similarstructures fromblast cmd claims there are no Blast Protein results when I had 2 sets

[Elaine Meng]

The following bug report has been submitted:
Platform:        macOS-14.7-arm64-arm-64bit
ChimeraX Version: 1.9.dev202410260116 (2024-10-26 01:16:29 UTC)
Description
I did two blastprotein searches to test "similarstructures fromblast" i.e. what would happen if I had two sets of results (bp1 and bp2), and it gave me an error saying there weren't any Blast Protein results.

Log:
> open /Users/meng/Desktop/startup.cxc

> alias reset view orient; view initial

> alias start tool show $1

> alias whereprefs info path user unversioned config

> alias captut open help:user/tutorials/binding-sites.html#cap-example

> alias previewts toolshed url https://cxtoolshed-
> preview.rbvi.ucsf.edu;toolshed reload available

> alias normalts toolshed url https://cxtoolshed.rbvi.ucsf.edu;toolshed reload
> available

> alias btut open
> https://www.cgl.ucsf.edu/home/meng/chimerax/vdocs/user/tutorials/binding-
> sites.html; ui dockable false "Help Viewer"

> alias stut open https://www.rbvi.ucsf.edu/chimerax/data/conservation-
> coloring/conservation-coloring.html; ui dockable false "Help Viewer"

> alias ltut open https://www.rbvi.ucsf.edu/chimerax/data/loop-modeling/loop-
> modeling.html; ui dockable false "Help Viewer"

> alias mtut open https://www.rbvi.ucsf.edu/chimerax/data/mole-channel/mole-
> channel.html; ui dockable false "Help Viewer"; windowsize 600 800

executed startup.cxc  
UCSF ChimeraX version: 1.9.dev202410260116 (2024-10-26)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  
Unable to load numpy_formathandler accelerator from OpenGL_accelerate  

> open /Users/meng/Desktop/keep/1hxz_foldseek_pdb.sms format sms

Summary of feedback from opening
/Users/meng/Desktop/keep/1hxz_foldseek_pdb.sms  
---  
notes | > open /Users/meng/Downloads/ChimeraX/PDB/1hxz.cif1hxz.cif title:  
Miniprotein MP-2 complex with streptavidin [more info...]  
  
  
  
  
| Chain information for 1hxz.cif #1  
  
---  
  
  
Chain  
| Description  
| UniProt  
  
  
  
  
  
A B  
| STREPTAVIDIN  
| SAV_STRAV 11-139  
  
  
  
C D  
| MP-2  
|  
  
  
  
  
  
1hxz.cif mmCIF Assemblies  
  
---  
1| author_and_software_defined_assembly  
  
  
Found 14 similar structures to 1hxz.cif #1/D in pdb database using foldseek,
name fs1  
  
Read 14 similar structures to 1hxz.cif #1/D in pdb database using foldseek,
name fs1  

> blastprotein /D

Webservices job id: EPYDL1AEJZQAASJT  

> blastprotein /A

Webservices job id: K14UDC803WK5MO0S  

> keep

Invalid "save" argument: Expected true or false (or 1 or 0)  

> similarstructures fromblast save true saveDirectory keep

No BLAST search has been done  




OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,1
      Model Number: MK1F3LL/A
      Chip: Apple M1 Pro
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 16 GB
      System Firmware Version: 11881.1.1
      OS Loader Version: 10151.140.19.700.2

Software:

    System Software Overview:

      System Version: macOS 14.7 (23H124)
      Kernel Version: Darwin 23.6.0
      Time since boot: 8 hours, 52 minutes

Graphics/Displays:

    Apple M1 Pro:

      Chipset Model: Apple M1 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 16
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      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: Yes
          Connection Type: Internal


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[Elaine Meng]

Seems to work OK if I close one set and try again. Prioritize as desired, most people only have one set at a time. They do have names, however, that could be referred to (bp1, bp2 ...)

[Tom Goddard]

Yep, the current code decides if there are multiple blast results open it won't use either because it doesn't currently provide a way to name the results. I could add an option to name the blast results.

[Tom Goddard]

Fixed.

I added an optional first argument to the "similarstructures fromblast" command that lists the blast results instance name as given in the title bar of the blast results, eg. "sim fromblast bp1".