[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:

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:

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 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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