From: Ekta Khurana (ekta.khurana_at_yale.edu)
Date: Wed Feb 09 2011 - 13:23:19 CST

Thank you all for the replies.
As discussed, in the short term it seems it might be easier to use stand
alone version of STAMP - although it seems the calculation of Qres was also
added in Multiseq and STAMP does not do that (so I need to compute those
values after STAMP alignment).
In the long term it will be nice to be able to do it with Multiseq - eg
labelling the residues by Qres and other options are really nice !

Best,
Ekta

On Tue, Feb 8, 2011 at 1:11 PM, Anurag Sethi <anurag.sethi_at_gmail.com> wrote:

> 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/
>>
>>
>

-- 
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/