Opened 6 months ago

Closed 6 months ago

#17634 closed defect (duplicate)

Crash in garbage collection

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

Description 

The following bug report has been submitted:
Platform:        Linux-6.8.0-59-generic-x86_64-with-glibc2.35
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 0x000074c8171d5640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 324 in wait
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 622 in wait
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1392 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap

Current thread 0x000074c8c026cb80 (most recent call first):
  Garbage-collecting
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/mouse_modes/mousemodes.py", line 798 in decode_modifier_bits
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/mouse_modes/mousemodes.py", line 790 in key_modifiers
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/mouse_modes/mousemodes.py", line 555 in _event_type
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/mouse_modes/mousemodes.py", line 534 in _dispatch_mouse_event
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/mouse_modes/mousemodes.py", line 651 in 
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/ui/graphics.py", line 61 in event
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/ui/gui.py", line 275 in event_loop
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
  File "/usr/lib/ucsf-chimerax/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, 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, 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.dssp._dssp, chimerax.alignment_algs._nw, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp, chimerax.mlp._mlp (total: 58)
===== 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
> /home/leonf/phd/Analysis_FAT10_Simulation_Triplicates/Clusters_CD_UMAP/CD_UMAP_Clusters_Coarse_min_samples4000_random_choice/CD_UMAP_Cluster_coarse0.pdb
> /home/leonf/phd/Analysis_FAT10_Simulation_Triplicates/Clusters_CD_UMAP/CD_UMAP_Clusters_Coarse_min_samples4000_random_choice/CD_UMAP_Cluster_coarse1.pdb

Chain information for CD_UMAP_Cluster_coarse0.pdb  
---  
Chain | Description  
1.1/A 1.2/A 1.3/A 1.4/A 1.5/A 1.6/A 1.7/A 1.8/A 1.9/A 1.10/A | No description
available  
  
Chain information for CD_UMAP_Cluster_coarse1.pdb  
---  
Chain | Description  
2.1/A 2.2/A 2.3/A 2.4/A 2.5/A 2.6/A 2.7/A 2.8/A 2.9/A 2.10/A | No description
available  
  

> hide :1/88

> hide :1-87

> hide :1-87 cartoons

> mmaker #1:88-160 to #2 :88-160

Specify a single 'to' model only  

> mmaker #1:88-160 to #2.1 :88-160

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker CD_UMAP_Cluster_coarse1.pdb, chain A (#2.1) with
CD_UMAP_Cluster_coarse0.pdb, chain A (#1.1), sequence alignment score = 352.4  
RMSD between 57 pruned atom pairs is 1.014 angstroms; (across all 73 pairs:
1.810)  
  
Matchmaker CD_UMAP_Cluster_coarse1.pdb, chain A (#2.1) with
CD_UMAP_Cluster_coarse0.pdb, chain A (#1.2), sequence alignment score = 333.2  
RMSD between 55 pruned atom pairs is 1.002 angstroms; (across all 73 pairs:
2.387)  
  
Matchmaker CD_UMAP_Cluster_coarse1.pdb, chain A (#2.1) with
CD_UMAP_Cluster_coarse0.pdb, chain A (#1.3), sequence alignment score = 338  
RMSD between 51 pruned atom pairs is 1.103 angstroms; (across all 73 pairs:
3.384)  
  
Matchmaker CD_UMAP_Cluster_coarse1.pdb, chain A (#2.1) with
CD_UMAP_Cluster_coarse0.pdb, chain A (#1.4), sequence alignment score = 347  
RMSD between 60 pruned atom pairs is 1.106 angstroms; (across all 73 pairs:
2.145)  
  
Matchmaker CD_UMAP_Cluster_coarse1.pdb, chain A (#2.1) with
CD_UMAP_Cluster_coarse0.pdb, chain A (#1.5), sequence alignment score = 356  
RMSD between 49 pruned atom pairs is 1.173 angstroms; (across all 73 pairs:
1.907)  
  
Matchmaker CD_UMAP_Cluster_coarse1.pdb, chain A (#2.1) with
CD_UMAP_Cluster_coarse0.pdb, chain A (#1.6), sequence alignment score = 329  
RMSD between 57 pruned atom pairs is 0.946 angstroms; (across all 73 pairs:
1.940)  
  
Matchmaker CD_UMAP_Cluster_coarse1.pdb, chain A (#2.1) with
CD_UMAP_Cluster_coarse0.pdb, chain A (#1.7), sequence alignment score = 336.8  
RMSD between 46 pruned atom pairs is 1.055 angstroms; (across all 73 pairs:
2.510)  
  
Matchmaker CD_UMAP_Cluster_coarse1.pdb, chain A (#2.1) with
CD_UMAP_Cluster_coarse0.pdb, chain A (#1.8), sequence alignment score = 332.6  
RMSD between 49 pruned atom pairs is 1.201 angstroms; (across all 73 pairs:
3.021)  
  
Matchmaker CD_UMAP_Cluster_coarse1.pdb, chain A (#2.1) with
CD_UMAP_Cluster_coarse0.pdb, chain A (#1.9), sequence alignment score = 348.8  
RMSD between 56 pruned atom pairs is 1.087 angstroms; (across all 73 pairs:
2.562)  
  
Matchmaker CD_UMAP_Cluster_coarse1.pdb, chain A (#2.1) with
CD_UMAP_Cluster_coarse0.pdb, chain A (#1.10), sequence alignment score = 343.4  
RMSD between 55 pruned atom pairs is 0.929 angstroms; (across all 73 pairs:
2.243)  
  

> show :125,126

> color :125 green

> select ~sel & ##selected

Nothing selected  

> select ~sel & ##selected

Nothing selected  

> hide :125

> color byhetero

> color bychain

> color bypolymer

> rainbow

> coulombic

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for CD_UMAP_Cluster_coarse0.pdb_A SES surface #1.1.1:
minimum, -15.03, mean 1.79, maximum 33.15  
Coulombic values for CD_UMAP_Cluster_coarse0.pdb_A SES surface #1.2.1:
minimum, -10.06, mean 2.20, maximum 15.17  
Coulombic values for CD_UMAP_Cluster_coarse0.pdb_A SES surface #1.3.1:
minimum, -11.60, mean 1.84, maximum 14.41  
Coulombic values for CD_UMAP_Cluster_coarse0.pdb_A SES surface #1.4.1:
minimum, -10.20, mean 1.98, maximum 17.11  
Coulombic values for CD_UMAP_Cluster_coarse0.pdb_A SES surface #1.5.1:
minimum, -10.21, mean 1.90, maximum 13.04  
Coulombic values for CD_UMAP_Cluster_coarse0.pdb_A SES surface #1.6.1:
minimum, -12.52, mean 1.76, maximum 20.29  
Coulombic values for CD_UMAP_Cluster_coarse0.pdb_A SES surface #1.7.1:
minimum, -12.67, mean 2.07, maximum 19.90  
Coulombic values for CD_UMAP_Cluster_coarse0.pdb_A SES surface #1.8.1:
minimum, -10.58, mean 1.80, maximum 15.61  
Coulombic values for CD_UMAP_Cluster_coarse0.pdb_A SES surface #1.9.1:
minimum, -15.39, mean 2.19, maximum 15.76  
Coulombic values for CD_UMAP_Cluster_coarse0.pdb_A SES surface #1.10.1:
minimum, -8.79, mean 1.62, maximum 15.26  
Coulombic values for CD_UMAP_Cluster_coarse1.pdb_A SES surface #2.1.1:
minimum, -12.00, mean 1.78, maximum 16.20  
Coulombic values for CD_UMAP_Cluster_coarse1.pdb_A SES surface #2.2.1:
minimum, -10.76, mean 1.65, maximum 14.41  
Coulombic values for CD_UMAP_Cluster_coarse1.pdb_A SES surface #2.3.1:
minimum, -10.83, mean 1.79, maximum 17.48  
Coulombic values for CD_UMAP_Cluster_coarse1.pdb_A SES surface #2.4.1:
minimum, -11.31, mean 1.90, maximum 16.95  
Coulombic values for CD_UMAP_Cluster_coarse1.pdb_A SES surface #2.5.1:
minimum, -11.43, mean 1.91, maximum 18.24  
Coulombic values for CD_UMAP_Cluster_coarse1.pdb_A SES surface #2.6.1:
minimum, -14.98, mean 1.69, maximum 15.73  
Coulombic values for CD_UMAP_Cluster_coarse1.pdb_A SES surface #2.7.1:
minimum, -13.04, mean 1.40, maximum 39.30  
Coulombic values for CD_UMAP_Cluster_coarse1.pdb_A SES surface #2.8.1:
minimum, -10.56, mean 2.10, maximum 17.61  
Coulombic values for CD_UMAP_Cluster_coarse1.pdb_A SES surface #2.9.1:
minimum, -10.08, mean 1.80, maximum 17.93  
Coulombic values for CD_UMAP_Cluster_coarse1.pdb_A SES surface #2.10.1:
minimum, -10.22, mean 2.20, maximum 23.07  
To also show corresponding color key, enter the above coulombic command and
add key true  

> mlp

Map values for surface "CD_UMAP_Cluster_coarse0.pdb_A SES surface": minimum
-26.46, mean -4.988, maximum 25.07  
Map values for surface "CD_UMAP_Cluster_coarse0.pdb_A SES surface": minimum
-25.64, mean -5.089, maximum 24.12  
Map values for surface "CD_UMAP_Cluster_coarse0.pdb_A SES surface": minimum
-26.38, mean -4.622, maximum 23.39  
Map values for surface "CD_UMAP_Cluster_coarse0.pdb_A SES surface": minimum
-25.76, mean -4.752, maximum 22.57  
Map values for surface "CD_UMAP_Cluster_coarse0.pdb_A SES surface": minimum
-24.22, mean -4.811, maximum 23.2  
Map values for surface "CD_UMAP_Cluster_coarse0.pdb_A SES surface": minimum
-26.45, mean -5.082, maximum 22.75  
Map values for surface "CD_UMAP_Cluster_coarse0.pdb_A SES surface": minimum
-27.8, mean -4.642, maximum 23.01  
Map values for surface "CD_UMAP_Cluster_coarse0.pdb_A SES surface": minimum
-25.83, mean -5.068, maximum 23.69  
Map values for surface "CD_UMAP_Cluster_coarse0.pdb_A SES surface": minimum
-26.71, mean -4.826, maximum 23.5  
Map values for surface "CD_UMAP_Cluster_coarse0.pdb_A SES surface": minimum
-25.17, mean -4.77, maximum 22.63  
Map values for surface "CD_UMAP_Cluster_coarse1.pdb_A SES surface": minimum
-26.37, mean -4.293, maximum 24.43  
Map values for surface "CD_UMAP_Cluster_coarse1.pdb_A SES surface": minimum
-25.23, mean -4.417, maximum 25.08  
Map values for surface "CD_UMAP_Cluster_coarse1.pdb_A SES surface": minimum
-26.35, mean -4.397, maximum 23.62  
Map values for surface "CD_UMAP_Cluster_coarse1.pdb_A SES surface": minimum
-27.69, mean -4.75, maximum 23.18  
Map values for surface "CD_UMAP_Cluster_coarse1.pdb_A SES surface": minimum
-26.59, mean -4.494, maximum 23.04  
Map values for surface "CD_UMAP_Cluster_coarse1.pdb_A SES surface": minimum
-24.73, mean -4.69, maximum 23.07  
Map values for surface "CD_UMAP_Cluster_coarse1.pdb_A SES surface": minimum
-25.25, mean -5.329, maximum 23.33  
Map values for surface "CD_UMAP_Cluster_coarse1.pdb_A SES surface": minimum
-28.16, mean -5.024, maximum 25.38  
Map values for surface "CD_UMAP_Cluster_coarse1.pdb_A SES surface": minimum
-23.32, mean -4.569, maximum 23.18  
Map values for surface "CD_UMAP_Cluster_coarse1.pdb_A SES surface": minimum
-27.46, mean -4.766, maximum 24.38  
To also show corresponding color key, enter the above mlp command and add key
true  

> hide surfaces

> color #1 #FF8C00

> color #2 #8FBC8F

> color #2 #800080

> color #2 :125 #9400D3

> show :125

> color #1 #FFFFE0

> color #1 :125 #FAF0E6

> color #1 :125 #FFFFE0

> color #1 :125 red

> color #2 :125 orange

> color #2 :126 purple

> color #1 :126 blue

> color #2 :126 green

> close

> open
> /home/leonf/phd/Analysis_FAT10_Simulation_Triplicates/Clusters_CD_UMAP/CD_UMAP_Clusters_Coarse_min_samples4000_random_choice/CD_UMAP_Cluster_coarse0.pdb
> /home/leonf/phd/Analysis_FAT10_Simulation_Triplicates/Clusters_CD_UMAP/CD_UMAP_Clusters_Coarse_min_samples4000_random_choice/CD_UMAP_Cluster_coarse1.pdb

Chain information for CD_UMAP_Cluster_coarse0.pdb  
---  
Chain | Description  
1.1/A 1.2/A 1.3/A 1.4/A 1.5/A 1.6/A 1.7/A 1.8/A 1.9/A 1.10/A | No description
available  
  
Chain information for CD_UMAP_Cluster_coarse1.pdb  
---  
Chain | Description  
2.1/A 2.2/A 2.3/A 2.4/A 2.5/A 2.6/A 2.7/A 2.8/A 2.9/A 2.10/A | No description
available  
  

> hide :1-87 cartoons

> show :125-126

> ui mousemode right "translate selected models"

Drag select of 100 atoms, 777 residues, 80 bonds  

> select clear

Drag select of 100 atoms, 780 residues, 80 bonds  


===== 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: 3.3.0 NVIDIA 535.183.01
OpenGL renderer: NVIDIA GeForce GTX 1080 Ti/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=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:0
Manufacturer: Micro-Star International Co., Ltd.
Model: MS-7B49
OS: Ubuntu 22.04 Jammy Jellyfish
Architecture: 64bit ELF
Virtual Machine: none
CPU: 12 Intel(R) Core(TM) i7-8700K CPU @ 3.70GHz
Cache Size: 12288 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            62Gi        25Gi        24Gi       155Mi        13Gi        36Gi
	Swap:          2.0Gi       0.0Ki       2.0Gi

Graphics:
	01:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP102 [GeForce GTX 1080 Ti] [10de:1b06] (rev a1)	
	Subsystem: ZOTAC International (MCO) Ltd. GP102 [GeForce GTX 1080 Ti] [19da:4471]	
	Kernel driver in use: nvidia

Installed Packages:
    alabaster: 0.7.16
    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: 2.12.2
    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-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: 2.6.1
    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
    distro: 1.7.0
    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
    MolecularDynamicsViewer: 1.4
    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: 23.2
    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
    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 Eric Pettersen, 6 months ago

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, 6 months ago

Resolution: → duplicate
Status: accepted → closed
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