Opened 11 months ago
Closed 11 months ago
#16428 closed defect (duplicate)
Problem fetching UniProt entry
Reported by: | Owned by: | pett | |
---|---|---|---|
Priority: | normal | Milestone: | |
Component: | Input/Output | 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: 1.4 (2022-06-03 23:39:42 UTC) Description (Describe the actions that caused this problem to occur here) Log: Startup Messages --- warnings | Data format provider 'LAMMPS coordinates' supplied unknown keywords with format description: {'default_for': '.data'} Data format provider 'LAMMPS trajectory' supplied unknown keywords with format description: {'default_for': '.dump'} Data format provider 'LAMMPS coordinates' supplied unknown keywords with format description: {'default_for': '.data'} Data format provider 'LAMMPS trajectory' supplied unknown keywords with format description: {'default_for': '.dump'} UCSF ChimeraX version: 1.4 (2022-06-03) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX QMainWindowLayout::tabPosition called with out-of-bounds value '0' > open 5KWY format mmcif fromDatabase pdb 5kwy title: Structure of human NPC1 middle lumenal domain bound to NPC2 [more info...] Chain information for 5kwy #1 --- Chain | Description | UniProt A B | Niemann-Pick C1 protein | NPC1_HUMAN C D | Epididymal secretory protein E1 | NPC2_HUMAN Non-standard residues in 5kwy #1 --- C3S — cholest-5-en-3-yl hydrogen sulfate (cholesterol-sulfate) 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) Drag select of 17 residues > select up 199 atoms, 202 bonds, 27 residues, 1 model selected > select up 1050 atoms, 1081 bonds, 134 residues, 1 model selected > select ~sel 4806 atoms, 4851 bonds, 686 residues, 1 model selected > hide sel cartoons > hide sel atoms > show sel atoms > hide sel atoms > select clear Drag select of 57 atoms, 132 residues, 55 bonds > show sel atoms > hide sel atoms > select ligand 120 atoms, 126 bonds, 6 residues, 1 model selected > show sel atoms > select clear Drag select of 60 atoms, 63 bonds > hide sel atoms > color sel bychain [Repeated 1 time(s)] > select clear > color bychain [Repeated 1 time(s)] > select ligand 120 atoms, 126 bonds, 6 residues, 1 model selected > color sel lime > color sel forest green > select clear > ui tool show "Show Sequence Viewer" > sequence chain /C /D Alignment identifier is 1 > select /C-D:40 12 atoms, 10 bonds, 2 residues, 1 model selected > select /C-D:40 12 atoms, 10 bonds, 2 residues, 1 model selected > select /C-D:50 12 atoms, 10 bonds, 2 residues, 1 model selected > select /C-D:50 12 atoms, 10 bonds, 2 residues, 1 model selected > select /C-D:51 18 atoms, 16 bonds, 2 residues, 1 model selected > select /C-D:51 18 atoms, 16 bonds, 2 residues, 1 model selected > open P61916 'P61916' has no suffix > open P61916 'P61916' has no suffix > toolshed show > ui tool show "Model Panel" > log metadata #1 Metadata for 5kwy #1 --- Title | Structure of human NPC1 middle lumenal domain bound to NPC2 Citation | Li, X., Saha, P., Li, J., Blobel, G., Pfeffer, S.R. (2016). Clues to the mechanism of cholesterol transfer from the structure of NPC1 middle lumenal domain bound to NPC2. Proc.Natl.Acad.Sci.USA, 113, 10079-10084. PMID: 27551080. DOI: 10.1073/pnas.1611956113 Non-standard residues | C3S — cholest-5-en-3-yl hydrogen sulfate (cholesterol- sulfate) 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) Gene source | Homo sapiens (human) Experimental method | X-ray diffraction Resolution | 2.4Å > log chains #1 Chain information for 5kwy #1 --- Chain | Description | UniProt A B | Niemann-Pick C1 protein | NPC1_HUMAN C D | Epididymal secretory protein E1 | NPC2_HUMAN > log metadata #1 Metadata for 5kwy #1 --- Title | Structure of human NPC1 middle lumenal domain bound to NPC2 Citation | Li, X., Saha, P., Li, J., Blobel, G., Pfeffer, S.R. (2016). Clues to the mechanism of cholesterol transfer from the structure of NPC1 middle lumenal domain bound to NPC2. Proc.Natl.Acad.Sci.USA, 113, 10079-10084. PMID: 27551080. DOI: 10.1073/pnas.1611956113 Non-standard residues | C3S — cholest-5-en-3-yl hydrogen sulfate (cholesterol- sulfate) 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) Gene source | Homo sapiens (human) Experimental method | X-ray diffraction Resolution | 2.4Å > log chains #1 Chain information for 5kwy #1 --- Chain | Description | UniProt A B | Niemann-Pick C1 protein | NPC1_HUMAN C D | Epididymal secretory protein E1 | NPC2_HUMAN > log_chains Unknown command: log_chains > log chains Chain information for 5kwy #1 --- Chain | Description | UniProt A B | Niemann-Pick C1 protein | NPC1_HUMAN C D | Epididymal secretory protein E1 | NPC2_HUMAN > chains Unknown command: chains > log chains Chain information for 5kwy #1 --- Chain | Description | UniProt A B | Niemann-Pick C1 protein | NPC1_HUMAN C D | Epididymal secretory protein E1 | NPC2_HUMAN > open log 'log' has no suffix > ui tool show Log > open NPC2_HUMAN fromDatabase uniprot Traceback (most recent call last): File "C:\Program Files\ChimeraX 1.4\bin\lib\site- packages\chimerax\ui\widgets\htmlview.py", line 335, in interceptRequest self._callback(info) File "C:\Program Files\ChimeraX 1.4\bin\lib\site- packages\chimerax\ui\widgets\htmlview.py", line 93, in _intercept return interceptor(request_info, *args) File "C:\Program Files\ChimeraX 1.4\bin\lib\site- packages\chimerax\log\tool.py", line 206, in link_intercept chimerax_intercept(request_info, *args, session=self.session, view=self, **kw) File "C:\Program Files\ChimeraX 1.4\bin\lib\site- packages\chimerax\ui\widgets\htmlview.py", line 470, in chimerax_intercept session.ui.thread_safe(defer, session, qurl.url(no_formatting), from_dir) File "C:\Program Files\ChimeraX 1.4\bin\lib\site-packages\chimerax\ui\gui.py", line 399, in thread_safe func(*args, **kw) File "C:\Program Files\ChimeraX 1.4\bin\lib\site- packages\chimerax\ui\widgets\htmlview.py", line 461, in defer cxcmd(session, topic) File "C:\Program Files\ChimeraX 1.4\bin\lib\site- packages\chimerax\ui\widgets\htmlview.py", line 479, in cxcmd run(session, cmd) File "C:\Program Files\ChimeraX 1.4\bin\lib\site- packages\chimerax\core\commands\run.py", line 38, in run results = command.run(text, log=log, return_json=return_json) File "C:\Program Files\ChimeraX 1.4\bin\lib\site- packages\chimerax\core\commands\cli.py", line 2897, in run result = ci.function(session, **kw_args) File "C:\Program Files\ChimeraX 1.4\bin\lib\site- packages\chimerax\open_command\cmd.py", line 118, in cmd_open models = Command(session, registry=registry).run(provider_cmd_text, log=log)[0] File "C:\Program Files\ChimeraX 1.4\bin\lib\site- packages\chimerax\core\commands\cli.py", line 2897, in run result = ci.function(session, **kw_args) File "C:\Program Files\ChimeraX 1.4\bin\lib\site- packages\chimerax\open_command\cmd.py", line 153, in provider_open models, status = collated_open(session, database_name, ident, File "C:\Program Files\ChimeraX 1.4\bin\lib\site- packages\chimerax\open_command\cmd.py", line 457, in collated_open return remember_data_format() File "C:\Program Files\ChimeraX 1.4\bin\lib\site- packages\chimerax\open_command\cmd.py", line 428, in remember_data_format models, status = func(*func_args, **func_kw) File "C:\Program Files\ChimeraX 1.4\bin\lib\site- packages\chimerax\uniprot\\__init__.py", line 26, in fetch return fetch_uniprot(session, ident, ignore_cache=ignore_cache) File "C:\Program Files\ChimeraX 1.4\bin\lib\site- packages\chimerax\uniprot\fetch_uniprot.py", line 22, in fetch_uniprot accession, entry = map_uniprot_ident(ident, return_value="both") ValueError: too many values to unpack (expected 2) ValueError: too many values to unpack (expected 2) File "C:\Program Files\ChimeraX 1.4\bin\lib\site- packages\chimerax\uniprot\fetch_uniprot.py", line 22, in fetch_uniprot accession, entry = map_uniprot_ident(ident, return_value="both") See log for complete Python traceback. > open NPC2_HUMAN fromDatabase uniprot Traceback (most recent call last): File "C:\Program Files\ChimeraX 1.4\bin\lib\site- packages\chimerax\ui\widgets\htmlview.py", line 335, in interceptRequest self._callback(info) File "C:\Program Files\ChimeraX 1.4\bin\lib\site- packages\chimerax\ui\widgets\htmlview.py", line 93, in _intercept return interceptor(request_info, *args) File "C:\Program Files\ChimeraX 1.4\bin\lib\site- packages\chimerax\log\tool.py", line 206, in link_intercept chimerax_intercept(request_info, *args, session=self.session, view=self, **kw) File "C:\Program Files\ChimeraX 1.4\bin\lib\site- packages\chimerax\ui\widgets\htmlview.py", line 470, in chimerax_intercept session.ui.thread_safe(defer, session, qurl.url(no_formatting), from_dir) File "C:\Program Files\ChimeraX 1.4\bin\lib\site-packages\chimerax\ui\gui.py", line 399, in thread_safe func(*args, **kw) File "C:\Program Files\ChimeraX 1.4\bin\lib\site- packages\chimerax\ui\widgets\htmlview.py", line 461, in defer cxcmd(session, topic) File "C:\Program Files\ChimeraX 1.4\bin\lib\site- packages\chimerax\ui\widgets\htmlview.py", line 479, in cxcmd run(session, cmd) File "C:\Program Files\ChimeraX 1.4\bin\lib\site- packages\chimerax\core\commands\run.py", line 38, in run results = command.run(text, log=log, return_json=return_json) File "C:\Program Files\ChimeraX 1.4\bin\lib\site- packages\chimerax\core\commands\cli.py", line 2897, in run result = ci.function(session, **kw_args) File "C:\Program Files\ChimeraX 1.4\bin\lib\site- packages\chimerax\open_command\cmd.py", line 118, in cmd_open models = Command(session, registry=registry).run(provider_cmd_text, log=log)[0] File "C:\Program Files\ChimeraX 1.4\bin\lib\site- packages\chimerax\core\commands\cli.py", line 2897, in run result = ci.function(session, **kw_args) File "C:\Program Files\ChimeraX 1.4\bin\lib\site- packages\chimerax\open_command\cmd.py", line 153, in provider_open models, status = collated_open(session, database_name, ident, File "C:\Program Files\ChimeraX 1.4\bin\lib\site- packages\chimerax\open_command\cmd.py", line 457, in collated_open return remember_data_format() File "C:\Program Files\ChimeraX 1.4\bin\lib\site- packages\chimerax\open_command\cmd.py", line 428, in remember_data_format models, status = func(*func_args, **func_kw) File "C:\Program Files\ChimeraX 1.4\bin\lib\site- packages\chimerax\uniprot\\__init__.py", line 26, in fetch return fetch_uniprot(session, ident, ignore_cache=ignore_cache) File "C:\Program Files\ChimeraX 1.4\bin\lib\site- packages\chimerax\uniprot\fetch_uniprot.py", line 22, in fetch_uniprot accession, entry = map_uniprot_ident(ident, return_value="both") ValueError: too many values to unpack (expected 2) ValueError: too many values to unpack (expected 2) File "C:\Program Files\ChimeraX 1.4\bin\lib\site- packages\chimerax\uniprot\fetch_uniprot.py", line 22, in fetch_uniprot accession, entry = map_uniprot_ident(ident, return_value="both") See log for complete Python traceback. OpenGL version: 3.3.0 - Build 32.0.101.5768 OpenGL renderer: Intel(R) Iris(R) Xe Graphics OpenGL vendor: Intel Python: 3.9.11 Locale: en_GB.cp1252 Qt version: PyQt6 6.3.0, Qt 6.3.0 Qt runtime version: 6.3.0 Qt platform: windows Manufacturer: Dell Inc. Model: Latitude 5420 OS: Microsoft Windows 10 Pro (Build 19045) Memory: 33,706,872,832 MaxProcessMemory: 137,438,953,344 CPU: 8 11th Gen Intel(R) Core(TM) i5-1145G7 @ 2.60GHz OSLanguage: en-US Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 Babel: 2.10.1 backcall: 0.2.0 blockdiag: 3.0.0 certifi: 2022.5.18.1 cftime: 1.6.0 charset-normalizer: 2.0.12 ChimeraX-AddCharge: 1.2.3 ChimeraX-AddH: 2.1.11 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2.1 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.4.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.39.1 ChimeraX-AtomicLibrary: 7.0 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.1 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.1 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.7 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.2 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.1 ChimeraX-CommandLine: 1.2.3 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.4 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.1 ChimeraX-DistMonitor: 1.1.5 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0 ChimeraX-FunctionKey: 1.0 ChimeraX-Geometry: 1.2 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1 ChimeraX-Hbonds: 2.1.2 ChimeraX-Help: 1.2 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 ChimeraX-Label: 1.1.1 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.1 ChimeraX-Map: 1.1 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 2.0.6 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.7 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.5.5 ChimeraX-ModelPanel: 1.3.2 ChimeraX-ModelSeries: 1.0 ChimeraX-Mol2: 2.0 ChimeraX-Morph: 1.0 ChimeraX-MouseModes: 1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.2 ChimeraX-OpenCommand: 1.9 ChimeraX-PDB: 2.6.6 ChimeraX-PDBBio: 1.0 ChimeraX-PDBImages: 1.2 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 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: 2.6 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.1 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.8 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.0.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.1.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.1 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.18.3 ChimeraX-uniprot: 2.2 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.1.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0 ChimeraX-WebServices: 1.1.0 ChimeraX-Zone: 1.0 colorama: 0.4.4 comtypes: 1.1.10 cxservices: 1.2 cycler: 0.11.0 Cython: 0.29.26 debugpy: 1.6.0 decorator: 5.1.1 docutils: 0.17.1 entrypoints: 0.4 filelock: 3.4.2 fonttools: 4.33.3 funcparserlib: 1.0.0 grako: 3.16.5 h5py: 3.7.0 html2text: 2020.1.16 idna: 3.3 ihm: 0.27 imagecodecs: 2021.11.20 imagesize: 1.3.0 ipykernel: 6.6.1 ipython: 7.31.1 ipython-genutils: 0.2.0 jedi: 0.18.1 Jinja2: 3.0.3 jupyter-client: 7.1.0 jupyter-core: 4.10.0 kiwisolver: 1.4.2 line-profiler: 3.4.0 lxml: 4.7.1 lz4: 3.1.10 MarkupSafe: 2.1.1 matplotlib: 3.5.1 matplotlib-inline: 0.1.3 MolecularDynamicsViewer: 1.4 msgpack: 1.0.3 nest-asyncio: 1.5.5 netCDF4: 1.5.8 networkx: 2.6.3 numexpr: 2.8.1 numpy: 1.22.1 openvr: 1.16.802 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pickleshare: 0.7.5 Pillow: 9.0.1 pip: 21.3.1 pkginfo: 1.8.2 prompt-toolkit: 3.0.29 psutil: 5.9.0 pycollada: 0.7.2 pydicom: 2.2.2 Pygments: 2.11.2 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 PyQt6-commercial: 6.3.0 PyQt6-Qt6: 6.3.0 PyQt6-sip: 13.3.1 PyQt6-WebEngine-commercial: 6.3.0 PyQt6-WebEngine-Qt6: 6.3.0 python-dateutil: 2.8.2 pytz: 2022.1 pywin32: 303 pyzmq: 23.1.0 qtconsole: 5.3.0 QtPy: 2.1.0 RandomWords: 0.3.0 requests: 2.27.1 scipy: 1.7.3 setuptools: 59.8.0 sfftk-rw: 0.7.2 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 4.3.2 sphinx-autodoc-typehints: 1.15.2 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 suds-community: 1.0.0 tables: 3.7.0 tifffile: 2021.11.2 tinyarray: 1.2.4 tornado: 6.1 traitlets: 5.1.1 urllib3: 1.26.9 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.37.1 wheel-filename: 1.3.0 WMI: 1.5.1
Change History (2)
comment:1 by , 11 months ago
Component: | Unassigned → Input/Output |
---|---|
Owner: | set to |
Platform: | → all |
Project: | → ChimeraX |
Status: | new → accepted |
Summary: | ChimeraX bug report submission → Problem fetching UniProt entry |
comment:2 by , 11 months ago
Resolution: | → duplicate |
---|---|
Status: | accepted → closed |
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