VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Sun Jul 06 2014 - 16:02:34 CDT

There isn't a direct way of doing this. Indirectly, you'd need to first
calculate the reference point, then use math operations to determine if
it is less than a distance away from the reference point. For example,
if you determined your center of mass to be at the point (x0, y0, z0),
this selection string will get you the points within radius of the
center of mass.

sqr(x-x0)+sqr(y+y0)+sqr(z-z0) < sqr(radius)

-Josh Vermaas

On 7/4/14, 10:48 AM, Gurunath Katagi wrote:
> Dear All,
> I am trying to calculate the number of tyrosine within certain
> distance from the geometric centre of the molecule.
>
> If the calculation was based on some atom, then it would have been
> <selection> within <distance> of protein
>
> Now I that i am not getting which atom to take reference from, can you
> please let me know how to go about this..?
> eg; <selection> within <distance> of <center of mass>
>
> thank you
> Gurunath