AMBER Archive (2009)
Subject: Re: [AMBER] Need help with point to plane distance calculation in nab
From: IN SUK JOUNG (i.joung_at_gmail.com)
Date: Thu Jan 08 2009 - 13:41:09 CST
I think I made a mistake here.
The distance should be multiplied by sqrt( A^2 + B^2 + 1 ).
That is, distance = abs( ( z - Ax - By - C ) / ( A^2 + B^2
+ 1 ) ) * sqrt( A^2 + B^2 + 1 );
On Thu, Jan 8, 2009 at 12:16 PM, M. L. Dodson <
> IN SUK JOUNG wrote:
>> My rough calculation gives...
>> When the point is (x,y,z), distance = abs( ( z - Ax - By - C ) / ( A^2 +
>> + 1 ) )
>> You should check if it is valid by yourself.
> Thank you very much. Could I impose on you some more to describe in
> words where the two terms come from? In other words, how you derived
> the formula (or give me a reference if this is a well known
> relationship)? I would be grateful for this as I want to understand
> how it comes about. This will be a (minor) point in a publication,
> and I need to justify the algorithm.
> Also, let me be sure I understand your nomenclature: In the expression
> ( z - Ax - By - C ), are x, y, and z the coordinates of the single
> atom (given by aex2) that I want to know the distance from the plane
> for? In other words, what I am calling X and Y? (Z would be the z
> coord for aex2.)
> Hope I am clear.
> Thanks again.
> Bud Dodson
> On Thu, Jan 8, 2009 at 11:39 AM, M. L. Dodson <
>> activesitedynamics_at_comcast.net> wrote:
>> 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.
>>> 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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