From: Axel Kohlmeyer (
Date: Fri Aug 04 2006 - 07:01:53 CDT

On Fri, 4 Aug 2006, andrea spitaleri wrote:

AS> Hi all,
AS> quick and I guess easy question:
AS> I have a cubic box of water+protein and I'd like to visualize the protein and water molecules lying
AS> on the edge of the box. That what I did:
AS> set pro [atomselect 0 "protein"]
AS> set edge [atomselect 0 "water and not (water within 10 of protein)"]

you can try using 'same residue and (water...)', so you always get
complete water molecules.

AS> Is it correct or there is a quickest way?. And then what about for a triclinic and octahedron box?
AS> How do I set the different cutoff long the xyz directions?

you can also build selections based on x-, y- and z-coordinates.
e.g. 'same residue as (name OW and x > 0.0 and x < 2.0)'


AS> Thanks in advance
AS> Regards
AS> andrea

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.