From: Boris Steipe (boris.steipe_at_utoronto.ca)
Date: Mon Nov 23 2009 - 09:48:34 CST

So you are looking for a sequence alignment based on a structure
superposition?

That's a bit of an ill-posed question. Imagine that your
superposition places a residue in the middle between two residues of
another structure? How would you define which one of them it is to be
aligned with? If you think you can just choose whatever is the
closest residue, what happens if more than one residue map onto one
other? ...

What you have in principle is a clustering problem where you need to
ensure that each cluster contains exactly one and only one residue
from each structure and the cluster metric is rmsd within the cluster.

That said - since RMSD transformations are (usually) calculated from
paired coordinate sets, it should be possible to get the information
about which pairs were used from the original superposition
algorithm. I.e. you would be better off not to try to recover the
information from the result, but getting it from the procedure. Many
superposition algorithms I have seen output that information somewhere.

HTH,
Boris

PS: would the STAMP superposition even be significantly different
from your original one?

On 23-Nov-09, at 6:43 AM, Tomek Wlodarski wrote:

> 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/ Fax: 217-244-6078
>