VMD-L Mailing List

From: Ekta Khurana (ekta.khurana_at_yale.edu)
Date: Tue Feb 08 2011 - 08:06:16 CST

Hi Jerome,

yes that is true and sequence alignment is not the biggest concern since it
can be done
in another way. I am more interested in using Multiseq for structural
alignment - I did not explore
other structural alignment tools much yet but they will likely do the job as
well.

Ekta

On Tue, Feb 8, 2011 at 4:43 AM, Jérôme Hénin <jhenin_at_ifr88.cnrs-mrs.fr>wrote:

> Hi Ekta,
>
> Maybe you have specific reasons to want to use Multiseq, but in this
> case, wouldn't it be easier to build your toolchain directly out of
> command-line structure and sequence alignment programs?
>
> Cheers,
> Jerome
>
>
> On 8 February 2011 06:33, Ekta Khurana <ekta.khurana_at_yale.edu> wrote:
> > 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/
> >
> 

-- 
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/