id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 6026 Incomplete retrieval of AlphaFold prediction thomas.lenz@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.14393 ChimeraX Version: 1.4.dev202201260121 (2022-01-26 01:21:26 UTC) Description ChimeraX 1.4.dev202201260121 Tools --> Structure Prediction --> AlphaFold Sequence: Uniprot identifier: Q16539,P49137 --> Predict sequences: MSQERPTFYRQELNKTIWEVPERYQNLSPVGSGAYGSVCAAFDTKTGLRVAVKKLSRPFQSIIHAKRTYRELRLLKHMKHENVIGLLDVFTPARSLEEFNDVYLVTHLMGADLNNIVKCQKLTDDHVQFLIYQILRGLKYIHSADIIHRDLKPSNLAVNEDCELKILDFGLARHTDDEMTGYVATRWYRAPEIMLNWMHYNQTVDIWSVGCIMAELLTGRTLFPGTDHIDQLKLILRLVGTPGAELLKKISSESARNYIQSLTQMPKMNFANVFIGANPLAVDLLEKMLVLDSDKRITAAQALAHAYFAQYHDPDDEPVADPYDQSFESRDLLIDEWKSLTYDEVISFVPPPLDQEEMES, MLSNSQGQSPPVPFPAPAPPPQPPTPALPHPPAQPPPPPPQQFPQFHVKSGLQIKKNAIIDDYKVTSQVLGLGINGKVLQIFNKRTQEKFALKMLQDCPKARREVELHWRASQCPHIVRIVDVYENLYAGRKCLLIVMECLDGGELFSRIQDRGDQAFTEREASEIMKSIGEAIQYLHSINIAHRDVKPENLLYTSKRPNAILKLTDFGFAKETTSHNSLTTPCYTPYYVAPEVLGPEKYDKSCDMWSLGVIMYILLCGYPPFYSNHGLAISPGMKTRIRMGQYEFPNPEWSEVSEEVKMLIRNLLKTEPTQRMTITEFMNHPWIMQSTKVPQTPLHTSRVLKEDKERWEDVKEEMTSALATMRVDYEQIKIKKIEDASNPLLLKRRKKARALEAAALAH 2 sequences, total length 760 (= 360 + 400) Have Colab GPU runtime Searching sequence databases (245 Gbytes). Search will take 49 minutes or more. Finding fastest mirror for sequence databases using europe Searching uniprot sequence database, 98 Gbytes 1 2 3 4 5 --------------------------------------------------------------------------- ContentTooShortError Traceback (most recent call last) in () 649 seq_list = seq_list[1:] 650 --> 651 run_prediction(seq_list, is_prokaryote=is_prokaryote) 8 frames /usr/lib/python3.7/urllib/request.py in urlretrieve(url, filename, reporthook, data) 286 raise ContentTooShortError( 287 ""retrieval incomplete: got only %i out of %i bytes"" --> 288 % (read, size), result) 289 290 return result ContentTooShortError: Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.4.dev202201260121 (2022-01-26) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > ui tool show AlphaFold > alphafold match Q16539,P49137 Fetching AlphaFold database settings from https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database.json Fetching compressed AlphaFold Q16539 from https://alphafold.ebi.ac.uk/files/AF-Q16539-F1-model_v2.cif Fetching compressed AlphaFold P49137 from https://alphafold.ebi.ac.uk/files/AF-P49137-F1-model_v2.cif 2 AlphaFold models found using UniProt identifiers: Q16539 (UniProt Q16539), P49137 (UniProt P49137) Opened 2 AlphaFold models > alphafold predict Q16539,P49137 Running AlphaFold prediction [Repeated 2 time(s)] > color bfactor #1 palette alphafold 2907 atoms, 360 residues, atom bfactor range 27.1 to 98.9 > hide #2 models > color bfactor #2 palette alphafold 3202 atoms, 400 residues, atom bfactor range 30.9 to 98.8 > hide #1 models > show #2 models > matchmaker #2 #1 Missing required ""to"" argument > matchmaker #2 to #1 Parameters --- Chain pairing | bb 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 AlphaFold Q16539, chain A (#1) with AlphaFold P49137, chain A (#2), sequence alignment score = 365.6 RMSD between 119 pruned atom pairs is 1.085 angstroms; (across all 314 pairs: 18.825) > show #1 models > hide #1 models > show #1 models > hide #2 models > show #2 models > hide #2 models > show #2 models > hide #2 models > show #2 models > hide #2 models > color #1 blue > color #2 red > show #2 models > load Q16644 Unknown command: load Q16644 > open Q16644 'Q16644' has no suffix Fetching Q16644 UniProt info from https://www.uniprot.org/uniprot/Q16644.xml > alphafold match Q16644 Fetching compressed AlphaFold Q16644 from https://alphafold.ebi.ac.uk/files/AF-Q16644-F1-model_v2.cif 1 AlphaFold model found using UniProt identifier: Q16644 (UniProt Q16644) Opened 1 AlphaFold model Fetching Q15746 UniProt info from https://www.uniprot.org/uniprot/Q15746.xml > alphafold match Q15746 Fetching compressed AlphaFold Q15746 from https://alphafold.ebi.ac.uk/files/AF-Q15746-F1-model_v2.cif 1 AlphaFold model found using UniProt identifier: Q15746 (UniProt Q15746) Opened 1 AlphaFold model > color #3 green > color #4 yellow > matchmaker #3 to #1 Parameters --- Chain pairing | bb 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 AlphaFold Q16539, chain A (#1) with AlphaFold Q16644, chain A (#3), sequence alignment score = 378.5 RMSD between 135 pruned atom pairs is 1.136 angstroms; (across all 309 pairs: 17.338) > matchmaker #4 to #1 Parameters --- Chain pairing | bb 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 AlphaFold Q16539, chain A (#1) with AlphaFold Q15746, chain A (#4), sequence alignment score = 414 RMSD between 124 pruned atom pairs is 0.970 angstroms; (across all 306 pairs: 20.792) > hide cartoons > show cartoons > hide atoms > show atoms > hide atoms > hide #1 models > hide #4 models Drag select of 5 residues Drag select of 28 residues > select #3 3016 atoms, 3084 bonds, 382 residues, 1 model selected > ~select #3 Nothing selected > hide #3 models > show #1 models > show #4 models > hide #2 models > hide #1 models > show #1 models > hide #1 models > show #2 models > show #1 models > hide #4 models > show #4 models > hide #4 models > show #3 models > show #4 models > alphafold predict Q16539,P49137 Running AlphaFold prediction > help help:credits.html OpenGL version: 3.3.0 NVIDIA 353.62 OpenGL renderer: GeForce GT 630M/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Locale: de_DE.cp1252 Qt version: PyQt5 5.15.2, Qt 5.15.2 Qt platform: windows Manufacturer: Dell Inc. Model: XPS L421X OS: Microsoft Windows 10 Enterprise 2016 LTSB (Build 14393) Memory: 8,461,746,176 MaxProcessMemory: 137,438,953,344 CPU: 4 Intel(R) Core(TM) i7-3667U CPU @ 2.00GHz OSLanguage: de-DE Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 Babel: 2.9.1 backcall: 0.2.0 blockdiag: 3.0.0 certifi: 2021.10.8 cftime: 1.5.2 charset-normalizer: 2.0.10 ChimeraX-AddCharge: 1.2.2 ChimeraX-AddH: 2.1.11 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.2.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.33.1 ChimeraX-AtomicLibrary: 5.0 ChimeraX-AtomSearch: 2.0 ChimeraX-AtomSearchLibrary: 1.0 ChimeraX-AxesPlanes: 2.1 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.0 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.6.1 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: 2.2.2 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.1 ChimeraX-CommandLine: 1.2 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.4.dev202201260121 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: 1.0 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: 1.1 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 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: 2.5 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.5.1 ChimeraX-ModelPanel: 1.3.1 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: 1.8 ChimeraX-PDB: 2.6.5 ChimeraX-PDBBio: 1.0 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 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.4.6 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: 1.7.4 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 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.16 ChimeraX-uniprot: 2.2 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.0.1 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: 1.0 ChimeraX-Zone: 1.0 colorama: 0.4.4 comtypes: 1.1.10 cxservices: 1.1 cycler: 0.11.0 Cython: 0.29.26 debugpy: 1.5.1 decorator: 5.1.1 docutils: 0.17.1 entrypoints: 0.3 filelock: 3.4.2 fonttools: 4.29.0 funcparserlib: 1.0.0a0 grako: 3.16.5 h5py: 3.6.0 html2text: 2020.1.16 idna: 3.3 ihm: 0.26 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: 4.9.1 kiwisolver: 1.3.2 line-profiler: 3.4.0 lxml: 4.7.1 lz4: 3.1.10 MarkupSafe: 2.0.1 matplotlib: 3.5.1 matplotlib-inline: 0.1.3 msgpack: 1.0.3 nest-asyncio: 1.5.4 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: 9.0.0 pip: 21.3.1 pkginfo: 1.8.2 prompt-toolkit: 3.0.24 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: 3.0.7 PyQt5-commercial: 5.15.2 PyQt5-sip: 12.8.1 PyQtWebEngine-commercial: 5.15.2 python-dateutil: 2.8.2 pytz: 2021.3 pywin32: 303 pyzmq: 22.3.0 qtconsole: 5.2.2 QtPy: 2.0.0 RandomWords: 0.3.0 requests: 2.27.1 scipy: 1.7.3 setuptools: 59.8.0 sfftk-rw: 0.7.1 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: 1.26.8 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.37.1 wheel-filename: 1.3.0 WMI: 1.5.1 }}} " defect closed normal Structure Prediction nonchimerax all ChimeraX