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

[Steve Chou]

Hi Elaine,
Thanks for your prompt response! You're right.
====================================
match #1/A at CA:10-20 to #2/B at CA:10-20
====================================
match #1/A at CA:10-30 to #2/B at CA:10-30
====================================
The above two gave the same result, because it used the same atoms for the
alignment.
But the following order ("@CA goes after :10-337) does not work for 'match'.
===================================
match #1/A:10-20 at CA to #2/B:10-20 at CA
===================================
The order ("@CA goes after :10-337) works for 'align'.
===================================
align #1/A:10-20 at CA to #2/B:10-20 at CA
===================================
All the best,
Steve

On Fri, Feb 8, 2019 at 4:07 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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)
> > ==================
> > Thanks a bunch!
> > Steve
> >
> > --
> > Steve Chou
> >
> >
> > _______________________________________________
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>
>

-- 
Steve Chou
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