VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Jan 05 2011 - 19:17:55 CST

On Wed, Jan 5, 2011 at 7:12 PM, prabhakar g <prabha.iisc_at_googlemail.com> wrote:
> Dear VMD users,
> I am new to VMD and would like to get some help related to orienting a
> protein molecule. I have a protein molecule and want to save the coordinates
> of the protein molecule in all possible orientations(each orientation
> seperately). I came across the Orient package of
> VMD.(http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/orient/),
>  in that there is a script for orienting the molecule along its principal
> axis. Could some one help  me to modify the script so that I can save all
> possible orientation of the molecule. Thanks in advance.

you have to be more specific about what you mean with
"all possible orientations". if taken literally, that number would
be practically infinite.

in any case, the script needs no modification.
if you look at the example commands, you can
specify any reference vector that you want and
the script will compute the transformation matrix
required to do that transformation.

the rest of the steps that are needed to save the data in any
which way you like, you can easily pick up from working your
way through the scripting parts of the VMD user's guide and
the VMD scripting tutorials.

cheers,
    axel.

> Sincerely
> prabh 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.