The following bug report has been submitted:
Platform: Linux-6.5.0-35-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.8rc202406060152 (2024-06-06 01:52:35 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x00007572fb7fa640 (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 0x0000757461479b80 (most recent call first):
Garbage-collecting
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/grako/ast.py", line 63 in update
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/grako/ast.py", line 19 in __init__
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/grako/ast.py", line 90 in copy
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/grako/contexts.py", line 642 in _try
File "/usr/lib/ucsf-chimerax/lib/python3.11/contextlib.py", line 137 in __enter__
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/grako/contexts.py", line 679 in _choice
File "/usr/lib/ucsf-chimerax/lib/python3.11/contextlib.py", line 137 in __enter__
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py", line 370 in _residue_
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/grako/contexts.py", line 497 in _invoke_rule
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/grako/contexts.py", line 458 in _call
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/grako/contexts.py", line 59 in wrapper
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py", line 359 in block7
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/grako/contexts.py", line 787 in _positive_closure
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py", line 361 in _chain_
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/grako/contexts.py", line 497 in _invoke_rule
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/grako/contexts.py", line 458 in _call
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/grako/contexts.py", line 59 in wrapper
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py", line 323 in block0
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/grako/contexts.py", line 787 in _positive_closure
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py", line 325 in _model_parts_
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/grako/contexts.py", line 497 in _invoke_rule
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/grako/contexts.py", line 458 in _call
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/grako/contexts.py", line 59 in wrapper
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py", line 200 in _model_
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/grako/contexts.py", line 497 in _invoke_rule
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/grako/contexts.py", line 458 in _call
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/grako/contexts.py", line 59 in wrapper
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py", line 157 in block0
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/grako/contexts.py", line 787 in _positive_closure
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py", line 159 in _model_list_
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/grako/contexts.py", line 497 in _invoke_rule
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/grako/contexts.py", line 458 in _call
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/grako/contexts.py", line 59 in wrapper
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py", line 136 in _as_term_
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/grako/contexts.py", line 497 in _invoke_rule
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/grako/contexts.py", line 458 in _call
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/grako/contexts.py", line 59 in wrapper
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py", line 89 in _atom_specifier_
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/grako/contexts.py", line 497 in _invoke_rule
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/grako/contexts.py", line 458 in _call
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/grako/contexts.py", line 59 in wrapper
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/grako/contexts.py", line 206 in parse
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 192 in _parse_unquoted
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 121 in parse
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/std_commands/defattr.py", line 180 in defattr
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/add_charge/charge.py", line 81 in add_standard_charges
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/add_charge/charge.py", line 34 in add_charges
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/coulombic/coulombic.py", line 110 in assign_charges
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/coulombic/cmd.py", line 102 in cmd_coulombic
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3213 in run
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49 in run
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 535 in run
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 592 in run_expanded_command
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 72 in func_plus_tip
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 338 in run
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 419 in run_shortcut
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 401 in try_shortcut
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 1386 in run_provider
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/shortcuts/__init__.py", line 66 in run_provider
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/toolshed/__init__.py", line 1306 in run_provider
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/toolshed/info.py", line 397 in run_provider
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/toolbar/tool.py", line 205 in callback
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 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.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, chimerax.pdb_lib._load_libs, chimerax.surface._surface, lxml._elementpath, lxml.etree, 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, PIL._imagingmath, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 60)
===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8rc202406060152 (2024-06-06)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> help help:quickstart
> open /home/renatafioravanti/Documents/HLA-
> Arena/pMHC_TEs/HLA-A0201-FLMQYHIFL.pdb
Chain information for HLA-A0201-FLMQYHIFL.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
> select /A
4280 atoms, 4345 bonds, 272 residues, 1 model selected
> hide sel atoms
> select clear
> select /C
172 atoms, 175 bonds, 9 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> show sel cartoons
> select clear
> select
6092 atoms, 6184 bonds, 381 residues, 1 model selected
> show sel surfaces
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for HLA-A0201-FLMQYHIFL.pdb_A SES surface #1.1: minimum,
-18.06, mean -0.69, maximum 11.24
Coulombic values for HLA-A0201-FLMQYHIFL.pdb_B SES surface #1.2: minimum,
-17.33, mean -0.15, maximum 14.11
Coulombic values for HLA-A0201-FLMQYHIFL.pdb_C SES surface #1.3: minimum,
-9.91, mean 0.03, maximum 10.11
To also show corresponding color key, enter the above coulombic command and
add key true
> graphics silhouettes true
> lighting soft
> select clear
> select
6092 atoms, 6184 bonds, 381 residues, 1 model selected
> volume style mesh
No volumes specified
> transparency sel 50
> select clear
> select
6092 atoms, 6184 bonds, 381 residues, 1 model selected
> select clear
> select /C
172 atoms, 175 bonds, 9 residues, 1 model selected
> hide sel surfaces
> style sel stick
Changed 172 atom styles
> show sel atoms
> hide sel cartoons
> select clear
> select /C
172 atoms, 175 bonds, 9 residues, 1 model selected
> show sel surfaces
> select
6092 atoms, 6184 bonds, 381 residues, 1 model selected
> lighting soft
> volume style surface
No volumes specified
> transparency sel 0
> lighting full
> lighting soft
> lighting full
> lighting soft
> select clear
> select
6092 atoms, 6184 bonds, 381 residues, 1 model selected
> graphics silhouettes false
> select clear
> close session
> open /home/renatafioravanti/Documents/HLA-
> Arena/pMHC_TEs/HLA-A0201-FLMQYHIFL.pdb /home/renatafioravanti/Documents/HLA-
> Arena/pMHC_TEs/HLA-A0201-FLSIPFFFV.pdb
Chain information for HLA-A0201-FLMQYHIFL.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
Chain information for HLA-A0201-FLSIPFFFV.pdb #2
---
Chain | Description
A | No description available
B | No description available
C | No description available
> select #1/A#2/A
8560 atoms, 8690 bonds, 544 residues, 2 models selected
> hide sel atoms
> select clear
> select #1/C#2/C
334 atoms, 341 bonds, 18 residues, 2 models selected
> show sel cartoons
> hide sel atoms
> select clear
> select
12174 atoms, 12359 bonds, 762 residues, 2 models selected
> ui tool show Matchmaker
> select clear
> select #1/A
4280 atoms, 4345 bonds, 272 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #2/A to #1/A pairing ss
Parameters
---
Chain pairing | ss
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 HLA-A0201-FLMQYHIFL.pdb, chain A (#1) with HLA-A0201-FLSIPFFFV.pdb,
chain A (#2), sequence alignment score = 1469.8
RMSD between 272 pruned atom pairs is 0.052 angstroms; (across all 272 pairs:
0.052)
> matchmaker #2/A to #1/A pairing ss
Parameters
---
Chain pairing | ss
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 HLA-A0201-FLMQYHIFL.pdb, chain A (#1) with HLA-A0201-FLSIPFFFV.pdb,
chain A (#2), sequence alignment score = 1469.8
RMSD between 272 pruned atom pairs is 0.052 angstroms; (across all 272 pairs:
0.052)
> select clear
> select #1/A
4280 atoms, 4345 bonds, 272 residues, 1 model selected
> hide sel cartoons
> select #1/C
172 atoms, 175 bonds, 9 residues, 1 model selected
> hide sel cartoons
> select #1/B
1640 atoms, 1664 bonds, 100 residues, 1 model selected
> hide sel cartoons
> show #1 target m
> hide #2 target m
> show #1 target m
> show sel cartoons
> select #1/A
4280 atoms, 4345 bonds, 272 residues, 1 model selected
> show sel cartoons
> select #1/C
172 atoms, 175 bonds, 9 residues, 1 model selected
> show sel cartoons
> select
12174 atoms, 12359 bonds, 762 residues, 2 models selected
> coulombic sel & #1
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8rc202406060152 (2024-06-06)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.6 (Core Profile) Mesa 23.2.1-1ubuntu3.1~22.04.2
OpenGL renderer: Mesa Intel(R) HD Graphics 630 (KBL GT2)
OpenGL vendor: Intel
Python: 3.11.4
Locale: pt_BR.UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: xcb
XDG_SESSION_TYPE=wayland
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
WAYLAND_DISPLAY=wayland-0
GNOME_SETUP_DISPLAY=:1
DISPLAY=:0
Manufacturer: Dell Inc.
Model: XPS 8920
OS: Ubuntu 22.04 Jammy Jellyfish
Architecture: 64bit ELF
Virtual Machine: none
CPU: 8 Intel(R) Core(TM) i7-7700 CPU @ 3.60GHz
Cache Size: 8192 KB
Memory:
total used free shared buff/cache available
Mem: 31Gi 2.4Gi 20Gi 597Mi 8.1Gi 27Gi
Swap: 2.0Gi 0B 2.0Gi
Graphics:
00:02.0 VGA compatible controller [0300]: Intel Corporation HD Graphics 630 [8086:5912] (rev 04)
Subsystem: Dell HD Graphics 630 [1028:07dc]
Kernel driver in use: i915
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2024.6.2
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57
ChimeraX-AtomicLibrary: 14.0.5
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
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: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8rc202406060152
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: 1.2.4
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: 1.1.10
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: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.16
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: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
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: 3.0.15
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: 1.16.5
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: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
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: 1.1.4
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: 4.53.0
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: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
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: 4.2.2
prompt-toolkit: 3.0.46
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: 1.1.0
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: 26.0.3
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: 4.12.1
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Of course as we approach the actual release these become more frequent! This one's short enough that I can see if I can reproduce it.