Opened 20 months ago

Closed 20 months ago

#14687 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-12.4-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 0x00007000135ff000 (most recent call first):
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 324 in wait
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 622 in wait
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1392 in run
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Current thread 0x000000011e794600 (most recent call first):
  Garbage-collecting
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/_weakrefset.py", line 58 in _commit_removals
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/_weakrefset.py", line 33 in __exit__
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/_weakrefset.py", line 64 in __iter__
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/nucleotides/_data.py", line 519 in 
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/nucleotides/_data.py", line 519 in rebuild
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 149 in invoke
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 248 in _activate
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 217 in activate
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 393 in activate_trigger
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 65 in draw_new_frame
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 150 in _redraw_timer_callback
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 275 in event_loop
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1069 in 
  File "", line 88 in _run_code
  File "", line 198 in _run_module_as_main

Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, chimerax.surface._surface, chimerax.pdb_lib._load_libs, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 56)


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  "legacyInfo" : {
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}
===== Log before crash start =====
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
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  

> help help:quickstart

> open 4YIT

Summary of feedback from opening 4YIT fetched from pdb  
---  
notes | Fetching compressed mmCIF 4yit from
http://files.rcsb.org/download/4yit.cif  
Fetching CCD CA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/CA/CA.cif  
  
4yit title:  
Crystal Structure of LAGLIDADG Meganuclease I-AabMI Bound to Uncleaved DNA
[more info...]  
  
Chain information for 4yit #1  
---  
Chain | Description  
A D | Meganuclease I-AabMI  
B | DNA (25-MER)  
C | DNA (25-MER)  
E | DNA (25MER)  
F | DNA (25-MER)  
  
Non-standard residues in 4yit #1  
---  
CA — calcium ion  
  
4yit mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  

> show cartoons

> hide target a

> preset cartoons/nucleotides ribbons/slabs

Using preset: Cartoons/Nucleotides / Ribbons/Slabs  
Changed 6138 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    nucleotides tube/slab shape box

  

> select /E

485 atoms, 541 bonds, 25 residues, 1 model selected  

> select /A

2074 atoms, 2106 bonds, 10 pseudobonds, 281 residues, 3 models selected  

> select /B

506 atoms, 562 bonds, 28 residues, 1 model selected  

> select /C

524 atoms, 586 bonds, 27 residues, 1 model selected  

> select add /A

2598 atoms, 2692 bonds, 10 pseudobonds, 308 residues, 3 models selected  

> select add /B

3104 atoms, 3254 bonds, 10 pseudobonds, 336 residues, 3 models selected  

> save /Users/petergogarten/Downloads/ChimeraX/PDB/chainA+DNA.pdb selectedOnly
> true relModel #1

> close session

> open /Users/petergogarten/Downloads/ChimeraX/PDB/chainA+DNA.pdb

Summary of feedback from opening
/Users/petergogarten/Downloads/ChimeraX/PDB/chainA+DNA.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 12 12 PRO D 3
GLU D 13 1 11  
Start residue of secondary structure not found: HELIX 13 13 HIS D 40 LYS D 42
1 3  
Start residue of secondary structure not found: HELIX 14 14 ASP D 43 LYS D 55
1 13  
Start residue of secondary structure not found: HELIX 15 15 THR D 73 TYR D 87
1 15  
Start residue of secondary structure not found: HELIX 16 16 LYS D 92 ASN D 109
1 18  
17 messages similar to the above omitted  
Cannot find LINK/SSBOND residue ASP (209 )  
Cannot find LINK/SSBOND residue GLY (12 )  
Cannot find LINK/SSBOND residue GLU (13 )  
Cannot find LINK/SSBOND residue ALA (168 )  
Cannot find LINK/SSBOND residue GLU (169 )  
4 messages similar to the above omitted  
  
Chain information for chainA+DNA.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> select add /B

506 atoms, 562 bonds, 28 residues, 1 model selected  

> select add /C

1030 atoms, 1148 bonds, 55 residues, 1 model selected  

> show sel target ab

> nucleotides sel fill

> cartoon hide sel

> select /A

2074 atoms, 2106 bonds, 10 pseudobonds, 281 residues, 3 models selected  

> select helix

1084 atoms, 1099 bonds, 142 residues, 1 model selected  

> color sel red

> select strand

474 atoms, 478 bonds, 58 residues, 1 model selected  

> color sel yellow

> save /Users/petergogarten/Downloads/ChimeraX/PDB/chainA+DNA_colored.pdb
> relModel #1

> open 1lws

Summary of feedback from opening 1lws fetched from pdb  
---  
note | Fetching compressed mmCIF 1lws from
http://files.rcsb.org/download/1lws.cif  
  
1lws title:  
Crystal structure of the intein homing endonuclease PI-SceI bound to its
recognition sequence [more info...]  
  
Chain information for 1lws #2  
---  
Chain | Description | UniProt  
A | ENDONUCLEASE PI-SCEI | VATA_YEAST 1-454  
B | PI-SceI DNA recognition region top strand |  
C | PI-SceI DNA recognition region bottom strand |  
  
Non-standard residues in 1lws #2  
---  
CA — calcium ion  
  

> ui tool show Matchmaker

> matchmaker #!2 to #1/A pairing bs

Parameters  
---  
Chain pairing | bs  
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 chainA+DNA.pdb, chain A (#1) with 1lws, chain A (#2), sequence
alignment score = 47.1  
RMSD between 10 pruned atom pairs is 1.368 angstroms; (across all 173 pairs:
28.731)  
  
Drag select of 10 residues  

> select #2/C

682 atoms, 760 bonds, 34 residues, 1 model selected  

> select add #1/C

1206 atoms, 1346 bonds, 61 residues, 2 models selected  

> cartoon hide sel

> select add #1/B

1712 atoms, 1908 bonds, 89 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> ui mousemode right rotate

> lighting soft

> lighting simple

> lighting full

> lighting soft

> lighting simple

> set bgColor white

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> select add #2

5786 atoms, 6130 bonds, 98 pseudobonds, 552 residues, 5 models selected  

> select subtract #2

1030 atoms, 1148 bonds, 55 residues, 1 model selected  

> select add #1

3104 atoms, 3254 bonds, 14 pseudobonds, 336 residues, 3 models selected  

> select subtract #1

Nothing selected  

> select add #1

3104 atoms, 3254 bonds, 14 pseudobonds, 336 residues, 3 models selected  

> select add #2

7860 atoms, 8236 bonds, 112 pseudobonds, 833 residues, 7 models selected  

> select subtract #2

3104 atoms, 3254 bonds, 14 pseudobonds, 336 residues, 3 models selected  

> select add #2

7860 atoms, 8236 bonds, 112 pseudobonds, 833 residues, 7 models selected  

> select subtract #2

3104 atoms, 3254 bonds, 14 pseudobonds, 336 residues, 3 models selected  

> select add #2

7860 atoms, 8236 bonds, 112 pseudobonds, 833 residues, 7 models selected  

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> select subtract #2

3104 atoms, 3254 bonds, 14 pseudobonds, 336 residues, 3 models selected  

> select add #2

7860 atoms, 8236 bonds, 112 pseudobonds, 833 residues, 7 models selected  

> select subtract #1

4756 atoms, 4982 bonds, 98 pseudobonds, 497 residues, 4 models selected  

> select add #1

7860 atoms, 8236 bonds, 112 pseudobonds, 833 residues, 7 models selected  

> select subtract #1

4756 atoms, 4982 bonds, 98 pseudobonds, 497 residues, 4 models selected  

> select add #1

7860 atoms, 8236 bonds, 112 pseudobonds, 833 residues, 7 models selected  

> select subtract #1

4756 atoms, 4982 bonds, 98 pseudobonds, 497 residues, 4 models selected  

> select subtract #2

Nothing selected  

> log metadata #1

No models had metadata

> log chains #1

Chain information for chainA+DNA.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> close #1

> show target m

> log metadata #2

Metadata for 1lws #2  
---  
Title | Crystal structure of the intein homing endonuclease PI-SceI bound to
its recognition sequence  
Citations | Moure, C.M., Gimble, F.S., Quiocho, F.A. (2002). Crystal structure
of the intein homing endonuclease PI-SceI bound to its recognition sequence.
Nat.Struct.Biol., 9, 764-770. PMID: 12219083. DOI: 10.1038/nsb840  
Duan, X., Gimble, F.S., Quiocho, F.A. (1997). Crystal structure of PI-SceI, a
homing endonuclease with protein splicing activity. Cell(Cambridge,Mass.), 89,
555-564. DOI: 10.1016/S0092-8674(00)80237-8  
Non-standard residue | CA — calcium ion  
Gene source | Saccharomyces cerevisiae (baker's yeast)  
Experimental method | X-ray diffraction  
Resolution | 3.5Å  
  
> log chains #2

Chain information for 1lws #2  
---  
Chain | Description | UniProt  
A | ENDONUCLEASE PI-SCEI | VATA_YEAST 1-454  
B | PI-SceI DNA recognition region top strand |  
C | PI-SceI DNA recognition region bottom strand |  
  

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> show cartoons

> view #2 clip false

> open /Users/petergogarten/Downloads/ChimeraX/PDB/chainA+DNA_colored.pdb

Chain information for chainA+DNA_colored.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> select helix

2087 atoms, 2107 bonds, 268 residues, 2 models selected  


===== 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 ATI-4.8.54
OpenGL renderer: AMD Radeon Pro 575X OpenGL Engine
OpenGL vendor: ATI Technologies 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: iMac
      Model Identifier: iMac19,1
      Processor Name: 6-Core Intel Core i5
      Processor Speed: 3.1 GHz
      Number of Processors: 1
      Total Number of Cores: 6
      L2 Cache (per Core): 256 KB
      L3 Cache: 9 MB
      Memory: 16 GB
      System Firmware Version: 1731.120.8.0.0
      OS Loader Version: 540.120.3~6
      SMC Version (system): 2.46f13

Software:

    System Software Overview:

      System Version: macOS 12.4 (21F79)
      Kernel Version: Darwin 21.5.0
      Time since boot: 24 days 22:12

Graphics/Displays:

    Radeon Pro 575X:

      Chipset Model: Radeon Pro 575X
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 4 GB
      Vendor: AMD (0x1002)
      Device ID: 0x67df
      Revision ID: 0x00c4
      ROM Revision: 113-D0008A-042
      VBIOS Version: 113-D0008A14GP-003
      EFI Driver Version: 01.B1.042
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        iMac:
          Display Type: Built-In Retina LCD
          Resolution: Retina 5K (5120 x 2880)
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    appnope: 0.1.3
    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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