Opened 13 months ago

Closed 13 months ago

#16098 closed defect (duplicate)

Crash in garbage collection

Reported by: chimerax-bug-report@… 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-13.2.1-arm64-arm-64bit
ChimeraX Version: 1.7 (2023-12-19 08:36:03 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Thread 0x00000002a7927000 (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 0x00000001f90ec140 (most recent call first):
  Garbage-collecting
  File "", line 1219 in _handle_fromlist
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/ctypes_support.py", line 68 in residue_or_none
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/ctypes_support.py", line 71 in 
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/ctypes_support.py", line 71 in residues_or_nones
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 177 in get_prop
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/mmcif/__init__.py", line 123 in save
  File "/Applications/ChimeraX_Daily.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_Daily.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_Daily.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_Daily.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_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49 in run
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py", line 62 in display
  File "/Applications/ChimeraX_Daily.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_Daily.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_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 918 in init
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1069 in 
  File "", line 88 in _run_code
  File "", line 198 in _run_module_as_main

Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.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, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, 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.mmcif.mmcif_write (total: 53)


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  "procStartAbsTime" : 2376164476719,
  "procExitAbsTime" : 2419399781502,
  "procName" : "ChimeraX",
  "procPath" : "\/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
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  "sleepWakeUUID" : "FBAA3E21-9848-4B01-8125-3E82D6E4377F",
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  "ktriageinfo" : "VM - pmap_enter retried due to resource shortage\nVM - pmap_enter retried due to resource shortage\nVM - pmap_enter retried due to resource shortage\n",
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  "vmSummary" : "ReadOnly portion of Libraries: Total=1.6G resident=0K(0%) swapped_out_or_unallocated=1.6G(100%)\nWritable regions: Total=3.8G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=3.8G(100%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nAccelerate framework               384K        3 \nActivity Tracing                   256K        1 \nCG backing stores                 2944K        8 \nCG image                           416K       25 \nColorSync                          592K       29 \nCoreAnimation                     14.3M       20 \nCoreGraphics                       128K        7 \nCoreUI image data                 4768K       32 \nFoundation                          16K        1 \nKernel Alloc Once                   32K        1 \nMALLOC                             2.5G      217 \nMALLOC guard page                  192K       11 \nMALLOC_MEDIUM (reserved)         760.0M        8         reserved VM address space (unallocated)\nMach message                        64K        4 \nOpenGL GLSL                        384K        4 \nSTACK GUARD                        544K       34 \nStack                            161.3M       35 \nStack Guard                       56.0M        1 \nVM_ALLOCATE                      296.5M      294 \nVM_ALLOCATE (reserved)           160.0M        2         reserved VM address space (unallocated)\n__AUTH                            1886K      352 \n__AUTH_CONST                      24.7M      575 \n__CTF                               756        1 \n__DATA                            21.0M      715 \n__DATA_CONST                      37.3M      722 \n__DATA_DIRTY                      1977K      226 \n__FONT_DATA                        2352        1 \n__GLSLBUILTINS                    5174K        1 \n__LINKEDIT                       797.6M      146 \n__OBJC_CONST                      4677K      317 \n__OBJC_RO                         65.5M        1 \n__OBJC_RW                         1988K        1 \n__TEXT                           805.7M      743 \ndyld private memory                448K        3 \nmapped file                      225.0M       59 \nshared memory                     3296K       32 \n===========                     =======  ======= \nTOTAL                              5.8G     4632 \nTOTAL, minus reserved VM space     4.9G     4632 \n",
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},
  "reportNotes" : [
  "dyld_process_snapshot_create_for_process failed with 5"
]
}
===== Log before crash start =====
Startup Messages  
---  
warnings | Replacing fetcher for 'ngff' and format OME-Zarr from OME-Zarr
bundle with that from OME-Zarr bundle  
Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with
that from NMRSTAR bundle  
  
UCSF ChimeraX version: 1.8.dev202312230206 (2023-12-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> "/Users/msamso/Documents/ALL_LAB/PDB_DATASETS/Kavita/RyR1_Y523S_open_DAN_hybrid_v2/RyR1_Y522S_open_DAN_V2b_h
> copy.pdb"

Chain information for RyR1_Y522S_open_DAN_V2b_h copy.pdb #1  
---  
Chain | Description  
A B C D | No description available  
E F G H | No description available  
  

> close session

> open
> /Users/msamso/Documents/ALL_LAB/PDB_DATASETS/Kavita/RyR1_Y523S_open_DAN_hybrid_v2/RyR1_Y522S_open_DAN_V2b_h.pdb

Chain information for RyR1_Y522S_open_DAN_V2b_h.pdb #1  
---  
Chain | Description  
A B C D | No description available  
E F G H | No description available  
  

> save
> /Users/msamso/Documents/ALL_LAB/PDB_DATASETS/Kavita/RyR1_Y523S_open_DAN_hybrid_v2/RyR1_Y522S_open_DAN_v2h.cif
> relModel #1

Not saving entity_poly_seq for non-authoritative sequences  

> close session

> open
> /Users/msamso/Documents/ALL_LAB/PDB_DATASETS/Kavita/RyR1_Y523S_open_DAN_hybrid_v2/RyR1_Y522S_open_DAN_V2b_amber.pdb

Summary of feedback from opening
/Users/msamso/Documents/ALL_LAB/PDB_DATASETS/Kavita/RyR1_Y523S_open_DAN_hybrid_v2/RyR1_Y522S_open_DAN_V2b_amber.pdb  
---  
warnings | Ignored bad PDB record found on line 129753  
TER ***** SER D5037  
  
Ignored bad PDB record found on line 129993  
CONECT***************  
  
Ignored bad PDB record found on line 129994  
CONECT***************  
  
Ignored bad PDB record found on line 129995  
CONECT**********  
  
Ignored bad PDB record found on line 129996  
CONECT**********  
  
57 messages similar to the above omitted  
  
Chain information for RyR1_Y522S_open_DAN_V2b_amber.pdb #1  
---  
Chain | Description  
A B C D | No description available  
E F G H | No description available  
  

> close session

> open
> /Users/msamso/Documents/ALL_LAB/PDB_DATASETS/Kavita/RyR1_Y523S_open_DAN_hybrid_v2/RyR1_Y522S_open_DAN_V2b_amber.pdb

Summary of feedback from opening
/Users/msamso/Documents/ALL_LAB/PDB_DATASETS/Kavita/RyR1_Y523S_open_DAN_hybrid_v2/RyR1_Y522S_open_DAN_V2b_amber.pdb  
---  
warnings | Ignored bad PDB record found on line 129753  
TER ***** SER D5037  
  
Ignored bad PDB record found on line 129993  
CONECT***************  
  
Ignored bad PDB record found on line 129994  
CONECT***************  
  
Ignored bad PDB record found on line 129995  
CONECT**********  
  
Ignored bad PDB record found on line 129996  
CONECT**********  
  
57 messages similar to the above omitted  
  
Chain information for RyR1_Y522S_open_DAN_V2b_amber.pdb #1  
---  
Chain | Description  
A B C D | No description available  
E F G H | No description available  
  

> save
> /Users/msamso/Documents/ALL_LAB/PDB_DATASETS/Kavita/RyR1_Y523S_open_DAN_hybrid_v2/RyR1_Y522S_open_DAN_v2ba.cif
> relModel #1

Not saving entity_poly_seq for non-authoritative sequences  

> close session

> open
> /Users/msamso/Documents/ALL_LAB/PDB_DATASETS/Kavita/RyR1_Y523S_open_DAN_hybrid/RyR1_YS_open_DAN_hybrid01_SSAdjusted_real_space_refined_000.cif

Summary of feedback from opening
/Users/msamso/Documents/ALL_LAB/PDB_DATASETS/Kavita/RyR1_Y523S_open_DAN_hybrid/RyR1_YS_open_DAN_hybrid01_SSAdjusted_real_space_refined_000.cif  
---  
warnings | Skipping chem_comp category: Missing column 'type' near line 5009  
Missing entity information. Treating each chain as a separate entity.  
Unable to fetch template for 'U1C': will connect using distance criteria  
Bad residue range for struct_conf "126" near line 239  
Bad residue range for struct_conf "127" near line 240  
Bad residue range for struct_conf "128" near line 241  
Bad residue range for struct_conf "129" near line 242  
Bad residue range for struct_conf "130" near line 243  
20 messages similar to the above omitted  
Invalid residue range for struct_conf "151": invalid entity "B", near line 264  
Invalid residue range for struct_conf "152": invalid entity "B", near line 265  
Invalid residue range for struct_conf "153": invalid entity "B", near line 266  
Invalid residue range for struct_conf "154": invalid entity "B", near line 267  
Invalid residue range for struct_conf "155": invalid entity "B", near line 268  
454 messages similar to the above omitted  
Invalid sheet range for struct_sheet_range "73 1" near line 4806  
Invalid sheet range for struct_sheet_range "74 1" near line 4807  
Invalid sheet range for struct_sheet_range "75 1": invalid entity "B", near
line 4808  
Invalid sheet range for struct_sheet_range "76 1": invalid entity "B", near
line 4809  
Invalid sheet range for struct_sheet_range "77 1": invalid entity "B", near
line 4810  
192 messages similar to the above omitted  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Skipping chem_comp category: Missing column 'type' near line 135388  
Skipping chem_comp category: Missing column 'type' near line 135676  
Skipping chem_comp category: Missing column 'type' near line 135703  
Skipping chem_comp category: Missing column 'type' near line 135991  
  
Chain information for
RyR1_YS_open_DAN_hybrid01_SSAdjusted_real_space_refined_000.cif #1  
---  
Chain | Description  
A B C D | No description available  
E F G H | No description available  
  

> save
> /Users/msamso/Documents/ALL_LAB/PDB_DATASETS/Kavita/RyR1_Y523S_open_DAN_hybrid/abans.pdb
> relModel #1

> close session

> open
> /Users/msamso/Documents/ALL_LAB/PDB_DATASETS/Kavita/RyR1_Y523S_closed_DAN_hybrid_v2/RyR1_Y522S_closed_DAN_v2b.pdb

Chain information for RyR1_Y522S_closed_DAN_v2b.pdb #1  
---  
Chain | Description  
A B C D | No description available  
E F G H | No description available  
  

> close session

> open
> /Users/msamso/Documents/ALL_LAB/PDB_DATASETS/Kavita/RyR1_Y523S_open_DAN_hybrid_v2/RyR1_Y522S_open_DAN_v2b.pdb

Chain information for RyR1_Y522S_open_DAN_v2b.pdb #1  
---  
Chain | Description  
A B C D | No description available  
E F G H | No description available  
  

> save
> /Users/msamso/Documents/ALL_LAB/PDB_DATASETS/Kavita/RyR1_Y523S_open_DAN_hybrid_v2/RyR1_Y522S_open_DAN_v2b_a.pdb
> relModel #1 serialNumbering amber

> close session

> open
> /Users/msamso/Documents/ALL_LAB/PDB_DATASETS/Kavita/RyR1_Y523S_open_DAN_hybrid_v2/RyR1_Y522S_open_DAN_v2b_a.pdb

Summary of feedback from opening
/Users/msamso/Documents/ALL_LAB/PDB_DATASETS/Kavita/RyR1_Y523S_open_DAN_hybrid_v2/RyR1_Y522S_open_DAN_v2b_a.pdb  
---  
warnings | Ignored bad PDB record found on line 129905  
TER ***** SER D5037  
  
CONECT record to nonexistent atom: (128790, 128795)  
CONECT record for nonexistent atom: 128795  
  
Chain information for RyR1_Y522S_open_DAN_v2b_a.pdb #1  
---  
Chain | Description  
A B C D | No description available  
E F G H | No description available  
  

> save
> /Users/msamso/Documents/ALL_LAB/PDB_DATASETS/Kavita/RyR1_Y523S_open_DAN_hybrid_v2/RyR1_Y522S_open_DAN_v2b_a_nofix.cif
> fixedWidth false relModel #1

Not saving entity_poly_seq for non-authoritative sequences  


===== 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 (2023-12-19)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 Metal - 83
OpenGL renderer: Apple M2
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 Pro
      Model Identifier: Mac14,7
      Model Number: MNEJ3LL/A
      Chip: Apple M2
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 8 GB
      System Firmware Version: 8419.80.7
      OS Loader Version: 8419.80.7

Software:

    System Software Overview:

      System Version: macOS 13.2.1 (22D68)
      Kernel Version: Darwin 22.3.0
      Time since boot: 4 days, 3 hours, 35 minutes

Graphics/Displays:

    Apple M2:

      Chipset Model: Apple M2
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 10
      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: Yes
          Connection Type: Internal
        32V1W:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 75.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported


Installed Packages:
    alabaster: 0.7.13
    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: 2.12.1
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1.3
    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
    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
    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: 1.5.13
    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: 1.0.3
    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: 1.12.3
    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: 1.33.2
    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: 0.2.0
    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: 4.47.0
    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: 5.5.1
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.3
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.8
    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: 10.0.1
    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: 1.0.7
    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: 0.6.3
    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: 2023.3
    urllib3: 2.1.0
    wcwidth: 0.2.12
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9

Change History (2)

comment:1 by Eric Pettersen, 13 months ago

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

comment:2 by Eric Pettersen, 13 months ago

Resolution: → duplicate
Status: accepted → closed
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