Opened 20 months ago

Closed 20 months ago

#14712 closed defect (duplicate)

Crash in garbage collection

Reported by: chimerax-bug-report@… Owned by: pett
Priority: normal Milestone:
Component: Core Version:
Keywords: Cc: Tom Goddard
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-14.2.1-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 0x00000003234d8000 (most recent call first):
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 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

Thread 0x00000003224d5000 (most recent call first):
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 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

Thread 0x00000003214d2000 (most recent call first):
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 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

Thread 0x00000003204cf000 (most recent call first):
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 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

Thread 0x000000031f4cc000 (most recent call first):
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 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

Thread 0x000000031e4c9000 (most recent call first):
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 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

Thread 0x000000031d4c6000 (most recent call first):
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 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

Thread 0x000000031c4c3000 (most recent call first):
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 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

Thread 0x000000031b4c0000 (most recent call first):
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 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

Thread 0x000000031a4bd000 (most recent call first):
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 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

Thread 0x00000003194ba000 (most recent call first):
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 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

Thread 0x00000003184b7000 (most recent call first):
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 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

Thread 0x00000003174b4000 (most recent call first):
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 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

Thread 0x00000003164b1000 (most recent call first):
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 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 0x000000020262b240 (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/chimerax/core/state.py", line 217 in _copy
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/state.py", line 232 in copy_state
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py", line 310 in process
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py", line 273 in discovery
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py", line 636 in save
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py", line 912 in save
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core_formats/__init__.py", line 95 in save
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/cmd.py", line 101 in provider_save
  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/save_command/cmd.py", line 86 in cmd_save
  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/save_command/dialog.py", line 62 in display
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py", line 138 in show_save_file_dialog
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py", line 127 in 
  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, 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.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.alignment_algs._nw, PIL._imagingmath, chimerax.atom_search.ast, chimerax.chem_group._chem_group, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, numpy.linalg.lapack_lite (total: 62)


{"app_name":"ChimeraX","timestamp":"2024-03-06 15:10:43.00 +0200","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":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 14.2.1 (23C71)","roots_installed":0,"name":"ChimeraX","incident_id":"5C56EB09-7372-4AC9-B7DC-BF983A69B304"}
{
  "uptime" : 730000,
  "procRole" : "Foreground",
  "version" : 2,
  "userID" : 501,
  "deployVersion" : 210,
  "modelCode" : "Mac15,6",
  "coalitionID" : 50024,
  "osVersion" : {
    "train" : "macOS 14.2.1",
    "build" : "23C71",
    "releaseType" : "User"
  },
  "captureTime" : "2024-03-06 15:10:40.1535 +0200",
  "codeSigningMonitor" : 1,
  "incident" : "5C56EB09-7372-4AC9-B7DC-BF983A69B304",
  "pid" : 69786,
  "translated" : true,
  "cpuType" : "X86-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2024-03-06 09:37:13.6641 +0200",
  "procStartAbsTime" : 17332759898600,
  "procExitAbsTime" : 17567246185693,
  "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":"904A6D72-D15B-5953-B04F-9E4F03B7E420","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "21D38BA5-BA89-3F67-2661-149E865C554D",
  "codeSigningID" : "edu.ucsf.cgl.ChimeraX",
  "codeSigningTeamID" : "LWV8X224YF",
  "codeSigningFlags" : 570491649,
  "codeSigningValidationCategory" : 6,
  "codeSigningTrustLevel" : 4294967295,
  "wakeTime" : 4835,
  "sleepWakeUUID" : "F85D356E-CBA6-4CCD-AE45-F44981C6EFA8",
  "sip" : "enabled",
  "vmRegionInfo" : "0xa9 is not in any region.  Bytes before following region: 140723125223255\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      mapped file              7ffca7e40000-7ffcd0858000 [650.1M] r-x\/r-x SM=COW  ...t_id=8d8e3853",
  "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":69786},
  "vmregioninfo" : "0xa9 is not in any region.  Bytes before following region: 140723125223255\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      mapped file              7ffca7e40000-7ffcd0858000 [650.1M] r-x\/r-x SM=COW  ...t_id=8d8e3853",
  "extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
  "faultingThread" : 0,
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  "PC register does not match crashing frame (0x0 vs 0x7FF8A2A56A78)"
]
}
===== 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/chenlior/Downloads/neurosnap-65e81917f9757c5d089a433a/try2_rank_4.pdb
> /Users/chenlior/Downloads/neurosnap-65e81917f9757c5d089a433a/try2_rank_5.pdb
> /Users/chenlior/Downloads/neurosnap-65e81917f9757c5d089a433a/try2_rank_1.pdb
> /Users/chenlior/Downloads/neurosnap-65e81917f9757c5d089a433a/try2_rank_2.pdb
> /Users/chenlior/Downloads/neurosnap-65e81917f9757c5d089a433a/try2_rank_3.pdb

Chain information for try2_rank_4.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Chain information for try2_rank_5.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Chain information for try2_rank_1.pdb #3  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Chain information for try2_rank_2.pdb #4  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Chain information for try2_rank_3.pdb #5  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> hide #2 models

> hide #3 models

> hide #4 models

> hide #5 models

> hide #1 models

> show #4 models

> show #1 models

> show #2 models

> show #3 models

> show #5 models

> color bychain

> hide #1 models

> hide #2 models

> hide #3 models

> hide #5 models

> color /B: 79-85 yellow

> hide #4 models

> show #5 models

> hide #5 models

> show #4 models

> hide #4 models

> show #3 models

> show #3 surfaces

> color /B: 79-85 yellow

> hide #!3 models

> show #4 models

> show #4 surfaces

> color /B: 79-85 yellow

> hide #!4 surfaces

> show #!4 surfaces

> hide #!4 models

> show #!3 models

> hide #!3 models

> show #2 models

> show #2 surfaces

> color /B: 79-85 yellow

> hide #!2 models

> show #1 models

> show #1 surfaces

> show #!1 surfaces

> color /B: 79-85 yellow

> ui tool show AlphaFold

> alphafold match #1/A

Fetching AlphaFold database settings from
https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database3.json  
Fetching compressed AlphaFold A0A2K6QHE2 from
https://alphafold.ebi.ac.uk/files/AF-A0A2K6QHE2-F1-model_v4.cif  
1 AlphaFold model found using sequence similarity searches: A0A2K6QHE2 (chain
A)  
AlphaFold prediction matching try2_rank_4.pdb  
---  
Chain| UniProt Id| UniProt Name| RMSD| Length| Seen| % Id  
A | A0A2K6QHE2 | A0A2K6QHE2_RHIRO | 9.56 | 303 | 303 | 100  
  
Opened 1 AlphaFold model  

> alphafold search #1/A

> alphafold match P61586

1 AlphaFold model found using UniProt identifier: P61586 (UniProt P61586)  
Sequence Similarity  
---  
AlphaFold Model| Query Sequence| Identity %| Coverage %  
P61586 | P61586 | 100.0 | 100.0  
Opened 1 AlphaFold model  

> hide #!1 models

> hide #!6 models

> hide #6.1 models

> close #6

> open /Users/chenlior/Downloads/4p5o.pdb

4p5o.pdb title:  
Structure of an RBX1-UBC12~NEDD8-CUL1-DCN1 complex: A ring-E3- E2~ubiquitin-
like protein-substrate intermediate trapped In action [more info...]  
  
| Chain information for 4p5o.pdb #6  
---  
Chain | Description | UniProt  
A C | CUL-1 | CUL1_HUMAN 411-776  
B D | E3 ubiquitin-protein ligase RBX1 | RBX1_HUMAN 3-108  
E F | DCN1-like protein 1 | DCNL1_HUMAN 62-259  
G I | NEDD8-conjugating enzyme UBC12 | UBC12_HUMAN 2-183  
H K | NEDD8 | NEDD8_HUMAN 1-76  
  
Non-standard residues in 4p5o.pdb #6  
---  
AME — N-acetylmethionine  
ZN — zinc ion  
  

> hide #7 models

> color #!6 bychain

> color /E red

> undo

> color /E/F red

> delete /A/B/E/G/G

> delete /A/B/E/G/i

> undo

Undo failed, probably because structures have been modified.  

> undo

Undo failed, probably because structures have been modified.  

> undo

> open /Users/chenlior/Downloads/4p5o.pdb

4p5o.pdb title:  
Structure of an RBX1-UBC12~NEDD8-CUL1-DCN1 complex: A ring-E3- E2~ubiquitin-
like protein-substrate intermediate trapped In action [more info...]  
  
Chain information for 4p5o.pdb #1  
---  
Chain | Description | UniProt  
A C | CUL-1 | CUL1_HUMAN 411-776  
B D | E3 ubiquitin-protein ligase RBX1 | RBX1_HUMAN 3-108  
E F | DCN1-like protein 1 | DCNL1_HUMAN 62-259  
G I | NEDD8-conjugating enzyme UBC12 | UBC12_HUMAN 2-183  
H K | NEDD8 | NEDD8_HUMAN 1-76  
  
Non-standard residues in 4p5o.pdb #1  
---  
AME — N-acetylmethionine  
ZN — zinc ion  
  

> close #1

> close #6

> open /Users/chenlior/Downloads/4p5o.pdb

4p5o.pdb title:  
Structure of an RBX1-UBC12~NEDD8-CUL1-DCN1 complex: A ring-E3- E2~ubiquitin-
like protein-substrate intermediate trapped In action [more info...]  
  
Chain information for 4p5o.pdb #1  
---  
Chain | Description | UniProt  
A C | CUL-1 | CUL1_HUMAN 411-776  
B D | E3 ubiquitin-protein ligase RBX1 | RBX1_HUMAN 3-108  
E F | DCN1-like protein 1 | DCNL1_HUMAN 62-259  
G I | NEDD8-conjugating enzyme UBC12 | UBC12_HUMAN 2-183  
H K | NEDD8 | NEDD8_HUMAN 1-76  
  
Non-standard residues in 4p5o.pdb #1  
---  
AME — N-acetylmethionine  
ZN — zinc ion  
  

> select /A:416-776

2631 atoms, 2670 bonds, 3 pseudobonds, 327 residues, 2 models selected  

> select /B:23-104

619 atoms, 637 bonds, 1 pseudobond, 75 residues, 2 models selected  

> select /E:62-258

1614 atoms, 1653 bonds, 197 residues, 1 model selected  

> select /G:1-184

1384 atoms, 1415 bonds, 1 pseudobond, 171 residues, 2 models selected  

> select /H:1-76

584 atoms, 589 bonds, 76 residues, 1 model selected  

> select /F:64-258

1594 atoms, 1633 bonds, 195 residues, 1 model selected  

> select /E:62-258

1614 atoms, 1653 bonds, 197 residues, 1 model selected  

> select /B:23-104

619 atoms, 637 bonds, 1 pseudobond, 75 residues, 2 models selected  

> select /A:416-776

2631 atoms, 2670 bonds, 3 pseudobonds, 327 residues, 2 models selected  

> select /B:23-104

619 atoms, 637 bonds, 1 pseudobond, 75 residues, 2 models selected  

> select /E:62-258

1614 atoms, 1653 bonds, 197 residues, 1 model selected  

> select /G:1-184

1384 atoms, 1415 bonds, 1 pseudobond, 171 residues, 2 models selected  

> select /H:1-76

584 atoms, 589 bonds, 76 residues, 1 model selected  

> delete /A/B/E/I/K

> show sel cartoons

> hide sel atoms

> hide sel surfaces

> select clear

> show cartoons

> hide cartoons

> style stick

Changed 6745 atom styles  

> show cartoons

> hide surfaces

> hide atoms

> select /F

1594 atoms, 1633 bonds, 195 residues, 1 model selected  

> select /G

1384 atoms, 1415 bonds, 1 pseudobond, 171 residues, 2 models selected  

> hbonds sel reveal true

137 hydrogen bonds found  

> select clear

> hbonds reveal true

634 hydrogen bonds found  

> select ~sel & ##selected

Nothing selected  

> select /C

2556 atoms, 2591 bonds, 269 pseudobonds, 322 residues, 3 models selected  

> alphafold match P61586

1 AlphaFold model found using UniProt identifier: P61586 (UniProt P61586)  
Sequence Similarity  
---  
AlphaFold Model| Query Sequence| Identity %| Coverage %  
P61586 | P61586 | 100.0 | 100.0  
Opened 1 AlphaFold model  

> hide #!1 models

> select add #1

6745 atoms, 6870 bonds, 652 pseudobonds, 843 residues, 4 models selected  

> select subtract #1

Nothing selected  

> color /A: 79-74 red

> color 79-74 red

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color /A: 79-84 red

> color #2 bychain

> color /A: 79-84 red

> color /A: 17-23 yellow

> color #2 bychain

> undo

> show #2 cartoons

> show #2 surfaces

> color /A: 79-84 red

> color /A: 17-23 yellow

> hide #!2 surfaces

> color /A: 77-82 yellow

> color /A: 169-173 yellow

> show #!2 surfaces

> open /Users/chenlior/Downloads/7khh.pdb

7khh.pdb title:  
Ternary complex of VHL/BRD4-BD1/COMPOUND9 (4-(3,5-difluoropyridin-2-
yl)-N-(11-(((S)-1-((2S,4R)-4-hydroxy-2-((4-(4-methylthiazol-5-yl)
benzyl)carbamoyl)pyrrolidin-1-yl)-3,3-dimethyl-1-oxobutan-2-yl)
amino)-11-oxoundecyl)-10-methyl-7-((methylsulfonyl)methyl)-11-oxo-3,
4,10,11-tetrahydro-1H-1,4,10-triazadibenzo[Cd,F]azulene-6- carboxamide) [more
info...]  
  
| Chain information for 7khh.pdb #3  
---  
Chain | Description | UniProt  
A | elongin-B | ELOB_HUMAN 1-118  
B | elongin-C | ELOC_HUMAN 17-112  
C | von hippel-lindau disease tumor suppressor | VHL_HUMAN 55-213  
D | protein HUNK1 | BRD4_HUMAN 44-168  
  
Non-standard residues in 7khh.pdb #3  
---  
WEP —
N-[11-({7-(3,5-difluoropyridin-2-yl)-2-methyl-10-[(methylsulfonyl)methyl]-3-oxo-3,4,6,7-tetrahydro-2H-2,4,7-triazadibenzo[Cd,F]azulene-9-carbonyl}amino)undecanoyl]-3-methyl-
L-
valyl-(4R)-4-hydroxy-N-{[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl}-L-prolinamide  
  

> hide #!2 models

> color #!3 bychain

> hide #!3 atoms

> hbonds #!3 reveal true

1331 hydrogen bonds found  

> hbonds #!3 reveal true

1331 hydrogen bonds found  

> ~hbonds

> hide #!3 atoms

> show #!3 atoms

> hide #!3 atoms

> alphafold match Q9NQW6

1 AlphaFold model found using UniProt identifier: Q9NQW6 (UniProt Q9NQW6)  
Sequence Similarity  
---  
AlphaFold Model| Query Sequence| Identity %| Coverage %  
Q9NQW6 | Q9NQW6 | 100.0 | 100.0  
Opened 1 AlphaFold model  

> hide #!3 models

> color #4 bychain

> color /A:16-22 red

> show #4 surfaces

> color /A:16-22 red

Fetching compressed Q96FE5 UniProt info from
https://www.uniprot.org/uniprot/Q96FE5.xml  

> alphafold match Q96FE5

1 AlphaFold model found using UniProt identifier: Q96FE5 (UniProt Q96FE5)  
| Sequence Similarity  
---  
AlphaFold Model| Query Sequence| Identity %| Coverage %  
Q96FE5 | Q96FE5 | 100.0 | 100.0  
Opened 1 AlphaFold model  

> hide #!4 models

> color /A:415-428 red

> color #5 bychain

> color /A:415-428 red

> show #5 cartoons

> show #5 surfaces

> color /A:415-428 red

> hide #!5 surfaces

> close #5

> show #!3 models

> close #2

> close #4

> close #1

> open
> /Users/chenlior/Downloads/neurosnap-65e85e7bf9757c5d089a4378/try3_rank_1.pdb

| Chain information for try3_rank_1.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> hide #!3 models

> color #1 bychain

> show #!3 models

> hide #1 models

> color #!3 bychain

> hide #!3 models

> show #1 models

> ui tool show "Show Sequence Viewer"

> color /A:16-22 red

> sequence chain #1/A

Alignment identifier is 1/A  

> sequence chain #1/B

Alignment identifier is 1/B  

> sequence chain #3/A

Alignment identifier is 3/A  

> sequence chain #3/B

Alignment identifier is 3/B  

> sequence chain #3/C

Alignment identifier is 3/C  

> sequence chain #3/D

Alignment identifier is 3/D  

> hide #1 models

> show #!3 models

> select clear

> select #3/D:60-76,80-84,88-93,96-101,106-117,121-140,144-162

715 atoms, 722 bonds, 85 residues, 1 model selected  

> select #3/D:110-111

17 atoms, 16 bonds, 2 residues, 1 model selected  

> select #3/D:110-117

70 atoms, 69 bonds, 8 residues, 1 model selected  

> select #3/D:144-145

16 atoms, 15 bonds, 2 residues, 1 model selected  

> select #3/D:144-155

92 atoms, 91 bonds, 12 residues, 1 model selected  

> select #3/D:96

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #3/D:96-100

49 atoms, 50 bonds, 5 residues, 1 model selected  

> select #3/D:106

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #3/D:106-108

20 atoms, 19 bonds, 3 residues, 1 model selected  

> select #3/D:110

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #3/D:110-115

54 atoms, 53 bonds, 6 residues, 1 model selected  

> select clear

> select #3/D:41-49

63 atoms, 66 bonds, 9 residues, 1 model selected  

> select #3/D:50

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #3/D:50-79

260 atoms, 266 bonds, 30 residues, 1 model selected  

> select #3/D:80

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #3/D:80-109

244 atoms, 252 bonds, 30 residues, 1 model selected  

> select clear

> select #3/D:80

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #3/D:80-84

46 atoms, 49 bonds, 5 residues, 1 model selected  

> select #3/D:85

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #3/D:85-90

43 atoms, 43 bonds, 6 residues, 1 model selected  

> select #3/D:91

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #3/D:91-95

40 atoms, 40 bonds, 5 residues, 1 model selected  

> show sel atoms

> hide sel atoms

> select #3/D:60-76,80-84,88-93,96-101,106-117,121-140,144-162

715 atoms, 722 bonds, 85 residues, 1 model selected  

> select #3/D:168

10 atoms, 9 bonds, 1 residue, 1 model selected  

> select #3/D:41-168

1066 atoms, 1096 bonds, 128 residues, 1 model selected  

> hide #!3 models

> show #1 models

> select #1/B:1

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/B

5511 atoms, 5652 bonds, 702 residues, 1 model selected  

> select #1/B:44-45

15 atoms, 15 bonds, 2 residues, 1 model selected  

> select #1/B:44-96

442 atoms, 458 bonds, 53 residues, 1 model selected  

> select #1/B:44-96

442 atoms, 458 bonds, 53 residues, 1 model selected  

> select #1/B:169

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #1/B:44-169

1054 atoms, 1084 bonds, 126 residues, 1 model selected  

> show sel surfaces

> undo

> hide sel surfaces

> color (#!1 & sel) red

> select clear

> show #!1 surfaces

> delete #1/B: 180-

Missing or invalid "atoms" argument: only initial part "#1/B" of atom
specifier valid  

> delete #1/B: 180-702

> hide #!1 models

> show #!3 models

> delete /A

> delete /B

> undo

> open
> /Users/chenlior/Downloads/neurosnap-65e85e7bf9757c5d089a4378/try3_rank_1.pdb

Chain information for try3_rank_1.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> color #1 bychain

> delete #1/B: 180-702

> delete #1/B: 1-40

> hide #1 models

> show #!3 models

> hide #!3 models

> show #1 models

> delete #1/A: 1-30

> ui tool show "Show Sequence Viewer"

> delete #1/A: 204-30

> sequence chain #1/B

Alignment identifier is 1/B  

> delete #1/A: 220-680

> hide #1 models

> show #!3 models

> select clear

> select #3/C:71

7 atoms, 7 bonds, 1 residue, 1 model selected  

> select #3/C:71-81

86 atoms, 88 bonds, 11 residues, 1 model selected  

> select clear

> select #3/C:61

7 atoms, 7 bonds, 1 residue, 1 model selected  

> select clear

> hide #!3 models

> show #1 models

> delete #1/A: 30-55

> show #!3 models

> hide #!3 models

> show #1 surfaces

> hide #!1 models

> show #!3 models

> show #!3 surfaces

> hide #!3 models

> show #!3 models

> ui tool show "Show Sequence Viewer"

> sequence chain #1/A

Alignment identifier is 1/A  

> sequence chain #1/B

Destroying pre-existing alignment with identifier 1/B  
Alignment identifier is 1/B  

> sequence chain #3/C

Destroying pre-existing alignment with identifier 3/C  
Alignment identifier is 3/C  

> sequence chain #3/D

Alignment identifier is 3/D  

> select #3/D:124-168

369 atoms, 375 bonds, 45 residues, 1 model selected  

> select #3/D:41-168

1066 atoms, 1096 bonds, 128 residues, 1 model selected  

> hide #!3 models

> show #!1 models

> select #1/B:72

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/B:72-179

904 atoms, 927 bonds, 108 residues, 1 model selected  

> select #1/B:44

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/B:44-168

1047 atoms, 1077 bonds, 125 residues, 1 model selected  

> delete #1/B: 1-543

> undo

Undo failed, probably because structures have been modified.  

> open
> /Users/chenlior/Downloads/neurosnap-65e85e7bf9757c5d089a4378/try3_rank_1.pdb

Chain information for try3_rank_1.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> close #1

> color #2 bychain

> delete #1/B: 1-43

> ui tool show "Show Sequence Viewer"

> delete #1/B: 1-43

> sequence chain #2/A

Alignment identifier is 2/A  

> sequence chain #2/B

Alignment identifier is 2/B  

> select #2/B:169-170

16 atoms, 15 bonds, 2 residues, 1 model selected  

> select #2/B:169-263

697 atoms, 725 bonds, 95 residues, 1 model selected  

> select #2/B:702

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #2/B:702

9 atoms, 8 bonds, 1 residue, 1 model selected  

> delete #1/B: 169-702

> delete #2/B: 1-43

> delete #2/B: 169-702

> select #3/C:61

7 atoms, 7 bonds, 1 residue, 1 model selected  

> select #3/C:61-208

1212 atoms, 1244 bonds, 148 residues, 1 model selected  

> select #2/A:61-62

14 atoms, 14 bonds, 2 residues, 1 model selected  

> select #2/A:61-213

1252 atoms, 1284 bonds, 153 residues, 1 model selected  

> delete #2/A: 1-60

> select clear

> view

> cofr frontCenter

> view

> toolshed show

> show #2 surfaces

> hide #!2 models

> show #!3 models

> color #!3 bychain

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!3 models

> save /Users/chenlior/Downloads/vhl-brd-af2.cxs


===== 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 M3 Pro
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: Mac
      Model Identifier: Mac15,6
      Model Number: MRX33HB/A
      Chip: Unknown
      Total Number of Cores: 11 (5 performance and 6 efficiency)
      Memory: 18 GB
      System Firmware Version: 10151.61.4
      OS Loader Version: 10151.61.4

Software:

    System Software Overview:

      System Version: macOS 14.2.1 (23C71)
      Kernel Version: Darwin 23.2.0
      Time since boot: 35 days, 5 hours, 10 minutes

Graphics/Displays:

    Apple M3 Pro:

      Chipset Model: Apple M3 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 14
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3024 x 1964 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal


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 pett, 20 months ago

Cc: Tom Goddard added
Component: Unassigned → Core
Owner: set to pett
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Crash in garbage collection

comment:2 by pett, 20 months ago

Resolution: → duplicate
Status: accepted → closed
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