Opened 3 years ago

Closed 3 years ago

#6819 closed defect (duplicate)

invalid literal error in blast results

Reported by: chimerax-bug-report@… Owned by:
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:        Windows-10-10.0.19043
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open C:\Users\xrzsz\Documents\post-graduate\thesis\ACC\Alphafold\BADC2.cxs
> format session

Log from Tue May 10 12:07:22 2022UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 4HR7 format mmcif fromDatabase pdb

4hr7 title:  
Crystal Structure of Biotin Carboxyl Carrier Protein-Biotin Carboxylase
Complex from E.coli [more info...]  
  
Chain information for 4hr7 #1  
---  
Chain | Description | UniProt  
A C E F | Biotin carboxylase | ACCC_ECOLI  
B D G I | Biotin carboxyl carrier protein of acetyl-CoA carboxylase |
BCCP_ECOLI  
  
Non-standard residues in 4hr7 #1  
---  
EDO — 1,2-ethanediol (ethylene glycol)  
SO4 — sulfate ion  
  

> ui tool show AlphaFold

> alphafold predict #1/A

> alphafold predict
> MGTTLRSVKAIQLSTVPPAETEAIADVKDSDETKSTVVNTHLMPKSSEVEALISEITDSSSIAEFELKLGGFRLYVARKLTDESSPPPQQIQPVVAASATPEGVHTNGSATSSSLAITKTSSSSADRPQTLANKAADQGLVILQSPTVGYFRRSKTIKGKRTPTICKEKDIVKEGQVLCYIEQLGGQIPVESDVSGEIVKILREDGEPVGYNDALITVLPSFPGIKKLQ

> show atoms

> style stick

Changed 16137 atom styles  

> show cartoons

> set bgColor white

> set bgColor black

> show atoms

> hide atoms

Running AlphaFold prediction  
Chain information for best_model.pdb #2  
---  
Chain | Description  
A | No description available  
  
AlphaFold prediction finished  
Results in C:\Users\xrzsz/Downloads\ChimeraX\AlphaFold\prediction_1  
Chain information for best_model.pdb #3  
---  
Chain | Description  
A | No description available  
  
AlphaFold prediction finished  
Results in C:\Users\xrzsz/Downloads\ChimeraX\AlphaFold\prediction_2  

> hide #!1 models

> select #2

3473 atoms, 3497 bonds, 229 residues, 1 model selected  

> ~select #2

Nothing selected  

> select #3

3473 atoms, 3497 bonds, 229 residues, 1 model selected  

> select #2

3473 atoms, 3497 bonds, 229 residues, 1 model selected  

> ui tool show "Selection Inspector"

> show #!1 models

> select #1

16137 atoms, 15945 bonds, 7 pseudobonds, 2498 residues, 2 models selected  

> view #1 clip false

> hide #!1 models

> ~select #1

Nothing selected  

> select #2

3473 atoms, 3497 bonds, 229 residues, 1 model selected  

> select #3

3473 atoms, 3497 bonds, 229 residues, 1 model selected  

> select #2

3473 atoms, 3497 bonds, 229 residues, 1 model selected  

> view #2 clip false

> show #2 target m

> select #3

3473 atoms, 3497 bonds, 229 residues, 1 model selected  

> view #2 clip false

> show #2 target m

> select #2

3473 atoms, 3497 bonds, 229 residues, 1 model selected  

> show #2 target m

> view #2 clip false

> hide #3 models

> show #3 models

> hide #3 models

> show #3 models

> select #3

3473 atoms, 3497 bonds, 229 residues, 1 model selected  

> view #2 clip false

> select #2

3473 atoms, 3497 bonds, 229 residues, 1 model selected  

> view #2 clip false

[Repeated 1 time(s)]

> select #3

3473 atoms, 3497 bonds, 229 residues, 1 model selected  

> view #2 clip false

> select #2

3473 atoms, 3497 bonds, 229 residues, 1 model selected  

> view #2 clip false

> show #2 target m

> log metadata #2

The model has no metadata

> log chains #2

Chain information for best_model.pdb #2  
---  
Chain | Description  
A | No description available  
  

> show #!1 models

> select #3

3473 atoms, 3497 bonds, 229 residues, 1 model selected  

> hide #3 models

> ~select #3

Nothing selected  

> hide #2 models

> show #2 models

> show #3 models

> hide #2 models

> hide #3 models

> show #2 models

> show #3 models

> hide #2 models

> hide #3 models

> show #2 models

> hide #2 models

> hide #!1 models

> show #!1 models

> view #1 clip false

> show #2 models

> hide #2 models

> show #2 models

> hide #!1 models

> view #1 clip false

[Repeated 3 time(s)]

> select #2

3473 atoms, 3497 bonds, 229 residues, 1 model selected  

> ~select #2

Nothing selected  

> hide #2 models

> show #2 models

> view #2 clip false

> save C:/Users/xrzsz/Documents/post-graduate/thesis/ACC/Alphafold/BADC2.cxs

——— End of log from Tue May 10 12:07:22 2022 ———

opened ChimeraX session  

> ui tool show AlphaFold

> show #3 models

> hide #3 models

> alphafold search
> MGSSHHHHHHSQDPPSSAEGKEKNSLKESSASSPELATEESISEFLTQVTTLVKLVDSRDIVELQLKQLDCELVIRKKEALPQPQAPASYVMMQQPNQPSYAQQMAPPAAPAAAAPAPSTPASLPPPSPPTPAKSSLPTVKSPMAGTFYRSPAPGEPPFIKVGDKVQKGQVLCIVEAMKLMNEIESDHTGTVVDIVAEDGKPVSLDTPLFVVQP

ChimeraX REST job id: DTCINGKKLCR0QMT1  
BlastProtein finished.  
Parsing BLAST results.  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\blastprotein\ui\results.py", line 474, in run  
self._parse_results(self.database, self.results, self.sequence, self.atomspec)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\blastprotein\ui\results.py", line 529, in _parse_results  
blast_results.add_info(self.session, match_chains, sequence_only_hits)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\blastprotein\data_model\databases.py", line 196, in add_info  
matches[match]["protein_existence"] =
experimental_evidence[int(protein_existence)]  
ValueError: invalid literal for int() with base 10: ''  
  
ValueError: invalid literal for int() with base 10: ''  
  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\blastprotein\data_model\databases.py", line 196, in add_info  
matches[match]["protein_existence"] =
experimental_evidence[int(protein_existence)]  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 30.0.100.9865
OpenGL renderer: Intel(R) HD Graphics 620
OpenGL vendor: Intel
Manufacturer: LENOVO
Model: 20HRS0DS00
OS: Microsoft Windows 10 Home (Build 19043)
Memory: 8,437,510,144
MaxProcessMemory: 137,438,953,344
CPU: 4 Intel(R) Core(TM) i7-7500U CPU @ 2.70GHz
OSLanguage: zh-CN
Locale: ('en_US', 'cp936')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.10.8
    cftime: 1.5.1.1
    charset-normalizer: 2.0.9
    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: 1.31
    ChimeraX-AtomicLibrary: 4.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    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
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3
    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-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: 1.1
    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: 1.1.4
    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: 2.0.4
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    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: 1.7
    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: 1.0.1
    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: 1.6.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.7
    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: 0.29.24
    decorator: 5.1.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.8.0
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.3
    ParmEd: 3.2.0
    parso: 0.8.3
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.23
    psutil: 5.8.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.6
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pywin32: 228
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.3
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    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-jurko: 0.6
    tables: 3.6.1
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0
    WMI: 1.5.1

Change History (1)

comment:1 by Zach Pearson, 3 years ago

Component: Unassigned → Sequence
Platform: → all
Project: → ChimeraX
Resolution: → duplicate
Status: new → closed
Summary: ChimeraX bug report submission → invalid literal error in blast results

Duplicate of #5572.

Note: See TracTickets for help on using tickets.