AMBER Archive (2009)

Subject: [AMBER] Need help with point to plane distance calculation in nab

From: M. L. Dodson (activesitedynamics_at_comcast.net)
Date: Thu Jan 08 2009 - 12:39:16 CST

Hello all,

I'm having a brain cramp coming up with the correct algebra for an
algorithm giving the distance from a point to a plane along a normal
to the plane. In nab, I can calculate the least squares best fit of a
plane of form z = Ax + By + C to a series of atomic positions
(represented by a nab atom expression, complete_aex1, in the molecule
mol) by using:

plane(mol, complete_aex1, A, B, C),

where complete_aex1 is an atom expression identifying the atoms whose
positions are to be fit by the plane.

I want to calculate the distance from that plane to another atom
(given by aex2) ALONG A NORMAL to the plane.

I need the correct POINT in the plane where the normal intersects. At
first I set the x and y coords of the POINT to be the x and y coords
of the atom given by aex2, say X and Y. Then set z coord of the POINT
to be z = AX + BY + C. Then I calculated the distance between the
position of atom aex2 and that point in the plane. But this (pretty
clearly, it seems to me), is NOT along a normal to the plane.

Can any of you geometers out there hit me with a clue bat? An
algorithm will do. You do not need to know nab to answer.

Thanks,
Bud Dodson 

-- 
M. L. Dodson
Business Email: activesitedynamics-at-comcast-dot-net
Personal Email:	mldodson-at-comcast-dot-net
Phone:	eight_three_two-56_three-386_one

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