Hi TJ,
Yes, you could use the Rotamers tool or the "swapaa" command to perform virtual mutations.

Rotamers (in menu under Tools... Structure Editing) will show multiple conformations of the chosen residue type, in this case, leucine, and lets you choose interactively which one should replace the existing residue, in this case serine.  You would first select the residue you want to change (Ctrl-click on some atom or bond in that residue). Details:
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/rotamers/framerot.html>
...there is also an example of using Rotamers in this tutorial:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html>

The swapaa command will automatically choose the conformation for you and perform the replacement.  Use menu: Favorites... Command Line to show the command line.  Details and examples:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/swapaa.html>

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 Nov 25, 2012, at 1:26 PM, Tijesunimi Odebode wrote:

> Hello all,
>
> I am new to Chimera and I am trying to change a serine in the sequence of my protein to a leucine. Is there a way of doing that in Chimera? Thanks in advance for the help.
>
> TJ