[Chimera-users] Align two structures

[Elaine Meng]

Hi Catherine,
If you just give the model number it specifies the all the atoms in the model,for example: 
match #1 #0

However, in most cases this will not work because the two models don't have exactly the same numbers of atoms in exactly the same order for proper pairing.

Instead you probably want to use the matchmaker command, which will try to figure out the residue pairing for you automatically.  It just uses the alpha-carbons (1 atom per residue).  Example:

matchmaker #0 #1

...there are lots of possible options of this command, see
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html>

See aso the discussion of different ways to superimpose structures, and links therein:
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.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 Mar 31, 2022, at 10:16 AM, Catherine Jenifer Rajam Rajendran via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Hi,
> 
> I'm trying to use the "match" command to align two protein pdb structures. Instead of specifying which chains or atoms or residues to align, Is there a way to align the whole structure from the command line?
> 
> Thanks,
> Catherine