Hi Josh,
I guess you mean actually changing the 3D structure.  Yes, you can “swap” amino acids by replacing side chains with the Rotamers tool (menu: Tools.. Structure Editing… Rotamers) or the “swapaa” command.  This only does a simple replacement; it does not predict any large/overall changes in the structure.

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html>
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/rotamers/framerot.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/swapaa.html>

There is an example of using Rotamers in the Structure Analysis and Comparison tutorial.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.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 Jul 25, 2019, at 2:00 PM, Joshua Plank <jplan002@ucr.edu> wrote:
>
> Hi,
> I am wondering if it is possible to edit the amino acid sequence somehow? I have a .pdb file of the protein I'm interested in, but would like to change two of the amino acids to something else. Is this possible?
> thanks,
> Josh