VMD-L Mailing List

From: Shyno Mathew (sm3334_at_columbia.edu)
Date: Fri Apr 15 2016 - 14:49:45 CDT

Dear all,

I am using Multiseq for the first time. Here is the N-terminal portion of
the aligned proteins:

protein1: M P S . . E K T
protein2: . . . M K W . M

The dots after third residue in protein 1 means there are no aligned
residues at these positions. Since multiseq is considering only the alpha
carbons, it's not breaking the bonds between residues 3, 4 (Ser, Glu) in
protein 1, just want to confirm?

Also, I want to get the structure alignment of the protein throughout the
simulation with another protein. I understand I could do this by stand
alone version of STAMP. Since Multiseq uses a modified version of STAMP, I
prefer using Multiseq in text mode. I see a discussion from 2011 about
Multiseq in text mode, have things changed since?
Any suggestions regarding this or do you recommend another software?

thanks,
Shyno

On Wed, Apr 13, 2016 at 9:26 PM, Shyno Mathew <sm3334_at_columbia.edu> wrote:

> Dear all,
>
> I am trying to compare two proteins using Multiseq. Everything works ok
> for the sequence alignment. However, for the structural alignment using
> STAMP, I am not getting the QH values when highlighting the proteins as
> mentioned here in step 11.
>
> http://www.ks.uiuc.edu/Training/Tutorials/vmd/tutorial-html/node6.html
>
> While trying to color the protein according to structural identity, I am
> getting an error! Also, I see a discussion about similar error concluding
> there is a bug with Qres portion of multiseq. I am using vmd 1.9.2
> Is this bug fixed in the recent versions of vmd?
>
> http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/23627.html
>
>
> thanks,
> Shyno
>
> --
> Shyno Mathew
> PhD Candidate
> Department of Chemical Engineering
> Graduate Assistant
> Office of Graduate Student Affairs
> The Fu Foundation School Of Engineering and Applied Science
> Columbia University
> 

-- 
Shyno Mathew
PhD Candidate
Department of Chemical Engineering
Graduate Assistant
Office of Graduate Student Affairs
The Fu Foundation School Of Engineering and Applied Science
Columbia University