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Opened 18 months ago
Closed 18 months ago
#15202 closed defect (duplicate)
Crash in garbage collection
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| 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-14.4.1-x86_64-i386-64bit
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x0000000318807000 (most recent call first):
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 324 in wait
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 622 in wait
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1392 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x00000002044c6240 (most recent call first):
Garbage-collecting
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/ast.py", line 15 in __init__
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/ast.py", line 90 in copy
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 642 in _try
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/contextlib.py", line 137 in __enter__
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 665 in _option
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/contextlib.py", line 137 in __enter__
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py", line 334 in _chain_
File "/Applications/ChimeraX-1.7.1.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-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 458 in _call
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 59 in wrapper
File "/Applications/ChimeraX-1.7.1.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-1.7.1.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-1.7.1.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-1.7.1.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-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 458 in _call
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 59 in wrapper
File "/Applications/ChimeraX-1.7.1.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-1.7.1.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-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 458 in _call
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 59 in wrapper
File "/Applications/ChimeraX-1.7.1.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-1.7.1.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-1.7.1.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-1.7.1.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-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 458 in _call
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 59 in wrapper
File "/Applications/ChimeraX-1.7.1.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-1.7.1.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-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 458 in _call
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 59 in wrapper
File "/Applications/ChimeraX-1.7.1.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-1.7.1.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-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 458 in _call
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 59 in wrapper
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 206 in parse
File "/Applications/ChimeraX-1.7.1.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-1.7.1.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-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/std_commands/defattr.py", line 180 in defattr
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/add_charge/charge.py", line 81 in add_standard_charges
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/add_charge/charge.py", line 34 in add_charges
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/coulombic/coulombic.py", line 110 in assign_charges
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/coulombic/cmd.py", line 99 in cmd_coulombic
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2908 in run
File "/Applications/ChimeraX-1.7.1.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-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 525 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 582 in run_expanded_command
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 72 in func_plus_tip
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 339 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 420 in run_shortcut
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 402 in try_shortcut
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 1376 in run_provider
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/__init__.py", line 66 in run_provider
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/toolshed/__init__.py", line 1302 in run_provider
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/toolshed/info.py", line 397 in run_provider
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/toolbar/tool.py", line 205 in callback
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/Applications/ChimeraX-1.7.1.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-1.7.1.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.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.surface._surface, lxml._elementpath, lxml.etree, chimerax.pdb_lib._load_libs, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, 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.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp, chimerax.mlp._mlp (total: 58)
{"app_name":"ChimeraX","timestamp":"2024-05-14 14:05:40.00 -0400","app_version":"1.7.1","slice_uuid":"194a3167-3db5-3029-8d22-1d742b826bb9","build_version":"1.7.1.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":1,"is_first_party":0,"bug_type":"309","os_version":"macOS 14.4.1 (23E224)","roots_installed":0,"name":"ChimeraX","incident_id":"3D60ECD6-0EAE-42D1-B8C1-AA89985FFC93"}
{
"uptime" : 65000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookAir10,1",
"coalitionID" : 993,
"osVersion" : {
"train" : "macOS 14.4.1",
"build" : "23E224",
"releaseType" : "User"
},
"captureTime" : "2024-05-14 14:05:38.9804 -0400",
"codeSigningMonitor" : 1,
"incident" : "3D60ECD6-0EAE-42D1-B8C1-AA89985FFC93",
"pid" : 28475,
"translated" : true,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-05-14 13:26:50.2469 -0400",
"procStartAbsTime" : 1518822337731,
"procExitAbsTime" : 1574713184817,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.7.1.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.7.1","CFBundleVersion":"1.7.1.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"22A5FEA9-F7FF-5AAB-B316-41EDFD3D5EDD","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "C35DDF32-99BD-0DB2-8E1C-80A4763326FD",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"wakeTime" : 6663,
"sleepWakeUUID" : "F42007B3-0502-49CC-829E-E659C2E32C39",
"sip" : "enabled",
"vmRegionInfo" : "0xa9 is not in any region. Bytes before following region: 4362223447\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 104024000-104028000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.7.1.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":28475},
"vmregioninfo" : "0xa9 is not in any region. Bytes before following region: 4362223447\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 104024000-104028000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.7.1.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,
"threads" : 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"source" : "P",
"arch" : "x86_64",
"base" : 140703278686208,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.Foundation",
"size" : 12808180,
"uuid" : "2909ab97-ca3a-3424-bf8f-cd578c176777",
"path" : "\/System\/Library\/Frameworks\/Foundation.framework\/Versions\/C\/Foundation",
"name" : "Foundation",
"CFBundleVersion" : "2420"
}
],
"sharedCache" : {
"base" : 140703257919488,
"size" : 21474836480,
"uuid" : "b8d5ff9b-b3b6-327c-a409-07449b1e60da"
},
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"logWritingSignature" : "32bbae1b2b96c0f978f07cdb4c59aa6d2194a637",
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "61675b89201f677a9a4cbd65",
"factorPackIds" : {
"HEALTH_FEATURE_AVAILABILITY" : "65a855f5f087695cfac03d1f"
},
"deploymentId" : 240000119
},
{
"rolloutId" : "6112d17137f5d11121dcd4e2",
"factorPackIds" : {
},
"deploymentId" : 240000550
}
],
"experiments" : [
{
"treatmentId" : "a34d22a1-a1a5-4126-a477-0c499e502c6a",
"experimentId" : "65835bc103dc58766bab2d27",
"deploymentId" : 400000011
},
{
"treatmentId" : "5d85d104-adc7-4ebf-8b7c-96d84fdad9cc",
"experimentId" : "6384d56b96e8d228551ec182",
"deploymentId" : 400000032
}
]
},
"reportNotes" : [
"PC register does not match crashing frame (0x0 vs 0x7FF8981E2A78)"
]
}
===== Log before crash start =====
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/genya/moreAlphaFold/AF3/fold_opa3_3/fold_opa3_3_model_0.cif
Chain information for fold_opa3_3_model_0.cif #1
---
Chain | Description
A B C | .
> close
> open
> /Users/genya/moreAlphaFold/AF3/fold_opa3_3_iars2/fold_opa3_3_iars2_model_0.cif
Chain information for fold_opa3_3_iars2_model_0.cif #1
---
Chain | Description
A B C | .
D | .
> open
> /Users/genya/moreAlphaFold/AF3/fold_opa3_4_iars2nomts/fold_opa3_4_iars2nomts_model_0.cif
Chain information for fold_opa3_4_iars2nomts_model_0.cif #2
---
Chain | Description
A B C D | .
E | .
> hide #1 models
> select #2
13308 atoms, 13610 bonds, 1685 residues, 1 model selected
> show sel cartoons
> hide sel atoms
> select #2/e
7684 atoms, 7874 bonds, 969 residues, 1 model selected
> color sel dark grey
> select #2/e:1-60
484 atoms, 494 bonds, 60 residues, 1 model selected
> hide sel cartoons
> select #2/a-d
5624 atoms, 5736 bonds, 716 residues, 1 model selected
> color sel goldenrod
> select #2/a-d:1-30
924 atoms, 936 bonds, 120 residues, 1 model selected
> color sel dark salmon
> select #2/a-d:80-100
572 atoms, 572 bonds, 84 residues, 1 model selected
> color sel saddle brown
> select #2/a-d:152-159,115-140
1072 atoms, 1076 bonds, 136 residues, 1 model selected
> color sel cornflower blue
> select clear
> lighting simple
> open
> /Users/genya/moreAlphaFold/AF3/fold_opa3_3_iars2/fold_opa3_3_iars2_model_0.cif
Chain information for fold_opa3_3_iars2_model_0.cif #3
---
Chain | Description
A B C | .
D | .
> hide #2 models
> hide #3 models
> open /Users/genya/moreAlphaFold/AF3/fold_opa3_3/fold_opa3_3_model_0.cif
Chain information for fold_opa3_3_model_0.cif #4
---
Chain | Description
A B C | .
> select #4
4218 atoms, 4302 bonds, 537 residues, 1 model selected
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for fold_opa3_3_model_0.cif_A SES surface #4.1: minimum,
-13.06, mean 0.11, maximum 11.89
Coulombic values for fold_opa3_3_model_0.cif_B SES surface #4.2: minimum,
-13.01, mean 0.12, maximum 11.43
Coulombic values for fold_opa3_3_model_0.cif_C SES surface #4.3: minimum,
-14.06, mean 0.11, maximum 14.45
To also show corresponding color key, enter the above coulombic command and
add key true
> set bgColor white
> select #4\
Expected an objects specifier or a keyword
> select #4
4218 atoms, 4302 bonds, 537 residues, 1 model selected
> hide sel surfaces
> show #3 models
> hide #!4 models
> select #3
12230 atoms, 12515 bonds, 1549 residues, 1 model selected
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for fold_opa3_3_iars2_model_0.cif_A SES surface #3.1:
minimum, -15.75, mean 0.06, maximum 20.02
Coulombic values for fold_opa3_3_iars2_model_0.cif_B SES surface #3.2:
minimum, -13.84, mean 0.07, maximum 14.14
Coulombic values for fold_opa3_3_iars2_model_0.cif_C SES surface #3.3:
minimum, -13.32, mean 0.03, maximum 13.51
Coulombic values for fold_opa3_3_iars2_model_0.cif_D SES surface #3.4:
minimum, -19.42, mean -1.03, maximum 11.58
To also show corresponding color key, enter the above coulombic command and
add key true
> mlp sel
Map values for surface "fold_opa3_3_iars2_model_0.cif_A SES surface": minimum
-25.65, mean -2.179, maximum 22.94
Map values for surface "fold_opa3_3_iars2_model_0.cif_B SES surface": minimum
-25.96, mean -2.146, maximum 23.05
Map values for surface "fold_opa3_3_iars2_model_0.cif_C SES surface": minimum
-25.65, mean -2.134, maximum 23.06
Map values for surface "fold_opa3_3_iars2_model_0.cif_D SES surface": minimum
-29.98, mean -5.067, maximum 23.24
To also show corresponding color key, enter the above mlp command and add key
true
> show #!4 models
> hide #!3 models
> select #4/a-c:10,17,21,86,82,32,29,28,100
255 atoms, 231 bonds, 27 residues, 1 model selected
> show sel atoms
> style sel sphere
Changed 255 atom styles
> coulombic sel
Coulombic values for fold_opa3_3_model_0.cif_A SES surface #4.1: minimum,
-13.06, mean 0.11, maximum 11.89
Coulombic values for fold_opa3_3_model_0.cif_B SES surface #4.2: minimum,
-13.01, mean 0.12, maximum 11.43
Coulombic values for fold_opa3_3_model_0.cif_C SES surface #4.3: minimum,
-14.06, mean 0.11, maximum 14.45
To also show corresponding color key, enter the above coulombic command and
add key true
> hide sel surfaces
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A #1/B #1/C #2/A #2/B #2/C #2/D #3/A #3/B #3/C #4/A #4/B
> #4/C
Alignment identifier is 1
> select #1/A-C:2-33,35-60,73-142,146-164,168-173
> #2/A-D:2-33,35-60,73-142,146-164,168-173
> #3/A-C:2-33,35-60,73-142,146-164,168-173
> #4/A-C:2-33,35-60,73-142,146-164,168-173
15834 atoms, 16068 bonds, 1989 residues, 4 models selected
> select #4/a-c:10,17,21,86,82,32,29,28,100,101
291 atoms, 270 bonds, 30 residues, 1 model selected
> show sel atoms
> select #4/a-c:10,17,21,86,82,32,29,28,100
255 atoms, 231 bonds, 27 residues, 1 model selected
> ui mousemode right clip
> ui mousemode right translate
> ui mousemode right clip
> ui mousemode right "clip rotate"
> ui mousemode right clip
> clip off
> select 4/c
Expected an objects specifier or a keyword
> select #4/c
1406 atoms, 1434 bonds, 179 residues, 1 model selected
> transparency #4/c 50
> transparency #4/c 50 All
> transparency #4/c 20 All
> transparency #4/c 75 All
> transparency #4/c 0 All
> clip off
> ui mousemode right translate
> select #4/c
1406 atoms, 1434 bonds, 179 residues, 1 model selected
> transparency #4/c 75
> transparency #4/c 75 All
> transparency #4/c 100 All
> graphics selection color black width 5
> transparency #3/c 90 All
> select clear
> transparency #3/c 60 All
> transparency #3/c 0 All
> select #3/c
1406 atoms, 1434 bonds, 179 residues, 1 model selected
> show #!4 cartoons
> close #1-2#3-4
> open /Users/genya/moreAlphaFold/AF3/fold_opa3_3/fold_opa3_3_model_0.cif
Chain information for fold_opa3_3_model_0.cif #1
---
Chain | Description
A B C | .
> open
> /Users/genya/moreAlphaFold/AF3/fold_opa3_3_iars2/fold_opa3_3_iars2_model_0.cif
Chain information for fold_opa3_3_iars2_model_0.cif #2
---
Chain | Description
A B C | .
D | .
> select #2
12230 atoms, 12515 bonds, 1549 residues, 1 model selected
> show sel cartoons
> hide sel atoms
> select #2/d
8012 atoms, 8213 bonds, 1012 residues, 1 model selected
> color sel dark grey
> select #2/d:1-60
451 atoms, 464 bonds, 60 residues, 1 model selected
> hide sel cartoons
> select #2/a-c
4218 atoms, 4302 bonds, 537 residues, 1 model selected
> color sel goldenrod
> select #2/a-c:1-30
693 atoms, 702 bonds, 90 residues, 1 model selected
> color sel dark salmon
> select #2/a-c:80-100
429 atoms, 429 bonds, 63 residues, 1 model selected
> color sel saddle brown
> select #2/a-c:152-159,115-140
804 atoms, 807 bonds, 102 residues, 1 model selected
> color sel cornflower blue
> select clear
> lighting simple
> hide #1 models
> select #1
4218 atoms, 4302 bonds, 537 residues, 1 model selected
> show sel cartoons
> hide sel atoms
> select #1/a-c
4218 atoms, 4302 bonds, 537 residues, 1 model selected
> color sel goldenrod
> select #1/a-c:1-30
693 atoms, 702 bonds, 90 residues, 1 model selected
> color sel dark salmon
> select #1/a-c:80-100
429 atoms, 429 bonds, 63 residues, 1 model selected
> color sel saddle brown
> select #1/a-c:152-159,115-140
804 atoms, 807 bonds, 102 residues, 1 model selected
> color sel cornflower blue
> select clear
> lighting simple
> show #1 models
> hide #2 models
> select #2/a-d:10,17,21,86,82,32,29,28,100
320 atoms, 290 bonds, 36 residues, 1 model selected
> select #1:10,17,21,86,82,32,29,28,100
255 atoms, 231 bonds, 27 residues, 1 model selected
> show sel atoms
> style sel sphere
Changed 255 atom styles
> color sel byhetero
> show #2 models
> hide #1 models
> show #1 models
> hide #2 models
> show #2 models
> hide #1 models
> select #2/a-c:10,17,21,86,82,32,29,28,100
255 atoms, 231 bonds, 27 residues, 1 model selected
> show sel atoms
> style sel sphere
Changed 255 atom styles
> color sel byhetero
> select #2/a-c:10,17,21,86,82,32,29,28,100,29,26
288 atoms, 261 bonds, 30 residues, 1 model selected
> show sel atoms
> style sel sphere
Changed 288 atom styles
> color sel byhetero
> show #1 models
> hide #2 models
> select #1
4218 atoms, 4302 bonds, 537 residues, 1 model selected
> coulombic sel
===== Log before crash end =====
Log:
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M1
OpenGL vendor: Apple
Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: MacBookAir10,1
Model Number: MGQN3LL/A
Chip: Unknown
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 10151.101.3
OS Loader Version: 10151.101.3
Software:
System Software Overview:
System Version: macOS 14.4.1 (23E224)
Kernel Version: Darwin 23.4.0
Time since boot: 1 day, 8 hours, 36 minutes
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
MNN:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.4.1
Babel: 2.14.0
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2022.12.7
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.13
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.2
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.5
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
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: 2.10.5
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: 1.3.2
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.3.2
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: 1.7.1
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.2
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
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: 1.1.8
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.1.4
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: 2.1.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6.1
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.14
ChimeraX-ModelPanel: 1.4
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-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.1
ChimeraX-PDB: 2.7.3
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
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
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-SelInspector: 1.0
ChimeraX-SeqView: 2.11
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.2
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.4
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.2
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: 1.33.3
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: 0.2.1
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 0.29.33
debugpy: 1.8.0
decorator: 5.1.1
docutils: 0.19
executing: 2.0.1
filelock: 3.9.0
fonttools: 4.47.2
funcparserlib: 2.0.0a0
glfw: 2.6.4
grako: 3.16.5
h5py: 3.10.0
html2text: 2020.1.16
idna: 3.6
ihm: 0.38
imagecodecs: 2023.9.18
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.1
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.7.1
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.4
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.6.0
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.8
numpy: 1.25.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.2.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 4.1.0
prompt-toolkit: 3.0.43
psutil: 5.9.5
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.16.1
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.2801
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2023.3.post1
pyzmq: 25.1.2
qtconsole: 5.4.3
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
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: 0.5.0
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4
traitlets: 5.9.0
typing-extensions: 4.9.0
tzdata: 2023.4
urllib3: 2.1.0
wcwidth: 0.2.13
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
Change History (2)
comment:1 by , 18 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 , 18 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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