From: Axel Kohlmeyer (
Date: Sat Feb 21 2009 - 11:03:44 CST

On Sat, 21 Feb 2009, wrote:

RP> Dear VMD users and developers,

dear regina,

RP> I would like to create a nice picture of peptide surrounded by water and I
RP> want the peptide to be presented by surface and maybe water too. Does anyone
RP> knows how to do it or maybe you can suggest some other nice way of
RP> presentation. I just don't want it to be presented in sticks and balls etc.

you could use SURF or MSMS to generate surfaces directly.
a second option would be to use the volmap tool to generate
a density map for a selection of atoms and then represent
that with an isosurface representation. the density maps can
be weighted by different atom parameters (mass, covalent radius,
unweighted) and there are other flags to play with, so there
are lots of options.

it is difficult to make a specific suggestions, since your
description of what you want to achieve is rather vague.


RP> Regina

Axel Kohlmeyer
   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
If you make something idiot-proof, the universe creates a better idiot.