VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Apr 05 2005 - 18:46:30 CDT

I don't have an easy answer for this one. You might find it easier
to identify those waters in some other way and use an atom selection
macro when you want to display them. You can certainly do a "within"
selection combined with some other qualifying selection to narrow it
down to a particular set of waters. I suspect that the interior waters
might coincidentally have sequential (or nearly so) atom indices, so
that might be an easy way to go.
  
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Mar 31, 2005 at 10:16:47AM +1000, Swarna Patra wrote:
> Hi,
> I want to find out waters within the the protein....I saw the example using
> within 2/3 of protein ..which gives water inside and outside of protein i.e
> near protein....I am interested only inside the protein....If anyone knows
> the script pl help me.
> regards
> swarna 

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NIH Resource for Macromolecular Modeling and Bioinformatics
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