From: Axel Kohlmeyer (
Date: Fri Aug 10 2012 - 02:08:02 CDT

On Thu, Aug 9, 2012 at 6:22 PM, Nate Hurley <> wrote:
> Hi all,
> I have two .pdb files. One has, in part, several molecular probes in
> various locations (on a protein). The other has a single molecule docked to
> that protein. I have a script that selects probes in the first .pdb. Is
> there a way that I can exclude probes that are within X of the molecule in
> the other .pdb? If VMD saw them each as being part of the same molecule it
> would be easy, but it would be best if I could do this without concatenating
> the two files. Is there a way to do this?


> Thanks!
> -Nate Hurley

Dr. Axel Kohlmeyer
International Centre for Theoretical Physics, Trieste. Italy.