VMD-L Mailing List

From: Leonardo Trabuco (ltrabuco_at_ks.uiuc.edu)
Date: Fri Nov 03 2006 - 14:17:55 CST

On Fri, Nov 03, 2006 at 09:44:20PM +0530, Sunita Patel wrote:
> How to align two peptide molecules containing different atoms using vmd?

To align protein or nucleic acid molecules with different number of
atoms, you can use the structural alignment tool of the MultiSeq plugin.
Open the plugin via Extensions->Analysis->MultiSeq, and then click on
Tools->Stamp Structural Alignment.

Of course, if you have exactly the same structure, you can use the
measure fit and move commands instead.

Best,
Leo 

-- 
Leonardo Trabuco, Ph.D. student
Theoretical and Computational Biophysics Group
University of Illinois at Urbana-Champaign