![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 6 months ago
Closed 6 months ago
#17419 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-15.3.2-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 0x00000001fd464840 (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, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 61)
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{
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"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac14,2",
"coalitionID" : 77862,
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"build" : "24D81",
"releaseType" : "User"
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"captureTime" : "2025-04-18 14:18:01.6829 +0900",
"codeSigningMonitor" : 1,
"incident" : "705D8CB7-B8AA-4D82-A4C2-F9FBB5F79E42",
"pid" : 22914,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-04-18 13:16:52.4693 +0900",
"procStartAbsTime" : 14917880517849,
"procExitAbsTime" : 15005933917423,
"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":"C17635AB-2CC7-55FD-94EA-1A09698D8823","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "B5A62B1D-6A4C-80F9-1C84-CE6A9B2C4266",
"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" : "25E59FC0-06F1-4EE2-A7CC-867C4A014450",
"wakeTime" : 13355,
"sleepWakeUUID" : "C830D4AC-39C0-4A07-84CD-5BF48F5EE8F4",
"sip" : "enabled",
"vmRegionInfo" : "0x72903e541978 is not in any region. Bytes after previous region: 20410133289337 \n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n owned unmapped memory unmapped-unmapped [ 57.3M] rw-\/rw- SM=PRV owned physical footprint (unmapped)\n---> \n UNUSED SPACE AT END",
"exception" : {"codes":"0x0000000000000001, 0x000072903e541978","rawCodes":[1,125963846556024],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x000072903e541978"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":22914},
"vmregioninfo" : "0x72903e541978 is not in any region. Bytes after previous region: 20410133289337 \n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n owned unmapped memory unmapped-unmapped [ 57.3M] rw-\/rw- SM=PRV owned physical footprint (unmapped)\n---> \n UNUSED SPACE AT END",
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"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" : "arm64",
"base" : 6382665728,
"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" : 6351241216,
"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"
},
{
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"arch" : "arm64",
"base" : 6351716352,
"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" : "arm64",
"base" : 6158565376,
"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" : 6158401536,
"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" : 6160171008,
"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" : 6158745600,
"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" : 6161498112,
"size" : 147456,
"uuid" : "1e310bc7-5f96-396b-816d-5b40a3dde12c",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/pdb\/_pdbio.cpython-311-darwin.so",
"name" : "_pdbio.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "arm64",
"base" : 6386876416,
"size" : 3817472,
"uuid" : "579ef19c-6e85-36be-a566-c980f789fbc0",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/lxml\/etree.cpython-311-darwin.so",
"name" : "etree.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "arm64",
"base" : 6158172160,
"size" : 131072,
"uuid" : "c8b24269-c8a2-3244-b044-b85c3449800d",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/lxml\/_elementpath.cpython-311-darwin.so",
"name" : "_elementpath.cpython-311-darwin.so"
},
{
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"arch" : "arm64",
"base" : 5821988864,
"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"
},
{
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"arch" : "arm64",
"base" : 5829361664,
"size" : 16384,
"uuid" : "644b1794-90c5-3838-9ffa-b772683aeb37",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/alignment_algs\/_sw.cpython-311-darwin.so",
"name" : "_sw.cpython-311-darwin.so"
},
{
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"base" : 5830492160,
"size" : 16384,
"uuid" : "02f24514-9c56-3aa2-806f-b6eae4e7cf23",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/alignment_algs\/libalign_algs.dylib",
"name" : "libalign_algs.dylib"
},
{
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"arch" : "arm64",
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"uuid" : "4e700338-6839-3c7c-9f41-a201e7f185e5",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/dssp\/_dssp.cpython-311-darwin.so",
"name" : "_dssp.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "arm64",
"base" : 5860589568,
"size" : 32768,
"uuid" : "93fd54d8-5d5e-319d-94c5-2702d533d751",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/alignment_algs\/_nw.cpython-311-darwin.so",
"name" : "_nw.cpython-311-darwin.so"
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"size" : 241656,
"uuid" : "eee9d0d3-dffc-37cb-9ced-b27cd0286d8c",
"path" : "\/usr\/lib\/system\/libsystem_kernel.dylib",
"name" : "libsystem_kernel.dylib"
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"uuid" : "984d08b8-f85c-36f5-9e17-5bff7fc779a3",
"path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
"name" : "libsystem_platform.dylib"
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"name" : "SkyLight"
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"uuid" : "5576e4fd-aad2-3608-8c8f-4eec421236f9",
"path" : "\/usr\/lib\/system\/libdispatch.dylib",
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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/kimbomin/Library/CloudStorage/Dropbox/share_dir/jieun_bomin/CB1_project/Chimera_Session/CB1_7FEE_5TGZ_keyresidues.cxs
> format session
opened ChimeraX session
> select : 170
44 atoms, 44 bonds, 4 residues, 4 models selected
> show (#!1-2 & sel) target ab
> label (#!1-2 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> show #3 models
> show #!4 models
> show sel target ab
> label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}"
> select : 356
50 atoms, 52 bonds, 4 residues, 4 models selected
> show sel target ab
> hide #!4 models
> hide #!3 models
> hide #!2 models
> select add #2
3578 atoms, 3648 bonds, 458 residues, 5 models selected
> select add #3
7507 atoms, 7584 bonds, 1011 residues, 6 models selected
> select add #4
10909 atoms, 11067 bonds, 1446 residues, 7 models selected
> select subtract #4
7499 atoms, 7577 bonds, 1010 residues, 5 models selected
> select subtract #3
3556 atoms, 3626 bonds, 456 residues, 3 models selected
> select subtract #2
14 atoms, 15 bonds, 1 residue, 1 model selected
> select add #1
4060 atoms, 4126 bonds, 520 residues, 2 models selected
> show #!4 models
> select add #4
7470 atoms, 7616 bonds, 956 residues, 4 models selected
> hide #!1 models
> select subtract #1
3410 atoms, 3490 bonds, 436 residues, 2 models selected
> color (#!4 & sel) #ffa4aeff
> hide #!4 models
> select subtract #4
Nothing selected
> show #!3 models
> show #!2 models
> hide #!3 models
> select add #2
3542 atoms, 3611 bonds, 455 residues, 2 models selected
> color (#!2 & sel) #abc5eeff
> color (#!2 & sel) #95a7f2ff
> color (#!2 & sel) #7177f2ff
> show #!3 models
> select add #3
7485 atoms, 7562 bonds, 1009 residues, 4 models selected
> select subtract #2
3943 atoms, 3951 bonds, 554 residues, 2 models selected
> hide #!2 models
> color (#!3 & sel) cornflower blue
> color sel byhetero
> show #!2 models
> select add #2
7485 atoms, 7562 bonds, 1009 residues, 4 models selected
> hide #!3 models
> select subtract #3
3542 atoms, 3611 bonds, 455 residues, 2 models selected
> color sel byhetero
> transparency 80 cartoons
> show #!1 models
> select add #1
7602 atoms, 7737 bonds, 975 residues, 4 models selected
> show #!3 models
> select add #3
11545 atoms, 11688 bonds, 1529 residues, 6 models selected
> show #!4 models
> select add #4
14955 atoms, 15178 bonds, 1965 residues, 8 models selected
> select clear
> select
> ::name="7DY"::name="7IC"::name="8D0"::name="9GF"::name="CLR"::name="FMN"::name="GOL"::name="HOH"::name="OLA"::name="OLC"::name="PEG"::name="SO4"::name="ZDG"
657 atoms, 560 bonds, 131 residues, 4 models selected
> hide sel target a
> ui tool show "Side View"
> select ::name="9GF"
27 atoms, 28 bonds, 1 residue, 1 model selected
> show sel target ab
> select ::name="7DY"
36 atoms, 38 bonds, 1 residue, 1 model selected
> show sel target ab
> hide #!2 models
> hide #!3 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!4 models
> show #!4 models
> select : 356
50 atoms, 52 bonds, 4 residues, 4 models selected
> hide #!4 models
> label (#!1 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> show #!2 models
> hide #!1 models
> ~label (#!2 & sel) residues
> show #!1 models
> select clear
Drag select of 3 atoms, 11 residues, 3 bonds
> select #1/A:388
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel target a
> select #2/A:387
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel target a
> select #1/A:388
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:387
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel target a
> select clear
> open
> "/private/var/folders/j3/26dx8rz97pq7ywn7507_0pcw0000gn/T/TemporaryItems/NSIRD_screencaptureui_1ij97B/스크린샷
> 2025-04-18 오후 1.39.43.png"
Failed opening file
/private/var/folders/j3/26dx8rz97pq7ywn7507_0pcw0000gn/T/TemporaryItems/NSIRD_screencaptureui_1ij97B/스크린샷
2025-04-18 오후 1.39.43.png:
Image mode RGBA is not supported (L, P, I;16, I;16B, I;16L, I;16S, F, F;32BF,
I, RGB)
> open /Users/kimbomin/Library/CloudStorage/Dropbox/9b54.cif
Summary of feedback from opening
/Users/kimbomin/Library/CloudStorage/Dropbox/9b54.cif
---
note | Fetching CCD A1AIW from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/W/A1AIW/A1AIW.cif
9b54.cif title:
Biased agonist bound CB1-Gi structure [more info...]
Chain information for 9b54.cif #5
---
Chain | Description | UniProt
A | Guanine nucleotide-binding protein G(i) subunit alpha-1 | GNAI1_HUMAN 1-354
B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | GBB1_HUMAN 2-340
C | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | GBG2_HUMAN 1-71
R | Cannabinoid receptor 1 | CNR1_HUMAN -6-472
S | scFv16 |
Non-standard residues in 9b54.cif #5
---
A1AIW — methyl
N-{6-(4-carbamimidamidobutoxy)-1-[(4-fluorophenyl)methyl]-1H-indazole-3-carbonyl}-3-methyl-
L-valinate
> select add #5
8512 atoms, 8689 bonds, 6 pseudobonds, 1111 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> ui tool show Matchmaker
> matchmaker #!5 to #1
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 7fee.pdb, chain A (#1) with 9b54.cif, chain R (#5), sequence
alignment score = 1173.5
RMSD between 164 pruned atom pairs is 1.217 angstroms; (across all 265 pairs:
4.059)
> select clear
> view
> ui tool show "Side View"
> transparency 80 cartoons
> select : 170
67 atoms, 65 bonds, 7 residues, 5 models selected
> show sel & #!1-2,5 atoms
> style sel & #!1-2,5 stick
Changed 45 atom styles
> show #!4 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> select : 356
64 atoms, 67 bonds, 5 residues, 5 models selected
> show sel & #!1-2,4-5 atoms
> style sel & #!1-2,4-5 stick
Changed 50 atom styles
> color sel & #!1-2,4-5 byhetero
> select #1/A:356
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #1/A:355
6 atoms, 5 bonds, 1 residue, 1 model selected
Drag select of 2 atoms, 23 residues, 1 bonds
> show sel atoms
> undo
> select #4/A:478
14 atoms, 15 bonds, 1 residue, 1 model selected
> hide #!2 models
> hide #!1 models
> hide #!5 models
Drag select of 4 residues
> show sel atoms
> undo
> select #4/A:478
14 atoms, 15 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> show #!2 models
> show #!1 models
> show #!5 models
> show #!3 models
> hide sel atoms
> undo
> select ~sel
23453 atoms, 23850 bonds, 6 pseudobonds, 3075 residues, 10 models selected
> hide sel atoms
> select clear
> select : 356
64 atoms, 67 bonds, 5 residues, 5 models selected
> show sel atoms
> select : 170
67 atoms, 65 bonds, 7 residues, 5 models selected
> show sel target ab
> select clear
> select ::name="7DY"
36 atoms, 38 bonds, 1 residue, 1 model selected
> show sel target ab
> select clear
> save
> /Users/kimbomin/Dropbox/share_dir/jieun_bomin/CB1_project/Chimera_Session/CB1_Ago_Anta_crystals.cxs
> select ::name="A1AIW"
73 atoms, 75 bonds, 1 residue, 1 model selected
> show sel target ab
> select H
35 atoms, 1 residue, 1 model selected
> hide sel target a
> select
> ::name="7DY"::name="7IC"::name="8D0"::name="9GF"::name="A1AIW"::name="CLR"::name="FMN"::name="GOL"::name="HOH"::name="OLA"::name="OLC"::name="PEG"::name="SO4"::name="ZDG"
730 atoms, 635 bonds, 132 residues, 5 models selected
> hide sel target a
> select ::name="A1AIW"
73 atoms, 75 bonds, 1 residue, 1 model selected
> show sel target ab
> select clear
> select ::name="A1AIW"
73 atoms, 75 bonds, 1 residue, 1 model selected
> select ::name="7DY"
36 atoms, 38 bonds, 1 residue, 1 model selected
> show sel target ab
> select ::name="9GF"
27 atoms, 28 bonds, 1 residue, 1 model selected
> show sel target ab
> select : 155
73 atoms, 72 bonds, 7 residues, 5 models selected
> show sel target ab
> style sel stick
Changed 73 atom styles
> color sel byhetero
> select add #5
8556 atoms, 8733 bonds, 6 pseudobonds, 1115 residues, 6 models selected
> select subtract #5
44 atoms, 44 bonds, 4 residues, 4 models selected
> select add #4
3443 atoms, 3523 bonds, 439 residues, 5 models selected
> select add #3
7375 atoms, 7463 bonds, 992 residues, 6 models selected
> select add #2
10906 atoms, 11063 bonds, 1446 residues, 7 models selected
> select subtract #2
7364 atoms, 7452 bonds, 991 residues, 5 models selected
> select subtract #3
3421 atoms, 3501 bonds, 437 residues, 3 models selected
> select subtract #4
11 atoms, 11 bonds, 1 residue, 1 model selected
> label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}"
> select clear
> hide #!4 models
> hide #!5 models
> hide #!1 models
> hide #!2 models
> show #!2 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!4 models
> hide #!4 models
> show #!5 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 M2
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: Mac14,2
Model Number: Z15Y0001VKH/A
Chip: Apple M2
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 8 GB
System Firmware Version: 11881.81.4
OS Loader Version: 11881.81.4
Software:
System Software Overview:
System Version: macOS 15.3.2 (24D81)
Kernel Version: Darwin 24.3.0
Time since boot: 9일 2시간 30분
Graphics/Displays:
Apple M2:
Chipset Model: Apple M2
Type: GPU
Bus: Built-In
Total Number of Cores: 8
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: No
Connection Type: Internal
LG HDR QHD:
Resolution: 1920 x 1080 (1080p FHD - Full 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 , 6 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 , 6 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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