VMD-L Mailing List

From: Jerome Henin (jhenin_at_vitae.cmm.upenn.edu)
Date: Sun Sep 03 2006 - 17:54:17 CDT

Hi Neela,
The following page, for example, explains how these 4x4 transformation
matrices are defined:
http://documents.wolfram.com/applications/visualizer/A2OrientationCommands/A2.8.html

You don't have to apply the transformation manually, the move command of
atomselect does it for you.

By the way, why on earth did you CC the NAMD mailing list on this?
Jerome

On Sunday 03 September 2006 16:34, you 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