VMD-L Mailing List

From: Tomek Wlodarski (tomek.wlodarski_at_gmail.com)
Date: Mon Nov 23 2009 - 05:43:14 CST

Dear John,

Thanks for reply!
Maybe I was not precise in my question...
Let say I have 10 structures opened with VMD, and they are already
structurally aligned by some other software. Now I am starting this Multiseq
plugin and I get multiseq window with sequences and I would like to have
those sequences aligned in such way that they resemble alignment of
structures. This alignment of sequences I can obtained after Stamp.
Can I obtained structure based sequence alignment without starting Stamp?
Just based on already superimposed structures?
Thanks!
Best

tomek

On Mon, Nov 16, 2009 at 10:28 PM, John Stone <johns_at_ks.uiuc.edu> wrote:

>
> Hi,
> I'm puzzled by your question. I believe if if you do just
> a sequence alignment, the alignment of the structures should have
> no impact on the results. Even if STAMP realigned the structures,
> the sequence alignment part of the result should be completely
> independent of the structure alignment.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Sat, Nov 14, 2009 at 03:02:43PM +0100, Tomek Wlodarski wrote:
> > Dear all,
> >
> > I have structures structurally aligned by other program than STAMP.
> > It is possible that when I will import all of the structures into VMD,
> > Multiseq plugin would generate sequence alignment based on how
> structures
> > are aligned?
> > Thanks for any suggestions and ideas!
> > Best!
> >
> > tomek
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ <http://www.ks.uiuc.edu/%7Ejohns/>
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>