VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
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)'

ciao,
   axel.

AS> Thanks in advance
AS>
AS> Regards
AS>
AS> andrea
AS> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   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
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If you make something idiot-proof, the universe creates a better idiot.