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Opened 18 months ago
Closed 18 months ago
#15057 closed defect (can't reproduce)
Crash in garbage collection
| Reported by: | 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: Linux-6.8.0-76060800daily20240311-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.8.dev202404262304 (2024-04-26 23:04:27 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 0x0000728d28bd8b80 (most recent call first):
Garbage-collecting
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/sim_matrices/__init__.py", line 57 in read_matrix_file
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/sim_matrices/__init__.py", line 132 in _init
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/sim_matrices/__init__.py", line 72 in matrices
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/sim_matrices/options.py", line 28 in
File "", line 241 in _call_with_frames_removed
File "", line 940 in exec_module
File "", line 690 in _load_unlocked
File "", line 1147 in _find_and_load_unlocked
File "", line 1176 in _find_and_load
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/match_maker/tool.py", line 101 in __init__
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/match_maker/__init__.py", line 44 in start_tool
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/toolshed/__init__.py", line 1282 in start_tool
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/toolshed/info.py", line 571 in start_tool
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/ui/cmd.py", line 219 in ui_tool_show
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3209 in run
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49 in run
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/ui/gui.py", line 1787 in
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/ui/gui.py", line 283 in event_loop
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1006 in init
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1169 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.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, 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, chimerax.surface._surface, 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.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, chimerax.alignment_algs._sw, chimerax.alignment_algs._nw, PIL._imagingmath, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp (total: 57)
===== Log before crash start =====
UCSF ChimeraX version: 1.8.dev202404262304 (2024-04-26)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 7y0d format mmcif fromDatabase pdb
7y0d title:
Cryo-EM structure of the Mycobacterium smegmatis DNA integrity scanning
protein (MsDisA). [more info...]
Chain information for 7y0d #1
---
Chain | Description | UniProt
A B C D E F G H | DNA integrity scanning protein DisA | DISA_MYCS2 1-372
> close
> ui tool show AlphaFold
Fetching compressed D0LZ74 UniProt info from
https://www.uniprot.org/uniprot/D0LZ74.xml
> alphafold match D0LZ74
Fetching compressed AlphaFold D0LZ74 from
https://alphafold.ebi.ac.uk/files/AF-D0LZ74-F1-model_v4.cif
1 AlphaFold model found using UniProt identifier: D0LZ74 (UniProt D0LZ74)
Sequence Similarity
---
AlphaFold Model| Query Sequence| Identity %| Coverage %
D0LZ74 | D0LZ74 | 100.0 | 100.0
Opened 1 AlphaFold model
Fetching compressed D0LZ73 UniProt info from
https://www.uniprot.org/uniprot/D0LZ73.xml
> alphafold match D0LZ73Fetching compressed AlphaFold D0LZ73 from
> https://alphafold.ebi.ac.uk/files/AF-D0LZ73-F1-model_v4.cif
1 AlphaFold model found using UniProt identifier: D0LZ73 (UniProt D0LZ73)
| Sequence Similarity
---
AlphaFold Model| Query Sequence| Identity %| Coverage %
D0LZ73 | D0LZ73 | 100.0 | 100.0
Opened 1 AlphaFold model
> alphafold predict D0LZ73Please cite ColabFold: Making protein folding
> accessible to all. Nature Methods (2022) if you use these predictions.
Running AlphaFold prediction
Alphafold prediction send sequence to Google Colab returned: None
Running AlphaFold prediction
> ui tool show "AlphaFold Error Plot"Fetching PAE using AlphaFold database
> version 4
> alphafold pae #2 uniprotId D0LZ73 version 4Fetching compressed AlphaFold PAE
> D0LZ73 from
> https://alphafold.ebi.ac.uk/files/AF-D0LZ73-F1-predicted_aligned_error_v4.json
> color #2:53-53 lime> color #2:62-62 magenta> color #2:52-52 lime> color
> #2:72-72 magenta> color #2:59-59 lime> color #2:84-84 magenta> color
> #2:102-102 lime> color #2:78-78 magenta> color #2:58-59 lime> color #2:80-82
> magenta> color #2:45-125 lime> color #2:83-83 lime> color #2:95-95 magenta>
> color #2:97-131 lime> color #2:106-106 lime> color #2:76-76 magenta> color
> #2:119-131 lime> color #2:4-95 magenta> color #2:105-131 lime> alphafold pae
> #2 colorDomains true> color bfactor #2 palette alphafold1037 atoms, 131
> residues, atom bfactor range 34.5 to 98.9
> close> alphafold match D0LZ73,D0LZ742 AlphaFold models found using UniProt
> identifiers: D0LZ73 (UniProt D0LZ73), D0LZ74 (UniProt D0LZ74)
| Sequence Similarity
---
AlphaFold Model| Query Sequence| Identity %| Coverage %
D0LZ73 | D0LZ73 | 100.0 | 100.0
| Sequence Similarity
---
AlphaFold Model| Query Sequence| Identity %| Coverage %
D0LZ74 | D0LZ74 | 100.0 | 100.0
Opened 2 AlphaFold models
Fetching PAE using AlphaFold database version 4
> alphafold pae #2 uniprotId D0LZ73,D0LZ74 version 4Invalid "uniprotId"
> argument: Invalid UniProt identifier "D0LZ73,D0LZ74"
> close> open 7kkj | Summary of feedback from opening 7kkj fetched from pdb
---
warnings | Atom H1 is not in the residue template for GLN /A:1
Atom H1 is not in the residue template for GLN /C:1
notes | Fetching compressed mmCIF 7kkj from http://files.rcsb.org/download/7kkj.cif
Fetching CCD CL from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/L/CL/CL.cif
7kkj title:
Structure of anti-SARS-CoV-2 Spike nanobody mNb6 [more info...]
Chain information for 7kkj #1
---
Chain | Description
A C | Synthetic nanobody mNb6
Non-standard residues in 7kkj #1
---
CL — chloride ion
SO4 — sulfate ion
7kkj mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
170 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> select /A:1-118
1762 atoms, 1781 bonds, 118 residues, 1 model selected
> select /C:1-119
1769 atoms, 1788 bonds, 119 residues, 1 model selected
> select :CL
1 atom, 1 residue, 1 model selected
> select :CL
1 atom, 1 residue, 1 model selected
> select :SO4
20 atoms, 16 bonds, 4 residues, 1 model selected
> select :CL
1 atom, 1 residue, 1 model selected
> sym #1 assembly 1
Made 1 copies for 7kkj assembly 1
> view
> sym #1 assembly 2
Made 1 copies for 7kkj assembly 2
> view
> hide #!2 models
> hide #!3 models
> hide #2.1 models
> hide #3.1 models
> show #1 models
> hide #1 models
> show #!3 models
> hide #!3 models
> show #3.1 models
> hide #3.1 models
> show #2.1 models
> hide #2.1 models
> hide #!2 models
> hide #!3 models
> show #!2 models
> show #2.1 models
> show #2.1 atoms
> hide #2.1 cartoons
> style #2.1 sphere
Changed 1842 atom styles
> style #2.1 ball
Changed 1842 atom styles
> lighting soft
> lighting full
> select #2.1/A:105@OH
1 atom, 1 residue, 1 model selected
> select up
21 atoms, 21 bonds, 1 residue, 1 model selected
> select up
111 atoms, 113 bonds, 9 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> select down
21 atoms, 21 bonds, 1 residue, 1 model selected
> select clear
> preset "initial styles" "original look"
Using preset: Initial Styles / Original Look
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> show #!3 models
> show #3.1 models
> coulombic
The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics:
7kkj #1/C SER 119 OG
7kkj #3.1/C SER 119 OG
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 7kkj_A SES surface #1.1: minimum, -14.35, mean 1.79,
maximum 15.82
Coulombic values for 7kkj_C SES surface #1.2: minimum, -13.58, mean 1.82,
maximum 16.66
Coulombic values for 7kkj_A SES surface #2.1.1: minimum, -13.88, mean 1.85,
maximum 14.79
Coulombic values for 7kkj_C SES surface #3.1.1: minimum, -13.59, mean 1.82,
maximum 16.65
> color bfactor
7366 atoms, 746 residues, 4 surfaces, atom bfactor range 18.9 to 93.5
> open 7kkj fromDatabase eds
Summary of feedback from opening 7kkj fetched from eds
---
note | Fetching map 7kkj from http://www.ebi.ac.uk/pdbe/coordinates/files/7kkj.ccp4
Opened eds 7kkj as #4, grid size 72,120,76, pixel 0.619,0.594,0.611, shown at
level 1.17, step 1, values float32
> hide #!2 models
> hide #!2.1 models
> hide #!3 models
> delete #3
> delete #2
> delete #1
> delete #2
> hide cartoons
> show atoms
> close
> open 7kkl
Summary of feedback from opening 7kkl fetched from pdb
---
notes | Fetching compressed mmCIF 7kkl from http://files.rcsb.org/download/7kkl.cif
Fetching CCD NAG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/NAG/NAG.cif
7kkl title:
SARS-CoV-2 Spike in complex with neutralizing nanobody mNb6 [more info...]
Chain information for 7kkl #1
---
Chain | Description | UniProt
A C D | Spike glycoprotein | SPIKE_SARS2 1-1208
B E F | Synthetic nanobody mNb6 |
Non-standard residues in 7kkl #1
---
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> select /B:2-119
1752 atoms, 1771 bonds, 118 residues, 1 model selected
> color /B,E,F gold
> show /D,F cartoons
> open 22910 fromDatabase emdb
Summary of feedback from opening 22910 fetched from emdb
---
notes | Fetching compressed map 22910 from ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-22910/map/emd_22910.map.gz
Fetching map header 22910 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-22910/header/emd-22910.xml
Opened emdb 22910 as #2, grid size 384,384,384, pixel 0.834, shown at level 2,
step 2, values float32, fit PDB 7kkl
> close #
Expected a models specifier or a keyword
> close #`
Expected a models specifier or a keyword
> close #1
> open 6vxx
Summary of feedback from opening 6vxx fetched from pdb
---
note | Fetching compressed mmCIF 6vxx from http://files.rcsb.org/download/6vxx.cif
6vxx title:
Structure of the SARS-CoV-2 spike glycoprotein (closed state) [more info...]
Chain information for 6vxx #1
---
Chain | Description | UniProt
A B C | Spike glycoprotein | SPIKE_SARS2 14-1211
Non-standard residues in 6vxx #1
---
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> color bychain
> ui mousemode right "translate selected models"
> select /B:511
7 atoms, 6 bonds, 1 residue, 1 model selected
> view matrix models #1,1,0,0,-51.373,0,1,0,-42.557,0,0,1,-34.014
> fitmap #1 inMap #2
Fit molecule 6vxx (#1) to map emdb 22910 (#2) using 23694 atoms
average map value = 0.8398, steps = 64
shifted from previous position = 3.11
rotated from previous position = 2.68 degrees
atoms outside contour = 19639, contour level = 2
Position of 6vxx (#1) relative to emdb 22910 (#2) coordinates:
Matrix rotation and translation
0.99907855 0.00276815 0.04282964 -57.72343914
-0.00196585 0.99982202 -0.01876331 -38.78439566
-0.04287396 0.01866182 0.99890618 -29.72575711
Axis 0.39967695 0.91526085 -0.05055616
Axis point -780.98932449 0.00000000 798.41750100
Rotation angle (degrees) 2.68352493
Shift along axis -57.06574651
> view matrix models
> #1,0.99908,0.0027682,0.04283,-101.92,-0.0019658,0.99982,-0.018763,-112.63,-0.042874,0.018662,0.99891,69.333
> view matrix models
> #1,0.99908,0.0027682,0.04283,-102.59,-0.0019658,0.99982,-0.018763,-111.72,-0.042874,0.018662,0.99891,63.852
> ui mousemode right rotate
> ui mousemode right translate
> ui mousemode right rotate
> select /A:351
12 atoms, 12 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> select clear
> select /A:351
12 atoms, 12 bonds, 1 residue, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.91856,0.01898,-0.39483,-2.7182,-0.19615,0.88908,-0.4136,31.619,0.34319,0.45736,0.82039,-78.909
> view matrix models
> #1,0.84693,-0.023981,-0.53117,48.59,-0.29753,0.80656,-0.51082,89.963,0.44067,0.59067,0.67596,-99.535
> view matrix models
> #1,0.99544,-0.012699,0.094496,-109.64,0.0094147,0.99934,0.035123,-125.79,-0.09488,-0.034073,0.99491,87.541
> ui mousemode right "move picked models"
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.99544,-0.012699,0.094496,-144.71,0.0094147,0.99934,0.035123,-190.99,-0.09488,-0.034073,0.99491,188.9
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.97853,-0.053835,0.19895,-153.79,0.024018,0.98849,0.14936,-215.43,-0.2047,-0.14137,0.96856,241.22
> view matrix models
> #1,-0.40794,0.46518,0.78561,-68.492,-0.86643,-0.46856,-0.17246,350.93,0.28788,-0.75104,0.59419,332.67
> view matrix models
> #1,-0.98157,-0.16183,0.10162,324.42,-0.17261,0.97903,-0.10815,-119.57,-0.081992,-0.1237,-0.98893,593.3
> ui mousemode right "move picked models"
> view matrix models
> #1,-0.98157,-0.16183,0.10162,392,-0.17261,0.97903,-0.10815,2.5084,-0.081992,-0.1237,-0.98893,410.22
> fitmap #1 inMap #2
Fit molecule 6vxx (#1) to map emdb 22910 (#2) using 23694 atoms
average map value = 3.158, steps = 200
shifted from previous position = 18.3
rotated from previous position = 8.62 degrees
atoms outside contour = 9753, contour level = 2
Position of 6vxx (#1) relative to emdb 22910 (#2) coordinates:
Matrix rotation and translation
-0.98914104 -0.14697110 0.00025202 398.67132134
-0.14697114 0.98914116 0.00014353 -16.74849456
-0.00027036 0.00010489 -1.00000025 376.96958113
Axis -0.07376318 0.99727578 -0.00007172
Axis point 198.74101209 0.00000000 188.45823675
Rotation angle (degrees) 179.98499384
Shift along axis -46.13717099
> select clear
> show atoms
> style sphere
Changed 23694 atom styles
> color zone #2 near #1 distance 5
> close
> open 7kkj 7kkl
Summary of feedback from opening 7kkj fetched from pdb
---
warnings | Atom H1 is not in the residue template for GLN /A:1
Atom H1 is not in the residue template for GLN /C:1
7kkj title:
Structure of anti-SARS-CoV-2 Spike nanobody mNb6 [more info...]
Chain information for 7kkj #1
---
Chain | Description
A C | Synthetic nanobody mNb6
Non-standard residues in 7kkj #1
---
CL — chloride ion
SO4 — sulfate ion
7kkj mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
170 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
7kkl title:
SARS-CoV-2 Spike in complex with neutralizing nanobody mNb6 [more info...]
Chain information for 7kkl #2
---
Chain | Description | UniProt
A C D | Spike glycoprotein | SPIKE_SARS2 1-1208
B E F | Synthetic nanobody mNb6 |
Non-standard residues in 7kkl #2
---
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> hide atoms
> show cartoons
> color #1 red
> color #2/F gold
> ui tool show Matchmaker
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.8.dev202404262304 (2024-04-26)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 3.3.0 NVIDIA 550.67
OpenGL renderer: NVIDIA GeForce RTX 2070 SUPER/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: xcb
XDG_SESSION_TYPE=x11
DESKTOP_SESSION=pop
XDG_SESSION_DESKTOP=pop
XDG_CURRENT_DESKTOP=pop:GNOME
DISPLAY=:1
Manufacturer: Dell Inc.
Model: Precision 7530
OS: Pop!_OS 22.04 jammy
Architecture: 64bit ELF
Virtual Machine: none
CPU: 12 Intel(R) Core(TM) i7-8750H CPU @ 2.20GHz
Cache Size: 9216 KB
Memory:
total used free shared buff/cache available
Mem: 31Gi 3.9Gi 20Gi 779Mi 6.9Gi 24Gi
Swap: 47Gi 0B 47Gi
Graphics:
00:02.0 VGA compatible controller [0300]: Intel Corporation CoffeeLake-H GT2 [UHD Graphics 630] [8086:3e9b]
DeviceName: Onboard - Video
Subsystem: Dell CoffeeLake-H GT2 [UHD Graphics 630] [1028:0831]
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
asttokens: 2.4.1
Babel: 2.14.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2024.2.2
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.16
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.5
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57
ChimeraX-AtomicLibrary: 14.0.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.4
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.3
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.4
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: 1.8.dev202404262304
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
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: 1.1.9
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: 1.2
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: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.15
ChimeraX-ModelPanel: 1.5
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-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.4
ChimeraX-PDB: 2.7.5
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: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
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-Segmentations: 1.0.3
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
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: 1.38
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.1
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: 0.2.2
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
distro: 1.9.0
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.51.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.2
jedi: 0.19.1
Jinja2: 3.1.3
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.10
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 24.0
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.1
prompt-toolkit: 3.0.43
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.2
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
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: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4
traitlets: 5.14.2
typing-extensions: 4.11.0
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.10
Change History (2)
comment:1 by , 18 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Core |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in garbage collection |
comment:2 by , 18 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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We've still got some crashes in garbage collection, just not as many.