VMD-L Mailing List

From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Tue Feb 08 2011 - 03:43:39 CST

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/
>