VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Mon May 11 2009 - 13:11:50 CDT

On Mon, 2009-05-11 at 13:35 -0400, Mark M Huntress wrote:

> I am trying to select waters near my protein, so my selection is
> "within 3.8 of protein" but this gives me many water atoms (lone H's
> and lone O's) that don't include the whole molecule, because the other
> atoms are outside of the 3.8 Å cutoff range. Is there a way I can
> select the whole water molecules and not extra atoms? I need to save a
> file that is realistic.

mark,

you get whole molecules if you change the selection text
to "same residue as (...)" and put your old text with the
ellipsis is.

cheers,
   axel.

> Thanks,
> Mark 

-- 
=======================================================================
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.