Blast protein should align loaded structures even when raw query sequence used

[goddard@…]

The following bug report has been submitted:
Platform:        macOS-14.4.1-arm64-arm-64bit
ChimeraX Version: 1.8.dev202404021803 (2024-04-02 18:03:23 UTC)
Description
Selecting two structures in the Blast protein results table and pressing Load Structures loads them but they are not aligned if the query sequences was given as a "raw sequence" instead of a reference PDB chain.  It would be useful it more than one structure is loaded if they were all aligned to the first structure.

This is especially important when a large number (100) of structures are loaded because it then become extremely tedious to try to align them afterwards using matchmaker because there is no way to automatically specify which chains of the 100 should be aligned.

Log:
UCSF ChimeraX version: 1.8.dev202404021803 (2024-04-02)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> ui tool show "Blast Protein"

> blastprotein
> MAALSGGGGGGAEPGQALFNGDMEPEAGAGAGAAASSAADPAIPEEVWNIKQMIKLTQEHIEALLDKFGGEHNPPSIYLEAYEEYTSKLDALQQREQQLLESLGNGTDFSVSSSASMDTVTSSSSSSLSVLPSSLSVFQNPTDVARSNPKSPQKPIVRVFLPNKQRTVVPARCGVTVRDSLKKALMMRGLIPECCAVYRIQDGEKKPIGWDTDISWLTGEELHVEVLENVPLTTHNFVRKTFFTLAFCDFCRKLLFQGFRCQTCGYKFHQRCSTEVPLMCVNYDQLDLLFVSKFFEHHPIPQEEASLAETALTSGSSPSAPASDSIGPQILTSPSPSKSIPIPQPFRPADEDHRNQFGQRDRSSSAPNVHINTIEPVNIDDLIRDQGFRGDGGSTTGLSATPPASLPGSLTNVKALQKSPGPQRERKSSSSSEDRNRMKTLGRRDSSDDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDVAVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHHLHIIETKFEMIKLIDIARQTAQGMDYLHAKSIIHRDLKSNNIFLHEDLTVKIGDFGLATVKSRWSGSHQFEQLSGSILWMAPEVIRMQDKNPYSFQSDVYAFGIVLYELMTGQLPYSNINNRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARSLPKIHRSASEPSLNRAGFQTEDFSLYACASPKTPIQAGGYGAFPVH
> database pdb cutoff 1e-100 matrix BLOSUM62 maxSeqs 100 version None name bp1

Webservices job id: Q8ER60WIBDKA8OQD  

> open pdb:6Q0K

6q0k title:  
Structure of a MAPK pathway complex [more info...]  
  
Chain information for 6q0k #1  
---  
Chain | Description | UniProt  
A B | Serine/threonine-protein kinase B-raf | BRAF_HUMAN 1-766  
X Y | 14-3-3 protein zeta/delta | 1433Z_HUMAN 1-245  
  

> select clear

> open pdb:7MFD

Summary of feedback from opening 7MFD fetched from pdb  
---  
warning | Atom NZ has no neighbors to form bonds with according to residue template for LYS /D:103  
  
7mfd title:  
Autoinhibited BRAF:(14-3-3)2:MEK complex with the BRAF RBD resolved [more
info...]  
  
Chain information for 7mfd #2  
---  
Chain | Description | UniProt  
A | Serine/threonine-protein kinase B-raf | BRAF_HUMAN 1-766  
B | Dual specificity mitogen-activated protein kinase kinase 1 | MP2K1_HUMAN 1-393  
C D | 14-3-3 protein zeta/delta | 1433Z_HUMAN 1-245  
  
Non-standard residues in 7mfd #2  
---  
CHU —
N-(3-fluoro-4-{[4-methyl-2-oxo-7-(pyrimidin-2-yloxy)-2H-chromen-3-yl]methyl}pyridin-2-yl)-N'-methylsulfuric
diamide (CH5126766)  
ZN — zinc ion  
  

> select clear

Already setting window visible!  




OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M2 Ultra
OpenGL vendor: Apple

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: Mac Studio
      Model Identifier: Mac14,14
      Model Number: Z1800003VLL/A
      Chip: Apple M2 Ultra
      Total Number of Cores: 24 (16 performance and 8 efficiency)
      Memory: 64 GB
      System Firmware Version: 10151.101.3
      OS Loader Version: 10151.101.3

Software:

    System Software Overview:

      System Version: macOS 14.4.1 (23E224)
      Kernel Version: Darwin 23.4.0
      Time since boot: 2 days, 12 hours, 48 minutes

Graphics/Displays:

    Apple M2 Ultra:

      Chipset Model: Apple M2 Ultra
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 60
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        PHL 278B1:
          Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported


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