From: Navendu bhatnagar (navendu.bhatnagar_at_gmail.com)
Date: Fri Jun 05 2009 - 17:26:16 CDT

Hello all,

I need to align my molecule to the principal axes. When going through the
mailing lists I came across a script / method to perform this shared by
Peter.

The message is as follows :

*For example, for your case, if the long axis of your molecule is along the
> vector {a b c}, you can rotate it to align it with the z axis as follows:
>
> set sel [atomselect top all]
> set M [transvecinv {a b c}]
> $sel move $M
> set M [transaxis y -90]
> $sel move $M
>
> This performs your task in two steps: transvec inv rotates your vector to
be
> along the x axis, and then transaxis rotates about the y axis to align
your
> vector with z. *

I want to use the above script but I am not sure on how to get the vector
corresponding to the long axis of my molecule.

Please share the ideas / suggestions on this.

Thanks,

NAVENDU BHATNAGAR