![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 5 months ago
Closed 5 months ago
#17719 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-15.4.1-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 0x00000002025fcc80 (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, chimerax.surface._surface, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, psutil._psutil_osx, psutil._psutil_posix, PIL._imagingmath, chimerax.graphics._graphics, chimerax.atomic._ribbons, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize (total: 53)
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"procRole" : "Background",
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"modelCode" : "Mac14,7",
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"build" : "24E263",
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"codeSigningMonitor" : 1,
"incident" : "13754E2A-6746-449D-A6D6-B2E3925C4E3B",
"pid" : 5132,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-05-18 11:01:01.4377 +0200",
"procStartAbsTime" : 6601499667728,
"procExitAbsTime" : 6977020379874,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
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"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "B362EAEC-D592-0B8A-05EB-D3BB388A7463",
"appleIntelligenceStatus" : {"state":"available"},
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRm+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkZDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"bootSessionUUID" : "48E5351C-FEB6-40CC-B43C-BB7C25A7D393",
"wakeTime" : 27,
"sleepWakeUUID" : "2D2821E4-4F72-476F-B326-CD26B1749312",
"sip" : "enabled",
"vmRegionInfo" : "0x52ede26051e8 is not in any region. Bytes after previous region: 90700622352873 Bytes before following region: 14371457576472\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL reserved VM address space (unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000001, 0x0000d2ede26051e8","rawCodes":[1,231919147045352],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000d2ede26051e8 -> 0x000052ede26051e8 (possible pointer authentication failure)"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":5132},
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"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/OpenGL_accelerate\/numpy_formathandler.cpython-311-darwin.so",
"name" : "numpy_formathandler.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "arm64",
"base" : 13167689728,
"size" : 49152,
"uuid" : "12c53516-421d-3f7a-a81e-95bcfdb8a3ff",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/OpenGL_accelerate\/nones_formathandler.cpython-311-darwin.so",
"name" : "nones_formathandler.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "arm64",
"base" : 13252116480,
"size" : 32768,
"uuid" : "a55a4181-c446-3fa3-8fd6-27f845527eab",
"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",
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"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" : 13030834176,
"size" : 32768,
"uuid" : "8abbdcef-1901-3d4b-9e6b-a38214b79214",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PIL\/_imagingmath.cpython-311-darwin.so",
"name" : "_imagingmath.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "arm64",
"base" : 13039140864,
"size" : 16384,
"uuid" : "de871a78-14f2-3e72-9bde-e4f2c7493f1b",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/graphics\/_graphics.cpython-311-darwin.so",
"name" : "_graphics.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "arm64",
"base" : 13012172800,
"size" : 81920,
"uuid" : "3133c77c-8bf7-32a3-b5db-cbfe2e50ce9d",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/atomic\/_ribbons.cpython-311-darwin.so",
"name" : "_ribbons.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "arm64",
"base" : 5830934528,
"size" : 81920,
"uuid" : "d7bd530c-3353-37a6-b81f-ee3179d65811",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/lz4\/_version.cpython-311-darwin.so",
"name" : "_version.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "arm64",
"base" : 5838471168,
"size" : 180224,
"uuid" : "87eed069-25fc-30f6-aa30-1e54859d92e2",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/lz4\/frame\/_frame.cpython-311-darwin.so",
"name" : "_frame.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "arm64",
"base" : 5831081984,
"size" : 131072,
"uuid" : "c1a3c2d3-b21b-3231-839d-fcbc83ca2028",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/core\/_serialize.cpython-311-darwin.so",
"name" : "_serialize.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "arm64",
"base" : 5838995456,
"size" : 131072,
"uuid" : "650aead6-ce16-39bb-9ba1-4bf9986b96d6",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/msgpack\/_cmsgpack.cpython-311-darwin.so",
"name" : "_cmsgpack.cpython-311-darwin.so"
},
{
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"arch" : "arm64e",
"base" : 6768455680,
"size" : 242444,
"uuid" : "225cb279-20a9-381d-a163-d2be263f5327",
"path" : "\/usr\/lib\/system\/libsystem_kernel.dylib",
"name" : "libsystem_kernel.dylib"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6768701440,
"size" : 51784,
"uuid" : "8d27ec9a-d919-31a4-8df8-31a2fd2e593c",
"path" : "\/usr\/lib\/system\/libsystem_pthread.dylib",
"name" : "libsystem_pthread.dylib"
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"path" : "\/usr\/lib\/system\/libsystem_c.dylib",
"name" : "libsystem_c.dylib"
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"uuid" : "27ed40c8-6b18-3266-93a7-387fb33ca186",
"path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
"name" : "libsystem_platform.dylib"
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"size" : 21564928,
"uuid" : "1d6df541-4a74-3a0e-8a8f-15aee6f93da9",
"path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
"name" : "AppKit",
"CFBundleVersion" : "2575.50.27"
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{
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"arch" : "arm64e",
"base" : 6866669568,
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"size" : 5394304,
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"name" : "SkyLight"
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"size" : 288544,
"uuid" : "3329eb0a-e722-3db0-a627-e27297282a0f",
"path" : "\/usr\/lib\/system\/libdispatch.dylib",
"name" : "libdispatch.dylib"
},
{
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"arch" : "arm64e",
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"size" : 5500928,
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"size" : 3174368,
"uuid" : "6cc82a38-f1b5-3f2b-876b-9b3d7b278490",
"path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
"name" : "HIToolbox"
},
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"source" : "P",
"arch" : "arm64e",
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"size" : 633476,
"uuid" : "aca43a8d-6369-3a2c-af92-3d4c458523d6",
"path" : "\/usr\/lib\/dyld",
"name" : "dyld"
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"arch" : "arm64e",
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"path" : "\/System\/Library\/Frameworks\/Foundation.framework\/Versions\/C\/Foundation",
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"arch" : "arm64e",
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"size" : 305408,
"uuid" : "c211ddea-e3c5-351d-8619-900c01bedfc9",
"path" : "\/usr\/lib\/system\/libxpc.dylib",
"name" : "libxpc.dylib"
}
],
"sharedCache" : {
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"size" : 5020123136,
"uuid" : "bb86a9b4-8362-37b8-b028-212703af6f30"
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"vmSummary" : "ReadOnly portion of Libraries: Total=1.9G resident=0K(0%) swapped_out_or_unallocated=1.9G(100%)\nWritable regions: Total=9.8G written=92.0M(1%) resident=5429K(0%) swapped_out=86.7M(1%) unallocated=9.7G(99%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 384K 3 \nActivity Tracing 256K 1 \nCG image 15.8M 43 \nColorSync 704K 38 \nCoreAnimation 6864K 389 \nCoreGraphics 48K 3 \nCoreServices 624K 2 \nCoreUI image data 5520K 41 \nFoundation 32K 2 \nKernel Alloc Once 32K 1 \nMALLOC 9.1G 133 \nMALLOC guard page 288K 18 \nMach message 64K 3 \nOpenGL GLSL 384K 4 \nSTACK GUARD 56.6M 38 \nStack 199.8M 38 \nVM_ALLOCATE 318.9M 243 \nVM_ALLOCATE (reserved) 96.0M 3 reserved VM address space (unallocated)\n__AUTH 5487K 696 \n__AUTH_CONST 77.2M 943 \n__CTF 824 1 \n__DATA 33.9M 1081 \n__DATA_CONST 36.8M 1098 \n__DATA_DIRTY 2775K 342 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 650.0M 150 \n__OBJC_RO 61.3M 1 \n__OBJC_RW 2391K 1 \n__TEXT 1.3G 1077 \n__TEXT (graphics) 19.3M 41 \n__TPRO_CONST 128K 2 \ndyld private memory 2592K 22 \nmapped file 306.5M 86 \npage table in kernel 5429K 1 \nshared memory 3184K 25 \n=========== ======= ======= \nTOTAL 12.3G 6573 \nTOTAL, minus reserved VM space 12.2G 6573 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"logWritingSignature" : "77699024059010918b294963d3e2c20641326fbd",
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}
===== 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/annguyen/Downloads/cryosparc_P8_J16_class_03_00042_volume.mrc
Opened cryosparc_P8_J16_class_03_00042_volume.mrc as #1, grid size
128,128,128, pixel 4.48, shown at level 0.714, step 1, values float32
> volume #1 level 0.1916
> ui tool show "Hide Dust"
> surface dust #1 size 49.27
> volume #1 level 0.1446
> volume #1 level 0.2804
> lighting simple
> lighting soft
> open /Users/annguyen/Downloads/cryosparc_P8_J16_class_02_00042_volume.mrc
Opened cryosparc_P8_J16_class_02_00042_volume.mrc as #2, grid size
128,128,128, pixel 4.48, shown at level 0.612, step 1, values float32
> ui mousemode right "translate selected models"
> select add #2
2 models selected
> view matrix models #2,1,0,0,75.331,0,1,0,185.38,0,0,1,-208.74
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.89649,-0.067195,0.43794,485.65,0.15418,0.87935,0.45053,38.689,-0.41538,0.47141,-0.77797,318.01
> view matrix models
> #2,-0.54237,0.3241,-0.77511,649.02,-0.52271,-0.85246,0.0093171,843.41,-0.65773,0.41021,0.63176,-28.353
> view matrix models
> #2,-0.84379,-0.42043,-0.33356,805.08,0.041419,-0.67069,0.74058,413.17,-0.53508,0.61107,0.58334,-103.5
> volume #2 level 0.321
> view matrix models
> #2,-0.93301,0.35059,-0.081067,514.38,-0.18657,-0.27868,0.94209,302.92,0.3077,0.89411,0.32542,-390.27
> view matrix models
> #2,-0.74246,-0.35871,0.56575,508.28,-0.12139,0.90261,0.41299,43.421,-0.6588,0.23795,-0.7137,409.64
> view matrix models
> #2,-0.92712,-0.27944,0.24973,626.75,-0.19072,0.92541,0.32747,81.135,-0.32261,0.25598,-0.91126,351.79
> select add #1
4 models selected
> select subtract #2
2 models selected
> view matrix models
> #1,-0.42787,-0.23197,-0.87357,712.86,0.27867,0.88556,-0.37165,64.001,0.85981,-0.40245,-0.31426,260.25
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.42787,-0.23197,-0.87357,770.61,0.27867,0.88556,-0.37165,116.42,0.85981,-0.40245,-0.31426,7.5245
> view matrix models
> #1,-0.42787,-0.23197,-0.87357,765.65,0.27867,0.88556,-0.37165,124.23,0.85981,-0.40245,-0.31426,4.2964
> view matrix models
> #1,-0.42787,-0.23197,-0.87357,770.74,0.27867,0.88556,-0.37165,108.22,0.85981,-0.40245,-0.31426,7.5417
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.1352,-0.69508,-0.70611,773.6,-0.68492,0.58052,-0.44031,480.23,0.71596,0.42409,-0.55456,-118.72
> view matrix models
> #1,-0.31623,-0.6713,-0.67034,806.22,-0.53732,0.70908,-0.45662,407.71,0.78185,0.21579,-0.58494,-68.614
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.31623,-0.6713,-0.67034,797.6,-0.53732,0.70908,-0.45662,420.01,0.78185,0.21579,-0.58494,-74.229
> view matrix models
> #1,-0.31623,-0.6713,-0.67034,800.06,-0.53732,0.70908,-0.45662,422.01,0.78185,0.21579,-0.58494,-75.834
> view matrix models
> #1,-0.31623,-0.6713,-0.67034,806.14,-0.53732,0.70908,-0.45662,433.2,0.78185,0.21579,-0.58494,-87.555
Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(NoModifier)
Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ControlModifier)
Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(AltModifier)
Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(NoModifier)
Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ControlModifier)
Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(AltModifier)
Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x1e' and Carbon '\x0' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> volume flip #1
Opened cryosparc_P8_J16_class_03_00042_volume.mrc z flip as #3, grid size
128,128,128, pixel 4.48, shown at step 1, values float32
> select subtract #1
Nothing selected
> select add #3
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.14249,-0.3567,0.92329,211.85,-0.98783,-0.00758,-0.15537,688.97,0.06242,-0.93419,-0.35127,392.59
> view matrix models
> #3,0.010751,-0.14262,0.98972,85.615,-0.9987,-0.050937,0.0035088,659.74,0.049913,-0.98847,-0.14298,353.02
> ui tool show "Fit in Map"
> fitmap #3 inMap #2
Fit map cryosparc_P8_J16_class_03_00042_volume.mrc z flip in map
cryosparc_P8_J16_class_02_00042_volume.mrc using 56970 points
correlation = 0.7959, correlation about mean = 0.4424, overlap = 1.931e+04
steps = 148, shift = 40.4, angle = 17.2 degrees
Position of cryosparc_P8_J16_class_03_00042_volume.mrc z flip (#3) relative to
cryosparc_P8_J16_class_02_00042_volume.mrc (#2) coordinates:
Matrix rotation and translation
0.32058201 0.59613022 -0.73610865 259.06315302
-0.78165732 -0.27244640 -0.56105686 758.83316483
-0.53501310 0.75524945 0.37862813 112.56395137
Axis 0.68697526 -0.10495100 -0.71906208
Axis point 577.15071940 243.25118652 0.00000000
Rotation angle (degrees) 106.65559624
Shift along axis 17.38920517
> volume #1 level 0.1889
> volume #1 color #b2b2b28f
> hide #!1 models
> color #3 #b2b2b2a0 models
> color #3 #b2b2b2a1 models
> volume #3 level 0.2584
> ui tool show "Side View"
> lighting soft
> volume #3 color #b2b2b2c8
> volume #3 color #b2b2b2c7
> surface dust #1 size 25.24
> surface dust #3 size 17.35
> open /Users/annguyen/Downloads/cryosparc_P8_J16_class_00_00042_volume.mrc
Opened cryosparc_P8_J16_class_00_00042_volume.mrc as #4, grid size
128,128,128, pixel 4.48, shown at level 0.834, step 1, values float32
> volume #4 level 0.0726
> select add #3
3 models selected
> select subtract #3
Nothing selected
> select add #4
3 models selected
> view matrix models
> #4,0.27094,0.33695,0.9017,-143.24,0.57742,0.6926,-0.43231,44.343,-0.77018,0.63779,-0.0069077,329.13
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.27094,0.33695,0.9017,-68.77,0.57742,0.6926,-0.43231,173.83,-0.77018,0.63779,-0.0069077,168.9
> view matrix models
> #4,0.27094,0.33695,0.9017,-115.06,0.57742,0.6926,-0.43231,140.81,-0.77018,0.63779,-0.0069077,119.9
> view matrix models
> #4,0.27094,0.33695,0.9017,-403.77,0.57742,0.6926,-0.43231,286.2,-0.77018,0.63779,-0.0069077,287.17
> volume flip #4
Opened cryosparc_P8_J16_class_00_00042_volume.mrc z flip as #5, grid size
128,128,128, pixel 4.48, shown at step 1, values float32
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.27094,0.33695,0.9017,-403.77,0.57742,0.6926,-0.43231,286.2,-0.77018,0.63779,-0.0069077,287.17
> select subtract #4
Nothing selected
> close #4
> select add #5
2 models selected
> view matrix models
> #5,0.27128,-0.33628,-0.90184,298.68,0.9181,-0.1909,0.34735,222.13,-0.28897,-0.92221,0.25695,522.73
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.27128,-0.33628,-0.90184,594.65,0.9181,-0.1909,0.34735,189.51,-0.28897,-0.92221,0.25695,437.5
> view matrix models
> #5,0.27128,-0.33628,-0.90184,571.22,0.9181,-0.1909,0.34735,81.639,-0.28897,-0.92221,0.25695,342.73
> view matrix models
> #5,0.27128,-0.33628,-0.90184,596.23,0.9181,-0.1909,0.34735,86.515,-0.28897,-0.92221,0.25695,343.32
> fitmap #5 inMap #3
Fit map cryosparc_P8_J16_class_00_00042_volume.mrc z flip in map
cryosparc_P8_J16_class_03_00042_volume.mrc z flip using 69265 points
correlation = 0.9197, correlation about mean = 0.7079, overlap = 2.925e+04
steps = 80, shift = 2.97, angle = 9.31 degrees
Position of cryosparc_P8_J16_class_00_00042_volume.mrc z flip (#5) relative to
cryosparc_P8_J16_class_03_00042_volume.mrc z flip (#3) coordinates:
Matrix rotation and translation
-0.99281795 0.11908966 -0.01140899 539.69042112
0.11710079 0.98688324 0.11112550 -61.67629565
0.02449323 0.10899139 -0.99374089 523.64074749
Axis -0.05924702 -0.99671515 -0.05521505
Axis point 269.31246390 0.00000000 265.96707099
Rotation angle (degrees) 178.96803163
Shift along axis 0.58580219
> volume #5 level 0.06543
> volume #2 level 0.1734
> surface dust #5 size 26.86
> surface dust #2 size 26.86
> volume #3 level 0.2479
> volume #3 color #b2b2b2
> volume #5 color #b2b2ffc5
> volume #5 color #b2b2ffc4
> volume #5 level 0.01881
> surface dust #5 size 27.25
> surface dust #5 size 138.75
> surface dust #5 size 125.7
> volume #3 level 0.1706
> surface dust #3 size 17.96
> surface dust #3 size 60.9
> volume #3 level 0.09331
> surface dust #3 size 61.5
> surface dust #3 size 261.97
> volume #3 level 0.1566
> volume #3 level 0.1601
> volume #3 level 0.2093
> volume #3 level 0.1917
> volume #5 level 0.05467
> volume #3 level 0.2093
> volume #3 level 0.2303
> volume #3 level 0.2936
> ui mousemode right "mark plane"
> ui mousemode right "mark surface"
> marker #4 position 310,300.4,33.63 color yellow radius 1
> marker change #4 radius 9
> volume #3 color #b2b2b2e8
> volume #5 color #b2b2ff
> volume #2 color #ffffb2d9
> volume #5 color #b2b2ffd3
> volume #5 color #b2b2ffd4
> volume #2 color #ffffb2
> volume #3 color #b2b2b2
> surface dust #3 size 267.27
> surface dust #3 size 33.9
> surface undust #3
> volume #1 level 0.4805
> hide #!1 models
> volume #3 level 0.2584
> volume #5 color #b2b2ffc0
> volume #5 color #b2b2ffbf
> volume #3 level 0.4165
> volume #3 level 0.2163
> volume #5 level 0.03674
> volume #3 level 0.1214
> volume #3 level 0.2128
Window position QRect(1158,923 862x100) outside any known screen, using
primary screen
> ui tool show "Side View"
> marker #4 position 314.8,297.4,26.65 color yellow radius 9
> marker #4 position 316.2,291.4,20.04 color yellow radius 9
> marker #4 position 322.9,287.4,15.66 color yellow radius 9
> marker #4 position 320.9,279.5,11.95 color yellow radius 9
> ui mousemode right "delete markers"
> marker delete #4:5
> marker delete #4:4
> ui mousemode right "delete markers"
> marker delete #4:3
> select add #4
2 atoms, 2 residues, 1 model selected
> marker delete #4:2
> ui mousemode right "translate selected models"
> view matrix models #4,1,0,0,-23.909,0,1,0,-2.2519,0,0,1,-6.2181
> view matrix models #4,1,0,0,-30.737,0,1,0,-6.7589,0,0,1,-3.2501
> view matrix models #4,1,0,0,-19.548,0,1,0,-1.9014,0,0,1,-5.0098
> view matrix models #4,1,0,0,-22.733,0,1,0,-26.641,0,0,1,-0.87727
> view matrix models #4,1,0,0,-8.6351,0,1,0,-27.47,0,0,1,-5.0959
> lighting full
> save "/Users/annguyen/ownCloud - Anh Nguyen@oc.biophys.mpg.de/Chimera
> sessions/18-05-25-scSec72-scRibo-10xbin.cxs" includeMaps true
===== 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
> open /Users/annguyen/Downloads/cryosparc_P8_J60_002_volume_map.mrc
Opened cryosparc_P8_J60_002_volume_map.mrc as #1, grid size 250,250,250, pixel
2.29, shown at level 0.525, step 1, values float32
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M2
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.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 Pro
Model Identifier: Mac14,7
Model Number: Z16U000NJD/A
Chip: Apple M2
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 11881.101.1
OS Loader Version: 11881.101.1
Software:
System Software Overview:
System Version: macOS 15.4.1 (24E263)
Kernel Version: Darwin 24.4.0
Time since boot: 6 days, 23 hours, 35 minutes
Graphics/Displays:
Apple M2:
Chipset Model: Apple M2
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
LG Monitor:
Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus)
UI Looks like: 2560 x 1440 @ 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-EMalign: 0.1.1
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
finufft: 2.3.1
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 , 5 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 , 5 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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