AMBER Archive (2003)

Subject: Re: AMBER: plane angle.

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Mon Sep 22 2003 - 13:42:40 CDT

> Three points or 2 axis are needed to define a plane in Carnal.

And in euclidean geometry generally.

> How is it possible to create an "average" plane formed by more than 3 atoms?

It is not possible to do this in the general case: what would
be the average plane defined by, say, six points forming a
cube?

> For example if I study the interaction between 2 saccharides,
> how is it possible to create an "average" plane of a sugar rings
> and later calculate the plane angle?

I believe that the pucker code actually does effectively
calculate a mean plane (not sure what would happen in the
degenerate cases like the cube). See src/carnal/pucker.c
code after the comment <<Calculate R', R">>. Note that this
is for an arbitrary number of atoms, so may be what you
want if you plan to program something.

This code

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