VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Tue Jul 10 2007 - 08:49:38 CDT

On Tue, 10 Jul 2007, sally cii wrote:

sally,

if you want selections to select whole molecules/residues,
you have to prefix each of the subselections with 'same residue as (..)'
and then add the corresponding parentheses to ensure proper
logical precedence. if your gas molecule is small, i suggest to pick
a reference atom and then prefix the whole selection with 'same residue
as' this way you have a consistent selection criterion.

cheers,
   axel.

SC> Hi, Olaf,
SC>
SC> Thank you, I think that works OK. I still have a small question, the
SC> selection of (within r1 of name FE) and (not within r2 of name FE) should be
SC> the result of (within r1 of name FE) minus the result of (within r2 of name
SC> FE), right? However, some residue ID that existed in the result of (within
SC> r2 of name FE) still exist in the result using selection (within r1 of name
SC> FE) and (not within r2 of name FE). Is this happening because they are of
SC> exactly r2 distance with FE?
SC>
SC> Regards,
SC> Sally
SC>
SC> On 7/10/07, Olaf Lenz <olenz_at_fias.uni-frankfurt.de> wrote:
SC> >
SC> > -----BEGIN PGP SIGNED MESSAGE-----
SC> > Hash: SHA1
SC> >
SC> > Hi!
SC> >
SC> > The problem was wrong brackets. Try:
SC> > (within $r1 of name FE) and (not within $r2 of name FE)
SC> >
SC> > Olaf
SC> > -----BEGIN PGP SIGNATURE-----
SC> > Version: GnuPG v1.4.1 (GNU/Linux)
SC> > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org
SC> >
SC> > iD8DBQFGk2LOtQ3riQ3oo/oRAiMSAJ45hyG27AQT8mGfD+IVoQ5P7k4NnwCfWW4c
SC> > btepTvmBsgl93XLyR4+wVUM=
SC> > =M8xS
SC> > -----END PGP SIGNATURE-----
SC> >
SC> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
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If you make something idiot-proof, the universe creates a better idiot.