VMD-L Mailing List

From: Daniel Gaston (daniel.gaston_at_dal.ca)
Date: Mon Apr 20 2009 - 18:57:33 CDT

The gaps should be just what we expect, gaps in the sequence alignment
(that is implied by the structural alignment) due to indel events.
Presumably these proteins are from different organisms?

Dan

Karne, Sai Harish Babu wrote:
> Hi All,
>
> I am new to VMD, I am using the multiseq to plot the per residue RMSD
> plot for a bunch of proteins (same proteins but different pdb_id's).
> After I align the structures using the STAMP from tools option in
> Multiseq, I notice some gaps (represented by dashes in the multiseq
> window). Can anyone tell me what this gaps or dashes signify. I looked
> in the aquaporin and evolutionary tutorials but not much information
> about the gaps.
>
> Thanks in advance
> Harish.
>