VMD-L Mailing List

From: Karne, Sai Harish Babu (saikarne_at_iupui.edu)
Date: Mon Apr 20 2009 - 21:04:53 CDT

Hi Daniel,

Thanks for the reply.

Harish.

Quoting Daniel Gaston <daniel.gaston_at_dal.ca>:

> 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.
>>
>