From: Axel Kohlmeyer (
Date: Fri Jan 09 2009 - 08:16:12 CST

On Fri, 9 Jan 2009, Max wrote:

M> Hi all,

hi max,

M> Is it possible to highlight molecule's substructures in VMD? I mean, I

yes and no. VMD has to be able to identify them, and since VMD does
not have any knowledge of chemistry, the file that you provide has
to have some indication of it (atom types, residue names, some index


M> would like to highlight a specific functional group, a carboxylic_acid or a
M> benzene ring, for example. If it's no possible, does anyone know about any
M> script or plugin which might do it?
M> Thanks
M> Max

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.