From: Tristan Bereau (bereau_at_cmu.edu)
Date: Fri Oct 10 2008 - 15:28:33 CDT

Hello,

First of all, although this is my first contribution to this
mailing-list, I have been already working with VMD for a few months and
am very happy with it !

I have been using the STRIDE algorithm with and without VMD, and am
wondering how VMD can determine the orientation of a beta-sheet. As far
as I understand, a beta sheet is simply characterized with a "E" letter
code in STRIDE, independently of the orientation (i.e. parallel or
antiparallel). However, VMD displays a direction to all its beta-sheets.
I've been able to work out a script that tries to determine this
orientation from the hydrogen bonds detected by STRIDE (when invoking
"stride -h ..."). Parallel and antiparallel sheets have very different
hydrogen bond patterns. Still, there are some cases where there doesn't
seem to be enough information coming from H-bonds to distinguish the
orientation (e.g. there is only one hydrogen bond detected).
Does VMD use another way to determine hydrogen bond patterns ?

Thank you for your help,

Tristan