![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 11 months ago
Closed 11 months ago
#16479 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-15.2-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 0x00000001fc8b8240 (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.surface._surface, chimerax.map._map, 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, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, psutil._psutil_osx, psutil._psutil_posix, PIL._imagingmath (total: 52)
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{
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"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro18,1",
"coalitionID" : 9202,
"osVersion" : {
"train" : "macOS 15.2",
"build" : "24C101",
"releaseType" : "User"
},
"captureTime" : "2024-12-16 15:37:29.8728 -0500",
"codeSigningMonitor" : 1,
"incident" : "CFC95088-BFB0-4F5A-9A1A-A7642ED3654B",
"pid" : 34715,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-12-16 01:14:29.6073 -0500",
"procStartAbsTime" : 698992574595,
"procExitAbsTime" : 1002997668685,
"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":"B8543864-1889-5D36-8740-ED1966E1426D","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "1A6C8CA6-7E03-1215-A189-1F1376BD7E7F",
"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" : "358B6A8F-C0A5-4CCD-B75C-6B07A91BCB46",
"wakeTime" : 14,
"sleepWakeUUID" : "BFB08011-1D7D-4E8C-BF1A-4C3D4BF95F5C",
"sip" : "enabled",
"vmRegionInfo" : "0x6379ae32acb8 is not in any region. Bytes after previous region: 3810142121145 \n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n owned unmapped memory unmapped-unmapped [256.5M] rw-\/rw- SM=PRV owned physical footprint (unmapped)\n---> \n UNUSED SPACE AT END",
"exception" : {"codes":"0x0000000000000001, 0x00006379ae32acb8","rawCodes":[1,109374264749240],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00006379ae32acb8"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":34715},
"vmregioninfo" : "0x6379ae32acb8 is not in any region. Bytes after previous region: 3810142121145 \n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n owned unmapped memory unmapped-unmapped [256.5M] rw-\/rw- SM=PRV owned physical footprint (unmapped)\n---> \n UNUSED SPACE AT END",
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"faultingThread" : 0,
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"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" : 5901942784,
"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" : 6441484288,
"size" : 475136,
"uuid" : "0c6e9a11-e483-3d7d-a88f-8ad0507af167",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/mmcif\/mmcif.cpython-311-darwin.so",
"name" : "mmcif.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "arm64",
"base" : 13265616896,
"size" : 409600,
"uuid" : "1ab8e5e2-c699-3efb-8f77-d375e3793c8f",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/mmcif\/_mmcif.cpython-311-darwin.so",
"name" : "_mmcif.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "arm64",
"base" : 5901795328,
"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",
"base" : 5902286848,
"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" : 5637439488,
"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" : "arm64e",
"base" : 6760783872,
"size" : 241656,
"uuid" : "dfc9530c-e75b-3d1c-a9a6-85c8a709d6a7",
"path" : "\/usr\/lib\/system\/libsystem_kernel.dylib",
"name" : "libsystem_kernel.dylib"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6761025536,
"size" : 53248,
"uuid" : "f1661613-b1c8-320d-b69d-97f174130e29",
"path" : "\/usr\/lib\/system\/libsystem_pthread.dylib",
"name" : "libsystem_pthread.dylib"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6759559168,
"size" : 532476,
"uuid" : "67989e50-e562-3062-9ff9-44bd90648e66",
"path" : "\/usr\/lib\/system\/libsystem_c.dylib",
"name" : "libsystem_c.dylib"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6761263104,
"size" : 32764,
"uuid" : "d215e3b2-fa4f-328a-a080-7650c0991858",
"path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
"name" : "libsystem_platform.dylib"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6824058880,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.AppKit",
"size" : 21204992,
"uuid" : "4251ee1c-062c-3b9a-b6e2-751f77ef9f4a",
"path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
"name" : "AppKit",
"CFBundleVersion" : "2575.30.19"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6857641984,
"CFBundleShortVersionString" : "1.600.0",
"CFBundleIdentifier" : "com.apple.SkyLight",
"size" : 5427200,
"uuid" : "122276c2-e3a9-3406-ace8-a2c2a4756ca0",
"path" : "\/System\/Library\/PrivateFrameworks\/SkyLight.framework\/Versions\/A\/SkyLight",
"name" : "SkyLight"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6759256064,
"size" : 290816,
"uuid" : "9c7ff4a8-9d78-3aed-b64d-979574a26d8f",
"path" : "\/usr\/lib\/system\/libdispatch.dylib",
"name" : "libdispatch.dylib"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6761492480,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.CoreFoundation",
"size" : 5197824,
"uuid" : "41fdd393-3acc-328d-8108-e59a3a947ec5",
"path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
"name" : "CoreFoundation",
"CFBundleVersion" : "3208"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6951055360,
"CFBundleShortVersionString" : "2.1.1",
"CFBundleIdentifier" : "com.apple.HIToolbox",
"size" : 3178496,
"uuid" : "83159ee1-0ca4-3a91-887a-db80b7029337",
"path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
"name" : "HIToolbox"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6757359616,
"size" : 532288,
"uuid" : "4ce86d18-f3fa-3d2a-a1b8-e7cd8a52fb0d",
"path" : "\/usr\/lib\/dyld",
"name" : "dyld"
},
{
"size" : 0,
"source" : "A",
"base" : 0,
"uuid" : "00000000-0000-0000-0000-000000000000"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6780305408,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.Foundation",
"size" : 14979072,
"uuid" : "b39c1e42-f15f-3671-b63e-6be7bdad0fcd",
"path" : "\/System\/Library\/Frameworks\/Foundation.framework\/Versions\/C\/Foundation",
"name" : "Foundation",
"CFBundleVersion" : "3208"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6758985728,
"size" : 270328,
"uuid" : "d2681e0d-7831-3d34-b6bc-ce8723de184b",
"path" : "\/usr\/lib\/system\/libsystem_malloc.dylib",
"name" : "libsystem_malloc.dylib"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6757023744,
"size" : 335012,
"uuid" : "9ced21b4-d02c-31c0-bf0d-508c1a74fd93",
"path" : "\/usr\/lib\/libobjc.A.dylib",
"name" : "libobjc.A.dylib"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6757908480,
"size" : 307200,
"uuid" : "daaac055-2ed3-3b40-bafb-39bb74137dd8",
"path" : "\/usr\/lib\/system\/libxpc.dylib",
"name" : "libxpc.dylib"
}
],
"sharedCache" : {
"base" : 6756548608,
"size" : 4861722624,
"uuid" : "e36100c7-89e7-3970-8938-8483ccd7019a"
},
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"logWritingSignature" : "0d16f4a4a336a01cd3dcdaa65ac230ac5c7b724f",
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "60da5e84ab0ca017dace9abf",
"factorPackIds" : {
},
"deploymentId" : 240000008
},
{
"rolloutId" : "6246d6a916a70b047e454124",
"factorPackIds" : {
},
"deploymentId" : 240000010
}
],
"experiments" : [
{
"treatmentId" : "45f4e2a5-551b-4bc2-a2dc-19c244dda8f8",
"experimentId" : "6643969b3099cf28e049862f",
"deploymentId" : 400000007
}
]
}
}
===== 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/gyanaprakashmahapatra/Library/CloudStorage/OneDrive-
> Personal/SYNMIKRO/Ph.D/Projects/Supercomplex/Chlamydomonas/CryoSPARC/composite
> map of PSI and CytC6_J111_J116.pdb"
Summary of feedback from opening
/Users/gyanaprakashmahapatra/Library/CloudStorage/OneDrive-
Personal/SYNMIKRO/Ph.D/Projects/Supercomplex/Chlamydomonas/CryoSPARC/composite
map of PSI and CytC6_J111_J116.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 LEU A 3 ASN A 13 1 11
Start residue of secondary structure not found: HELIX 2 2 LYS A 33 TYR A 39 1
7
Start residue of secondary structure not found: HELIX 3 3 VAL A 46 ASN A 55 1
10
Start residue of secondary structure not found: HELIX 4 4 GLU A 69 ASP A 85 1
17
Chain information for composite map of PSI and CytC6_J111_J116.pdb
---
Chain | Description
1.2/1 1.2/Z | No description available
1.2/3 | No description available
1.2/4 | No description available
1.2/5 | No description available
1.2/6 | No description available
1.2/7 | No description available
1.2/8 | No description available
1.2/9 | No description available
1.1/A | No description available
1.2/A | No description available
1.2/B | No description available
1.2/C | No description available
1.2/D | No description available
1.2/E | No description available
1.2/F | No description available
1.2/G | No description available
1.2/I | No description available
1.2/J | No description available
1.2/K | No description available
1.2/L | No description available
> open "/Users/gyanaprakashmahapatra/Library/CloudStorage/OneDrive-
> Personal/SYNMIKRO/Ph.D/Projects/Supercomplex/Chlamydomonas/CryoSPARC/composite
> map of PSI and CytC6_J111_J116.mrc"
Opened composite map of PSI and CytC6_J111_J116.mrc as #2, grid size
704,704,705, pixel 0.73,0.73,0.73, shown at step 1, values float32
> volume #2 region 0,0,0,703,703,704 step 4
> volume #2 change image level -0.02945,0 level 0.1587,0.8 level 1.138,1
> volume #2 step 1
> volume #2 level 0.15
> hide atoms
> show cartoons
Computing secondary structure
> surface dust #2 size 7.3
> select ::name="HEC"
43 atoms, 46 bonds, 4 pseudobonds, 1 residue, 2 models selected
> show sel atoms
> select clear
Color zone shortcut requires 1 displayed atomic model and 1 map, got 2 atomic
models, 1 maps.
> hide #!1.1 models
> show #!1.1 models
> hide #!1.2 models
> color zone #2 near #1.1 distance 4.38
> olor zone #2 near #1.1 distance 4
Unknown command: olor zone #2 near #1.1 distance 4
> color zone #2 near #1.1 distance 4
> color zone #2 near #1.1 distance 3.5
> color zone #2 near #1.1 distance 3
> color zone #2 near #1.1 distance 2
> color zone #2 near #1.1 distance 1.5
> color zone #2 near #1.1 distance 1
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 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 #!1.1 models
> show #!1.1 models
> ui tool show "Color Zone"
> color zone #2 near #1.1 distance 1
> help help:user/tools/colorzone.html
> color #1.1#2.2#!1-2 magenta
> color zone #2 near #1.1 distance 1
> ui tool show "Color Actions"
> color cyan
> color medium blue
> color lime
> color forest green
> color cyan
> color light sea green
> color blue
> color cornflower blue
> lighting soft
> lighting flat
> lighting soft
> color zone #2 near #1.1 distance 1
> color zone #2 near #1.1 distance 1.04
> color zone #2 near #1.1 distance 0.87
> show #2.1 models
> hide #2.1 models
> hide #2.2 models
> show #2.2 models
> color zone #2 near #1.1 distance 1
> show #!1.2 models
> hide #!1.2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> hide #!1 models
> show #!1 models
> hide #!1.1 models
> show #!1.1 models
> show #!1.2 models
> hide #!1.2 models
> show #!1.2 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.2 models
> show #!1.2 models
> hide #!1.1 models
> hide #!1.2 models
> hide #!1 models
> show #!1 models
> show #!1.1 models
> show #!1.2 models
> hide #!1 models
> show #!1 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
> select #1.1/A#1.2/A
19474 atoms, 19811 bonds, 204 pseudobonds, 964 residues, 4 models selected
> select #1.1/A
776 atoms, 725 bonds, 17 pseudobonds, 158 residues, 2 models selected
> show #!2 models
> color zone #2 near #1.1 distance 0.87
> color (#!1.1 & sel) cyan
> color (#!1.1 & sel) forest green
> color (#!1.1 & sel) magenta
> select clear
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> volume #2 color #6495ed3b
> select #2
3 models selected
> select #2
3 models selected
> select #2
3 models selected
> select #2
3 models selected
> select clear
> color zone #2 near #1.1 distance 1
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> volume #2 color cornflowerblue
> ui tool show "Color Zone"
> color zone #2 near #1.1 distance 1
> color zone #2 near #1.1 distance 2.14
> color zone #2 near #1.1 distance 2.25
> color zone #2 near #1.1 distance 2.38
> color zone #2 near #1.1 distance 1.78
> color single #2
> color zone #2 near #1.1 distance 1.78
> help help:user/tools/colorzone.html
> volume splitbyzone #2
Opened composite map of PSI and CytC6_J111_J116.mrc 0 as #3.1, grid size
704,704,705, pixel 0.73,0.73,0.73, shown at level 0.15, step 1, values float32
Opened composite map of PSI and CytC6_J111_J116.mrc 1 as #3.2, grid size
704,704,705, pixel 0.73,0.73,0.73, shown at level 0.15, step 1, values float32
> hide #!3.1 models
> color #3.2 #ff00ff32 models
> color #3.2 #ff00ff30 models
> color #1.1 #0096ffff
> color #1.1 #76d6ffff
> color #1.1 #7a81ffff
> color #1.1 #00fdffff
> color #1.2 #76d6ffff
> color #1.2 #00fdffff
> hide #!1.2 models
> show #!1.2 models
> hide #!1.1 models
> show #!1.1 models
Cell requested for row 2 is out of bounds for table with 7 rows! Resizing
table model.
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3.2 models
> show #!3.2 models
> hide #!3 models
> show #!3.1 models
> color #3.2 #ff00ff90 models
> color #3.2 #ff00ff8f models
> set bgColor white
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> hide #!3.1 models
> show #!2 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> show #!3.1 models
> hide #!3.1 models
> hide #!3.2 models
> show #!3.2 models
> color #3.2 #ff00ff43 models
> color #3.2 #ff00ffac models
> color #3.2 #ff00ffad models
> show #!3.1 models
> color #3.2 magenta models
> hide #!1 models
> hide #!2 models
> hide #!3 models
> hide #!3.1 models
> hide #!3.2 models
> show #!3.2 models
> show #!3.1 models
> hide #!3.1 models
> show #!3.1 models
> hide #!3.1 models
> show #!3.1 models
> color #3.1 #6495edf9 models
> color #3.1 cornflowerblue models
> hide #!3.1 models
> hide #!3 models
> show #!3 models
> show #!2 models
> show #!1 models
> show #!3.1 models
> hide #!3.1 models
> show #!3.1 models
> hide #!3.1 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!2 models
> hide #!1 models
> hide #!3.2 models
> hide #!3 models
> show #!1 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!3.1 models
> volume #3.1 level 0.2433
> volume #3.1 color cornflowerblue
> volume #3.1 level 0.15
> surface dust #3.1 size 7.3
> show #!3.2 models
> color #3.2 #ff00ff32 models
> color #3.2 #ff00ff33 models
> color #3.2 #ff00ff60 models
> color #3.2 #ff00ff5e models
> hide #!3.2 models
> show #!3.2 models
> hide #!3 models
> show #!3 models
> hide #!3.1 models
> show #!3.1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> color #3.1 #6495ed00 models
> color #3.1 #6495ed49 models
> color #3.1 #6495ed4a models
> color #3.1 #6495ed1a models
> color #3.1 cornflowerblue models
> color #3.2 magenta models
> color #3.2 #ff00ff3a models
> color #3.2 #ff00ff4a models
> color #3.2 #ff00ff4e models
> color #3.2 #ff00ff4d models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> color #1.1 #00f900ff
> color #1.2 #00f900ff
> color #1.1 #008f00ff
> color #1.1 #4f8f00ff
> color #1.1 #8efa00ff
> color #1.2 #8efa00ff
Cell requested for row 3 is out of bounds for table with 7 rows! Resizing
table model.
> hide #!3.1 models
> show #!3.1 models
> hide #!3.1 models
> show #!3.1 models
> color #3.1 #6495edd2 models
> color #3.1 #6495edb7 models
> color #3.1 #6495edb8 models
> color #3.1 #6495edf5 models
> color #3.1 #6495edfc models
> color #3.1 cornflowerblue models
> color #3.1 #6495ed00 models
> color #3.1 #6495ed90 models
> color #3.1 #6495ed88 models
> color #3.1 #6495ed80 models
> save /Users/gyanaprakashmahapatra/Desktop/image8.png supersample 3
> hide #!3 models
> show #!3 models
> select ~sel & ##selected
Nothing selected
> rotate axis 90 #3
Unknown command: rotate axis 90 #3
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> save /Users/gyanaprakashmahapatra/Desktop/image9.png supersample 3
> hide #!3.1 models
> show #!3.1 models
> save /Users/gyanaprakashmahapatra/Desktop/image10.png supersample 3
> ui tool show "Side View"
> save /Users/gyanaprakashmahapatra/Desktop/image11.png supersample 3
> ui tool show "Side View"
> select #1.2/9
3773 atoms, 3853 bonds, 60 pseudobonds, 171 residues, 3 models selected
> hide sel cartoons
> color #3.1 cornflowerblue models
> select #1.2/G
1530 atoms, 1549 bonds, 10 pseudobonds, 84 residues, 3 models selected
> hide sel cartoons
> color #3.1 #6495ed6b models
> ui tool show "Map Eraser"
> ui tool show "Side View"
Can only have one displayed volume when erasing
> hide #!3 models
> show #!3 models
> hide #!3.1 models
> show #!3.1 models
> hide #!3.2 models
> show #!3.2 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #!1 models
> show #!1 models
> hide #4 models
> show #4 models
> hide #!3 models
> show #!3 models
> hide #!3.2 models
> volume erase #3.1 center 261.68,245.18,182.61 radius 23.159
> volume erase #3.1 center 287.72,252.88,263.76 radius 12.609
> volume erase #3.1 center 276.88,253.65,264.81 radius 7.7198
> close #4
> show #!3.2 models
> save /Users/gyanaprakashmahapatra/Desktop/image12.png supersample 3
> save /Users/gyanaprakashmahapatra/Desktop/image13.png supersample 3
===== 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 M1 Pro
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 Pro
Model Identifier: MacBookPro18,1
Model Number: MK193LL/A
Chip: Apple M1 Pro
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 16 GB
System Firmware Version: 11881.61.3
OS Loader Version: 11881.61.3
Software:
System Software Overview:
System Version: macOS 15.2 (24C101)
Kernel Version: Darwin 24.2.0
Time since boot: 3 days, 4 hours, 10 minutes
Graphics/Displays:
Apple M1 Pro:
Chipset Model: Apple M1 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 16
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3456 x 2234 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
LS27D70xE:
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 , 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 |
That is fine. I did not want to completely shut-off the flow of reports of this crash. The message came up in red so I hope they saw it and read it. A bit discouraged that we already have a crash report just a few days after release.
Note:
See TracTickets
for help on using tickets.
Well, I have good news and I have bad news. The good news is that your auto-detection of the cause of a crash worked and an appropriate message was displayed to the user. The bad news is that the user reported the bug anyway.