[chimerax-users] How to align two molecules using a subset of atoms in ChimeraX?

[Elaine Meng]

Hi Steve,
I couldn’t tell exactly without having those structures, but did you really mean chain B of model #2?  Your first command (the one that works) has chain A of both models.

However, if you are just trying to match exactly those atoms, use the “align” command, not matchmaker.  For example, something like

align #1/A:10-20 at ca to #2/A:10-20 at ca

<http://rbvi.ucsf.edu/chimerax/docs/user/commands/align.html>

Align uses the atoms you tell it to use and pairs them in order.  Matchmaker figures out the residue pairing automatically by making a sequence alignment… this is especially useful for aligning structures that happen to have different residue numbering, homologs with different sequence lengths, etc.  When if figures out the pairing, it automatically only uses CA atoms of each pair, so you wouldn’t need to give them in the command.

<http://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html>

So generally, one would just specify the whole chain and not give specific residues with “matchmaker” except to suppress using parts of the structure you want to exclude from the sequence alignment.  Nevertheless, the error message is unexpected so I will report it as a bug.

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

> On Feb 8, 2019, at 12:46 PM, Steve Chou <stevezchou at gmail.com> wrote:
> 
> Dear ChimeraX support team,
> I tried the following command first - it worked well.
> ==================
> match #1/A to #2/A
> ==================
> Then I tried to align the two molecules using parts of them - it didn't work and complained that "No chains in reference structure PROT.pdb #2 compatible with BLOSUM-62 similarity matrix."
> ==================
> matchmaker #1/A:10-20 at CA to #2/B:10-20 at CA
> ==================
> System Info:
> ==================
> Platform: Linux-3.10.0-862.el7.x86_64-x86_64-with-redhat-7.5-Maipo
> ChimeraX version: 0.9 (2019-02-05)
> ==================
> Thank a bunch!
> Steven
> 
> -- 
> Steve Chou
> 
> 
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