"Show in sequence viewer" error when no hits

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.3.dev202104210709 (2021-04-21 07:09:28 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.3.dev202104210709 (2021-04-21)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/wei/Downloads/7ENA.cif

Summary of feedback from opening /Users/wei/Downloads/7ENA.cif  
---  
warnings | Missing entity information. Treating each chain as a separate
entity.  
Unable to infer polymer connectivity due to unspecified label_seq_id for
residue "DC" near line 343985  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
note | Fetching CCD SF4 from http://ligand-expo.rcsb.org/reports/S/SF4/SF4.cif  
  
Chain information for 7ENA.cif #1  
---  
Chain | Description  
0 | No description available  
1 | No description available  
2 | No description available  
3 | No description available  
4 | No description available  
5 | No description available  
6 | No description available  
7 | No description available  
8 | No description available  
9 | No description available  
BA | No description available  
DA | No description available  
DB | No description available  
DD | No description available  
DE | No description available  
DF | No description available  
DG | No description available  
DH | No description available  
DI | No description available  
DJ | No description available  
DL | No description available  
DO | No description available  
DP | No description available  
DQ | No description available  
Dc | No description available  
Dd | No description available  
De | No description available  
Df | No description available  
Di | No description available  
Dj | No description available  
Dk | No description available  
Dl | No description available  
Dm | No description available  
EA | No description available  
EB | No description available  
FA | No description available  
FB | No description available  
PA | No description available  
PB | No description available  
PC | No description available  
PD | No description available  
PE | No description available  
PF | No description available  
PG | No description available  
PH | No description available  
PI | No description available  
PJ | No description available  
PK | No description available  
PL | No description available  
X | No description available  
Y | No description available  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
e | No description available  
f | No description available  
g | No description available  
h | No description available  
i | No description available  
j | No description available  
k | No description available  
l | No description available  
m | No description available  
n | No description available  
o | No description available  
p | No description available  
q | No description available  
r | No description available  
s | No description available  
t | No description available  
u | No description available  
v | No description available  
w | No description available  
x | No description available  
z | No description available  
  

> hide cartoons

> hide atoms

> show cartoons

> select /a:420

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select up

147 atoms, 149 bonds, 18 residues, 1 model selected  

> select up

3586 atoms, 3661 bonds, 469 residues, 1 model selected  

> ui tool show "Show Sequence Viewer"

> sequence chain /a

Alignment identifier is 1/a  

> blastprotein 1/a:1

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: appBlastProtein2Service1620428587404-1675947675  
Opal status URL prefix:
http://webservices.rbvi.ucsf.edu/appBlastProtein2Service1620428587404-1675947675  
stdout.txt = standard output  
stderr.txt = standard error  
BlastProtein finished.  
Traceback (most recent call last):  
File
"/private/var/folders/z_/y75k2tcj3ln_z9l34tvw4jp80000gn/T/AppTranslocation/0EC30BB3-3AE6-4066-AB6E-EF7855986B00/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/widgets/htmlview.py", line 324, in interceptRequest  
self._callback(info)  
File
"/private/var/folders/z_/y75k2tcj3ln_z9l34tvw4jp80000gn/T/AppTranslocation/0EC30BB3-3AE6-4066-AB6E-EF7855986B00/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/widgets/htmlview.py", line 85, in _intercept  
return interceptor(request_info, *args)  
File
"/private/var/folders/z_/y75k2tcj3ln_z9l34tvw4jp80000gn/T/AppTranslocation/0EC30BB3-3AE6-4066-AB6E-EF7855986B00/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/htmltool.py", line 112, in _navigate  
self.session.ui.thread_safe(self.handle_scheme, url)  
File
"/private/var/folders/z_/y75k2tcj3ln_z9l34tvw4jp80000gn/T/AppTranslocation/0EC30BB3-3AE6-4066-AB6E-EF7855986B00/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 366, in thread_safe  
func(*args, **kw)  
File
"/private/var/folders/z_/y75k2tcj3ln_z9l34tvw4jp80000gn/T/AppTranslocation/0EC30BB3-3AE6-4066-AB6E-EF7855986B00/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/blastprotein/tool.py", line 115, in handle_scheme  
id_list = [int(n) for n in query["ids"][0].split(',')]  
KeyError: 'ids'  
  
KeyError: 'ids'  
  
File
"/private/var/folders/z_/y75k2tcj3ln_z9l34tvw4jp80000gn/T/AppTranslocation/0EC30BB3-3AE6-4066-AB6E-EF7855986B00/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/blastprotein/tool.py", line 115, in handle_scheme  
id_list = [int(n) for n in query["ids"][0].split(',')]  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-4.4.17
OpenGL renderer: AMD Radeon R9 M390 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:

    Hardware Overview:

      Model Name: iMac
      Model Identifier: iMac17,1
      Processor Name: Quad-Core Intel Core i5
      Processor Speed: 3.2 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 6 MB
      Memory: 16 GB
      System Firmware Version: 429.100.7.0.0
      SMC Version (system): 2.33f12

Software:

    System Software Overview:

      System Version: macOS 11.3 (20E232)
      Kernel Version: Darwin 20.4.0
      Time since boot: 3 days 9:54

Graphics/Displays:

    AMD Radeon R9 M390:

      Chipset Model: AMD Radeon R9 M390
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 2 GB
      Vendor: AMD (0x1002)
      Device ID: 0x6819
      Revision ID: 0x0000
      ROM Revision: 113-C408WA-799
      VBIOS Version: 113-C408W1-009
      EFI Driver Version: 01.00.799
      Metal Family: Supported, Metal GPUFamily macOS 2
      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: Yes
          Connection Type: Internal

Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.2
    Babel: 2.9.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.12.5
    cftime: 1.4.1
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.1
    ChimeraX-AddH: 2.1.6
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.17
    ChimeraX-AtomicLibrary: 3.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.3
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3.dev202104210709
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.1
    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: 1.1
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.2
    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: 1.2
    ChimeraX-MDcrds: 2.2
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0
    ChimeraX-ModelPanel: 1.1
    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: 2.0.1
    ChimeraX-OpenCommand: 1.5
    ChimeraX-PDB: 2.4.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.0.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.4
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4
    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: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.5
    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: 1.0.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.8
    ChimeraX-uniprot: 2.1
    ChimeraX-UnitCell: 1.0
    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: 0.29.21
    decorator: 5.0.7
    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: 0.17
    imagecodecs: 2020.5.30
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.7
    jupyter-core: 4.7.1
    kiwisolver: 1.3.1
    line-profiler: 2.1.2
    lxml: 4.6.2
    lz4: 3.1.0
    MarkupSafe: 1.1.1
    matplotlib: 3.3.2
    msgpack: 1.0.0
    netCDF4: 1.5.4
    networkx: 2.5
    numexpr: 2.7.3
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.14.1501
    packaging: 20.9
    ParmEd: 3.2.0
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 21.0.1
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.18
    psutil: 5.7.2
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.7.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.1
    pytz: 2021.1
    pyzmq: 22.0.3
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    setuptools: 50.3.2
    sfftk-rw: 0.6.7.dev1
    six: 1.15.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.2.2
    Sphinx: 3.2.1
    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: 2020.9.3
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.0.5
    urllib3: 1.25.11
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.0
    wheel-filename: 1.2.0

[Eric Pettersen]

This blast query produces no hits

[Eric Pettersen]

Hopefully the eventual rewrite of the BLAST gui will make this ticket obsolete

[Zach Pearson]

Should be fixed in tonight's build by ​https://github.com/RBVI/ChimeraX/commit/06c3c18a363e4a5f4366c60876f1f40f55f74d5f