VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Jul 13 2006 - 16:53:32 CDT

Hi,
  I'd suggest having a read through the VMD tutorial so you learn the
most basic steps of scripting in VMD, and then crack open the VMD User's
Guide for a few specific examples of atom selections, and looping over
atom coordinates etc. (see the analysis examples section) From there,
you may also want to have a quick look through the VMD script library
and between those three source of info you should be all set.

  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Jul 13, 2006 at 05:39:59PM -0400, Gustavo Seabra wrote:
> Thanks John,
>
> I can see how to build the algorithm. However, I don;t have any
> experience coding for VMD. Could you tell me where I can read some
> material about it, so I can try to start coding that?
>
> Thanks,
>
> Gustavo.
>
> On 7/13/06, John Stone <johns_at_ks.uiuc.edu> wrote:
> >
> >Gustavo,
> > If you want an exact quantile then you'll have to calculate the distances
> >for the candidates your interested in, sort them, and select the N you care
> >about. In VMD you'd do something like:
> > 1) select all waters within the max cutoff distance M
> > 2) calculate the distance D of each water molecule and add the index and
> > distance to a list or lists
> > 3) sort the list(s) by the distance (keeping the water index and distance
> > assocation intact, if they are in separate lists..)
> > 4) select the closest N waters from the sorted list
> >
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> >On Thu, Jul 13, 2006 at 01:39:31PM -0400, Gustavo Seabra wrote:
> >> Hi,
> >>
> >> I have a system of a small peptide in explicit water. I know, for
> >> example, how to select all waters within a certain distance of the
> >> peptide.
> >>
> >> Now, what I'd like to do instead is to select the 'N' waters closest
> >> to the peptide. Is that possible? I looked into the VMD manual and
> >> couldn't find anything. Maybe some script?
> >>
> >> Thanks a lot!
> >>
> >> Gustavo.
> >
> >--
> >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 

-- 
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