VMD-L Mailing List

From: Richard Swenson (swenson_at_hec.utah.edu)
Date: Tue Jun 12 2007 - 15:23:31 CDT

Thanks John,

I implemented a similar algorithm to what you proposed and it seems to work
well enough.

Richard

On 6/12/07, John Stone <johns_at_ks.uiuc.edu> wrote:
>
>
> Richard,
> Probably the easiest way to implement this currently would be to
> use the "within" selection to search by increasing radius. We don't
> have anything like the "nearest" command you suggest presently, but the
> returning a specified quantile from the full set can be implemented by
> looping over an increasing radius r until you get a non-empty selection
> result, at which point you can simply loop over the selected candidates
> and pick the members of the quantile you're interested in (in this case
> 1).
> If people would find this sort of thing very useful, it would be pretty
> easy
> to implement it as a new "measure" command, but that only makes sense if
> enough people would use it.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Mon, Jun 11, 2007 at 09:23:57AM -0600, Richard Swenson wrote:
> > Hi All,
> >
> > I am wondering if anyone knows of an efficient way to select the closest
> > atom of a given type to a reference atom. Something like this would be
> > great:
> >
> > atomselect top "name P and nearest index 4000"
> >
> > where the keyword nearest selects the phosphorus atom (P) closest to the
> > atom with the index 4000.
> >
> > Thanks for you help,
> > Richard
>
> --
> 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
>