Opened 8 months ago
Closed 8 months ago
#17337 closed defect (duplicate)
Crash in chem_group on Windows
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Analysis | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.19045
ChimeraX Version: 1.10.dev202504020144 (2025-04-02 01:44:35 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Windows fatal exception: access violation
Windows fatal exception: access violation
Thread 0x0000160cWindows fatal exception: access violation
(most recent call first):
File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\threading.py", line 324 in wait
File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\threading.py", line 622 in wait
File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\threading.py", line 1392 in run
File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\threading.py", line 1038 in _bootstrap_inner
File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\threading.py", line 995 in _bootstrap
Thread 0x00001fdc (most recent call first):
File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\multiprocessing\pool.py", line 579 in _handle_results
File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\threading.py", line 975 in run
File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\threading.py", line 1038 in _bootstrap_inner
File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\threading.py", line 995 in _bootstrap
Thread 0x00003060 (most recent call first):
File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\multiprocessing\pool.py", line 531 in _handle_tasks
File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\threading.py", line 975 in run
File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\threading.py", line 1038 in _bootstrap_inner
File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\threading.py", line 995 in _bootstrap
Thread 0x00003264 (most recent call first):
File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\multiprocessing\connection.py", line 810 in _exhaustive_wait
File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\multiprocessing\connection.py", line 878 in wait
File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\multiprocessing\pool.py", line 502 in _wait_for_updates
File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\multiprocessing\pool.py", line 522 in _handle_workers
File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\threading.py", line 975 in run
File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\threading.py", line 1038 in _bootstrap_inner
File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\threading.py", line 995 in _bootstrap
Thread 0x00002788 (most recent call first):
File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\multiprocessing\pool.py", line 114 in worker
File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\threading.py", line 975 in run
File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\threading.py", line 1038 in _bootstrap_inner
File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\threading.py", line 995 in _bootstrap
Thread 0x000009d8 (most recent call first):
File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\multiprocessing\pool.py", line 114 in worker
File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\threading.py", line 975 in run
File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\threading.py", line 1038 in _bootstrap_inner
File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\threading.py", line 995 in _bootstrap
Thread 0x000023dc (most recent call first):
File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\multiprocessing\pool.py", line 114 in worker
File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\threading.py", line 975 in run
File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\threading.py", line 1038 in _bootstrap_inner
File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\threading.py", line 995 in _bootstrap
Thread 0x00001078 (most recent call first):
File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\multiprocessing\pool.py", line 114 in worker
File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\threading.py", line 975 in run
File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\threading.py", line 1038 in _bootstrap_inner
File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\threading.py", line 995 in _bootstrap
Thread 0x00000fe0 (most recent call first):
File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\site-packages\chimerax\chem_group\support.py", line 40 in call_c_plus_plus
File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\site-packages\chimerax\chem_group\chem_group.py", line 233 in find_group
File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\site-packages\chimerax\hbonds\hbond.py", line 771 in _find_acceptors
File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\site-packages\chimerax\hbonds\hbond.py", line 498 in find_hbonds
File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\site-packages\chimerax\addh\hbond.py", line 259 in add_hydrogens
File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\site-packages\chimerax\addh\cmd.py", line 184 in hbond_add_hydrogens
File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\site-packages\chimerax\addh\cmd.py", line 77 in cmd_addh
File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\site-packages\chimerax\coulombic\coulombic.py", line 95 in assign_charges
File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\site-packages\chimerax\coulombic\cmd.py", line 102 in cmd_coulombic
File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 3215 in run
File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\site-packages\chimerax\core\commands\run.py", line 49 in run
File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\site-packages\chimerax\shortcuts\shortcuts.py", line 537 in run
File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\site-packages\chimerax\shortcuts\shortcuts.py", line 594 in run_expanded_command
File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\site-packages\chimerax\shortcuts\shortcuts.py", line 72 in func_plus_tip
File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\site-packages\chimerax\shortcuts\shortcuts.py", line 340 in run
File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\site-packages\chimerax\shortcuts\shortcuts.py", line 421 in run_shortcut
File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\site-packages\chimerax\shortcuts\shortcuts.py", line 403 in try_shortcut
File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\site-packages\chimerax\shortcuts\shortcuts.py", line 1394 in run_provider
File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\site-packages\chimerax\shortcuts\__init__.py", line 66 in run_provider
File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\site-packages\chimerax\core\toolshed\__init__.py", line 1419 in run_provider
File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\site-packages\chimerax\core\toolshed\info.py", line 397 in run_provider
File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\site-packages\chimerax\toolbar\tool.py", line 215 in callback
File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\site-packages\chimerax\ui\gui.py", line 339 in event_loop
File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\site-packages\chimerax\core\__main__.py", line 1054 in init
File "D:\Program Files\ChimeraX 1.10.dev202504020144\bin\Lib\site-packages\chimerax\core\__main__.py", line 1217 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
===== Log before crash start =====
> ui mousemode right clip
> ui mousemode right "clip rotate"
> ui mousemode right clip
> show cartoons
> show surfaces
> show target m
> color byelement
> color byhetero
> color byelement
> color black
> color lime
> mlp
Map values for surface "AF-A6ZIB7-F1-model_v4.pdb_A SES surface": minimum
-29.54, mean -2.111, maximum 24.99
To also show corresponding color key, enter the above mlp command and add key
true
> coulombic
===== Log before crash end =====
Log:
Startup Messages
---
warning | Your computer has Intel graphics driver 8190 with a known bug that causes all Qt user interface panels to be blank. ChimeraX can partially fix this but may make some panel titlebars and edges black. Hopefully newer Intel graphics drivers will fix this.
UCSF ChimeraX version: 1.10.dev202504020144 (2025-04-02)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open C:\\\Users\\\ZHANG\\\Desktop\\\3dd5.pdb
3dd5.pdb title:
Glomerella cingulata E600-cutinase complex [more info...]
Chain information for 3dd5.pdb #1
---
Chain | Description | UniProt
A B C D E F G H | cutin hydrolase | CUTI_COLGL 31-224
Non-standard residues in 3dd5.pdb #1
---
DEP — diethyl phosphonate
OpenGL version: 3.3.0 - Build 27.20.100.8190
OpenGL renderer: Intel(R) UHD Graphics 630
OpenGL vendor: Intel
Python: 3.11.4
Locale: zh_CN.cp936
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: windows
Manufacturer: LENOVO
Model: 90J4000FCD
OS: Microsoft Windows 10 家庭中文版 (Build 19045)
Memory: 8,468,692,992
MaxProcessMemory: 137,438,953,344
CPU: 4 Intel(R) Core(TM) i3-8100 CPU @ 3.60GHz
OSLanguage: zh-CN
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
asttokens: 3.0.0
auditwheel: 6.3.0
babel: 2.17.0
beautifulsoup4: 4.13.3
blockdiag: 3.0.0
blosc2: 3.2.1
build: 1.2.2.post1
certifi: 2025.1.31
cftime: 1.6.4.post1
charset-normalizer: 3.4.1
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.7
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.20
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.1.1
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.5
ChimeraX-AtomicLibrary: 14.1.13
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
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: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.10.dev202504020144
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
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: 1.4.1
ChimeraX-Hbonds: 2.5.1
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.5.3
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
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: 2.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.8
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
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-MutationScores: 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: 1.14.1
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.7
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: 1.1.2
ChimeraX-ProfileGrids: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.3
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
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: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.1
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
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: 2.5.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.45
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
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
comtypes: 1.4.10
contourpy: 1.3.1
coverage: 7.8.0
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.12
debugpy: 1.8.13
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.0
filelock: 3.18.0
fonttools: 4.56.0
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h5py: 3.13.0
html2text: 2024.2.26
idna: 3.10
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.1.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.6
jupyter_client: 8.6.3
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.8
line_profiler: 4.2.0
lxml: 5.3.1
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.10.1
matplotlib-inline: 0.1.7
msgpack: 1.1.0
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 24.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pickleshare: 0.7.5
pillow: 10.4.0
pip: 25.0.1
pkginfo: 1.11.1
platformdirs: 4.3.7
pluggy: 1.5.0
prompt_toolkit: 3.0.50
psutil: 7.0.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.32
Pygments: 2.18.0
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.9
PyOpenGL-accelerate: 3.1.9
pyopenxr: 1.1.4501
pyparsing: 3.2.3
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.8.1
PyQt6-Qt6: 6.8.2
PyQt6-WebEngine-commercial: 6.8.0
PyQt6-WebEngine-Qt6: 6.8.2
PyQt6_sip: 13.10.0
pytest: 8.3.5
pytest-cov: 6.1.0
python-dateutil: 2.9.0.post0
pytz: 2025.2
pywin32: 310
pyzmq: 26.3.0
qtconsole: 5.5.2
QtPy: 2.4.3
qtshim: 1.1
RandomWords: 0.4.0
requests: 2.32.3
roman-numerals-py: 3.1.0
scipy: 1.14.0
setuptools: 75.8.2
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.1.0
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.7.1
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.4
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.13.0
tzdata: 2025.2
urllib3: 2.3.0
wcwidth: 0.2.13
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.13
WMI: 1.5.1
Change History (2)
comment:1 by , 8 months ago
| Component: | Unassigned → Structure Analysis |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in chem_group on Windows |
comment:2 by , 8 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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