BLAST gui shows wrong database and chain when the blastprotein command is run

[goddard@…]

The following bug report has been submitted:
Platform:        macOS-10.15.7-x86_64-i386-64bit
ChimeraX Version: 1.3.dev202108070803 (2021-08-07 08:03:28 UTC)
Description
The blastprotein command shows results in the user interface with the wrong database and chain shown in the GUI menus.  This is very misleading.  For instance "blast #1/B database alphafold" bring up results showing chain A was searched in the PDB database.  There is some text below that says #1/B and database alphafold, but it is much less visible than the wrong settings shown in the menus.

The menus should be set to show the correct settings for the displayed results.  In the current implementation this would require messing with the BLAST gui JavaScript -- not too hard.  But probably better to replace the html / javascript gui with Qt as has been discussed before.


Log:
UCSF ChimeraX version: 1.3.dev202108070803 (2021-08-07)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 3nos format mmcif fromDatabase pdb

Summary of feedback from opening 3nos fetched from pdb  
---  
warnings | Unknown polymer entity '3' near line 7769  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
  
3nos title:  
Human endothelial nitric oxide synthase with arginine substrate [more info...]  
  
Chain information for 3nos #1  
---  
Chain | Description | UniProt  
A B | endothelial nitric-oxide synthase | NOS3_HUMAN  
  
Non-standard residues in 3nos #1  
---  
H4B — 5,6,7,8-tetrahydrobiopterin  
HEM — protoporphyrin IX containing Fe (HEME)  
ZN — zinc ion  
  

> blastprotein #1/B database alphafold

ChimeraX REST job id: job_0d_j1om7  
BlastProtein finished.  
Parsing BLAST results.  




OpenGL version: 4.1 ATI-3.10.19
OpenGL renderer: AMD Radeon Pro Vega 20 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro15,3
      Processor Name: 8-Core Intel Core i9
      Processor Speed: 2.4 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: 1554.100.64.0.0 (iBridge: 18.16.14556.0.0,0)

Software:

    System Software Overview:

      System Version: macOS 10.15.7 (19H1030)
      Kernel Version: Darwin 19.6.0
      Time since boot: 95 days 3 minutes

Graphics/Displays:

    Intel UHD Graphics 630:

      Chipset Model: Intel UHD Graphics 630
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3e9b
      Revision ID: 0x0002
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal: Supported, feature set macOS GPUFamily2 v1

    Radeon Pro Vega 20:

      Chipset Model: Radeon Pro Vega 20
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x8
      VRAM (Total): 4 GB
      Vendor: AMD (0x1002)
      Device ID: 0x69af
      Revision ID: 0x00c0
      ROM Revision: 113-D2060I-087
      VBIOS Version: 113-D20601MA0T-016
      Option ROM Version: 113-D20601MA0T-016
      EFI Driver Version: 01.01.087
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal: Supported, feature set macOS GPUFamily2 v1
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2880 x 1800 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          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: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.5.30
    cftime: 1.5.0
    chardet: 4.0.0
    charset-normalizer: 2.0.4
    ChimeraX-AddCharge: 1.1.4
    ChimeraX-AddH: 2.1.10
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.28.1
    ChimeraX-AtomicLibrary: 4.1
    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
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    ChimeraX-ChemGroup: 2.0
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    ChimeraX-ConnectStructure: 2.0
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    ChimeraX-Core: 1.3.dev202108070803
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    ChimeraX-Crystal: 1.0
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    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
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    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.2
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    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
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    ChimeraX-Label: 1.1
    ChimeraX-ListInfo: 1.1.1
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    ChimeraX-MapData: 2.0
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    ChimeraX-MapFit: 2.0
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    ChimeraX-MatchMaker: 2.0
    ChimeraX-MDcrds: 2.4
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
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    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.5.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.1
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    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0
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    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
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    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
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    ChimeraX-Toolbar: 1.1
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    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.11.1
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    ChimeraX-UnitCell: 1.0
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[Zach Pearson]

The blastprotein Qt GUI does not show the control panel if run from the command line. If this is acceptable behavior then this ticket is obsolete. If we want to show the control panel (the previous behavior in 1.2.5), then an easy mechanism exists to display the right parameters. Let me know!

[goddard@…]

In the old BLAST gui even when run from the command-line it puts a line of text above the table of results that says what the settings are.  Here is an example of what it shows

Results for: chain: #1/H, database: pdb, cutoff: 0.001, maxSeqs: 100, matrix: BLOSUM62

I would think that a separate results panel should have something similar that says what settings produced the results.  Otherwise if you have multiple results panels it may be easy to mix them up.  Probably the maxSeqs and matrix can be omitted as seldom used -- maybe they could be included only if they differ from the defaults.

[Zach Pearson]

OK, the query parameters are shown in the results window as of ​https://github.com/RBVI/ChimeraX/commit/bbfd6360eeed48af23fc9897f9c104bdc6d94451

Should be in tomorrow's build.