From: Axel Kohlmeyer (
Date: Tue Aug 12 2008 - 10:37:45 CDT

On Tue, 12 Aug 2008, Roman Petrenko wrote:

RP> Dear all,
RP> i am making a movie in vmd and want to display only those hydrogen
RP> bonds which are formed between a protein and water molecules
RP> (protein-protein HB are ok as well).
RP> is there any way to do it?

how about selecting "within 3.0 of protein" for the hbonds
representation? you also want to enable "Update Selection Every Frame"
in the Trajectory tab...



RP> the problem is if i display only protein (no water) and choose Hbonds
RP> representation, then only protein-protein HB are displayed.
RP> if i display everything (protein+water), then protein-water HBs are
RP> visually hidden by numerous useless hydrogen bonds between water
RP> molecules.

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.