VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Tue Dec 02 2008 - 11:29:25 CST

On 12/2/08, Björn Windshügel <windshuegel_at_zbh.uni-hamburg.de> wrote:
> Hi all,

hi bjoern,

> I have a problem regarding the rotation of molecules. For some reason I'd
> like
> to rotate a protein around the X- and Z-axis for 180 degrees and save the
> new
> coordinates.
> First I have used the "orient" script to align the principal axes with the
> x,
> y and z directions. Then I use the following commands:
> set sel [atomselect top "all"]
> $sel move [trans z 180]
>
> What I would expect is rotation of the molecule along the z axis but in
> addition to the rotation the protein is also translated in x and y direction
> (real coordinates, not just the view).
> Can anyone explain why this happens and how to avoid it? Would be great to
> get
> some ideas to solve the problem.

the question is, whether the "orient" script (which one?) does
the proper translation of the molecule in real coordinates.
have you verified that?

cheers,
   axel.

>
>
> With best regards,
>
> Bjoern
>
>
>
>
>
> --
> Dr. Björn Windshügel
>
> Centre for Bioinformatics
> University of Hamburg
> Bundesstr. 43
> 20146 Hamburg
>
> Email: windshuegel_at_zbh.uni-hamburg.de
> Phone: +49-40-42838-7372
> Fax: +49-40-42838-7352
>
> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
  Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.