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@ca #0:212-243@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