Foldseek ligands does not dock all altlocs to query

[goddard@…]

The following bug report has been submitted:
Platform:        macOS-14.5-arm64-arm-64bit
ChimeraX Version: 1.9.dev202407240247 (2024-07-24 02:47:28 UTC)
Description
The foldseek ligands command only repositions the current ligand altloc to align to the query leaving other altlocs at their original position in the hit structures.  The easiest way to handle this is probably to remove any extra altlocs with residue.clean_alt_locs().

Log:
UCSF ChimeraX version: 1.9.dev202407240247 (2024-07-24)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/goddard/Downloads/ChimeraX/Foldseek/8jnb_B/pdb100.m8 format
> foldseek

Summary of feedback from opening
/Users/goddard/Downloads/ChimeraX/Foldseek/8jnb_B/pdb100.m8  
---  
notes | 8jnb.pdb title:  
Craf ras-binding domain chimera, ligand complex [more info...]  
  
  
  
  
| Chain information for 8jnb.pdb #1  
  
---  
  
  
Chain  
| Description  
| UniProt  
  
  
  
  
  
B  
| raf proto-oncogene serine/threonine-protein kinase, craf  
| RAF1_HUMAN 50-101 114-141, BRAF_HUMAN 102-113  
  
  
  
  
  
  
  
Non-standard residues in 8jnb.pdb #1  
  
---  
  
  
  
  
USX — 2-[4-[[(2S)-1-ethanoyl-3-oxidanylidene-2H-indol-2-yl]methyl]-2-methoxy-
phenoxy]ethanamide  
  
  
  
  
3 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
Foldseek search for similar structures to /B in pdb100 found 845 hits  
  

> foldseek ligands

Found 4 ligands in 1 hits: CBY, HOH, NAG  




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[Tom Goddard]

Fixed.

I made foldseek ligands keep only one altloc for each ligand (the default one after opening the structure).