id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
6348	Parsing BlastProtein results failed: 'hits'	goddard@…	Zach Pearson	"{{{
The following bug report has been submitted:
Platform:        macOS-12.2.1-arm64-arm-64bit
ChimeraX Version: 1.4.dev202203071951 (2022-03-07 19:51:09 UTC)
Description
Doing an AlphaFold search from gui with 7PUA chain Ug I get this error pasing result ""hits"".

Log:
UCSF ChimeraX version: 1.4.dev202203071951 (2022-03-07)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 7pua format mmcif fromDatabase pdb

Summary of feedback from opening 7pua fetched from pdb  
---  
warnings | Unknown polymer entity '88' near line 240142  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
  
7pua title:  
Middle assembly intermediate of the Trypanosoma brucei mitoribosomal small
subunit [more info...]  
  
Chain information for 7pua #1  
---  
Chain | Description | UniProt  
CA | 9S rRNA |  
CB | 9S rRNA |  
CC | uS3m |  
CE | Ribosomal_S5_C domain-containing protein | D0A335_TRYB9  
CF | bS6m | Q38BW5_TRYB2  
CH | 30S ribosomal protein S8, putative | C9ZZU9_TRYB9  
CI | uS9m | Q57W62_TRYB2  
CJ | LysM domain-containing protein | C9ZPU0_TRYB9  
CK | uS11m | Q389T7_TRYB2  
CL | uS12m |  
CN | uS14m | Q580I0_TRYB2  
CO | uS15m | Q4GZ99_TRYB2  
CP | bS16m | Q384N9_TRYB2  
CQ | 30S Ribosomal protein S17, putative | C9ZYU9_TRYB9  
CR | bS18m | D0A3A4_TRYB9  
CS | uS19m | A0A3L6L621_9TRYP  
CU | bS21m | Q580M9_TRYB2  
Ca | mS22 | Q38DR3_TRYB2  
Cb | mS23 | C9ZNU0_TRYB9  
Cd | mS26 | Q38DK6_TRYB2  
Cg | mS29 | Q585C2_TRYB2  
Ci | mS33 | Q57WW0_TRYB2  
Cj | mS34 | Q57UK0_TRYB2  
Ck | mS35 | Q387C7_TRYB2  
Cm | mS37 | Q38C96_TRYB2  
Cn | mS38 | Q57VQ9_TRYB2  
Cp | Protein FYV4, mitochondrial | Q389L3_TRYB2  
DB | mS49 | C9ZJE4_TRYB9  
DC | mS50 | A0A3L6L3Q2_9TRYP  
DD | mS51 | D0A752_TRYB9  
DE | mS52 | Q386Q7_TRYB2  
DF | mS53 | C9ZXX4_TRYB9  
DG | mS54 | C9ZNY4_TRYB9  
DH | mS55 | A0A3L6LGC8_9TRYP  
DI | mS56 | A0A3L6L6C6_9TRYP  
DJ | mS57 | Q584U8_TRYB2  
DK | mS58 | A0A3L6L3U6_9TRYP  
DL | mS59 | D0A232_TRYB9  
DO | mS62 | Q383D1_TRYB2  
DP | mS63 | C9ZXR0_TRYB9  
DR | mS65 | C9ZPP1_TRYB9  
DT | Rhodanese domain-containing protein | Q586G5_TRYB2  
DU | Ubiquitin-like domain-containing protein | C9ZKC1_TRYB9  
DV | mS69 | Q57UZ6_TRYB2  
DW | mS70 | D0A8P6_TRYB9  
DX | mS71 | Q383G5_TRYB2  
DY | mS72 | Q57YD4_TRYB2  
DZ | mS73 | Q587C4_TRYB2  
Da | mS74 | A0A3L6KY67_9TRYP  
F2 | PPR_long domain-containing protein | C9ZIL7_TRYB9  
F3 | mt-SAF3 | Q38E61_TRYB2  
F5 | mt-SAF5 | D0AAF7_TRYB9  
F6 | DUF4460 domain-containing protein | Q38FQ8_TRYB2  
F7 | mt-SAF7 | Q57UW6_TRYB2  
F9 | mt-SAF9 | C9ZSL5_TRYB9  
FM FN | mt-SAF21 | C9ZJW2_TRYB9  
FO | mt-SAF22 | Q389F9_TRYB2  
FP | mt-SAF23 | D0A963_TRYB9  
FW | LMWPc domain-containing protein | Q38FI3_TRYB2  
FX | mt-SAF27 | Q57YK5_TRYB2  
FZ | mt-SAF29 | A0A3L6KWY8_9TRYP  
Fb | mt-SAF31 | Q581U4_TRYB2  
Fc | Acyl carrier protein | Q57WW9_TRYB2  
Fd | DUF4379 domain-containing protein | Q581T4_TRYB2  
Ff | DNA photolyase, putative | D0A9A9_TRYB9  
Fg | Acyl transferase-like protein, putative | C9ZYZ4_TRYB9  
Fh | mt-SAF37 | Q38A63_TRYB2  
Fi | mt-SAF38 | C9ZNX5_TRYB9  
IA | Translation initiation factor IF-2, putative | C9ZSN7_TRYB9  
IB | mt-SAF39 | D0A0V4_TRYB9  
U8 | Unk8 |  
UC | UnkC |  
UD | UnkD |  
UF | UnkF |  
UG | UnkG |  
UI | UnkI |  
UK | UnkK |  
UM UN UQ | Unk |  
UP | UnkP |  
Ua | Unka |  
Ug | Unkg |  
  
Non-standard residues in 7pua #1  
---  
ATP — adenosine-5'-triphosphate  
FDA — dihydroflavine-adenine dinucleotide  
MG — magnesium ion  
PM8 —
S-(2-{[N-(2-hydroxy-4-{[hydroxy(oxido)phosphino]oxy}-3,3-dimethylbutanoyl)-β-alanyl]amino}ethyl)
decanethioate  
PO4 — phosphate ion  
ZN — zinc ion  
  

> ui tool show AlphaFold

> alphafold match #1/Ug

No AlphaFold model with similar sequence for chain Ug  

Opened 0 AlphaFold model  

> alphafold search #1/Ug

Webservices job id:
72VCVYYLUXPSD1GMUU6A105YR17ES8ZQ8H8GQG37T10SPD347CXAGGCTQ0II3C21  
BlastProtein finished.  
Parsing BLAST results.  
Parsing BlastProtein results failed: 'hits'  




OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M1 Max
OpenGL vendor: Apple

Locale: UTF-8
Qt version: PyQt6 6.2.2, Qt 6.2.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,2
      Chip: Apple M1 Max
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 32 GB
      System Firmware Version: 7429.81.3
      OS Loader Version: 7429.81.3

Software:

    System Software Overview:

      System Version: macOS 12.2.1 (21D62)
      Kernel Version: Darwin 21.3.0
      Time since boot: 2 days 6:19

Graphics/Displays:

    Apple M1 Max:

      Chipset Model: Apple M1 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 32
      Vendor: Apple (0x106b)
      Metal Family: Supported, Metal GPUFamily Apple 7
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3456 x 2234 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.2
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2021.5.30
    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: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.36.2
    ChimeraX-AtomicLibrary: 6.1.1
    ChimeraX-AtomSearch: 2.0.1
    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: 1.2.1
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4.dev202203071951
    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-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: 2.7
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.2
    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: 1.8
    ChimeraX-PDB: 2.6.6
    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: 2.4.7
    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
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.16.2
    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: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.26
    debugpy: 1.5.1
    decorator: 5.1.1
    docutils: 0.17.1
    entrypoints: 0.4
    filelock: 3.4.2
    fonttools: 4.29.1
    funcparserlib: 1.0.0a0
    grako: 3.16.5
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.26
    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: 4.9.2
    kiwisolver: 1.3.2
    line-profiler: 3.4.0
    lxml: 4.7.1
    lz4: 3.1.10
    MarkupSafe: 2.1.0
    matplotlib: 3.5.1
    matplotlib-inline: 0.1.3
    msgpack: 1.0.3
    nest-asyncio: 1.5.4
    networkx: 2.6.3
    numpy: 1.22.1
    openvr: 1.16.802
    packaging: 21.0
    ParmEd: 3.4.3
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.0.0
    pip: 21.3.1
    pkginfo: 1.8.2
    prompt-toolkit: 3.0.28
    psutil: 5.9.0
    ptyprocess: 0.7.0
    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
    PyQt6: 6.2.2
    PyQt6-Qt6: 6.2.3
    PyQt6-sip: 13.2.0
    PyQt6-WebEngine: 6.2.1
    PyQt6-WebEngine-Qt6: 6.2.3
    python-dateutil: 2.8.2
    pytz: 2021.3
    pyzmq: 22.3.0
    qtconsole: 5.2.2
    QtPy: 2.0.1
    requests: 2.27.1
    scipy: 1.7.3
    setuptools: 59.8.0
    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
    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

}}}
"	defect	closed	normal	1.4	Sequence		fixed						all	ChimeraX