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Opened 10 months ago
Closed 9 months ago
#16595 closed defect (duplicate)
Crash in garbage collection
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-12.1-x86_64-i386-64bit
ChimeraX Version: 1.8.dev202404050126 (2024-04-05 01:26:12 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 0x0000000119f2a600 (most recent call first):
Garbage-collecting
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 161 in
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 161 in __iter__
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 907 in atomspec_atoms
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 627 in _add_model_parts
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 476 in _check
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 490 in _check
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 470 in find_matches
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 612 in find_matches
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 455 in find_matches
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 1011 in find_matches
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 1008 in evaluate
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 1098 in evaluate
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/args.py", line 36 in parse
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/args.py", line 71 in parse
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2495 in _parse_arg
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2791 in _process_keyword_arguments
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2865 in run
File "/Applications/ChimeraX_Daily.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_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/match_maker/tool.py", line 303 in run_matchmaker
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 283 in event_loop
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1069 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, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, 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, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, PIL._imagingmath, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize (total: 60)
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{
"uptime" : 200000,
"procLaunch" : "2025-01-09 13:42:12.4085 -0600",
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookAir7,2",
"procStartAbsTime" : 207062406964958,
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"captureTime" : "2025-01-09 14:45:02.5900 -0600",
"incident" : "99BD80AF-1537-4B9C-98C9-6E007140D611",
"bug_type" : "309",
"pid" : 47220,
"procExitAbsTime" : 209822643275641,
"cpuType" : "X86-64",
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
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"crashReporterKey" : "5F0E6A8E-1AB0-AADA-C9D5-7F27A7CF2221",
"wakeTime" : 2204,
"sleepWakeUUID" : "1AEA5609-8F08-41B7-AE58-FA1945F12B42",
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"vmRegionInfo" : "0xa9 is not in any region. Bytes before following region: 4462108503\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 109f66000-109f6a000 [ 16K] r-x\/r-x SM=COW ...acOS\/ChimeraX",
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"path" : "\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/atomic\/cymol.cpython-311-darwin.so",
"name" : "cymol.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4789276672,
"size" : 1196032,
"uuid" : "d54465fc-3a07-34e5-95fa-6c6ebe8244b4",
"path" : "\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/atomic_lib\/lib\/libatomstruct.dylib",
"name" : "libatomstruct.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4586446848,
"size" : 1720320,
"uuid" : "d186fce2-169a-3875-8ca4-f2fcd55371cf",
"path" : "\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/QtCore.abi3.so",
"name" : "QtCore.abi3.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4578947072,
"size" : 5373952,
"uuid" : "f4950342-54e3-3755-a88f-e2a6406c1fc3",
"path" : "\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtCore.framework\/Versions\/A\/QtCore",
"name" : "QtCore"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4709670912,
"size" : 4931584,
"uuid" : "6b647ba7-e77f-36aa-937c-028f9cb4875c",
"path" : "\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtWidgets.framework\/Versions\/A\/QtWidgets",
"name" : "QtWidgets"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4703543296,
"size" : 2867200,
"uuid" : "04d3e498-8e36-3f03-9aa5-8a19040cc57f",
"path" : "\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/QtWidgets.abi3.so",
"name" : "QtWidgets.abi3.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4691054592,
"size" : 7274496,
"uuid" : "57e18c1d-e3ae-37c5-ada4-dcc62718794e",
"path" : "\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtGui.framework\/Versions\/A\/QtGui",
"name" : "QtGui"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4725571584,
"size" : 655360,
"uuid" : "a9df58b1-89b1-36c8-9d9e-fe251bf025f2",
"path" : "\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/plugins\/platforms\/libqcocoa.dylib",
"name" : "libqcocoa.dylib"
},
{
"source" : "P",
"arch" : "x86_64h",
"base" : 140703607099392,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.CoreFoundation",
"size" : 5255168,
"uuid" : "eab0e216-2a9e-31ce-9164-fdf3ebcf7bd3",
"path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
"name" : "CoreFoundation",
"CFBundleVersion" : "1856.105"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703754420224,
"CFBundleShortVersionString" : "2.1.1",
"CFBundleIdentifier" : "com.apple.HIToolbox",
"size" : 3112960,
"uuid" : "535dbc28-4d26-3609-86bb-5c40227b648c",
"path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
"name" : "HIToolbox"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703651594240,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.AppKit",
"size" : 15265792,
"uuid" : "d23b9681-3764-3298-a716-fbb511dd5a7c",
"path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
"name" : "AppKit",
"CFBundleVersion" : "2113.20.111"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4462108672,
"CFBundleShortVersionString" : "1.8.0",
"CFBundleIdentifier" : "edu.ucsf.cgl.ChimeraX",
"size" : 16384,
"uuid" : "194a3167-3db5-3029-8d22-1d742b826bb9",
"path" : "\/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
"name" : "ChimeraX",
"CFBundleVersion" : "1.8.0.0"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4729774080,
"size" : 442368,
"uuid" : "cef5a27a-d50b-3020-af03-1734b19bc8c5",
"path" : "\/usr\/lib\/dyld",
"name" : "dyld"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5101391872,
"size" : 183599104,
"uuid" : "af091873-5278-3492-8e76-7c22e65c04ac",
"path" : "\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtWebEngineCore.framework\/Versions\/A\/QtWebEngineCore",
"name" : "QtWebEngineCore"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703606104064,
"size" : 364544,
"uuid" : "c006ac8c-2c1c-3ca5-9085-9a754386bf42",
"path" : "\/usr\/lib\/libc++.1.dylib",
"name" : "libc++.1.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140704014761984,
"CFBundleShortVersionString" : "17612",
"CFBundleIdentifier" : "com.apple.JavaScriptCore",
"size" : 20119552,
"uuid" : "5f124536-07f4-328b-a93e-2b6ddab37fee",
"path" : "\/System\/Library\/Frameworks\/JavaScriptCore.framework\/Versions\/A\/JavaScriptCore",
"name" : "JavaScriptCore",
"CFBundleVersion" : "17612.3.6.1.6"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4592009216,
"size" : 66404352,
"uuid" : "7048d1fd-b9a9-3f6a-b752-ae8be69f6c3f",
"path" : "\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/numpy\/.dylibs\/libopenblas64_.0.dylib",
"name" : "libopenblas64_.0.dylib"
}
],
"sharedCache" : {
"base" : 140703603556352,
"size" : 15216738304,
"uuid" : "40432a03-88d3-305f-9c0c-e7549e71d927"
},
"vmSummary" : "ReadOnly portion of Libraries: Total=1.5G resident=0K(0%) swapped_out_or_unallocated=1.5G(100%)\nWritable regions: Total=2.1G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=2.1G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 768K 6 \nActivity Tracing 256K 1 \nCG backing stores 544K 4 \nCG image 436K 47 \nColorSync 244K 29 \nCoreAnimation 916K 74 \nCoreGraphics 12K 2 \nCoreServices 624K 2 \nCoreUI image data 2768K 40 \nFoundation 52K 2 \nIOKit 7940K 1 \nJS JIT generated code 1.0G 3 \nKernel Alloc Once 8K 1 \nMALLOC 729.3M 437 \nMALLOC guard page 32K 8 \nMALLOC_LARGE (reserved) 384K 1 reserved VM address space (unallocated)\nMach message 16K 3 \nOpenGL GLSL 384K 4 \nSTACK GUARD 132K 33 \nStack 174.8M 34 \nStack Guard 56.0M 1 \nVM_ALLOCATE 168.0M 154 \nWebKit Malloc 1128K 7 \n__DATA 38.5M 699 \n__DATA_CONST 40.1M 404 \n__DATA_DIRTY 1776K 234 \n__FONT_DATA 4K 1 \n__GLSLBUILTINS 5176K 1 \n__LINKEDIT 672.1M 161 \n__OBJC_RO 81.8M 1 \n__OBJC_RW 3136K 2 \n__TEXT 817.8M 704 \n__UNICODE 588K 1 \ndyld private memory 1056K 3 \nmapped file 210.6M 55 \nshared memory 2976K 27 \n=========== ======= ======= \nTOTAL 3.9G 3187 \nTOTAL, minus reserved VM space 3.9G 3187 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "607844aa04477260f58a8077",
"factorPackIds" : {
"SIRI_MORPHUN_ASSETS" : "6103050cbfe6dc472e1c982a"
},
"deploymentId" : 240000066
},
{
"rolloutId" : "60da5e84ab0ca017dace9abf",
"factorPackIds" : {
},
"deploymentId" : 240000008
},
{
"rolloutId" : "602ad4dac86151000cf27e46",
"factorPackIds" : {
"SIRI_DICTATION_ASSETS" : "6193d03f2171a2330e561dfc"
},
"deploymentId" : 240000303
},
{
"rolloutId" : "601d9415f79519000ccd4b69",
"factorPackIds" : {
"SIRI_TEXT_TO_SPEECH" : "621d4d0f680160486b9e1c98"
},
"deploymentId" : 240000416
},
{
"rolloutId" : "63582c5f8a53461413999550",
"factorPackIds" : {
},
"deploymentId" : 240000002
},
{
"rolloutId" : "5fb4245a1bbfe8005e33a1e1",
"factorPackIds" : {
},
"deploymentId" : 240000021
},
{
"rolloutId" : "5f72dc58705eff005a46b3a9",
"factorPackIds" : {
},
"deploymentId" : 240000015
},
{
"rolloutId" : "60f8ddccefea4203d95cbeef",
"factorPackIds" : {
},
"deploymentId" : 240000025
},
{
"rolloutId" : "5fc94383418129005b4e9ae0",
"factorPackIds" : {
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"deploymentId" : 240000614
},
{
"rolloutId" : "60186475825c62000ccf5450",
"factorPackIds" : {
},
"deploymentId" : 240000083
},
{
"rolloutId" : "5ffde50ce2aacd000d47a95f",
"factorPackIds" : {
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}
],
"experiments" : [
]
}
}
===== Log before crash start =====
Startup Messages
---
notes | available bundle cache has not been initialized yet
Database-fetch provider 'redo' in bundle Map specified unknown data format
'MTZ'
UCSF ChimeraX version: 1.8.dev202404050126 (2024-04-05)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/adrianadejesus/Downloads/ChimeraX/AlphaFold/delta/Munia-trimero-
> resultado/best_model_munia.pdb
Chain information for best_model_munia.pdb #1
---
Chain | Description
A B C | No description available
> color #1 #db151eff
> color #1 #db0c00ff
> open "/Users/adrianadejesus/Desktop/coronavirus/Deltacoronavirus/color
> rbd/munia-rbd-color.pdb"
munia-rbd-color.pdb title:
SWISS-MODEL SERVER (https://swissmodel.expasy.org) Munia coronavirus
HKU13-3514 [more info...]
Chain information for munia-rbd-color.pdb
---
Chain | Description
2.1/A 2.2/A 2.1/B 2.2/B 2.1/C 2.2/C | No description available
> ui tool show Matchmaker
> hide #!2 models
> show #!2 models
> hide #2.1 models
> hide #2.2 models
> show #2.1 models
> show #2.2 models
> color #2 #0dbfbbff models
> color #2 #03adbfff models
> hide #2.2 models
> show #2.2 models
> hide #2.1 models
> show #2.1 models
> ui tool show Matchmaker
> matchmaker #2.1/A#2.1/B#2.1/C to #1/A#1/B#1/C pairing ss
Parameters
---
Chain pairing | ss
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 best_model_munia.pdb, chain A (#1) with munia-rbd-color.pdb, chain
A (#2.1), sequence alignment score = 633.2
Matchmaker best_model_munia.pdb, chain B (#1) with munia-rbd-color.pdb, chain
B (#2.1), sequence alignment score = 633.2
Matchmaker best_model_munia.pdb, chain C (#1) with munia-rbd-color.pdb, chain
C (#2.1), sequence alignment score = 629.6
RMSD between 6 pruned atom pairs is 1.203 angstroms; (across all 366 pairs:
22.383)
> ui tool show Matchmaker
> matchmaker #2.2/A#2.2/B#2.2/C to #1/A#1/B#1/C pairing ss
Parameters
---
Chain pairing | ss
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 best_model_munia.pdb, chain A (#1) with munia-rbd-color.pdb, chain
A (#2.2), sequence alignment score = 633.2
Matchmaker best_model_munia.pdb, chain B (#1) with munia-rbd-color.pdb, chain
B (#2.2), sequence alignment score = 633.2
Matchmaker best_model_munia.pdb, chain C (#1) with munia-rbd-color.pdb, chain
C (#2.2), sequence alignment score = 629.6
RMSD between 6 pruned atom pairs is 1.203 angstroms; (across all 366 pairs:
22.383)
> save /Users/adrianadejesus/Desktop/image1.png supersample 3
> save "/Users/adrianadejesus/Desktop/alineamientos 3d/RBD-SW-AP/munia.cxs"
> close session
> open /Users/adrianadejesus/Downloads/ChimeraX/AlphaFold/delta/wigeon-
> coronavirus-resultados/best_model_wigeon.pdb
Chain information for best_model_wigeon.pdb #1
---
Chain | Description
A B C | No description available
> color #1 #db1a12ff
> color #1 #db0004ff
> open "/Users/adrianadejesus/Desktop/coronavirus/Deltacoronavirus/color
> rbd/wigeon rbd-color.pdb"
wigeon rbd-color.pdb title:
SWISS-MODEL SERVER (https://swissmodel.expasy.org) wigeon HKU20 [more info...]
Chain information for wigeon rbd-color.pdb #2
---
Chain | Description
A B C | No description available
> color #2 #12efd2ff
> color #2 #0fe9efff
> ui tool show Matchmaker
> matchmaker #2/A#2/B#2/C to #1/A#1/B#1/C pairing ss
Parameters
---
Chain pairing | ss
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 best_model_wigeon.pdb, chain A (#1) with wigeon rbd-color.pdb,
chain A (#2), sequence alignment score = 394.3
Matchmaker best_model_wigeon.pdb, chain B (#1) with wigeon rbd-color.pdb,
chain B (#2), sequence alignment score = 397.9
Matchmaker best_model_wigeon.pdb, chain C (#1) with wigeon rbd-color.pdb,
chain C (#2), sequence alignment score = 394.3
RMSD between 5 pruned atom pairs is 1.520 angstroms; (across all 306 pairs:
26.496)
> save /Users/adrianadejesus/Desktop/image1.png supersample 3
> save "/Users/adrianadejesus/Desktop/alineamientos 3d/RBD-SW-AP/wigeon.cxs"
> close session
> open /Users/adrianadejesus/Downloads/ChimeraX/AlphaFold/delta/White-eye-
> trimero-resultados/best_model_white-eye.pdb
Chain information for best_model_white-eye.pdb #1
---
Chain | Description
A B C | No description available
> open "/Users/adrianadejesus/Desktop/coronavirus/Deltacoronavirus/color
> rbd/WE-RBD-color.pdb"
WE-RBD-color.pdb title:
SWISS-MODEL SERVER (https://swissmodel.expasy.org) White-eye HKU16 [more
info...]
Chain information for WE-RBD-color.pdb #2
---
Chain | Description
A B C | No description available
> color #1 #db1613ff
> color #1 #db0705ff
> color #2 #00ebefff
> color #2 #09e1efff
> ui tool show Matchmaker
> matchmaker #2/A#2/B#2/C to #1/A#1/B#1/C pairing ss
Parameters
---
Chain pairing | ss
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 best_model_white-eye.pdb, chain A (#1) with WE-RBD-color.pdb, chain
A (#2), sequence alignment score = 522
Matchmaker best_model_white-eye.pdb, chain B (#1) with WE-RBD-color.pdb, chain
B (#2), sequence alignment score = 522
Matchmaker best_model_white-eye.pdb, chain C (#1) with WE-RBD-color.pdb, chain
C (#2), sequence alignment score = 518.4
RMSD between 56 pruned atom pairs is 1.178 angstroms; (across all 339 pairs:
5.081)
> save /Users/adrianadejesus/Desktop/image1.png supersample 3
> save "/Users/adrianadejesus/Desktop/alineamientos 3d/RBD-SW-AP/WE.cxs"
> close session
> open /Users/adrianadejesus/Downloads/ChimeraX/AlphaFold/delta/Sparrow-
> trimero-resultados/best_model_sparrow.pdb
Chain information for best_model_sparrow.pdb #1
---
Chain | Description
A B C | No description available
> open "/Users/adrianadejesus/Desktop/coronavirus/Deltacoronavirus/color
> rbd/sparrow-rbd-color.pdb"
sparrow-rbd-color.pdb title:
SWISS-MODEL SERVER (https://swissmodel.expasy.org) sparrow rbd [more info...]
Chain information for sparrow-rbd-color.pdb #2
---
Chain | Description
A B C | No description available
> color #1 #db0400ff
> color #1 #db1600ff
> color #1 #db1000ff
> color #2 #00efefff
> ui tool show Matchmaker
> matchmaker #2/A#2/B#2/C to #1/A#1/B#1/C pairing ss
Parameters
---
Chain pairing | ss
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 best_model_sparrow.pdb, chain A (#1) with sparrow-rbd-color.pdb,
chain A (#2), sequence alignment score = 390.9
Matchmaker best_model_sparrow.pdb, chain B (#1) with sparrow-rbd-color.pdb,
chain B (#2), sequence alignment score = 384.9
Matchmaker best_model_sparrow.pdb, chain C (#1) with sparrow-rbd-color.pdb,
chain C (#2), sequence alignment score = 384.9
RMSD between 5 pruned atom pairs is 1.013 angstroms; (across all 303 pairs:
27.726)
> save /Users/adrianadejesus/Desktop/image1.png supersample 3
> save "/Users/adrianadejesus/Desktop/alineamientos 3d/RBD-SW-AP/sparrow.cxs"
> close session
> open /Users/adrianadejesus/Downloads/ChimeraX/AlphaFold/gamma/IBV-trimero-
> resultados/best_model_IBV.pdb
Chain information for best_model_IBV.pdb #1
---
Chain | Description
A B C | No description available
> open /Users/adrianadejesus/Desktop/coronavirus/Gammacoronavirus/RBD-
> SW/ibv/IBV-RBD.pdb
IBV-RBD.pdb title:
SWISS-MODEL SERVER (https://swissmodel.expasy.org) RBD IBV [more info...]
Chain information for IBV-RBD.pdb #2
---
Chain | Description
A | No description available
> color #1 #db2318ff
> color #2 #1aecefff
> color #2 #00dbefff
> ui tool show Matchmaker
===== Log before crash end =====
Log:
Startup Messages
---
notes | available bundle cache has not been initialized yet
Database-fetch provider 'redo' in bundle Map specified unknown data format
'MTZ'
UCSF ChimeraX version: 1.8.dev202404050126 (2024-04-05)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 INTEL-18.3.5
OpenGL renderer: Intel(R) HD Graphics 6000
OpenGL vendor: Intel Inc.
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 Air
Model Identifier: MacBookAir7,2
Processor Name: Dual-Core Intel Core i5
Processor Speed: 1.8 GHz
Number of Processors: 1
Total Number of Cores: 2
L2 Cache (per Core): 256 KB
L3 Cache: 3 MB
Hyper-Threading Technology: Enabled
Memory: 8 GB
System Firmware Version: 428.60.3.0.0
OS Loader Version: 540.60.2~89
SMC Version (system): 2.27f2
Software:
System Software Overview:
System Version: macOS 12.1 (21C52)
Kernel Version: Darwin 21.2.0
Time since boot: 36 days 5:12
Graphics/Displays:
Intel HD Graphics 6000:
Chipset Model: Intel HD Graphics 6000
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x1626
Revision ID: 0x0009
Metal Family: Supported, Metal GPUFamily macOS 1
Displays:
Color LCD:
Display Type: LCD
Resolution: 1440 x 900 (Widescreen eXtended Graphics Array Plus)
UI Looks like: 1440 x 900
Framebuffer Depth: 24-Bit Color (ARGB8888)
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: 2.14.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.1.1
certifi: 2023.11.17
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.16
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.4.3
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.5
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.56.1
ChimeraX-AtomicLibrary: 14.0.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
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: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8.dev202404050126
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
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: 1.1.9
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: 1.5.15
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: 1.1
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.1
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: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.3
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: 1.0
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: 1.16.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2
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: 1.37.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
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: 1.1.3
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: 3.0.9
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.1
fonttools: 4.50.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.10.0
html2text: 2024.2.26
idna: 3.6
ihm: 0.43
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: 3.1.3
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: 5.1.0
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.3
matplotlib-inline: 0.1.6
msgpack: 1.0.8
ndindex: 1.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.2.1
nibabel: 5.0.1
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: 4.2.0
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: 2.3.0
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3302
pyparsing: 3.1.2
pyproject-hooks: 1.0.0
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: 25.1.2
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.12.0
setuptools: 69.2.0
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: 2.0.0
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: 0.6.1
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4
traitlets: 5.14.1
typing-extensions: 4.10.0
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 , 9 months ago
| 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 , 9 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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