VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Fri Oct 10 2008 - 16:50:59 CDT

On Fri, 10 Oct 2008, Tristan Bereau wrote:

TB> Hello,

hello tristan,

TB>
TB> First of all, although this is my first contribution to this
TB> mailing-list, I have been already working with VMD for a few months and
TB> am very happy with it !
TB>
TB> I have been using the STRIDE algorithm with and without VMD, and am
TB> wondering how VMD can determine the orientation of a beta-sheet. As far

to get an answer to this kind of question, you (usually) have to look
into the source code. in this case you can find the details in
DrawMolItemRibbons.C and BaseMolecule.C.

what happens is that VMD analyses protein structures and collects
a list of fragments in N to C direction. when drawing the beta
sheet representation, it uses this fragment list and draws the
arrowhead at the position of the last residue (i.e. the "C-term")
that is labeled at beta sheet.

cheers,
   axel.

TB> as I understand, a beta sheet is simply characterized with a "E" letter
TB> code in STRIDE, independently of the orientation (i.e. parallel or
TB> antiparallel). However, VMD displays a direction to all its beta-sheets.
TB> I've been able to work out a script that tries to determine this
TB> orientation from the hydrogen bonds detected by STRIDE (when invoking
TB> "stride -h ..."). Parallel and antiparallel sheets have very different
TB> hydrogen bond patterns. Still, there are some cases where there doesn't
TB> seem to be enough information coming from H-bonds to distinguish the
TB> orientation (e.g. there is only one hydrogen bond detected).
TB> Does VMD use another way to determine hydrogen bond patterns ?
TB>
TB> Thank you for your help,
TB>
TB> Tristan
TB> 

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