VMD-L Mailing List

From: Leonardo Trabuco (ltrabuco_at_ks.uiuc.edu)
Date: Tue Feb 08 2011 - 08:18:44 CST

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
>> >>  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/
> 

-- 
Leonardo Trabuco, Postdoctoral fellow (Russell group)
CellNetworks, University of Heidelberg, Germany
http://www.russelllab.org/people/leo/