Hi Sabuj,
There is no user interface way to do that (you'd have to get into code)... however, your question is quite timely, as there is a new plugin that provides a Rotamers-type interface to hundreds of nonstandard residues.  It also makes a new command "swapnaa" to access these residues via command line.

This SwissSidechain plugin is provided by the Molecular Modelling Group at SIB.  Information and download:
<http://ludwig-sun1.unil.ch/~dgfeller/SwissSidechain/chimera.html>

You can browse the SwissSidechain database to see if it includes your residue of interest:
<http://ludwig-sun1.unil.ch/~dgfeller/SwissSidechain/table.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 Dec 5, 2011, at 10:31 AM, Sabuj Pattanayek wrote:

Hi,

How do I add custom residues so that they're usable with swapaa or the

rotamer tool?

Thanks,

Sabuj

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