VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Sat Apr 15 2006 - 17:17:16 CDT

Margaret,
  Are you trying to identify waters enclosed in internal cavities, or
are you looking for something waters near specific residues?

The latter case is simpler as you could do something like:
  water within 5 of (residue 5 6 7 38 49)

  John Stone
  vmd_at_ks.uiuc.edu

On Sat, Apr 15, 2006 at 05:54:25PM -0400, Margaret Shun Cheung wrote:
>
> Dear VMD wizards,
>
> I am struggling with the tcl syntax (VMD tkconsole).
> I'd like to select water molecules between two residues in a trajectory
> (eg 100 frames).
>
> The "within 5 of protein" seems to only select waters around proteins. But
> how could I identify water molecules that are enclosed between two or more
> residues?
> Thank you very much for your help!
> Sincerely,
>
> Margaret S. Cheung,
> Ph. D. Postdoctoral Fellow,
>
> ------------------------------------------------------------
> Room 2117 Tel: (301) 405-4892
> Inst. for Phys. Sci. & Tech. Fax: (301) 314-9404
> University of Maryland http://glue.umd.edu/~mscheung
> College Park, MD 20742-2431 email: mscheung_at_ipst.umd.edu
> ------------------------------------------------------------ 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078