![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 8 months ago
Closed 8 months ago
#17045 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-15.3.1-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX.
Fatal Python error: Segmentation fault
Current thread 0x00000001fe470840 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, chimerax.pdb_lib._load_libs, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, 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, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, PIL._imagingmath, psutil._psutil_osx, psutil._psutil_posix, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets (total: 57)
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{
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"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac15,12",
"coalitionID" : 15207,
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"build" : "24D70",
"releaseType" : "User"
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"captureTime" : "2025-03-07 15:23:11.3412 -0800",
"codeSigningMonitor" : 1,
"incident" : "11934D43-E35C-4D78-89D6-86D58F19FCE5",
"pid" : 46313,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-03-07 11:02:09.9703 -0800",
"procStartAbsTime" : 3435494438327,
"procExitAbsTime" : 3786061830041,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.9.0","CFBundleVersion":"1.9.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"292D261C-48B5-505D-96AA-1C3B54C1D842","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "3587406A-7241-238D-D039-C9AD257A1AF4",
"lowPowerMode" : 1,
"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" : "AD9AFBF0-22AA-4C3E-83DC-1D67B1EAF023",
"wakeTime" : 1,
"sleepWakeUUID" : "AD508E97-E744-475A-951C-225B89762F8F",
"sip" : "enabled",
"vmRegionInfo" : "0 is not in any region. Bytes before following region: 4364992512\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 1042c8000-1042cc000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000000","rawCodes":[1,0],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000000"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":46313},
"vmregioninfo" : "0 is not in any region. Bytes before following region: 4364992512\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 1042c8000-1042cc000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
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"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/psutil\/_psutil_osx.abi3.so",
"name" : "_psutil_osx.abi3.so"
},
{
"source" : "P",
"arch" : "arm64",
"base" : 12909101056,
"size" : 16384,
"uuid" : "a516c5bc-1157-318a-a306-5c9b350e0c09",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/psutil\/_psutil_posix.abi3.so",
"name" : "_psutil_posix.abi3.so"
},
{
"source" : "P",
"arch" : "arm64",
"base" : 12938395648,
"size" : 737280,
"uuid" : "cc06500d-d418-3365-b197-36b1304a819e",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/QtOpenGL.abi3.so",
"name" : "QtOpenGL.abi3.so"
},
{
"source" : "P",
"arch" : "arm64",
"base" : 12911443968,
"size" : 49152,
"uuid" : "b32a8c32-a5e0-3a8b-9a0d-00a26b160215",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/QtOpenGLWidgets.abi3.so",
"name" : "QtOpenGLWidgets.abi3.so"
},
{
"source" : "P",
"arch" : "arm64",
"base" : 6414090240,
"size" : 49152,
"uuid" : "cd4f396b-89fe-36fd-a488-6f5b3d4b0282",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtOpenGLWidgets.framework\/Versions\/A\/QtOpenGLWidgets",
"name" : "QtOpenGLWidgets"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6789259264,
"size" : 241656,
"uuid" : "eee9d0d3-dffc-37cb-9ced-b27cd0286d8c",
"path" : "\/usr\/lib\/system\/libsystem_kernel.dylib",
"name" : "libsystem_kernel.dylib"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6789500928,
"size" : 53248,
"uuid" : "642faf7a-874e-37e6-8aba-2b0cc09a3025",
"path" : "\/usr\/lib\/system\/libsystem_pthread.dylib",
"name" : "libsystem_pthread.dylib"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6788034560,
"size" : 532476,
"uuid" : "92699527-645f-3d8d-aed8-1cfb0c034e15",
"path" : "\/usr\/lib\/system\/libsystem_c.dylib",
"name" : "libsystem_c.dylib"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6789738496,
"size" : 32748,
"uuid" : "984d08b8-f85c-36f5-9e17-5bff7fc779a3",
"path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
"name" : "libsystem_platform.dylib"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6852587520,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.AppKit",
"size" : 21221376,
"uuid" : "b88a44c1-d617-33dc-90ed-b6ab417c428e",
"path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
"name" : "AppKit",
"CFBundleVersion" : "2575.40.6"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6886207488,
"CFBundleShortVersionString" : "1.600.0",
"CFBundleIdentifier" : "com.apple.SkyLight",
"size" : 5427200,
"uuid" : "f66e0c94-99b5-3fcd-b726-3e3cbca668a3",
"path" : "\/System\/Library\/PrivateFrameworks\/SkyLight.framework\/Versions\/A\/SkyLight",
"name" : "SkyLight"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6787731456,
"size" : 290816,
"uuid" : "5576e4fd-aad2-3608-8c8f-4eec421236f9",
"path" : "\/usr\/lib\/system\/libdispatch.dylib",
"name" : "libdispatch.dylib"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6789967872,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.CoreFoundation",
"size" : 5197824,
"uuid" : "190e6a36-fcaa-3ea3-94bb-7009c44653da",
"path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
"name" : "CoreFoundation",
"CFBundleVersion" : "3302.1.400"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6979624960,
"CFBundleShortVersionString" : "2.1.1",
"CFBundleIdentifier" : "com.apple.HIToolbox",
"size" : 3178496,
"uuid" : "950f1236-acaf-379d-819f-6c6b0b5deabd",
"path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
"name" : "HIToolbox"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6785835008,
"size" : 532288,
"uuid" : "398a133c-9bcb-317f-a064-a40d3cea3c0f",
"path" : "\/usr\/lib\/dyld",
"name" : "dyld"
},
{
"size" : 0,
"source" : "A",
"base" : 0,
"uuid" : "00000000-0000-0000-0000-000000000000"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6808784896,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.Foundation",
"size" : 14974976,
"uuid" : "16d282d0-8b48-3e76-8036-fcb45dece518",
"path" : "\/System\/Library\/Frameworks\/Foundation.framework\/Versions\/C\/Foundation",
"name" : "Foundation",
"CFBundleVersion" : "3302.1.400"
}
],
"sharedCache" : {
"base" : 6785024000,
"size" : 4865835008,
"uuid" : "d272b91e-f9f0-3854-b5b9-508b21c25dcc"
},
"vmSummary" : "ReadOnly portion of Libraries: Total=1.9G resident=0K(0%) swapped_out_or_unallocated=1.9G(100%)\nWritable regions: Total=4.1G written=2506K(0%) resident=2506K(0%) swapped_out=0K(0%) unallocated=4.1G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 384K 3 \nActivity Tracing 256K 1 \nCG image 3376K 55 \nColorSync 736K 38 \nCoreAnimation 6160K 324 \nCoreGraphics 48K 3 \nCoreGraphics (reserved) 16K 1 reserved VM address space (unallocated)\nCoreImage 192K 6 \nCoreServices 80K 1 \nCoreUI image data 5344K 40 \nFoundation 32K 2 \nKernel Alloc Once 32K 1 \nMALLOC 3.4G 106 \nMALLOC guard page 288K 18 \nMach message 64K 3 \nOpenGL GLSL 384K 4 \nSTACK GUARD 56.6M 36 \nStack 191.2M 36 \nVM_ALLOCATE 294.4M 401 \nVM_ALLOCATE (reserved) 160.0M 2 reserved VM address space (unallocated)\n__AUTH 5288K 672 \n__AUTH_CONST 70.9M 920 \n__CTF 824 1 \n__DATA 33.4M 1064 \n__DATA_CONST 34.2M 1082 \n__DATA_DIRTY 2763K 342 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 637.6M 156 \n__OBJC_RW 2374K 1 \n__TEXT 1.3G 1102 \n__TPRO_CONST 272K 2 \ndyld private memory 32K 2 \nmapped file 587.4M 96 \nowned unmapped memory 90.5M 1 \npage table in kernel 2506K 1 \nshared memory 3200K 26 \n=========== ======= ======= \nTOTAL 6.8G 6552 \nTOTAL, minus reserved VM space 6.6G 6552 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"logWritingSignature" : "f465458cb810aa99eb40bd8302cb48a9e0ac260b",
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "642da32dea3b2418c750f848",
"factorPackIds" : {
"VISUAL_INTELLIGENCE_VICTORIA" : "66d8b2f77cd4b62688efd2cf"
},
"deploymentId" : 240000004
},
{
"rolloutId" : "5ffde50ce2aacd000d47a95f",
"factorPackIds" : {
},
"deploymentId" : 240000460
}
],
"experiments" : [
]
}
}
===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/sphulera/Library/CloudStorage/OneDrive-
> TheScrippsResearchInstitute/EM/Briney/PC94-A15_BG505_RM20A3/RealSpaceRefine_3/PC94A15_BG505_RM20A3_J1466_real_space_refined_003.pdb
Chain information for PC94A15_BG505_RM20A3_J1466_real_space_refined_003.pdb #1
---
Chain | Description
A C E | No description available
B D F | No description available
H | No description available
I K Q | No description available
L | No description available
M O S | No description available
> open /Users/sphulera/Library/CloudStorage/OneDrive-
> TheScrippsResearchInstitute/EM/Briney/PC94-A30_BG505_RM20A3/RealSpaceRefine_2/PC94-A30_BG505_RM20A3_P2661_real_space_refined_002.pdb
Chain information for PC94-A30_BG505_RM20A3_P2661_real_space_refined_002.pdb
#2
---
Chain | Description
A C E | No description available
B D F | No description available
H J P | No description available
I K Q | No description available
L N R | No description available
M O S | No description available
> open /Users/sphulera/Library/CloudStorage/OneDrive-
> TheScrippsResearchInstitute/EM/Briney/PC94-A31/RealSpaceRefine_4/PC94A31_BG505SOSIP_RM20A3_J1526_real_space_refined_052_updated.pdb
Chain information for
PC94A31_BG505SOSIP_RM20A3_J1526_real_space_refined_052_updated.pdb #3
---
Chain | Description
A | No description available
B D F | No description available
C | No description available
E | No description available
H | No description available
I | No description available
K Q | No description available
L | No description available
M O S | No description available
> mmaker #3/A to #1/A
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker PC94A15_BG505_RM20A3_J1466_real_space_refined_003.pdb, chain A (#1)
with PC94A31_BG505SOSIP_RM20A3_J1526_real_space_refined_052_updated.pdb, chain
A (#3), sequence alignment score = 2182.6
RMSD between 430 pruned atom pairs is 0.526 angstroms; (across all 435 pairs:
0.634)
> mmaker #2/A to #1/A
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker PC94A15_BG505_RM20A3_J1466_real_space_refined_003.pdb, chain A (#1)
with PC94-A30_BG505_RM20A3_P2661_real_space_refined_002.pdb, chain A (#2),
sequence alignment score = 2187.6
RMSD between 430 pruned atom pairs is 0.406 angstroms; (across all 437 pairs:
0.521)
> hide atoms
> show cartoons
> select ~/A,H,L
70464 atoms, 71771 bonds, 36 pseudobonds, 6482 residues, 6 models selected
> hide sel cartoons
> preset "overall look" "publication 2 (depth-cued)"
Using preset: Overall Look / Publication 2 (Depth-Cued)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes f
lighting depthCue t
> lighting soft
> dssp
Computing secondary structure
> select clear
> select /A:332
29 atoms, 26 bonds, 3 residues, 3 models selected
> show sel atoms
> select clear
> select #1/H,L
1805 atoms, 1854 bonds, 232 residues, 1 model selected
> ui tool show Axes/Planes/Centroids
> define centroid sel
Centroid 'centroid' placed at [261.75550803 228.82803546 133.81233518]
> select #2/H,L
3531 atoms, 3577 bonds, 232 residues, 1 model selected
> define centroid sel
Centroid 'centroid' placed at [210.96783093 141.31256075 152.24647267]
> select clear
> select #3/H,L
1832 atoms, 1883 bonds, 233 residues, 1 model selected
> define centroid sel
Centroid 'centroid' placed at [165.63171397 252.88298144 272.36567303]
> select clear
> hide #!1 models
> hide #!2 models
> show #!2 models
> show #!1 models
> hide #!2 models
> hide #!3 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> show #!3 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> ui tool show Distances
> ui mousemode right select
> select #1.2
1 atom, 1 residue, 1 model selected
> select #!1/A:332@CA
1 atom, 1 residue, 1 model selected
> select #1.2
1 atom, 1 residue, 1 model selected
> select add #!1/A:332@CA
2 atoms, 2 residues, 2 models selected
> distance #1.2 #!1/A:332@CA
Distance between PC94A15_BG505_RM20A3_J1466_real_space_refined_003.pdb #!1/A
ASN 332 CA and centroid #1.2: 36.124Å
> distance style color black
> distance style dashes 0
> hide #4.1 models
> select clear
> show #!2 models
> hide #!1 models
> hide #!4 models
> select #2.2
1 atom, 1 residue, 1 model selected
> select #!2/A:332@CA
1 atom, 1 residue, 1 model selected
> select add #2.2
2 atoms, 2 residues, 2 models selected
> distance #!2/A:332@CA #2.2
Distance between PC94-A30_BG505_RM20A3_P2661_real_space_refined_002.pdb #!2/A
ASN 332 CA and centroid #2.2: 35.510Å
> distance #!2/A:332@CA #2.2
Distance already exists; modify distance properties with 'distance style'
> show #!4 models
> show #4.1 models
> hide #4.1 models
> show #!3 models
> distance style color #ff2600
> distance style color black
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!2 models
> select clear
> show #!3 models
> hide #!2 models
> hide #!1 models
> select add #3.2
1 atom, 1 residue, 1 model selected
> select add #!3/A:332@CA
2 atoms, 2 residues, 2 models selected
> distance #3.2 #!3/A:332@CA
Distance between
PC94A31_BG505SOSIP_RM20A3_J1526_real_space_refined_052_updated.pdb #!3/A ASN
332 CA and centroid #3.2: 35.480Å
> hide #!4 models
> show #!4 models
> distance style color #0433ff
> distance style color black
> show #!2 models
> show #!1 models
> select clear
> angle #1.2 #1/A:332@ca #2.2
Angle between centroid #1.2,
PC94A15_BG505_RM20A3_J1466_real_space_refined_003.pdb #!1/A ASN 332 CA, and
centroid #2.2: 4.438
> angle #1.2 #1/A:332@ca #2.2
Angle between centroid #1.2,
PC94A15_BG505_RM20A3_J1466_real_space_refined_003.pdb #!1/A ASN 332 CA, and
centroid #2.2: 4.438
> angle #1.2 #1/A:332@ca #3.2
Angle between centroid #1.2,
PC94A15_BG505_RM20A3_J1466_real_space_refined_003.pdb #!1/A ASN 332 CA, and
centroid #3.2: 4.741
> angle #2.2 #1/A:332@ca #3.2
Angle between centroid #2.2,
PC94A15_BG505_RM20A3_J1466_real_space_refined_003.pdb #!1/A ASN 332 CA, and
centroid #3.2: 2.366
> hide #!1 models
> show #!1 models
> save /Users/sphulera/Desktop/image56.png supersample 3
> open /Users/sphulera/Library/CloudStorage/OneDrive-
> TheScrippsResearchInstitute/EM/Clinical_trial_samples/C101/1D07_GT1-1_RM20A3/RealSpaceRefine_1/1D07_GT1-1_RM20A3_J1753_real_space_refined_001.pdb
Chain information for 1D07_GT1-1_RM20A3_J1753_real_space_refined_001.pdb #5
---
Chain | Description
A C E | No description available
B D F | No description available
H I P | No description available
J K Q | No description available
L N R | No description available
M O S | No description available
> open /Users/sphulera/Library/CloudStorage/OneDrive-
> TheScrippsResearchInstitute/EM/Clinical_trial_samples/C101/1D07_GT1-1_RM20A3/1D07_GT1-1_RM20A3_P455_J1753_C3_3.02.mrc
Opened 1D07_GT1-1_RM20A3_P455_J1753_C3_3.02.mrc as #6, grid size 400,400,400,
pixel 1.03, shown at level 0.0606, step 2, values float32
> close #5
> close #6
> open /Users/sphulera/Library/CloudStorage/OneDrive-
> TheScrippsResearchInstitute/EM/Clinical_trial_samples/C101/1D07_GT1-1_RM20A3/J1692_40A_sphere_1D07.mrc
Opened J1692_40A_sphere_1D07.mrc as #5, grid size 400,400,400, pixel 1.03,
shown at level 0.000431, step 2, values float32
> close #5
> ui tool show "Side View"
> distance style radius 0.2
> save /Users/sphulera/Desktop/image57.png supersample 3
> transparentBackground true
Unknown command: transparentBackground true
> save /Users/sphulera/Desktop/image57.png width 709 height 757 supersample 3
> transparentBackground true
> hide #!1 models
> hide #!2 models
> hide #!3 models
> show #!1 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> hide #!2 models
> show #!1 models
> select /A
15387 atoms, 15726 bonds, 13 pseudobonds, 1409 residues, 6 models selected
> ui tool show "Color Actions"
> color (#!1 & sel) #00f900ff
> select clear
> select #1 /H
985 atoms, 1010 bonds, 126 residues, 1 model selected
> color sel byelement
> color sel byhetero
> color sel byelement
> color sel byhetero
> color sel orchid
> color sel dark orchid
> select #1 /L
820 atoms, 844 bonds, 106 residues, 1 model selected
> color sel orchid
> select clear
> select #2 /L
1611 atoms, 1635 bonds, 106 residues, 1 model selected
> show #!2 models
> hide #!1 models
> color sel lime
> color sel wheat
> select #2 /H
1920 atoms, 1942 bonds, 126 residues, 1 model selected
> color sel tan
> select clear
> show #!3 models
> hide #!2 models
> select #3 /H
1007 atoms, 1034 bonds, 127 residues, 1 model selected
> color sel light cyan
> select #3 /L
825 atoms, 849 bonds, 106 residues, 1 model selected
> color sel light cyan
> select #3 /H
1007 atoms, 1034 bonds, 127 residues, 1 model selected
> color sel cyan
> lighting soft
> select clear
> select #3 /L
825 atoms, 849 bonds, 106 residues, 1 model selected
> select #3 /H
1007 atoms, 1034 bonds, 127 residues, 1 model selected
> color sel royal blue
> select #3 /L
825 atoms, 849 bonds, 106 residues, 1 model selected
> color sel dark turquoise
> color sel medium aquamarine
> select clear
> show #!2 models
> show #!1 models
> select /A
15387 atoms, 15726 bonds, 13 pseudobonds, 1409 residues, 6 models selected
> color sel green
> color sel chartreuse
> select clear
> select /A
15387 atoms, 15726 bonds, 13 pseudobonds, 1409 residues, 6 models selected
> color sel green
> select clear
> select /A:332
29 atoms, 26 bonds, 3 residues, 3 models selected
> style sel stick
Changed 29 atom styles
> color sel byelement
> ui tool show "Color Actions"
> color sel forest green
> select clear
> select /A:332
29 atoms, 26 bonds, 3 residues, 3 models selected
> color sel byhetero
> select H
24423 atoms, 3174 residues, 1 model selected
> select clear
> select H
24423 atoms, 3174 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> hide #!3 models
> hide #!2 models
> hide #!1 models
> show #!1 models
> show #!2 models
> show #!3 models
> hide #!2 models
> hide #!1 models
> show #!1 models
> show #!2 models
> save /Users/sphulera/Desktop/image57.png width 709 height 757 supersample 3
> transparentBackground true
> hide #!2 models
> hide #!3 models
> show #!2 models
> hide #!1 models
> select #2 /L
822 atoms, 846 bonds, 106 residues, 1 model selected
> ui tool show "Color Actions"
> color sel wheat
> select clear
> select #2 /H
977 atoms, 999 bonds, 126 residues, 1 model selected
> color sel dark goldenrod
> show #!1 models
> show #!3 models
> hide #!3 models
> hide #!2 models
> show #!2 models
> show #!3 models
> select clear
> save /Users/sphulera/Desktop/image57.png width 709 height 757 supersample 3
> transparentBackground true
> hide #!1 models
> hide #!3 models
> show #!3 models
> hide #!2 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> show #!2 models
> show #!1 models
> hide #!3 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> show #!3 models
> hide #!2 models
> select #1 /H
985 atoms, 1010 bonds, 126 residues, 1 model selected
> ui tool show Axes/Planes/Centroids
> define centroid sel name centroid_HC_15
Centroid 'centroid_HC_15' placed at [268.73964061 223.60277462 137.52658883]
> select clear
> select #3 /H
1007 atoms, 1034 bonds, 127 residues, 1 model selected
> define centroid sel name centroid_HC_31
Centroid 'centroid_HC_31' placed at [157.8284002 248.42483714 268.66567825]
> select clear
> angle #1.3 #1/A:332@ca #3.3
Angle between centroid_HC_15 #1.3,
PC94A15_BG505_RM20A3_J1466_real_space_refined_003.pdb #!1/A ASN 332 CA, and
centroid_HC_31 #3.3: 8.910
> hide #1.1 models
> hide #2.1 models
> hide #2.2 models
> hide #3.2 models
> hide #1.2 models
> select #2 /H
977 atoms, 999 bonds, 126 residues, 1 model selected
> ui tool show Axes/Planes/Centroids
> define centroid sel name centroid_HC_30
Centroid 'centroid_HC_30' placed at [205.19048004 135.52411975 157.24736336]
> hide #2.3 models
> show #2.3 models
> hide #2.3 models
> show #2.3 models
> select clear
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> select #1 /L
820 atoms, 844 bonds, 106 residues, 1 model selected
> define centroid sel name centroid_LC_15
Centroid 'centroid_LC_15' placed at [253.36603171 235.10472073 129.35070122]
> select #3 /L
825 atoms, 849 bonds, 106 residues, 1 model selected
> define centroid sel name centroid_LC_31
Centroid 'centroid_LC_31' placed at [175.15648606 258.32461939 276.88190909]
> hide #!3 models
> select add #1.3
826 atoms, 849 bonds, 107 residues, 2 models selected
> select add #!1/A:332@CA
827 atoms, 849 bonds, 108 residues, 3 models selected
Either three or four atoms must be selected!
> select #1.3 #1/A:332@ca
2 atoms, 2 residues, 2 models selected
Either three or four atoms must be selected!
> select clear
> select #1.3
1 atom, 1 residue, 1 model selected
> select add #!1/A:332@CA
2 atoms, 2 residues, 2 models selected
Either three or four atoms must be selected!
> select clear
> distance #1.3 #1/A:332@ca
Distance between PC94A15_BG505_RM20A3_J1466_real_space_refined_003.pdb #!1/A
ASN 332 CA and centroid_HC_15 #1.3: 34.665Å
> show #!3 models
> distance #1/A:332@ca #3.3
Distance between PC94A15_BG505_RM20A3_J1466_real_space_refined_003.pdb #!1/A
ASN 332 CA and centroid_HC_31 #3.3: 33.088Å
> angle #1.3 #1/A:332@ca #3.3
Angle between centroid_HC_15 #1.3,
PC94A15_BG505_RM20A3_J1466_real_space_refined_003.pdb #!1/A ASN 332 CA, and
centroid_HC_31 #3.3: 8.910
> show #!2 models
> hide #!3 models
> show #!3 models
> hide #!2 models
> ui tool show "Side View"
> ui tool show Distances
> distance style color #929000
> distance style color black
> distance style color #0433ff
> distance style color #ff2600
> distance style color #941100
> distance style color black
> save /Users/sphulera/Desktop/image58.png width 709 height 757 supersample 3
> transparentBackground true
> show #!2 models
> hide #!3 models
> save /Users/sphulera/Desktop/image59.png width 709 height 757 supersample 3
> hide #3.3 models
> hide #3.4 models
> hide #1.3 models
> hide #1.4 models
> hide #2.3 models
> ui tool show "Side View"
> show #!3 models
> hide #!2 models
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 89.3
OpenGL renderer: Apple M3
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: Mac15,12
Model Number: Z1B600163LL/A
Chip: Apple M3
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 11881.81.4
OS Loader Version: 11881.81.4
Software:
System Software Overview:
System Version: macOS 15.3.1 (24D70)
Kernel Version: Darwin 24.3.0
Time since boot: 2 days, 22 minutes
Graphics/Displays:
Apple M3:
Chipset Model: Apple M3
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina Display
Resolution: 2560 x 1664 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
LG HDR 4K:
Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
Change History (2)
comment:1 by , 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 |
The message shown in the Bug reporting panel when you reported this bug explains what we know about this crash
"This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX."
The current ChimeraX daily build is using a newer version of the Qt window toolkit (6.8.2) that may not have this crashing problem on Macs with multiple displays.
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Reported by Swastik