VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Jan 23 2015 - 14:05:27 CST

On Fri, Jan 23, 2015 at 2:04 PM, Thomas C. Bishop <bishop_at_latech.edu> wrote:
> Dear VMD,
> I"m looking for a quick way to generate a list of atom pairs that are within
> a specified distance of each other.
> e.g find oxygen atoms that are within say 3A of each other.
>
> I thought I could use the within command
> set sel [atomselect top "within 3 of name O" ]
>
> This selects all atoms within the specified distance (in Å) from a
> selection,
> BUT ALSO INCLUDES THE SELECTION ITSELF.
>
> So the above sel includes ALL atoms named O b/c each oxygen is within 3 of
> itself :-)
>
> Maybe it's just Friday but I dont' see a simple solution here.
> This selection is being used to highlight various pairs associated with a
> radial distribution analysis.
>
> Any tips,tricks or solutions greatly appreciated.

you want to use "exwithin" instead of "within".

axel.

> Is it worthwhile to suggest a " -self" option be added to the within command
>
> Thanks in advance,
> Tom.
>
>
>
>
> --
> *******************************
> Thomas C. Bishop
> Tel: 318-257-5209
> Fax: 318-257-3823
> www.latech.edu/~bishop
> ******************************** 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.