VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Nov 16 2009 - 15:28:45 CST

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
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