From: Ana Celia Vila Verde (
Date: Fri Aug 10 2012 - 02:23:27 CDT

Dear Nate,

As far as I know, there's no way to do what you want from VMD's
graphical interface. It should be fairly straightforward to do it using
a tcl script going something like:
- load molecule 1 and 2 into pdb
- get distance of probe1 to the relevant atoms of molecule 2. This is
obviously the tricky step because you will need to decide which is the
relevant distance (e.g. distance to the center of mass of molecule 2, or
minimum distance to any atom of molecule 2, etc...)
-if {$distance < $referenceDistance} {
   select probe in molecule 1

I hope this points you in the right direction

On 8/9/12 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