VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Thu Jul 03 2008 - 12:24:16 CDT

On Thu, 3 Jul 2008, Jorgen Simonsen wrote:

JS> Hi,
JS>
JS> I have made a little script in order to calculate the dihedrale angle using
JS> VMD for atom selection - somehow my vector is pointing in the opposite
JS> direction because I get -1*MyAngle equals the angle from VMD if I make the
JS> following atom select in VMD
JS>
JS> residue 1 and name N CA CB CG

it is not entirely clear to me what you are doing exactly,
but i would like to remind you that the coordinats in atomselections
are ordered in the way they are read in from the coordinate
file and _not_ in the order you select them. a different order
may turn a right-handed definition of an angle into a left handed
one (or worse) and voila you have a different sign.

cheers,
   axel.

JS>
JS> and define the dehedral using the mouse consecutive first N then CA then CB
JS> nad last CG - let say I get 60 my script than gives me -60 where I calculate
JS> the angle like this
JS>
JS> n1 = Vector.cross((N-CA),(CB-CA))
JS> n2 = Vector.cross((CA-CB),(CG-CB))
JS> return Vector.angle(n1,n2)
JS>
JS> first generating the vector and then crossing them and lastly find the angle
JS> between them. Any help or correction appreciated.
JS>
JS> Thanks in advance
JS>
JS> Best
JS>
JS> Jorgen
JS>
JS>
JS>
JS>
JS>
JS>
JS>
JS> N CA CB CG
JS> 

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