VMD-L Mailing List

From: Ivan Gregoretti (ivangreg_at_gmail.com)
Date: Fri Mar 28 2014 - 16:57:16 CDT

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

Multiseq
https://www-s.ks.uiuc.edu/Research/vmd/plugins/multiseq/

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.

Cheers,

Ivan

Ivan Gregoretti, PhD
Bioinformatics

On Fri, Mar 28, 2014 at 4:37 PM, Hailin Huang <hailin.huang_at_my.liu.edu> 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