VMD-L Mailing List

From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Sun Sep 03 2006 - 21:59:46 CDT

A 4x4 matrix can encode translation, rotation, and scaling for something
called "homogenous coordinates". It's a computer graphics thing. Google
it or see http://bishopw.loni.ucla.edu/AIR5/homogenous.html

-Jim

On Sun, 3 Sep 2006, Neelanjana Sengupta wrote:

> Hi,
> I am writing a routine that will align a (C=O) of my simulated system along
> an axis, and then align th (C-N) along another axis. While I have figured
> out what I need to do, I do not understand why the Matrix Routines in vmd
> yield 4X4 matrices:
> http://www.ks.uiuc.edu/Research/vmd/current/ug/node176.html
>
> At the end, we would really like to mutliply our {x y z} vectors with the
> transformation matrix, right? So the transformation should be a 3X3 matrix.
> Could somebody point out what I am missing here?
>
> Thanks,
> Neela
>