VMD-L Mailing List

From: Ekta Khurana (ekta.khurana_at_yale.edu)
Date: Mon Feb 07 2011 - 23:33:00 CST

Hi John,

I have multiple groups (~ 100) with each group containing multiple pdbs
(hundreds). I want to do structural alignment
of pdbs within the same group and then print out Qres values for specific
residues of certain pdbs.
If I can do the same for sequence alignment too - that is do sequence
alignment of pdbs within each group and
print out sequence conservation of specific residues - that would be good.

Thanks a lot !
Ekta

On Mon, Feb 7, 2011 at 9:30 PM, John Stone <johns_at_ks.uiuc.edu> wrote:

>
> Hi,
> We are working on making the internal multiseq scripting
> interfaces available so that people can drive multiseq from
> within their own workflows, but this is an ongoing project and
> it isn't completed yet. If you could tell us what you want
> to do more specifically, we might be able to give you some tips
> on how to accomplish it within the versions of the Multiseq that are
> currently available. I'll ask my colleagues that develop
> Multiseq to chime in on this after you tell us exactly what
> you have in mind, and what kind of output or data you want
> for the results of your scripting.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Mon, Feb 07, 2011 at 02:11:57PM -0500, Ekta Khurana wrote:
> > Hi all,
> >
> > I would like to run Multiseq and STAMP structural alignment in text
> mode
> > so I can script it.
> > I could not find the commands for that in the user's guide.
> > Any help is appreciated.
> >
> > Thanks,
> > Ekta
>
> --
> 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
> 

-- 
Ekta Khurana, PhD
Yale University
Molecular Biophysics and Biochemistry Department
Bass 437, 266 Whitney Avenue
New Haven, CT 06520
Ph: 203-432-5405
Fax: 203-432-6946
Webpage:http://homes.gersteinlab.org/people/ekhurana/