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Opened 2 years ago
Closed 2 years ago
#9676 closed defect (duplicate)
javaScriptConsoleMessage KeyError
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Logging | 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: 1.5 (2022-11-24 00:03:27 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open \\\nas.ads.mwn.de\ge24kix\TUM-PC\Desktop\PhD-
> Project\3_Internship\3_Brian_Schoichet\7_tutorials\GAT1\binding_site.cxs
> format session
Log from Wed Aug 30 09:36:28 2023UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open \\\nas.ads.mwn.de\ge24kix\TUM-PC\Desktop\PhD-
> Project\3_Internship\3_Brian_Schoichet\7_tutorials\GAT1\binding_site.cxs
> format session
Log from Tue Aug 29 21:38:24 2023 Startup Messages
---
warning | Your computer has Intel graphics driver 7261 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: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open //nas.ads.mwn.de/ge24kix/TUM-PC/Desktop/PhD-
> Project/3_Internship/3_Brian_Schoichet/7_tutorials/GAT1/rec_and_xtal_minimized_water.pdb
rec_and_xtal_minimized_water.pdb title:
Cryo-em structure of human gaba transporter GAT1 bound with nipecotic acid In
nacl solution In an inward-occluded state At 2.4 angstrom [more info...]
Chain information for rec_and_xtal_minimized_water.pdb #1
---
Chain | Description
A | No description available
Non-standard residues in rec_and_xtal_minimized_water.pdb #1
---
ACE — (ACE)
ID7 — (3R)-piperidine-3-carboxylic acid
NA — sodium ion
NMA — (NMA)
> set bgColor white
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
20 atoms, 20 bonds, 1 residue, 1 model selected
> hbonds sel reveal true
4 hydrogen bonds found
> transparency protein 95 target r
> select /A:65
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> select /A:64
19 atoms, 18 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
Drag select of 1 pseudobonds
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
14 atoms, 13 bonds, 1 residue, 1 model selected
> hide sel atoms
> show sel atoms
> select /A:134
20 atoms, 20 bonds, 1 residue, 1 model selected
> select clear
> select /A:701@C4
1 atom, 1 residue, 1 model selected
> select up
20 atoms, 20 bonds, 1 residue, 1 model selected
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
20 atoms, 20 bonds, 1 residue, 1 model selected
> color sel yellow
> color sel byhetero
> select clear
> transparency protein 98 target r
> colour protein white
> color byhetero
> select clear
> select /A:701@C2
1 atom, 1 residue, 1 model selected
> colour protein cornflower blue target a
> color sel byhetero
> select /A:136
19 atoms, 18 bonds, 1 residue, 1 model selected
> select up
243 atoms, 245 bonds, 16 residues, 1 model selected
> select up
8390 atoms, 8526 bonds, 529 residues, 1 model selected
> select up
8418 atoms, 8550 bonds, 534 residues, 1 model selected
> color sel byhetero
> select clear
> graphics silhouettes true
> open //nas.ads.mwn.de/ge24kix/TUM-PC/Desktop/PhD-
> Project/3_Internship/3_Brian_Schoichet/7_tutorials/GAT1/matching_spheres.pdb
> open //nas.ads.mwn.de/ge24kix/TUM-PC/Desktop/PhD-
> Project/3_Internship/3_Brian_Schoichet/7_tutorials/GAT1/sitemap.pdb
sitemap.pdb title:
sitemap_1_3A_7e2y_site_3 [more info...]
Non-standard residues in sitemap.pdb #3
---
SIT — (SIT)
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
82 atoms, 830 bonds, 1 residue, 1 model selected
> style sel stick
Changed 82 atom styles
> style sel ball
Changed 82 atom styles
> style sel sphere
Changed 82 atom styles
> style sel stick
Changed 82 atom styles
> show sel surfaces
> select #3//chain_id='E ':1@@serial_number=64
Nothing selected
> select #3//chain_id='E ':1@@serial_number=67
Nothing selected
> transparency #3 98 target s
> transparency #3 70 target s
> hide #3 target a
> save //nas.ads.mwn.de/ge24kix/TUM-PC/Desktop/PhD-
> Project/3_Internship/3_Brian_Schoichet/7_tutorials/GAT1/binding_site.cxs
——— End of log from Tue Aug 29 21:38:24 2023 ———
opened ChimeraX session
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
19 atoms, 18 bonds, 1 residue, 1 model selected
> hide sel atoms
> save //nas.ads.mwn.de/ge24kix/TUM-PC/Desktop/PhD-
> Project/3_Internship/3_Brian_Schoichet/7_tutorials/GAT1/binding_site.cxs
——— End of log from Wed Aug 30 09:36:28 2023 ———
opened ChimeraX session
> hide #3 target s
> select #1/A:816@H1
1 atom, 1 residue, 1 model selected
> select up
3 atoms, 2 bonds, 1 residue, 1 model selected
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
3 atoms, 2 bonds, 1 residue, 1 model selected
> hide sel atoms
> open //nas.ads.mwn.de/ge24kix/TUM-PC/Desktop/PhD-
> Project/3_Internship/3_Brian_Schoichet/7_tutorials/GAT1/best_matching_gaba_opt/retro_docking_rand_sph_45/poses.mol2
Opened poses.mol2 containing 500 structures (10583 atoms, 10753 bonds)
> ui tool show ViewDockX
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 308, in
javaScriptConsoleMessage
self.Levels[level], msg))
KeyError: <JavaScriptConsoleMessageLevel.ErrorMessageLevel: 2>
KeyError:
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 308, in
javaScriptConsoleMessage
self.Levels[level], msg))
See log for complete Python traceback.
> hide #4.1-500 models
OpenGL version: 3.3.0 - Build 26.20.100.7261
OpenGL renderer: Intel(R) UHD Graphics 620
OpenGL vendor: Intel
Python: 3.9.11
Locale: en_US.cp1252
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: windows
Manufacturer: LENOVO
Model: 20N5S01K00
OS: Microsoft Windows 10 Education (Build 19045)
Memory: 16,915,587,072
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-8565U CPU @ 1.80GHz
OSLanguage: en-US
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
asttokens: 2.1.0
Babel: 2.11.0
backcall: 0.2.0
blockdiag: 3.0.0
build: 0.8.0
certifi: 2022.9.24
cftime: 1.6.2
charset-normalizer: 2.1.1
ChimeraX-AddCharge: 1.4
ChimeraX-AddH: 2.2.1
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.6
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.41.5
ChimeraX-AtomicLibrary: 8.0.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.7.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.1
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.2
ChimeraX-CommandLine: 1.2.4
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.5
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.3
ChimeraX-DockPrep: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
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-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.1
ChimeraX-MatchMaker: 2.0.9
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.8
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.6
ChimeraX-ModelPanel: 1.3.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.1
ChimeraX-MouseModes: 1.1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.9.1
ChimeraX-PDB: 2.6.8
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
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: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
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
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.7.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.1.3
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.24.3
ChimeraX-uniprot: 2.2.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.1.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.1
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0.1
colorama: 0.4.5
comtypes: 1.1.10
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.32
debugpy: 1.6.4
decorator: 5.1.1
docutils: 0.19
entrypoints: 0.4
executing: 1.2.0
filelock: 3.7.1
fonttools: 4.38.0
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.33
imagecodecs: 2022.7.31
imagesize: 1.4.1
importlib-metadata: 5.1.0
ipykernel: 6.15.3
ipython: 8.4.0
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.1.2
jupyter-client: 7.3.4
jupyter-core: 5.1.0
kiwisolver: 1.4.4
line-profiler: 3.5.1
lxml: 4.9.1
lz4: 4.0.2
MarkupSafe: 2.1.1
matplotlib: 3.5.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.0
networkx: 2.8.5
numexpr: 2.8.4
numpy: 1.23.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pickleshare: 0.7.5
Pillow: 9.2.0
pip: 22.2.2
pkginfo: 1.8.3
platformdirs: 2.5.4
prompt-toolkit: 3.0.33
psutil: 5.9.1
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.12.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
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: 2022.6
pywin32: 303
pyzmq: 24.0.1
qtconsole: 5.3.1
QtPy: 2.3.0
RandomWords: 0.4.0
requests: 2.28.1
scipy: 1.9.0
setuptools: 65.1.1
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 5.1.1
sphinx-autodoc-typehints: 1.19.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tifffile: 2022.7.31
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.2
traitlets: 5.3.0
urllib3: 1.26.13
wcwidth: 0.2.5
webcolors: 1.12
wheel: 0.37.1
wheel-filename: 1.4.1
WMI: 1.5.1
zipp: 3.11.0
Change History (2)
comment:1 by , 2 years ago
| Component: | Unassigned → Logging |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → javaScriptConsoleMessage KeyError |
comment:2 by , 2 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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Hi Alessandro,
--Eric