VMD-L Mailing List

From: Kirby Vandivort (kvandivo_at_ks.uiuc.edu)
Date: Tue Feb 08 2011 - 11:49:43 CST

Ekta,

Sorry for not responding earlier. I've been swamped with other things. As John
has mentioned, we are working to get MultiSeq fully scriptable. There are
definitely places where we haven't yet achieved that, but we ultimately want you
to be able to script it as thoroughly as you would anything else in VMD. Having
STAMP already included within MultiSeq, as well as other VMD features, does tend
to make it desirable to do this in many instances.

There are a couple of things that I would like to point you to.

There is a tutorial written that has examples of MultiSeq scripting in it:

http://www.ks.uiuc.edu/Training/Tutorials/#eteftu

It isn't going to be a script that does precisely what you want, but you can
hopefully take the TCL code and get a good idea of how to proceed. Particularly
with setting up the MultiSeq environment, etc. I've taken a look at the
genomeContext.tcl file and it looks like it should help.

If you can load each group of PDBs into VMD and operate on all of the PDBs
(instead of having the multiple groups loaded at the same time) that will also
serve to simplify things.

Beyond that, you will need to decompose several of the existing TCL procedures
to accomplish your goals. If you look at the multiseq.tcl file, there is a
procedure called 'menu_stamp'. If you are wanting to script this procedure, you
will want to use the contents of the procedure after the
[Stamp::showStampOptionsDialog $w] call. The array options stored in $options
are what you will need to fill in within your script. [I fully understand this
is something that could be simplified in future versions of the code to make it
more script-friendly]

Sequence Alignment will work similarly. There's a procedure in multiseq.tcl
called 'menu_seqAlign'.

This will hopefully be enough to get you moving in the right direction. Leo's
suggestion of having something like 'measure stamp' would be another interesting
direction to go. We'll add that one to our list.

Kirby

Ekta Khurana 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
> <mailto: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 <mailto: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 <mailto:johns_at_ks.uiuc.edu>
> Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/
> <http://www.ks.uiuc.edu/%7Ejohns/> 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/ 

-- 
Kirby Vandivort                      Theoretical and
Senior Research Programmer            Computational Biophysics
Email: kvandivo_at_ks.uiuc.edu          3061 Beckman Institute
http://www.ks.uiuc.edu/~kvandivo/    University of Illinois
Phone: (217) 244-1928                405 N. Mathews Ave
Fax  : (217) 244-6078                Urbana, IL  61801, USA