From: Ivan Gregoretti (
Date: Fri Mar 28 2014 - 16:57:16 CDT

Yes, there is, with one of VMD's plugins.


Elijah Roberts, John Eargle, Dan Wright, and Zaida Luthey-Schulten.
MultiSeq: Unifying sequence and structure data for evolutionary analysis.
BMC Bioinformatics, 2006, 7:382.

The user guide shows you how to use via a graphical user interface. It
may be difficult to run at the command line but I would be delighted
to be proved wrong by somebody in the list.



Ivan Gregoretti, PhD

On Fri, Mar 28, 2014 at 4:37 PM, Hailin Huang <> wrote:
> Dear Users,
> Is there a way I can align two protein structures at specific residues that are numbered differently? For example, how do I align residues 20-80 in structure A with residues 100-160 in structure B?
> Thanks,
> Hailin Huang