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Opened 3 months ago
Closed 3 months ago
#18292 closed defect (duplicate)
Crash in garbage collection
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| 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-13.7.6-x86_64-i386-64bit
ChimeraX Version: 1.7.dev202308300120 (2023-08-30 01:20:01 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x000070000f467000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 324 in wait
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 622 in wait
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1392 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x00007ff8581a7a00 (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/addh/cmd.py", line 1003 in to_h36
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/addh/cmd.py", line 1071 in _h_name
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/addh/cmd.py", line 938 in new_hydrogen
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/addh/cmd.py", line 899 in add_altloc_hyds
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/addh/hbond.py", line 898 in _attach_hydrogens
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/addh/hbond.py", line 214 in add_hydrogens
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/addh/cmd.py", line 173 in hbond_add_hydrogens
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/addh/cmd.py", line 66 in cmd_addh
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/coulombic/coulombic.py", line 84 in assign_charges
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/coulombic/cmd.py", line 88 in cmd_coulombic
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2897 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 38 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 514 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 571 in run_expanded_command
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 61 in func_plus_tip
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 328 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 409 in run_shortcut
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 391 in try_shortcut
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 1365 in run_provider
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/__init__.py", line 55 in run_provider
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/toolshed/__init__.py", line 1291 in run_provider
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/toolshed/info.py", line 386 in run_provider
File "/Applications/ChimeraX_Daily.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_Daily.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_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 893 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 1044 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.pdb_lib._load_libs, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, chimerax.surface._surface, 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, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, numpy.linalg.lapack_lite, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, chimerax.dssp._dssp, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.alignment_algs._sw, chimerax.alignment_algs._nw (total: 62)
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{
"uptime" : 120000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro14,1",
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"captureTime" : "2025-07-27 12:38:58.9348 +0530",
"incident" : "72AED648-4FB2-4C14-B38A-CD32A2DFDC9C",
"pid" : 29175,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-07-27 12:19:38.8522 +0530",
"procStartAbsTime" : 121867986406102,
"procExitAbsTime" : 123027995580911,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.7.0","CFBundleVersion":"1.7.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"08438299-4CDC-5D87-AC30-ED58C2379817","thirdParty":true},
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"crashReporterKey" : "15D25DF0-7659-D181-E945-A179084794A0",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 0,
"wakeTime" : 4576,
"sleepWakeUUID" : "FD61FFBE-917F-49CE-9234-58304F804BEA",
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"vmRegionInfo" : "0xa9 is not in any region. Bytes before following region: 140737486929751\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n shared memory 7fffffea4000-7fffffea5000 [ 4K] r-x\/r-x SM=SHM ",
"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":29175},
"vmregioninfo" : "0xa9 is not in any region. Bytes before following region: 140737486929751\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n shared memory 7fffffea4000-7fffffea5000 [ 4K] r-x\/r-x SM=SHM ",
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"faultingThread" : 0,
"threads" : 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"vmSummary" : "ReadOnly portion of Libraries: Total=1.1G resident=0K(0%) swapped_out_or_unallocated=1.1G(100%)\nWritable regions: Total=3.1G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=3.1G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 256K 2 \nActivity Tracing 256K 1 \nCG backing stores 2160K 4 \nCG image 372K 24 \nColorSync 264K 30 \nCoreAnimation 100K 14 \nCoreGraphics 12K 2 \nCoreUI image data 2900K 27 \nFoundation 36K 2 \nKernel Alloc Once 8K 1 \nMALLOC 2.2G 779 \nMALLOC guard page 32K 7 \nMALLOC_LARGE (reserved) 256K 1 reserved VM address space (unallocated)\nMALLOC_NANO (reserved) 384.0M 1 reserved VM address space (unallocated)\nMach message 16K 4 \nOpenGL GLSL 384K 4 \nSTACK GUARD 92K 23 \nStack 170.2M 24 \nStack Guard 56.0M 1 \nVM_ALLOCATE 268.1M 267 \n__CTF 824 1 \n__DATA 49.0M 772 \n__DATA_CONST 41.2M 398 \n__DATA_DIRTY 1802K 226 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 203.7M 154 \n__OBJC_RO 66.3M 1 \n__OBJC_RW 2013K 2 \n__TEXT 938.1M 778 \ndyld private memory 420K 4 \nmapped file 239.0M 63 \nshared memory 2992K 26 \n=========== ======= ======= \nTOTAL 4.6G 3646 \nTOTAL, minus reserved VM space 4.2G 3646 \n",
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"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
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{
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"factorPackIds" : {
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},
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{
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}
===== Log before crash start =====
UCSF ChimeraX version: 1.7.dev202308300120 (2023-08-30)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/jbaral/Desktop/Session for structures.cxs"
Opened cryosparc_P1_J136_007_volume_map_sharp.mrc as #1, grid size
420,420,420, pixel 0.833, shown at level 0.0875, step 1, values float32
Opened Zflippedcryosparc_P4_J97_008_volume_sharp_map.mrc as #3, grid size
512,512,512, pixel 0.833, shown at level 0.106, step 1, values float32
Log from Mon Jan 27 20:56:18 2025 Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.7.dev202308300120 (2023-08-30)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/jbaral/Library/CloudStorage/OneDrive-
> TheUniversityofMelbourne/Enigma/Structures of mKu- Cryo-EM/Submission 40bp
> supercomplex/Detailed/Maps-
> submitted/cryosparc_P1_J136_007_volume_map_sharp.mrc"
Opened cryosparc_P1_J136_007_volume_map_sharp.mrc as #1, grid size
420,420,420, pixel 0.833, shown at level 0.0303, step 2, values float32
> open "/Users/jbaral/Library/CloudStorage/OneDrive-
> TheUniversityofMelbourne/Enigma/Structures of mKu- Cryo-EM/Submission 40bp
> supercomplex/Detailed/Model/pdb_extract_29665-job-145.cif"
Summary of feedback from opening /Users/jbaral/Library/CloudStorage/OneDrive-
TheUniversityofMelbourne/Enigma/Structures of mKu- Cryo-EM/Submission 40bp
supercomplex/Detailed/Model/pdb_extract_29665-job-145.cif
---
warnings | Atom H1 is not in the residue template for ASP /A:28
Atom H1 is not in the residue template for ASP /A:56
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Chain information for pdb_extract_29665-job-145.cif #2
---
Chain | Description
A C E | No description available
B D F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
> volume #1 level 0.1222
> show cartoons
> hide atoms
> volume #1 step 1
> volume #1 level 0.136
> color bychain
> color zone #1 near #2 distance 5
> lighting soft
> surface dust #1 size 8.33
> volume #1 level 0.08753
[Repeated 1 time(s)]
> volume #1 level 0.091
> volume #1 level 0.09792
> volume #1 level 0.1014
> volume style mesh
> open "/Users/jbaral/Library/CloudStorage/OneDrive-
> TheUniversityofMelbourne/Enigma/Structures of mKu- Cryo-EM/Submission-1JEY
> supercomplex/Detailed/Maps-
> submitted/Zflippedcryosparc_P4_J97_008_volume_sharp_map.mrc"
Opened Zflippedcryosparc_P4_J97_008_volume_sharp_map.mrc as #3, grid size
512,512,512, pixel 0.833, shown at level 0.0237, step 2, values float32
> open "/Users/jbaral/Library/CloudStorage/OneDrive-
> TheUniversityofMelbourne/Enigma/Structures of mKu- Cryo-EM/Submission-1JEY
> supercomplex/Detailed/Model/pdb_extract_8499-J-318.cif"
Summary of feedback from opening /Users/jbaral/Library/CloudStorage/OneDrive-
TheUniversityofMelbourne/Enigma/Structures of mKu- Cryo-EM/Submission-1JEY
supercomplex/Detailed/Model/pdb_extract_8499-J-318.cif
---
warning | Missing or incomplete entity_poly_seq table. Inferred polymer
connectivity.
Chain information for pdb_extract_8499-J-318.cif #4
---
Chain | Description
A I K | No description available
B J L | No description available
C E G | No description available
D F H | No description available
> ui tool show matchmaker
> matchmaker #4 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker pdb_extract_29665-job-145.cif, chain C (#2) with
pdb_extract_8499-J-318.cif, chain I (#4), sequence alignment score = 1071
RMSD between 189 pruned atom pairs is 1.174 angstroms; (across all 226 pairs:
1.462)
> select add #4
24579 atoms, 25014 bonds, 1449 residues, 1 model selected
> select subtract #4
Nothing selected
> select add #4
24579 atoms, 25014 bonds, 1449 residues, 1 model selected
> select add #3
24579 atoms, 25014 bonds, 1449 residues, 3 models selected
> close #3
> close #4
> open "/Users/jbaral/Library/CloudStorage/OneDrive-
> TheUniversityofMelbourne/Enigma/Structures of mKu- Cryo-EM/Submission-1JEY
> supercomplex/Detailed/Maps-
> submitted/Zflippedcryosparc_P4_J97_008_volume_sharp_map.mrc"
Opened Zflippedcryosparc_P4_J97_008_volume_sharp_map.mrc as #3, grid size
512,512,512, pixel 0.833, shown at level 0.0237, step 2, values float32
> open "/Users/jbaral/Library/CloudStorage/OneDrive-
> TheUniversityofMelbourne/Enigma/Structures of mKu- Cryo-EM/Submission-1JEY
> supercomplex/Detailed/Model/pdb_extract_8499-J-318.cif"
Summary of feedback from opening /Users/jbaral/Library/CloudStorage/OneDrive-
TheUniversityofMelbourne/Enigma/Structures of mKu- Cryo-EM/Submission-1JEY
supercomplex/Detailed/Model/pdb_extract_8499-J-318.cif
---
warning | Missing or incomplete entity_poly_seq table. Inferred polymer
connectivity.
Chain information for pdb_extract_8499-J-318.cif #4
---
Chain | Description
A I K | No description available
B J L | No description available
C E G | No description available
D F H | No description available
> volume #3 level 0.09441
> surface dust #1 size 8.33
> surface dust #3 size 8.33
> hide #2 models
> hide #!1 models
> hide #4 cartoons
> hide #4 atoms
> show #4 cartoons
> volume #3 level 0.09441
> surface dust #3 size 8.33
[Repeated 1 time(s)]
> volume #3 step 1
> volume #3 level 0.1064
> ui tool show "Hide Dust"
> surface dust #3 size 8.61
[Repeated 1 time(s)]
> surface dust #3 size 42.93
> surface dust #3 size 43.65
> color bychain
> color zone #3 near #4 distance 5
[Repeated 1 time(s)]
> volume #!3 style mesh
> lighting soft
[Repeated 1 time(s)]
> show #2 models
> show #!1 models
Color zone shortcut requires 1 displayed atomic model and 1 map, got 2 atomic
models, 2 maps.
[Repeated 3 time(s)]
> select add #2
25454 atoms, 25961 bonds, 1477 residues, 1 model selected
> select add #1
25454 atoms, 25961 bonds, 1477 residues, 3 models selected
> color zone #1 near sel & #2 distance 5
> select subtract #2
2 models selected
> select subtract #1
Nothing selected
> select add #3
2 models selected
> select add #4
24579 atoms, 25014 bonds, 1449 residues, 3 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.34309,0.28801,0.89406,-104.44,0.093586,0.93661,-0.33763,62.709,-0.93463,0.19951,0.29439,301.28,#4,0.34309,0.28801,0.89406,-104.44,0.093586,0.93661,-0.33763,62.709,-0.93463,0.19951,0.29439,301.28
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.34309,0.28801,0.89406,-104.7,0.093586,0.93661,-0.33763,61.858,-0.93463,0.19951,0.29439,301.48,#4,0.34309,0.28801,0.89406,-104.7,0.093586,0.93661,-0.33763,61.858,-0.93463,0.19951,0.29439,301.48
> view matrix models
> #3,0.34309,0.28801,0.89406,-90.629,0.093586,0.93661,-0.33763,112.53,-0.93463,0.19951,0.29439,293.8,#4,0.34309,0.28801,0.89406,-90.629,0.093586,0.93661,-0.33763,112.53,-0.93463,0.19951,0.29439,293.8
> view matrix models
> #3,0.34309,0.28801,0.89406,-90.757,0.093586,0.93661,-0.33763,112.56,-0.93463,0.19951,0.29439,293.79,#4,0.34309,0.28801,0.89406,-90.757,0.093586,0.93661,-0.33763,112.56,-0.93463,0.19951,0.29439,293.79
> view matrix models
> #3,0.34309,0.28801,0.89406,-115.89,0.093586,0.93661,-0.33763,118.5,-0.93463,0.19951,0.29439,293.42,#4,0.34309,0.28801,0.89406,-115.89,0.093586,0.93661,-0.33763,118.5,-0.93463,0.19951,0.29439,293.42
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.29444,-0.7512,0.59077,178.21,0.29522,0.65944,0.69137,-76.141,-0.90893,-0.029162,0.41593,311.81,#4,0.29444,-0.7512,0.59077,178.21,0.29522,0.65944,0.69137,-76.141,-0.90893,-0.029162,0.41593,311.81
> view matrix models
> #3,-0.084383,-0.50622,0.85827,151.97,0.28726,0.81241,0.50741,-69.39,-0.95413,0.28936,0.07686,322.97,#4,-0.084383,-0.50622,0.85827,151.97,0.28726,0.81241,0.50741,-69.39,-0.95413,0.28936,0.07686,322.97
> set bgColor white
> view matrix models
> #3,-0.084383,-0.50622,0.85827,151.97,0.28726,0.81241,0.50741,-69.39,-0.95413,0.28936,0.07686,322.97,#4,-0.084383,-0.50622,0.85827,151.97,0.28726,0.81241,0.50741,-69.39,-0.95413,0.28936,0.07686,322.97
> select clear
> select add #3
2 models selected
> select add #4
24579 atoms, 25014 bonds, 1449 residues, 3 models selected
> view matrix models
> #3,-0.085186,-0.50897,0.85656,153.07,0.28686,0.81076,0.51028,-69.539,-0.95418,0.28918,0.076939,323,#4,-0.085186,-0.50897,0.85656,153.07,0.28686,0.81076,0.51028,-69.539,-0.95418,0.28918,0.076939,323
> view matrix models
> #3,-0.094515,-0.50117,0.86017,152.66,-0.089877,0.8648,0.494,2.6085,-0.99146,-0.03062,-0.12678,440.87,#4,-0.094515,-0.50117,0.86017,152.66,-0.089877,0.8648,0.494,2.6085,-0.99146,-0.03062,-0.12678,440.87
> view matrix models
> #3,-0.016743,-0.91762,0.39711,319.72,-0.062251,0.39735,0.91555,10.064,-0.99792,-0.0093911,-0.063776,424.82,#4,-0.016743,-0.91762,0.39711,319.72,-0.062251,0.39735,0.91555,10.064,-0.99792,-0.0093911,-0.063776,424.82
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.016743,-0.91762,0.39711,280.84,-0.062251,0.39735,0.91555,5.3813,-0.99792,-0.0093911,-0.063776,417.16,#4,-0.016743,-0.91762,0.39711,280.84,-0.062251,0.39735,0.91555,5.3813,-0.99792,-0.0093911,-0.063776,417.16
> view matrix models
> #3,-0.016743,-0.91762,0.39711,304.95,-0.062251,0.39735,0.91555,1.6131,-0.99792,-0.0093911,-0.063776,415.39,#4,-0.016743,-0.91762,0.39711,304.95,-0.062251,0.39735,0.91555,1.6131,-0.99792,-0.0093911,-0.063776,415.39
> view matrix models
> #3,-0.016743,-0.91762,0.39711,316.57,-0.062251,0.39735,0.91555,29.884,-0.99792,-0.0093911,-0.063776,407.21,#4,-0.016743,-0.91762,0.39711,316.57,-0.062251,0.39735,0.91555,29.884,-0.99792,-0.0093911,-0.063776,407.21
> select clear
> volume #1 level 0.07368
> volume #1 level 0.08753
> save "/Users/jbaral/Desktop/Session for structures.cxs" includeMaps true
——— End of log from Mon Jan 27 20:56:18 2025 ———
opened ChimeraX session
> set bgColor black
> volume style mesh
> transparency 50
> transparency 0
> hide #2 models
> show #2 models
> hide #!1 models
> hide #2 models
> show #2 models
> select #2/i.j
Expected an objects specifier or a keyword
> select #2/i,j
1392 atoms, 1500 bonds, 44 residues, 1 model selected
> select #2/i,j
1392 atoms, 1500 bonds, 44 residues, 1 model selected
> color sel red
> select #2/g,h
2345 atoms, 2528 bonds, 74 residues, 1 model selected
> color sel green
> hide #!3 models
> select #4/c,d
956 atoms, 1029 bonds, 30 residues, 1 model selected
> color sel green
> select #4/e,f
956 atoms, 1029 bonds, 30 residues, 1 model selected
> color sel red
> select #4/g,h
956 atoms, 1029 bonds, 30 residues, 1 model selected
> color sel red
> select protein
43428 atoms, 43860 bonds, 2718 residues, 2 models selected
> color sel grey
> select #2/a,b
7247 atoms, 7319 bonds, 453 residues, 1 model selected
> color sel salmon
> color sel magenta
> color sel purple
> select #4/a,b
7237 atoms, 7309 bonds, 453 residues, 1 model selected
> color sel purple
> select clear
> dssp
> select clear
> select nucleic0acid
Expected an objects specifier or a keyword
> select nucleic-acid
6605 atoms, 7115 bonds, 208 residues, 2 models selected
> show sel atoms
> nucleotides sel atoms
> style nucleic & sel stick
Changed 6605 atom styles
> nucleotides sel fill
> style nucleic & sel stick
Changed 6605 atom styles
> nucleotides sel tube/slab shape box
> select clear
Drag select of 1081 residues, 196 shapes
> select clear
> show #!3 models
> hide #!3 models
> select add #3
2 models selected
> select add #4
24579 atoms, 25014 bonds, 1449 residues, 3 models selected
Drag select of 6 residues
> select add #3
90 atoms, 6 residues, 3 models selected
> select add #4
24579 atoms, 25014 bonds, 1449 residues, 3 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.016743,-0.91762,0.39711,324.7,-0.062251,0.39735,0.91555,57.544,-0.99792,-0.0093911,-0.063776,405.92,#4,-0.016743,-0.91762,0.39711,324.7,-0.062251,0.39735,0.91555,57.544,-0.99792,-0.0093911,-0.063776,405.92
> view matrix models
> #3,-0.016743,-0.91762,0.39711,325.43,-0.062251,0.39735,0.91555,58.698,-0.99792,-0.0093911,-0.063776,401.46,#4,-0.016743,-0.91762,0.39711,325.43,-0.062251,0.39735,0.91555,58.698,-0.99792,-0.0093911,-0.063776,401.46
> open "/Users/jbaral/Desktop/PDB/40bp-mKu complex.pdb"
Chain information for 40bp-mKu complex.pdb #5
---
Chain | Description
A | No description available
B | No description available
G | No description available
H | No description available
> select clear
> select nucleic-acid
7933 atoms, 8546 bonds, 250 residues, 3 models selected
> show sel atoms
> nucleotides sel tube/slab shape box
> select clear
> select #2/a,b
7247 atoms, 7319 bonds, 453 residues, 1 model selected
> select #2/i,j
1392 atoms, 1500 bonds, 44 residues, 1 model selected
> select #2/g,h
2345 atoms, 2528 bonds, 74 residues, 1 model selected
> color sel green
> select clear
> select add #5
8575 atoms, 8750 bonds, 495 residues, 1 model selected
> view matrix models #5,1,0,0,14.741,0,1,0,58.275,0,0,1,-1.1596
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.29192,-0.22569,-0.92943,339.33,0.57813,0.81578,-0.016516,-5.5434,0.76194,-0.53251,0.36862,72.92
> view matrix models
> #5,-0.27737,0.43285,-0.85773,305.35,0.77536,0.62804,0.066206,-19.725,0.56735,-0.64669,-0.50982,279.18
> view matrix models
> #5,0.95312,0.20776,0.22001,-53.083,-0.20878,-0.074828,0.9751,122.79,0.21905,-0.97531,-0.027943,316.57
> view matrix models
> #5,0.95128,0.11714,0.28522,-47.445,-0.28047,-0.055535,0.95825,134.61,0.12809,-0.99156,-0.019975,333.96
> view matrix models
> #5,0.95141,0.11606,0.28521,-47.27,-0.28052,-0.055265,0.95826,134.57,0.12698,-0.9917,-0.020022,334.18
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.95141,0.11606,0.28521,-45.986,-0.28052,-0.055265,0.95826,136.22,0.12698,-0.9917,-0.020022,290.68
> select #5/a
3619 atoms, 3655 bonds, 226 residues, 1 model selected
> color sel purple
> select #5/b
3628 atoms, 3664 bonds, 227 residues, 1 model selected
> color sel salmon
> color sel gold
> select #5/g,h
1328 atoms, 1431 bonds, 42 residues, 1 model selected
> color sel green
> select clear
Drag select of 9 residues
> select clear
> open "/Users/jbaral/Desktop/PDB/40bp-mKu complex.pdb"
Chain information for 40bp-mKu complex.pdb #6
---
Chain | Description
A | No description available
B | No description available
G | No description available
H | No description available
> select add #6
8575 atoms, 8750 bonds, 495 residues, 1 model selected
> view matrix models #6,1,0,0,-0.010998,0,1,0,-0.051463,0,0,1,-0.070208
> view matrix models #6,1,0,0,15.188,0,1,0,65.243,0,0,1,44.568
> view matrix models #6,1,0,0,16.166,0,1,0,69.688,0,0,1,49.648
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.47844,-0.30628,-0.82298,304.74,0.53705,0.84355,-0.0017164,5.3677,0.69475,-0.44116,0.56807,84.263
> view matrix models
> #6,0.46195,0.12087,-0.87863,239.1,0.78181,0.41227,0.46776,-39.275,0.41877,-0.90301,0.095953,298.11
> view matrix models
> #6,-0.076661,0.26808,-0.96034,319.77,0.88336,0.46494,0.05927,3.9643,0.46239,-0.84378,-0.27245,343.28
> view matrix models
> #6,0.5439,0.29229,-0.7866,177.64,0.81734,0.027813,0.57549,6.2733,0.19008,-0.95593,-0.22377,402.66
> view matrix models
> #6,0.051683,0.14819,-0.98761,324.12,0.99627,0.060741,0.06125,57.937,0.069065,-0.98709,-0.14449,415.68
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.051683,0.14819,-0.98761,323.46,0.99627,0.060741,0.06125,56.427,0.069065,-0.98709,-0.14449,417.65
> coulombic sel
The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics:
40bp-mKu complex.pdb #6/A TYR 57 O
40bp-mKu complex.pdb #6/A ILE 29 O
Using Amber 20 recommended default charges and atom types for standard
residues
Hydrogen copy of 40bp-mKu complex.pdb #/A TYR 57 HXT bonded to atom that
should not have hydrogens (copy of 40bp-mKu complex.pdb #/A TYR 57 OXT)
> open "/Users/jbaral/Desktop/PDB/mKu dimer AF.pdb"
Chain information for mKu dimer AF.pdb #7
---
Chain | Description
A B | No description available
> open "/Users/jbaral/Desktop/PDB/mKu dimer AF DNA 21bp.pdb"
Chain information for mKu dimer AF DNA 21bp.pdb #8
---
Chain | Description
A B | No description available
C | No description available
D | No description available
> close #6
> close #7
> select add #8
5205 atoms, 5392 bonds, 588 residues, 1 model selected
> hide #8 models
> show #8 models
> hide #8 models
> select subtract #8
Nothing selected
> ui tool show Matchmaker
> matchmaker #8 to #5
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 40bp-mKu complex.pdb, chain B (#5) with mKu dimer AF DNA 21bp.pdb,
chain A (#8), sequence alignment score = 990.4
RMSD between 176 pruned atom pairs is 0.986 angstroms; (across all 227 pairs:
1.940)
> show #8 models
> select add #8
5205 atoms, 5392 bonds, 588 residues, 1 model selected
> view matrix models
> #8,0.65199,-0.70806,-0.27122,193.37,0.7582,0.61213,0.22458,259.45,0.0070107,-0.35206,0.93595,158.25
> view matrix models
> #8,0.65199,-0.70806,-0.27122,189.41,0.7582,0.61213,0.22458,256.42,0.0070107,-0.35206,0.93595,203.58
> view matrix models
> #8,0.65199,-0.70806,-0.27122,186.99,0.7582,0.61213,0.22458,251.8,0.0070107,-0.35206,0.93595,223.81
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.90296,0.42647,-0.052831,186.56,-0.37895,0.84818,0.37013,249.58,0.20266,-0.31419,0.92748,224.13
> coulombic sel
===== Log before crash end =====
Log:
Startup Messages
---
warnings | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
Registration file '/Users/jbaral/Library/Application
Support/ChimeraX/registration' has expired
UCSF ChimeraX version: 1.7.dev202308300120 (2023-08-30)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 INTEL-20.7.3
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 640
OpenGL vendor: Intel Inc.
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 Pro
Model Identifier: MacBookPro14,1
Processor Name: Dual-Core Intel Core i5
Processor Speed: 2.3 GHz
Number of Processors: 1
Total Number of Cores: 2
L2 Cache (per Core): 256 KB
L3 Cache: 4 MB
Hyper-Threading Technology: Enabled
Memory: 8 GB
System Firmware Version: 529.140.2.0.0
OS Loader Version: 577.140.2~30
SMC Version (system): 2.43f11
Software:
System Software Overview:
System Version: macOS 13.7.6 (22H625)
Kernel Version: Darwin 22.6.0
Time since boot: 7 days, 22 hours, 44 minutes
Graphics/Displays:
Intel Iris Plus Graphics 640:
Chipset Model: Intel Iris Plus Graphics 640
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x5926
Revision ID: 0x0006
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.2.1
Babel: 2.12.1
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: 1.6.2
charset-normalizer: 3.2.0
ChimeraX-AddCharge: 1.5.11
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.47.1
ChimeraX-AtomicLibrary: 10.0.8
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: 2.10.4
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: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7.dev202308300120
ChimeraX-CoreFormats: 1.1
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: 1.1.2
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
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9
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
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: 1.5.12
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: 1.10.2
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PhenixUI: 1.2.2
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: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.9
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.2
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-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: 1.31.4
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.4
contourpy: 1.1.0
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7.post1
decorator: 5.1.1
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.42.1
funcparserlib: 1.0.1
glfw: 2.6.2
grako: 3.16.5
h5py: 3.9.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.38
imagecodecs: 2023.7.10
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.0
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.3.1
jupyterlab-widgets: 3.0.8
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.3
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.7
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.5
numpy: 1.25.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 10.0.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.10.0
prompt-toolkit: 3.0.39
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
pyzmq: 25.1.1
qtconsole: 5.4.3
QtPy: 2.4.0
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: 2.4.1
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.7
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.5
sphinxcontrib-htmlhelp: 2.0.4
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.6
sphinxcontrib-serializinghtml: 1.1.9
stack-data: 0.6.2
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: 6.3.3
traitlets: 5.9.0
typing-extensions: 4.7.1
tzdata: 2023.3
urllib3: 2.0.4
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.8
Change History (2)
comment:1 by , 3 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 , 3 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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