VMD-L Mailing List

From: Gustavo Seabra (gustavo.seabra_at_gmail.com)
Date: Thu Jul 13 2006 - 16:59:58 CDT

Thanks!

Gustavo.

On 7/13/06, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> 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