From: Thomas C. Bishop (
Date: Thu Oct 03 2013 - 12:42:02 CDT

The magnitude of the cross product provides information about the sine of the angle between the vectors
but seems there must be an easy way that only involves scalars :-)


On 10/03/2013 11:37 AM, Axel Kohlmeyer wrote:
On Thu, Oct 3, 2013 at 5:40 PM, Peterson J <> wrote:
Hello VMD Users,

I am trying to calculate the angle between two domains of my protein. I have
calculated the inertia for both domains which provided me the center of mass
and the principal axes of each domain. But I have a problem calculating the
angle using the two principal axes. The 'measure angle' asks for three atom

How do I measure it?
how do you compute the angle between two vectors?