VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Tue Jan 30 2007 - 11:16:32 CST

On Tue, 30 Jan 2007, Prevost Martine wrote:

PM> Hello,
PM>
PM> I would like to compute the angle between each carbonyl backbone
PM> group and the largest inertia axis of a protein. Would it be
PM> possible to do that with available scripts in vmd ? If not could you

that should be doable. you'll have to do some custom tcl scripting
for yourself, though. first you create the required vectors and then
compute the angle with elementary vector algebra: the dot product
of the two normalized vectors is the cosine of the angle.

axel.

PM> suggest me ways to perform this type of calculation. I've seen that
PM> I could get the principal axes through the package orient but then
PM> ... Thank you very much.

PM>
PM> Best,
PM>
PM> Martine.
PM>
PM> --------------------------------------------
PM> Martine Prévost
PM> Structure et Fonction des Membranes biologiques
PM> et
PM> Bioinformatique génomique et structurale,
PM> CP 206/2
PM> Université Libre de Bruxelles
PM> Bld du Triomphe
PM> B-1050 Bruxelles
PM> Belgium
PM> Phone : 32-2-650 2049
PM> Fax : 32-2-650 5382
PM> E-mail: mprevost_at_ulb.ac.be
PM> --------------------------------------------
PM>
PM>
PM>
PM>
PM> 

-- 
=======================================================================
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.