VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Feb 02 2005 - 10:08:07 CST

Hi,
  VMD doesn't keep any internal list of dihedrals, it calculates them
on-the-fly as-needed, but doesn't store them otherwise. Thus, the only time
they exist is when you use label commands to measure them, and as you know,
VMD will let you measure anything you want, so really VMD is only providing
the means to evaluate arbitrary angles/dihedrals, not a specific indexed set.

  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Feb 01, 2005 at 10:47:38PM -0500, Paul R Brenner wrote:
>
> Thanks again for the reply Jan. I'm guessing the VMD authors decided to export
> only the atom indexs as they are the only items officially indexed in the pdb
> or psf. The only bookeeping required is to make sure you realize that VMD
> starts the atom indexing with zero. Providing indexs for the dihedrals based
> on the relational informatin in the psf is probably so less "standardized" that
> they felt such indices could easily lead to trouble when comunicated accross
> platforms.
>
> After reading your first response it dawned on me that with a little additional
> code I can use the atom indices to determine the backbone (or alpha helix, beta
> sheet, etc...) dihedrals within my MD software (I use Protomol).
>
> Regards,
> Paul
>
> Quoting Jan Saam <saam_at_charite.de>:
>
> > Paul,
> >
> > AFAIK, VMD keeps a list of dihedrals internally, but this list contains
> > all possible dihedrals, not only the protein backbone diheds. (Just like
> > the ones that are defined in the psf file.) Unfortunately, there is no
> > tcl procedure to access this info.
> >
> > Maybe this is a good feature request, I could use such a function, too.
> > John! Did you read this?
> >
> > If you just want the backbone diheds can build your own list by
> > selecting each resid in each segid and determine the dihedrals respectively.
> >
> > Jan
> >
> > Paul R Brenner wrote:
> > > Jan,
> > >
> > > Thanks for the reply. I am specifically interested in an index for the
> > dihedral
> > > itself (not an index of the atoms which make up the dihedral). I am hoping
> > that
> > > VMD has some way of indexing the dihedrals for a given set of atoms and can
> > > subsequently output them.
> > >
> > > Paul
> > >
> > > Quoting Jan Saam <saam_at_charite.de>:
> > >
> > >
> > >>Paul,
> > >>
> > >>I'm not sure, if I di understand you correctly, but I think the answer
> > >>is quite easy:
> > >>If you have an atomselection $sel then you can retrieve the indexes
> > >>either with
> > >>set myindexes [$sel list]
> > >>or
> > >>set myindexes [$sel get index]
> > >>
> > >>if you want them for a specific residue than you have to select
> > >>something like this:
> > >>
> > >>set psiindexes [atomselect top "protein and resid 5 and name N CA"]
> > >>set phiindexes [atomselect top "protein and resid 5 and name CA C"]
> > >>
> > >>Note that vmd outputs the indexxes in ascending order, not in the order
> > >>you typed the atom names. If you need to identify individual indexes
> > >>with atom names you have to select single atoms.
> > >>
> > >>Regards,
> > >> Jan
> > >>
> > >>Paul R Brenner wrote:
> > >>
> > >>>Is it possible to use VMD to output index information for the dihedrals of
> > >>
> > >>a
> > >>
> > >>>molecule. I see that I can use the get function within atomselect to get
> > >>
> > >>the
> > >>
> > >>>angle values (phi,psi) but what I am looking for is an index.
> > >>>
> > >>>(I then plan to align these indexes with those assigned by a molecular
> > >>
> > >>dynamics
> > >>
> > >>>program to selectively restrict their variation.)
> > >>>
> > >>>Thanks for any pointers,
> > >>>
> > >>>Paul R Brenner
> > >>>Graduate Research Associate
> > >>>Computer Science and Engineering
> > >>>The University of Notre Dame
> > >>>
> > >>>
> > >>>
> > >>>
> > >>>
> > >>>
> > >>>
> > >>
> > >
> > >
> > >
> > >
> >
> >
>
> 

-- 
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