VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Sun Nov 25 2007 - 12:49:29 CST

On Sun, 25 Nov 2007, aneesh cna wrote:

AC> hi Peter,
AC> Thank you for kind reply.Actually I want to calculate the surface
AC> hydrophobicity of a protein.

aneesh,

i don't think this is helping much.
could you please explain you mean by
"calculate the surface hydrophobicity"?

i.e.:
do you want to visualize which part of
the surface is hydrophobic?
or:
do you want to get some parameter showing
what fraction of the surface is hydrophobic?
or:
do you want to compute some "total hydrophobicity"
of your protein? in this case, you'd have to
specify, how you want to measure it.

can you give us an example, a program, or a paper
that does already what you want to do?

cheers,
   axel.

AC>
AC> with regadrs
AC> Aneesh
AC>
AC>
AC> On Nov 24, 2007 8:06 PM, Peter Freddolino <petefred_at_ks.uiuc.edu> wrote:
AC> > Hi Aneesh,
AC> > if you could be more specific about what you mean by "a hydrophobicity
AC> > plot" we may be able to help; there are multiple definitions I can think
AC> > of for what you may be looking for.
AC> > Best,
AC> > Peter
AC> >
AC> >
AC> > aneesh cna wrote:
AC> > > hello vmd users,
AC> > > I would like to know whether there is any way to get a
AC> > > hydrophobicity plot for a protein (with more than 200) residues using
AC> > > VMD.
AC> > >
AC> > > with regards
AC> > > Aneesh
AC> > >
AC> >
AC> 

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