VMD-L Mailing List

From: Himanshu Khandelia (hkhandel_at_memphys.sdu.dk)
Date: Wed Feb 14 2007 - 17:30:18 CST

This should do it:

http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/orient/

On Wed, 14 Feb 2007, s.schweizer_at_dkfz-heidelberg.de wrote:

> Hello,
>
> I want to align a molecule: I have a pdb file of tryptophan
> and I want to put the aromatic ring in the xy-plane, the z-axis
> is then perpendicular to the molecule.
>
> Can I do this with VMD and how is it done? Or do you know another program
> that can do this?
>
> The alignment has to be accurate, so I cannot move it by mouse in the
> xy-plane.
>
> Thanks in advance,
> Simon Schweizer
>