From: Neelanjana Sengupta (
Date: Sun Sep 03 2006 - 15:34:48 CDT


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?


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