VMD-L Mailing List

From: Amarda Shehu (shehua_at_cs.rice.edu)
Date: Fri Dec 08 2006 - 14:21:19 CST

Hi Myunggi,

I hope I understand your question right. It seems to me you want to do a
linear projection of these atom coordinates on a d=2 Euclidean space. You
can use pca (principal component analysis) and only use the two
eigenvectors corresponding to the largest two eignvalues. These two
vectors will be the basis for the best-fitting plane.

-Amarda

On Fri, 8 Dec 2006, Myunggi Yi wrote:

> Dear VMD users,
>
> Do you have any script for calculation of best fit
> plane through selected atoms?
>
> I can imagine for three atoms, but
> for more than three atoms I need some algorithm.
>
> Even if you have some idea or a seed for a script,
> let me know.
>
> Have a nice day.
>
>
> --
> Best wishes,
>
> MYUNGGI YI
> ==================================
> KLB 419
> Institute of Molecular Biophysics
> Florida State University
> Tallahassee, FL 32306
>
> Office: (850) 645-1334
> http://www.scs.fsu.edu/~myunggi
>