VMD-L Mailing List

From: Jorgen Simonsen (jorgen589_at_gmail.com)
Date: Thu Jul 03 2008 - 07:43:07 CDT

Hi,

I have made a little script in order to calculate the dihedrale angle using
VMD for atom selection - somehow my vector is pointing in the opposite
direction because I get -1*MyAngle equals the angle from VMD if I make the
following atom select in VMD

residue 1 and name N CA CB CG

and define the dehedral using the mouse consecutive first N then CA then CB
nad last CG - let say I get 60 my script than gives me -60 where I calculate
the angle like this

n1 = Vector.cross((N-CA),(CB-CA))
n2 = Vector.cross((CA-CB),(CG-CB))
return Vector.angle(n1,n2)

first generating the vector and then crossing them and lastly find the angle
between them. Any help or correction appreciated.

Thanks in advance

Best

Jorgen

N CA CB CG