Re: vmd-l: CoordinateTransformation

From: Jim Phillips (
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


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:
> 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

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