Opened 20 months ago

Closed 20 months ago

#14738 closed defect (duplicate)

Crash in garbage collection

Reported by: jan.binovsky@… 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:        Linux-5.4.0-172-generic-x86_64-with-glibc2.31
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

Current thread 0x00007f572d6b7740 (most recent call first):
  Garbage-collecting
  File "/cemcofsw/em/chimerax/1.7/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 161 in 
  File "/cemcofsw/em/chimerax/1.7/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 161 in __iter__
  File "/cemcofsw/em/chimerax/1.7/lib/python3.11/site-packages/chimerax/mmcif/__init__.py", line 123 in save
  File "/cemcofsw/em/chimerax/1.7/lib/python3.11/site-packages/chimerax/save_command/cmd.py", line 101 in provider_save
  File "/cemcofsw/em/chimerax/1.7/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2908 in run
  File "/cemcofsw/em/chimerax/1.7/lib/python3.11/site-packages/chimerax/save_command/cmd.py", line 86 in cmd_save
  File "/cemcofsw/em/chimerax/1.7/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2908 in run
  File "/cemcofsw/em/chimerax/1.7/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49 in run
  File "/cemcofsw/em/chimerax/1.7/lib/python3.11/site-packages/chimerax/save_command/dialog.py", line 62 in display
  File "/cemcofsw/em/chimerax/1.7/lib/python3.11/site-packages/chimerax/save_command/dialog.py", line 138 in show_save_file_dialog
  File "/cemcofsw/em/chimerax/1.7/lib/python3.11/site-packages/chimerax/toolbar/providers.py", line 38 in _file_save
  File "/cemcofsw/em/chimerax/1.7/lib/python3.11/site-packages/chimerax/toolbar/providers.py", line 56 in run_provider
  File "/cemcofsw/em/chimerax/1.7/lib/python3.11/site-packages/chimerax/toolbar/__init__.py", line 37 in run_provider
  File "/cemcofsw/em/chimerax/1.7/lib/python3.11/site-packages/chimerax/core/toolshed/__init__.py", line 1302 in run_provider
  File "/cemcofsw/em/chimerax/1.7/lib/python3.11/site-packages/chimerax/core/toolshed/info.py", line 397 in run_provider
  File "/cemcofsw/em/chimerax/1.7/lib/python3.11/site-packages/chimerax/toolbar/tool.py", line 165 in callback
  File "/cemcofsw/em/chimerax/1.7/lib/python3.11/site-packages/chimerax/ui/gui.py", line 275 in event_loop
  File "/cemcofsw/em/chimerax/1.7/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
  File "/cemcofsw/em/chimerax/1.7/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, openmm._openmm, openmm.app.internal.compiled, chimerax.pdb_lib._load_libs, lxml._elementpath, lxml.etree, scipy._lib._ccallback_c, scipy.special._ufuncs_cxx, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.sparse.linalg._isolve._iterative, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, scipy.linalg._flinalg, scipy.special._ellip_harm_2, scipy.interpolate._fitpack, scipy.interpolate.dfitpack, scipy.optimize._minpack2, scipy.optimize._group_columns, scipy._lib.messagestream, scipy.optimize._trlib._trlib, numpy.linalg.lapack_lite, scipy.optimize._lbfgsb, _moduleTNC, scipy.optimize._moduleTNC, scipy.optimize._cobyla, scipy.optimize._slsqp, scipy.optimize._minpack, scipy.optimize._lsq.givens_elimination, scipy.optimize._zeros, scipy.optimize.__nnls, scipy.optimize._highs.cython.src._highs_wrapper, scipy.optimize._highs._highs_wrapper, scipy.optimize._highs.cython.src._highs_constants, scipy.optimize._highs._highs_constants, scipy.linalg._interpolative, scipy.optimize._bglu_dense, scipy.optimize._lsap, scipy.spatial._ckdtree, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.spatial.transform._rotation, scipy.optimize._direct, scipy.interpolate._bspl, scipy.interpolate._ppoly, scipy.interpolate.interpnd, scipy.interpolate._rbfinterp_pythran, scipy.interpolate._rgi_cython, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, chimerax.mmcif.mmcif_write, chimerax.dssp._dssp (total: 122)
===== Log before crash start =====
Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  

> isolde shorthand
    
    
    Initialising ISOLDE-specific command aliases:
    Alias	Equivalent full command
    -------------------------------------------------
    st	isolde step {arguments}
    aw	isolde add water {arguments}
    awsf	isolde add water {arguments} sim false
    al	isolde add ligand {arguments}
    aa	isolde add aa $1 sel {arguments}
    ht	isolde mod his sel {arguments}
    so	setattr sel atoms occupancy {arguments}
    ab	isolde adjust bfactors {arguments}
    ss	isolde sim start sel
    rt	isolde release torsions sel {arguments}
    rd	isolde release distances sel {arguments}
    ra	rd; rt
    pf	isolde pepflip sel
    cf	isolde cisflip sel
    cbb	color bfactor {arguments}
    cbo	color byattr occupancy {arguments}
    cbc	color {arguments} bychain; color {arguments} byhet
    cs	clipper set contourSensitivity {arguments}
    

  

> lighting soft

> hide atoms

> show cartoons

> mousemode shift middleMode center

UCSF ChimeraX version: 1.7 (2023-12-19)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /home/janbinovsky/Projects/baseplate_building_phi812/baseplate/native_structures/native_complete/phenix_native_complete/RealSpaceRefine_22/nat_complete_rsr022_third.cif

Summary of feedback from opening
/home/janbinovsky/Projects/baseplate_building_phi812/baseplate/native_structures/native_complete/phenix_native_complete/RealSpaceRefine_22/nat_complete_rsr022_third.cif  
---  
warnings | Unknown polymer entity '1' near line 558  
Unknown polymer entity '2' near line 17874  
Unknown polymer entity '3' near line 22199  
Unknown polymer entity '4' near line 27698  
Unknown polymer entity '5' near line 32820  
16 messages similar to the above omitted  
Atom OG has no neighbors to form bonds with according to residue template for
SER /b:130  
Atom O has no neighbors to form bonds with according to residue template for
TYR /i:888  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for nat_complete_rsr022_third.cif #1  
---  
Chain | Description  
0 1 2 3 h i j l z | No description available  
4 | No description available  
5 6 7 n o p | No description available  
8 9 AA q r s | No description available  
A | No description available  
B | No description available  
C D | No description available  
E | No description available  
F | No description available  
G | No description available  
H J | No description available  
I K | No description available  
L O | No description available  
M N | No description available  
P Q | No description available  
R S V W Z a | No description available  
T U | No description available  
X Y | No description available  
b c d e f g t u v w x y | No description available  
k | No description available  
m | No description available  
  

> open
> /home/janbinovsky/Projects/phi812_paper/deposition_PDB/01_native_baseplate_complete/postprocess/bp_nat_complete_ref3Djob019_1-075apx_masked.mrc
> format mrc

Opened bp_nat_complete_ref3Djob019_1-075apx_masked.mrc as #2, grid size
840,840,840, pixel 1.08, shown at step 1, values float32  

> volume #2 region 0,0,0,839,839,839 step 4

> volume #2 step 1

> measure symmetry #2

Symmetry bp_nat_complete_ref3Djob019_1-075apx_masked.mrc: C3, center 420 420
422  

> sym #1 symmetry #2 addMmcifAssembly true

Made 3 copies for nat_complete_rsr022_third.cif symmetry #2  

> close #3

> show #!1 models

> save
> /home/janbinovsky/Projects/baseplate_building_phi812/baseplate/native_structures/native_complete/phenix_native_complete/RealSpaceRefine_22/nat_complete_rsr022_third_sym1.cif
> relModel #1

Not saving entity_poly_seq for non-authoritative sequences  

> close #1

> open
> /home/janbinovsky/Projects/baseplate_building_phi812/baseplate/native_structures/native_complete/phenix_native_complete/RealSpaceRefine_22/nat_complete_rsr022_third_sym1.cif

Summary of feedback from opening
/home/janbinovsky/Projects/baseplate_building_phi812/baseplate/native_structures/native_complete/phenix_native_complete/RealSpaceRefine_22/nat_complete_rsr022_third_sym1.cif  
---  
warnings | Unknown polymer entity '1' near line 307  
Unknown polymer entity '2' near line 17623  
Unknown polymer entity '3' near line 21948  
Unknown polymer entity '4' near line 27447  
Unknown polymer entity '5' near line 32569  
16 messages similar to the above omitted  
Atom OG has no neighbors to form bonds with according to residue template for
SER /b:130  
Atom O has no neighbors to form bonds with according to residue template for
TYR /i:888  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for nat_complete_rsr022_third_sym1.cif #1  
---  
Chain | Description  
0 1 2 3 h i j l z | No description available  
4 | No description available  
5 6 7 n o p | No description available  
8 9 AA q r s | No description available  
A | No description available  
B | No description available  
C D | No description available  
E | No description available  
F | No description available  
G | No description available  
H J | No description available  
I K | No description available  
L O | No description available  
M N | No description available  
P Q | No description available  
R S V W Z a | No description available  
T U | No description available  
X Y | No description available  
b c d e f g t u v w x y | No description available  
k | No description available  
m | No description available  
  
nat_complete_rsr022_third_sym1.cif mmCIF Assemblies  
---  
1| author defined symmetry  
  

> sym #1 assembly 1

Made 3 copies for nat_complete_rsr022_third_sym1.cif assembly 1  

> view

> close #3#3.1-3

> close #1

> close #2

> open
> /home/janbinovsky/Projects/phi812_paper/deposition_PDB/01_native_baseplate_complete/bp_nat_fitted/rsr022/nat_complete_rsr022_third_sym1.cif

Summary of feedback from opening
/home/janbinovsky/Projects/phi812_paper/deposition_PDB/01_native_baseplate_complete/bp_nat_fitted/rsr022/nat_complete_rsr022_third_sym1.cif  
---  
warnings | Unknown polymer entity '1' near line 307  
Unknown polymer entity '2' near line 17623  
Unknown polymer entity '3' near line 21948  
Unknown polymer entity '4' near line 27447  
Unknown polymer entity '5' near line 32569  
16 messages similar to the above omitted  
Atom OG has no neighbors to form bonds with according to residue template for
SER /b:130  
Atom O has no neighbors to form bonds with according to residue template for
TYR /i:888  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for nat_complete_rsr022_third_sym1.cif #1  
---  
Chain | Description  
0 1 2 3 h i j l z | No description available  
4 | No description available  
5 6 7 n o p | No description available  
8 9 AA q r s | No description available  
A | No description available  
B | No description available  
C D | No description available  
E | No description available  
F | No description available  
G | No description available  
H J | No description available  
I K | No description available  
L O | No description available  
M N | No description available  
P Q | No description available  
R S V W Z a | No description available  
T U | No description available  
X Y | No description available  
b c d e f g t u v w x y | No description available  
k | No description available  
m | No description available  
  
nat_complete_rsr022_third_sym1.cif mmCIF Assemblies  
---  
1| author defined symmetry  
  

> show cartoons

> hide atoms

> dssp

> save
> /home/janbinovsky/Projects/phi812_paper/deposition_PDB/01_native_baseplate_complete/bp_nat_fitted/rsr022/nat_complete_rsr022_third_sym2.cif
> 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  
  

> isolde shorthand
    
    
    Initialising ISOLDE-specific command aliases:
    Alias	Equivalent full command
    -------------------------------------------------
    st	isolde step {arguments}
    aw	isolde add water {arguments}
    awsf	isolde add water {arguments} sim false
    al	isolde add ligand {arguments}
    aa	isolde add aa $1 sel {arguments}
    ht	isolde mod his sel {arguments}
    so	setattr sel atoms occupancy {arguments}
    ab	isolde adjust bfactors {arguments}
    ss	isolde sim start sel
    rt	isolde release torsions sel {arguments}
    rd	isolde release distances sel {arguments}
    ra	rd; rt
    pf	isolde pepflip sel
    cf	isolde cisflip sel
    cbb	color bfactor {arguments}
    cbo	color byattr occupancy {arguments}
    cbc	color {arguments} bychain; color {arguments} byhet
    cs	clipper set contourSensitivity {arguments}
    

  

> lighting soft

> hide atoms

> show cartoons

> mousemode shift middleMode center

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: 3.3.0 NVIDIA 470.239.06
OpenGL renderer: NVIDIA GeForce RTX 3090/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.2
Locale: en_US.UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=xubuntu
XDG_SESSION_DESKTOP=xubuntu
XDG_CURRENT_DESKTOP=XFCE
DISPLAY=:0.0
Manufacturer: M Computers s.r.o.
Model: Super Server
OS: Ubuntu 20.04 Focal Fossa
Architecture: 64bit ELF
Virtual Machine: none
CPU: 32 AMD EPYC 7302P 16-Core Processor
Cache Size: 512 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:          251Gi        28Gi       220Gi       717Mi       2.3Gi       220Gi
	Swap:            0B          0B          0B

Graphics:
	01:00.0 VGA compatible controller [0300]: NVIDIA Corporation Device [10de:2204] (rev a1)	
	Subsystem: Gigabyte Technology Co., Ltd Device [1458:403b]	
	Kernel driver in use: nvidia

Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    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: 2023.11.17
    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-Clipper: 0.22.4
    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-ISOLDE: 1.7.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.8
    ChimeraX-LinuxSupport: 1.0.1
    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
    distro: 1.7.0
    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: 23.2
    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
    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 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

Hi Jan,

Thanks for reporting this problem. We believe it is fixed in the current daily build, so if you use that then you shouldn't run into this kind of crash again.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

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