6,#ffff00:3.8,#ff0000
Map values for surface "surface": minimum 3.082, mean 3.333, maximum 5.28
Map values for surface "cap far": minimum 3.133, mean 3.36, maximum 4.736
Map values for surface "cap near": minimum 3.133, mean 3.362, maximum 5.121
> key rainbow :3.0 :3.2 :3.4 :3.6 :3.8 showTool true
> ui mousemode right "color key"
> ui mousemode right "move planes"
> color sample #2.1 map #3 palette
> 3.1,#0000ff:3.2,#00ffff:3.4,#00ff00:3.6,#ffff00:3.8,#ff0000
Map values for surface "surface": minimum 3.082, mean 3.333, maximum 5.28
Map values for surface "cap far": minimum 3.133, mean 3.36, maximum 4.736
Map values for surface "cap near": minimum 3.133, mean 3.362, maximum 5.121
> color sample #2.1 map #3 palette
> 3.1,#0000ff:3.2,#00ffff:3.4,#00ff00:3.6,#ffff00:3.9,#ff0000
Map values for surface "surface": minimum 3.082, mean 3.333, maximum 5.28
Map values for surface "cap far": minimum 3.133, mean 3.36, maximum 4.736
Map values for surface "cap near": minimum 3.133, mean 3.362, maximum 5.121
> color sample #2.1 map #3 palette
> 3.1,#0000ff:3.2,#00ffff:3.3,#00ff00:3.4,#ffff00:3.5,#ff0000
Map values for surface "surface": minimum 3.082, mean 3.333, maximum 5.28
Map values for surface "cap far": minimum 3.133, mean 3.36, maximum 4.736
Map values for surface "cap near": minimum 3.133, mean 3.362, maximum 5.121
> volume #2 level 0.01223
> volume #2 level 0.009396
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #!3 models
> show #!3 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> volume #2 level 0.008829
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> color sample #2.1 map #3 palette #0000ff:#00ffff:#00ff00:#ffff00:#ff0000
Map values for surface "surface": minimum 3.081, mean 3.384, maximum 5.797
Map values for surface "cap far": minimum 3.133, mean 3.416, maximum 5.035
Map values for surface "cap near": minimum 3.133, mean 3.416, maximum 5.278
> color sample #2.1 map #3 palette
> 3.1,#0000ff:3.3,#00ffff:3.5,#00ff00:3.7,#ffff00:3.9,#ff0000
Map values for surface "surface": minimum 3.081, mean 3.384, maximum 5.797
Map values for surface "cap far": minimum 3.133, mean 3.416, maximum 5.035
Map values for surface "cap near": minimum 3.133, mean 3.416, maximum 5.278
> key rainbow :3.1 :3.3 :3.5 :3.7 :3.9 showTool true
> ui mousemode right "color key"
> volume #2 level 0.009585
> view orient
> turn x 90
> color sample #2.1 map #3 palette #0000ff:#00ffff:#00ff00:#ffff00:#ff0000
Map values for surface "surface": minimum 3.082, mean 3.365, maximum 5.762
> hide #1 models
> color sample #2.1 map #3 palette
> 3.1,#0000ff:3.3,#00ffff:3.5,#00ff00:3.7,#ffff00:3.9,#ff0000
Map values for surface "surface": minimum 3.082, mean 3.365, maximum 5.762
> key rainbow :3.1 :3.3 :3.5 :3.7 :3.9 showTool true
> view orient
> turn x 90
> color sample #2.1 map #3 palette #0000ff:#00ffff:#00ff00:#ffff00:#ff0000
Map values for surface "surface": minimum 3.082, mean 3.365, maximum 5.762
> color sample #2.1 map #3 palette
> 3.1,#0000ff:3.3,#00ffff:3.5,#00ff00:3.7,#ffff00:3.9,#ff0000
Map values for surface "surface": minimum 3.082, mean 3.365, maximum 5.762
> hide #!3 models
> ui tool show "Side View"
> hide #!2 models
> show #!2 models
> hide #4 models
> show #4 models
> ui tool show "Side View"
> view
> ui tool show "Side View"
> lighting soft
> lighting simple
> lighting soft
> lighting full
> lighting soft
> lighting simple
> lighting soft
> lighting simple
> turn x 90
> ui tool show "Side View"
> view orient
> turn x 90
> color sample #2.1 map #3 palette
> 3.1,#0000ff:3.3,#00ffff:3.5,#00ff00:3.7,#ffff00:3.9,#ff0000
Map values for surface "surface": minimum 3.082, mean 3.365, maximum 5.762
Map values for surface "cap far": minimum 3.13, mean 3.353, maximum 4.166
Map values for surface "cap near": minimum 3.133, mean 3.34, maximum 4.438
> volume #2 level 0.01147
> volume #2 level 0.01223
> volume #2 level 0.009962
> volume #2 level 0.01
> volume #2 level 0.011
> volume #2 level 0.01
> key rainbow :3.1 :3.3 :3.5 :3.7 :3.9 showTool true
> key size 0.2,0.05000
> key size 0.0000,0.05000
> key size 0.00000,0.05000
> key size 0.00000,0.5000
> key size 0.00000,0.0000
> key size 0.00000,0.2
> key size 0.00000,0.21000
> key size 0.00000,0.22000
> key size 0.00000,0.23000
> key size 0.00000,0.24000
> key size 0.00000,0.25000
> key size 0.01000,0.25000
> key size 0.02000,0.25000
> key size 0.03000,0.25000
> key size 0.04000,0.25000
> key size 0.05000,0.25000
> key pos 0.71000,0.08000
> key pos 0.72000,0.08000
> key pos 0.73000,0.08000
> key pos 0.74000,0.08000
> key pos 0.75000,0.08000
> key pos 0.76000,0.08000
> key pos 0.77000,0.08000
> key pos 0.78000,0.08000
> key pos 0.79000,0.08000
> key pos 0.80000,0.08000
> key pos 0.81000,0.08000
> key pos 0.82000,0.08000
> key pos 0.83000,0.08000
> key pos 0.84000,0.08000
> key pos 0.83000,0.08000
> key pos 0.83000,0.07000
> key pos 0.83000,0.08000
> key pos 0.83000,0.09000
> key pos 0.83000,0.10000
> key pos 0.83000,0.11000
> key pos 0.83000,0.12000
> key pos 0.83000,0.13000
> key pos 0.83000,0.14000
> key pos 0.83000,0.15000
> key pos 0.83000,0.16000
> key pos 0.83000,0.17000
> key pos 0.83000,0.18000
> key pos 0.83000,0.19000
> key pos 0.83000,0.20000
> key pos 0.83000,0.21000
> key pos 0.83000,0.22000
> key pos 0.83000,0.23000
> key pos 0.83000,0.24000
> key pos 0.83000,0.25000
> key pos 0.83000,0.26000
> save "/Users/menmt0930/Downloads/local resolution.cxs"
> save "/Users/menmt0930/Downloads/local resolution.png" width 897 height 782
> supersample 3 transparentBackground true
> key rainbow :3.1 :3.3 :3.5 :3.7 :3.9 showTool true
> key size 0.05000,0.24000
> key size 0.05000,0.25000
> key size 0.04000,0.25000
> key size 0.03000,0.25000
> key size 0.02000,0.25000
> key size 0.03000,0.25000
> key fontSize 23
> key fontSize 22
> key fontSize 21
> key fontSize 20
> key fontSize 19
> key fontSize 18
> key fontSize 17
> key fontSize 16
> key fontSize 15
> key fontSize 14
> key fontSize 15
> key fontSize 16
> save "/Users/menmt0930/Downloads/local resolution.png" width 897 height 782
> supersample 3
> save "/Users/menmt0930/Downloads/local resolution.cxs"
> save "/Users/menmt0930/Downloads/local resolution.png" width 897 height 782
> supersample 3 transparentBackground true
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/menmt0930/Downloads/8-layers_strand_copy.pdb
Chain information for 8-layers_strand_copy.pdb #1
---
Chain | Description
A1 A2 A3 A4 A5 A6 A7 A8 | No description available
B1 B2 B3 B4 B5 B6 B7 B8 | No description available
C1 C2 C3 | No description available
C4 | No description available
C5 C6 C7 | No description available
C8 | No description available
OpenGL version: 4.1 Metal - 89.3
OpenGL renderer: Apple M2 Ultra
OpenGL vendor: Apple
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: Mac Studio
Model Identifier: Mac14,14
Model Number: Z18000049VC/A
Chip: Apple M2 Ultra
Total Number of Cores: 24 (16 performance and 8 efficiency)
Memory: 128 GB
System Firmware Version: 11881.41.5
OS Loader Version: 11881.41.5
Software:
System Software Overview:
System Version: macOS 15.1.1 (24B91)
Kernel Version: Darwin 24.1.0
Time since boot: 1 day, 23 hours, 48 minutes
Graphics/Displays:
Apple M2 Ultra:
Chipset Model: Apple M2 Ultra
Type: GPU
Bus: Built-In
Total Number of Cores: 76
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
DELL S2721QS:
Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
DELL S2721QS:
Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
UI Looks like: 1920 x 1080 @ 30.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
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: 1.6.4
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: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
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: 1.2.7
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: 0.23.1
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: 1.8
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-ISOLDE: 1.8
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: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
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: 1.13.5
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: 3.0.15
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: 1.4.3
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: 4.53.0
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: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
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: 3.0.47
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: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
Change History (2)
comment:1 by , 11 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 , 11 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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