[chimerax-users] Residue priority for Matchmaker alignment?

[Elaine Meng]

Hi Steven,
If you want only part of the chain to be considered at all (which does not affect the alignment matrices, but simply ignores the rest of the chain) see the Matchmaker "also restrict to selection" option in the Chain Pairing section.
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/matchmaker.html#pairing>

Or, if you're using the matchmaker command, you would specify the residue ranges to use, see the paragraph right above the "Options" section.
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html>

Example: mm #2/A:1-100 to #1/A:85-150

Or, if you want to explicitly specify which atoms to least-squares fit between two structures, then use the "align" command instead of matchmaker, but then you have to be very careful to specify the same numbers of atoms in the two structures:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/align.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Nov 4, 2021, at 5:11 AM, Steven Truong via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Dear ChimeraX Admins,
> 
> I have a question about the Matchmaker (mmaker) command.  If I wanted to specify which residues to prioritize in the alignment, how would I specify that in the command line?  Is there a way to do this without changing the alignment algorithm/scoring matrix?  I have tried tinkering with the matrix but wasn’t able to get it to work.  I see that you can specify which chains to align, but I can’t seem to find the equivalent for residue ID numbers.
> 
> Thank you for your help,
> Steven Truong
> Vendruscolo Lab
> Cambridge University
> 
>  <Screen Shot 2021-11-04 at 12.07.36 PM.png>
> -users