Opened 4 years ago
Closed 4 years ago
#5284 closed defect (duplicate)
Blast: not enough values to unpack
Reported by: | Owned by: | Eric Pettersen | |
---|---|---|---|
Priority: | normal | Milestone: | |
Component: | Sequence | Version: | |
Keywords: | Cc: | ||
Blocked By: | Blocking: | ||
Notify when closed: | Platform: | all | |
Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: Darwin-19.6.0-x86_64-i386-64bit ChimeraX Version: 1.1.1 (2020-10-07 08:32:49 UTC) Description Blasting protein sequence through PDB Log: UCSF ChimeraX version: 1.1.1 (2020-10-07) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/luca/Downloads/AF-Q5T4T6-F1-model_v1.pdb AF-Q5T4T6-F1-model_v1.pdb title: Alphafold V2.0 prediction for synaptonemal complex protein 2-like (Q5T4T6) [more info...] Chain information for AF-Q5T4T6-F1-model_v1.pdb #1 --- Chain | Description A | synaptonemal complex protein 2-like > select ::name="CYS" 54 atoms, 45 bonds, 9 residues, 1 model selected > show sel atoms > color sel lime > select clear > open "/Users/luca/Dropbox (Cambridge > University)/SARS_CoV_2_NSP1/PDB_DEPO/pdb:cif/27.05.2021.pdb" Summary of feedback from opening /Users/luca/Dropbox (Cambridge University)/SARS_CoV_2_NSP1/PDB_DEPO/pdb:cif/27.05.2021.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 GLU A 8 LEU A 20 1 13 Start residue of secondary structure not found: HELIX 2 2 PRO A 22 VAL A 35 1 14 Start residue of secondary structure not found: HELIX 3 3 LYS A 50 ASP A 52 1 3 Start residue of secondary structure not found: HELIX 4 4 ASN A 62 LYS A 72 1 11 Start residue of secondary structure not found: HELIX 5 5 ARG A 87 HIS A 91 1 5 21 messages similar to the above omitted End residue of secondary structure not found: HELIX 27 27 PRO B 285 ASN B 298 1 14 Start residue of secondary structure not found: HELIX 28 28 ARG B 302 ILE B 316 1 15 Start residue of secondary structure not found: HELIX 29 29 THR B 319 ILE B 332 1 14 Start residue of secondary structure not found: HELIX 30 30 ASP B 337 GLY B 354 1 18 Start residue of secondary structure not found: HELIX 31 31 SER B 366 SER B 373 1 8 Start residue of secondary structure not found: HELIX 32 32 CYS B 384 TYR B 401 1 18 1 messages similar to the above omitted End residue of secondary structure not found: HELIX 34 34 HIS B 419 ASN B 433 1 15 Start residue of secondary structure not found: HELIX 35 35 HIS B 443 ILE B 454 1 12 Start residue of secondary structure not found: HELIX 36 36 GLU C 368 GLU C 371 1 4 Start residue of secondary structure not found: HELIX 37 37 SER C 409 LYS C 426 1 18 Start residue of secondary structure not found: HELIX 38 38 SER C 482 ARG C 491 1 10 Start residue of secondary structure not found: HELIX 39 39 LYS C 522 VAL C 526 1 5 31 messages similar to the above omitted End residue of secondary structure not found: HELIX 71 71 LYS D 212 TYR D 235 1 24 Start residue of secondary structure not found: HELIX 72 72 ASP D 275 SER D 280 1 6 Start residue of secondary structure not found: HELIX 73 73 GLU D 332 ASP D 336 1 5 Start residue of secondary structure not found: HELIX 74 74 TYR D 357 ARG D 371 1 15 Start residue of secondary structure not found: HELIX 75 75 HIS D 386 ASN D 391 1 6 Start residue of secondary structure not found: HELIX 76 76 PRO D 397 GLY D 412 1 16 56 messages similar to the above omitted End residue of secondary structure not found: SHEET 53 5353 ILE D 271 GLY D 274 0 Start residue of secondary structure not found: SHEET 54 5454 GLN D 283 ASP D 287 0 Start residue of secondary structure not found: SHEET 55 5555 SER D 295 LEU D 296 0 Start residue of secondary structure not found: SHEET 56 5656 VAL D 301 ILE D 307 0 Start residue of secondary structure not found: SHEET 57 5757 LEU D 314 LEU D 319 0 Start residue of secondary structure not found: SHEET 58 5858 SER D 340 CYS D 346 0 1 messages similar to the above omitted End residue of secondary structure not found: SHEET 60 6060 HIS D 419 VAL D 423 0 Start residue of secondary structure not found: SHEET 61 6161 VAL D 453 PHE D 455 0 Start residue of secondary structure not found: SHEET 62 6262 CYS D 460 ILE D 464 0 Start residue of secondary structure not found: SHEET 63 6363 ILE D 468 LEU D 471 0 Start residue of secondary structure not found: SHEET 64 6464 ILE D 485 SER D 486 0 Start residue of secondary structure not found: SHEET 65 6565 VAL D 537 ILE D 539 0 6 messages similar to the above omitted Chain information for 27.05.2021.pdb #2 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available > select #2 19743 atoms, 20171 bonds, 46 pseudobonds, 2446 residues, 3 models selected > view sel > hide #1 models > show sel cartoons > hide sel atoms > select clear > ui tool show "Side View" > open 4vfm Fetching url http://files.rcsb.org/download/4vfm.cif failed: HTTP Error 404: Not Found > open 4fvm Summary of feedback from opening 4fvm fetched from pdb --- note | Fetching compressed mmCIF 4fvm from http://files.rcsb.org/download/4fvm.cif 4fvm title: Crystal structure of yeast DNA polymerase α [more info...] Chain information for 4fvm #3 --- Chain | Description A | DNA polymerase α catalytic subunit A > ui tool show Matchmaker > matchmaker #3/A to #2/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 27.05.2021.pdb, chain A (#2) with 4fvm, chain A (#3), sequence alignment score = 1913.8 RMSD between 516 pruned atom pairs is 1.113 angstroms; (across all 790 pairs: 4.703) > ui tool show "Show Sequence Viewer" > sequence chain #3/A Alignment identifier is 3/A > show sel atoms > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > select clear > select #2/A:409 6 atoms, 5 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 6 atom styles > color sel byhetero > select #2/A:405 4 atoms, 3 bonds, 1 residue, 1 model selected > select up 137 atoms, 137 bonds, 18 residues, 1 model selected > show sel target ab > style sel stick Changed 137 atom styles > color sel byhetero > select clear > hide #!2 models > select #3/A:887 22 atoms, 21 bonds, 1 residue, 1 model selected > select up 412 atoms, 415 bonds, 27 residues, 1 model selected > view sel > show sel atoms > color sel byhetero > select H 6732 atoms, 829 residues, 1 model selected > hide sel atoms > select clear > select #3/A:886 14 atoms, 13 bonds, 1 residue, 1 model selected > select up 412 atoms, 415 bonds, 27 residues, 1 model selected > view sel > select clear > open 4fyd Summary of feedback from opening 4fyd fetched from pdb --- warnings | Atom HO5' is not in the residue template for C /E:1 Atom HO5' is not in the residue template for C /F:1 4fyd title: Crystal structure of yeast DNA polymerase α bound to DNA/RNA and dGTP [more info...] Chain information for 4fyd #4 --- Chain | Description A B | DNA polymerase α catalytic subunit A C D | DNA (5'-D(*TP*GP*ap*GP*CP*GP*TP*G*TP*GP*TP*ap*CP*CP*CP*CP*TP*GP*CP*CP*CP*GP*CP*CP*G)-3') E F | DNA/RNA (5'-R(*CP*GP*GP*CP*GP*GP*GP*CP*ap*G)-D(P*GP*G)-3') Non-standard residues in 4fyd #4 --- DGT — 2'-deoxyguanosine-5'-triphosphate 4fyd mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly > hide #!3 models > select #4 29108 atoms, 29492 bonds, 72 pseudobonds, 1754 residues, 3 models selected > view sel > show sel cartoons > hide sel atoms > select clear > select #4/B:891 12 atoms, 11 bonds, 1 residue, 1 model selected > select sel :< 10 1030 atoms, 1038 bonds, 9 pseudobonds, 76 residues, 3 models selected > show (#!4 & sel) target ab > style sel & #!4 stick Changed 694 atom styles > color sel & #!4 byhetero > select H 21096 atoms, 2581 residues, 2 models selected > delete atoms (#!4 & sel) > delete bonds (#!4 & sel) > select clear > select clear > select clear > select clear > select clear > select clear > select #4/B:889 8 atoms, 7 bonds, 1 residue, 1 model selected > select clear > select #4/B:891@CB 1 atom, 1 residue, 1 model selected > select up 8 atoms, 7 bonds, 1 residue, 1 model selected > view sel > select clear > ui tool show "Blast Protein" > blastprotein #1/A database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100 name > bp1 Web Service: BlastProtein2 is a Python wrapper that calls blastp to search nr or pdb for sequences similar to the given protein sequence Opal service URL: http://webservices.rbvi.ucsf.edu/opal2/services/BlastProtein2Service Opal job id: appBlastProtein2Service1632489728942-2089285466 Opal status URL prefix: http://webservices.rbvi.ucsf.edu/appBlastProtein2Service1632489728942-2089285466 stdout.txt = standard output stderr.txt = standard error BlastProtein finished. Fetching BLAST PDB info using URL: https://data.rcsb.org/rest/v1/core/entry/A Failed HTTP Error 404: Could not fetch entry information for A Traceback (most recent call last): File "/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/gui.py", line 629, in customEvent func(*args, **kw) File "/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/blastprotein/job.py", line 92, in on_finish self.tool.job_finished(self, p, self._params()) File "/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/blastprotein/tool.py", line 284, in job_finished self._show_results(job.atomspec, blast_results) File "/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/blastprotein/tool.py", line 326, in _show_results self._add_pdbinfo(pdb_chains) File "/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/blastprotein/tool.py", line 345, in _add_pdbinfo data = info.fetch_info(self.session, chain_ids) File "/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/blastprotein/pdbinfo.py", line 206, in fetch_info entry, auth_cid = pcid.split('_') ValueError: not enough values to unpack (expected 2, got 1) ValueError: not enough values to unpack (expected 2, got 1) File "/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/blastprotein/pdbinfo.py", line 206, in fetch_info entry, auth_cid = pcid.split('_') See log for complete Python traceback. OpenGL version: 4.1 ATI-3.10.19 OpenGL renderer: AMD Radeon Pro Vega 48 OpenGL Engine OpenGL vendor: ATI Technologies Inc.Hardware: Hardware Overview: Model Name: iMac Model Identifier: iMac19,1 Processor Name: 8-Core Intel Core i9 Processor Speed: 3.6 GHz Number of Processors: 1 Total Number of Cores: 8 L2 Cache (per Core): 256 KB L3 Cache: 16 MB Hyper-Threading Technology: Enabled Memory: 32 GB Boot ROM Version: 1554.80.3.0.0 SMC Version (system): 2.46f13 Software: System Software Overview: System Version: macOS 10.15.7 (19H524) Kernel Version: Darwin 19.6.0 Time since boot: 6 days 20:03 Graphics/Displays: Radeon Pro Vega 48: Chipset Model: Radeon Pro Vega 48 Type: GPU Bus: PCIe PCIe Lane Width: x16 VRAM (Total): 8 GB Vendor: AMD (0x1002) Device ID: 0x6869 Revision ID: 0x0000 ROM Revision: 113-D0650E-072 VBIOS Version: 113-D05001A1XG-011 Option ROM Version: 113-D05001A1XG-011 EFI Driver Version: 01.01.072 Metal: Supported, feature set macOS GPUFamily2 v1 Displays: iMac: Display Type: Built-In Retina LCD Resolution: 5120 x 2880 Retina Framebuffer Depth: 30-Bit Color (ARGB2101010) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal PyQt version: 5.12.3 Compiled Qt version: 5.12.4 Runtime Qt version: 5.12.9 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.0 Babel: 2.8.0 backcall: 0.2.0 blockdiag: 2.0.1 certifi: 2020.6.20 chardet: 3.0.4 ChimeraX-AddH: 2.1.1 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.1 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.6.1 ChimeraX-AtomSearch: 2.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 1.0.1 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.0 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.0 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.1 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.0 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-CommandLine: 1.1.3 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.1.1 ChimeraX-CoreFormats: 1.0 ChimeraX-coulombic: 1.0.1 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-DataFormats: 1.0 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1 ChimeraX-DistUI: 1.0 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: 1.0 ChimeraX-Hbonds: 2.0 ChimeraX-Help: 1.0 ChimeraX-HKCage: 1.0 ChimeraX-IHM: 1.0 ChimeraX-ImageFormats: 1.0 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0 ChimeraX-Label: 1.0 ChimeraX-ListInfo: 1.0 ChimeraX-Log: 1.1.1 ChimeraX-LookingGlass: 1.1 ChimeraX-Map: 1.0.1 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.0 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 1.1 ChimeraX-MDcrds: 2.0 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.0 ChimeraX-mmCIF: 2.2 ChimeraX-MMTF: 2.0 ChimeraX-Modeller: 1.0 ChimeraX-ModelPanel: 1.0 ChimeraX-ModelSeries: 1.0 ChimeraX-Mol2: 2.0 ChimeraX-Morph: 1.0 ChimeraX-MouseModes: 1.0 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0 ChimeraX-OpenCommand: 1.2.1 ChimeraX-PDB: 2.1 ChimeraX-PDBBio: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0 ChimeraX-PubChem: 2.0 ChimeraX-Read-Pbonds: 1.0 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.0 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.2 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SeqView: 2.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.0 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.0 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.0.4 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-Struts: 1.0 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.0 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.0 ChimeraX-ToolshedUtils: 1.0 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.2.3 ChimeraX-uniprot: 2.0 ChimeraX-ViewDockX: 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: 0.4.3 comtypes: 1.1.7 cxservices: 1.0 cycler: 0.10.0 Cython: 0.29.20 decorator: 4.4.2 distlib: 0.3.1 docutils: 0.16 filelock: 3.0.12 funcparserlib: 0.3.6 grako: 3.16.5 h5py: 2.10.0 html2text: 2020.1.16 idna: 2.10 ihm: 0.16 imagecodecs: 2020.5.30 imagecodecs-lite: 2020.1.31 imagesize: 1.2.0 ipykernel: 5.3.0 ipython: 7.15.0 ipython-genutils: 0.2.0 jedi: 0.17.2 Jinja2: 2.11.2 jupyter-client: 6.1.3 jupyter-core: 4.6.3 kiwisolver: 1.2.0 line-profiler: 2.1.2 lxml: 4.5.1 MarkupSafe: 1.1.1 matplotlib: 3.2.1 msgpack: 1.0.0 netifaces: 0.10.9 networkx: 2.4 numexpr: 2.7.1 numpy: 1.18.5 numpydoc: 1.0.0 openvr: 1.12.501 packaging: 20.4 parso: 0.7.1 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 7.1.2 pip: 20.2.2 pkginfo: 1.5.0.1 prompt-toolkit: 3.0.7 psutil: 5.7.0 ptyprocess: 0.6.0 pycollada: 0.7.1 pydicom: 2.0.0 Pygments: 2.6.1 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 2.4.7 PyQt5-commercial: 5.12.3 PyQt5-sip: 4.19.19 PyQtWebEngine-commercial: 5.12.1 python-dateutil: 2.8.1 pytz: 2020.1 pyzmq: 19.0.2 qtconsole: 4.7.4 QtPy: 1.9.0 RandomWords: 0.3.0 requests: 2.24.0 scipy: 1.4.1 setuptools: 49.4.0 sfftk-rw: 0.6.6.dev0 six: 1.15.0 snowballstemmer: 2.0.0 sortedcontainers: 2.2.2 Sphinx: 3.1.1 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 2.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 1.0.3 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.4 suds-jurko: 0.6 tables: 3.6.1 tifffile: 2020.6.3 tinyarray: 1.2.2 tornado: 6.0.4 traitlets: 5.0.4 urllib3: 1.25.10 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.34.2
Change History (2)
comment:1 by , 4 years ago
Component: | Unassigned → Sequence |
---|---|
Owner: | set to |
Platform: | → all |
Project: | → ChimeraX |
Status: | new → accepted |
Summary: | ChimeraX bug report submission → Blast: not enough values to unpack |
comment:2 by , 4 years ago
Resolution: | → duplicate |
---|---|
Status: | accepted → closed |
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Hi Luca,
--Eric