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Opened 12 months ago
Closed 12 months ago
#16121 closed defect (duplicate)
Crash in garbage collection
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.5-arm64-arm-64bit
ChimeraX Version: 1.8rc202405171936 (2024-05-17 19:36:10 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x0000000205764c00 (most recent call first):
Garbage-collecting
File "/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/ast.py", line 63 in update
File "/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/ast.py", line 19 in __init__
File "/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/ast.py", line 90 in copy
File "/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 642 in _try
File "/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/contextlib.py", line 137 in __enter__
File "/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 665 in _option
File "/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/contextlib.py", line 137 in __enter__
File "/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py", line 439 in _atom_
File "/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 497 in _invoke_rule
File "/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 458 in _call
File "/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 59 in wrapper
File "/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py", line 396 in block7
File "/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 787 in _positive_closure
File "/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py", line 398 in _residue_
File "/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 497 in _invoke_rule
File "/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 458 in _call
File "/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 59 in wrapper
File "/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py", line 344 in block2
File "/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 771 in _closure
File "/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py", line 346 in _chain_
File "/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 497 in _invoke_rule
File "/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 458 in _call
File "/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 59 in wrapper
File "/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py", line 323 in block0
File "/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 748 in _repeater
File "/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 789 in _positive_closure
File "/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py", line 325 in _model_parts_
File "/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 497 in _invoke_rule
File "/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 458 in _call
File "/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 59 in wrapper
File "/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py", line 200 in _model_
File "/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 497 in _invoke_rule
File "/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 458 in _call
File "/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 59 in wrapper
File "/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py", line 157 in block0
File "/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 787 in _positive_closure
File "/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py", line 159 in _model_list_
File "/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 497 in _invoke_rule
File "/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 458 in _call
File "/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 59 in wrapper
File "/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py", line 136 in _as_term_
File "/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 497 in _invoke_rule
File "/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 458 in _call
File "/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 59 in wrapper
File "/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py", line 89 in _atom_specifier_
File "/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 497 in _invoke_rule
File "/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 458 in _call
File "/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 59 in wrapper
File "/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 206 in parse
File "/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 192 in _parse_unquoted
File "/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 121 in parse
File "/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/args.py", line 123 in parse
File "/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2780 in _parse_arg
File "/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2926 in _process_positional_arguments
File "/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3166 in run
File "/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49 in run
File "/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/show_sequences/tool.py", line 74 in show_seqs
File "/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 285 in event_loop
File "/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1006 in init
File "/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1169 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, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, lxml._elementpath, lxml.etree, chimerax.surface._surface, chimerax.pdb_lib._load_libs, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, 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, PIL._imagingmath, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets (total: 55)
{"app_name":"ChimeraX","timestamp":"2024-10-11 13:37:02.00 -0500","app_version":"1.8.0","slice_uuid":"17982d98-65bc-3327-8526-577ec996453c","build_version":"1.8.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 14.5 (23F79)","roots_installed":0,"name":"ChimeraX","incident_id":"EFC7D5D0-1426-4D2E-8BC3-AE3C7A16AD6F"}
{
"uptime" : 6600,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac15,6",
"coalitionID" : 3619,
"osVersion" : {
"train" : "macOS 14.5",
"build" : "23F79",
"releaseType" : "User"
},
"captureTime" : "2024-10-11 13:37:01.7177 -0500",
"codeSigningMonitor" : 1,
"incident" : "EFC7D5D0-1426-4D2E-8BC3-AE3C7A16AD6F",
"pid" : 9654,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-10-11 13:34:09.3278 -0500",
"procStartAbsTime" : 154803583939,
"procExitAbsTime" : 158940763604,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.8-rc2024.05.17.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"CB4CAF32-F353-590D-B75D-53A2EB9DB1F8","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "90CF9E7A-0191-7709-E234-12B6F1C3F8AE",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRW+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkVDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"wakeTime" : 750,
"sleepWakeUUID" : "31A78EE0-6FEB-4F70-B0B5-891AE49F945A",
"sip" : "enabled",
"vmRegionInfo" : "0xa9 is not in any region. Bytes before following region: 4371775319\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 104940000-104944000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.8-rc2024.05.17.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x00000000000000a9","rawCodes":[1,169],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00000000000000a9"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":9654},
"vmregioninfo" : "0xa9 is not in any region. Bytes before following region: 4371775319\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 104940000-104944000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.8-rc2024.05.17.app\/Contents\/MacOS\/ChimeraX",
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
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"rolloutId" : "5fb4245a1bbfe8005e33a1e1",
"factorPackIds" : {
},
"deploymentId" : 240000021
}
],
"experiments" : [
{
"treatmentId" : "c47ab4cc-c9c3-4b5d-a87c-e2433ce02597",
"experimentId" : "6639bc6ba73d460582162323",
"deploymentId" : 400000006
},
{
"treatmentId" : "45f4e2a5-551b-4bc2-a2dc-19c244dda8f8",
"experimentId" : "6643969b3099cf28e049862f",
"deploymentId" : 400000007
}
]
}
}
===== Log before crash start =====
UCSF ChimeraX version: 1.8rc202405170741 (2024-05-17)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/maryam/Downloads/9ayf.pdb
9ayf.pdb title:
Structure of human calcium-sensing receptor In complex with GI1 (MINIGI1)
protein In detergent [more info...]
Chain information for 9ayf.pdb #1
---
Chain | Description | UniProt
A | adenylate cyclase-inhibiting G α protein | GNAI1_HUMAN 1-57 66-229
B | transducin β chain 1 | GBB1_HUMAN 2-340
G | G γ-I | GBG2_HUMAN 1-71
H | single-chain antibody fragment SCFV16 |
Q R | isoform 1 of extracellular calcium-sensing receptor | CASR_HUMAN -7-903
Non-standard residues in 9ayf.pdb #1
---
9IG — 3-(2-chlorophenyl)-N-[(1R)-1-(3-methoxyphenyl)ethyl]propan-1-amine
AV0 — lauryl maltose neopentyl glycol (2,2-didecylpropane-1,3-bis-B-D-
maltopyranoside; 2-decyl-2-{[(4-O-α-D-glucopyranosyl-β-D-
glucopyranosyl)oxy]methyl}DODECYL4-O-α-D-glucopyranosyl-β-D-glucopyranoside)
CA — calcium ion
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine;
2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine)
PO4 — phosphate ion
TCR — cyclomethyltryptophan
> hide atoms
> show atoms
> show cartoons
> style stick
Changed 19630 atom styles
> hide cartoons
> show cartoons
> hide atoms
> ui tool show "Show Sequence Viewer"
> sequence chain /B
Alignment identifier is 1/B
> ui tool show "Show Sequence Viewer"
> sequence chain /G
Alignment identifier is 1/G
> select clear
> select /G
447 atoms, 453 bonds, 58 residues, 1 model selected
> delete :1-51
> ui tool show "Show Sequence Viewer"
> sequence chain /B
Alignment identifier is 1/B
> delete :7-293
> ui tool show "Show Sequence Viewer"
> close #1
> open /Users/maryam/Downloads/9ayf.pdb format pdb
9ayf.pdb title:
Structure of human calcium-sensing receptor In complex with GI1 (MINIGI1)
protein In detergent [more info...]
Chain information for 9ayf.pdb #1
---
Chain | Description | UniProt
A | adenylate cyclase-inhibiting G α protein | GNAI1_HUMAN 1-57 66-229
B | transducin β chain 1 | GBB1_HUMAN 2-340
G | G γ-I | GBG2_HUMAN 1-71
H | single-chain antibody fragment SCFV16 |
Q R | isoform 1 of extracellular calcium-sensing receptor | CASR_HUMAN -7-903
Non-standard residues in 9ayf.pdb #1
---
9IG — 3-(2-chlorophenyl)-N-[(1R)-1-(3-methoxyphenyl)ethyl]propan-1-amine
AV0 — lauryl maltose neopentyl glycol (2,2-didecylpropane-1,3-bis-B-D-
maltopyranoside; 2-decyl-2-{[(4-O-α-D-glucopyranosyl-β-D-
glucopyranosyl)oxy]methyl}DODECYL4-O-α-D-glucopyranosyl-β-D-glucopyranoside)
CA — calcium ion
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine;
2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine)
PO4 — phosphate ion
TCR — cyclomethyltryptophan
> show cartoons
> show atoms
> hide atoms
> ui tool show "Show Sequence Viewer"
> sequence chain /B
Alignment identifier is 1/B
> delete :7-293
> ui tool show "Show Sequence Viewer"
> sequence chain /B
Alignment identifier is 1/B
> ui tool show "Show Sequence Viewer"
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.8rc202405170741 (2024-05-17)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M3 Pro
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac15,6
Model Number: Z1AX00298LL/A
Chip: Apple M3 Pro
Total Number of Cores: 11 (5 performance and 6 efficiency)
Memory: 18 GB
System Firmware Version: 10151.121.1
OS Loader Version: 10151.121.1
Software:
System Software Overview:
System Version: macOS 14.5 (23F79)
Kernel Version: Darwin 23.5.0
Time since boot: 2 hours, 59 minutes
Graphics/Displays:
Apple M3 Pro:
Chipset Model: Apple M3 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 14
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57
ChimeraX-AtomicLibrary: 14.0.5
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.4
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.4
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: 1.8rc202405170741
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.3
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.16
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.4
ChimeraX-PDB: 2.7.5
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.0.3
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.4
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.1
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.51.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.2
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.10
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.43
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4
traitlets: 5.14.2
typing-extensions: 4.11.0
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.10
Change History (2)
comment:1 by , 12 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Core |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in garbage collection |
comment:2 by , 12 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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