Dear Dr. Scoville,
(I changed the subject line because “question” is not useful to people searching for a topic)

You can build peptides, but it will not do conformational analysis for you.  I.e. you would get “a” shape but Chimera wouldn’t automatically figure out the range of possible shapes (since peptides are quite flexible) or which shapes would predominate.

Besides peptide building, there is general structural analysis: you can rotate bonds, measure distances, show molecular surface, measure surface area and enclosed volume, etc.  There is a full user manual with tutorials,
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/index.html>
<http://www.rbvi.ucsf.edu/Outreach/Tutorials/GettingStarted.html>
...and you can search for terms of interest with the menu: Help… Search Documentation. 

Chimera is free for noncommercial use.  For commercial use, contact chimera@cgl.ucsf.edu
Licensing:
<http://www.rbvi.ucsf.edu/chimera/docs/licensing.html>

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