VMD-L Mailing List

From: Anurag Sethi (anurag.sethi_at_gmail.com)
Date: Tue Feb 08 2011 - 12:11:29 CST

Ekta,

You can use the stand alone version of STAMP as Leonardo pointed out.
However, I would like to point out that Zan Schulten's post doc John Eargle
has made some changes to the version of STAMP in Multiseq(which may not even
be published/documented if I am right). So, the alignments you get from the
standalone version might be different from the version you get from within
Multiseq. However, I can provide example files for using standalon/multiseq
version of STAMP if required. I have not touched them for years and will
have to test them again though.

Anurag

On Tue, Feb 8, 2011 at 07:18, Leonardo Trabuco <ltrabuco_at_ks.uiuc.edu> wrote:

> Hi Ekta,
>
> As you know, MultiSeq uses STAMP for structural alignment
> (http://www.compbio.dundee.ac.uk/manuals/stamp.4.2/). In the short
> term, you might be better off learning how to use STAMP from the
> command-line and build your own workflow. But I always thought it
> would be really sweet to have a 'measure stamp' command in VMD that
> works in a similar way as 'measure fit'.
>
> Cheers,
> Leo
>
> On Tue, Feb 8, 2011 at 3:06 PM, Ekta Khurana <ekta.khurana_at_yale.edu>
> wrote:
> > 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<+12172443349>
> >> >> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078<+12172446078>
> >> >
> >> >
> >> >
> >> > --
> >> > Ekta Khurana, PhD
> >> > Yale University
> >> > Molecular Biophysics and Biochemistry Department
> >> > Bass 437, 266 Whitney Avenue
> >> > New Haven, CT 06520
> >> > Ph: 203-432-5405 <+12034325405>
> >> > Fax: 203-432-6946 <+12034326946>
> >> > 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 <+12034325405>
> > Fax: 203-432-6946 <+12034326946>
> > Webpage:http://homes.gersteinlab.org/people/ekhurana/
> >
>
>
>
> --
> Leonardo Trabuco, Postdoctoral fellow (Russell group)
> CellNetworks, University of Heidelberg, Germany
> http://www.russelllab.org/people/leo/
>
>