[Chimera-users] Homology Modeling

Elaine Meng meng at cgl.ucsf.edu
Thu Jan 17 11:13:25 PST 2013


Hi CE,
I guess this question is about alignment in 3D (superposition), not about homology modeling.

Chimera includes several different ways of superimposing structures or their parts, as outlined here:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/superposition.html>

I'm not sure of your exact situation, but it sounds like you may want to use the "match" command, for example:

match #1:482-513.A at ca #0:212-243 at ca

(superimpose model 1 residues 482-513 of chain A onto model 0 residues 212-243, using only atoms named CA)

Atom specification syntax is described here:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html>

If I misunderstood what you are doing, however, take a look at the first link above to see if one of the other methods might do what you want.

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

On Jan 17, 2013, at 10:55 AM, Chinaza Egbuta wrote:

> I have a protein with multiple modules that are homologous to each other.  I have generated a homology model of one module based on the structure of another.  However, I need to align a specific peptide that is identical between my two modules.  Is there a way to do this?
> 
> Thank you.
> 
> CE




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