VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Aug 06 2013 - 09:51:49 CDT

Hi,
  As Axel says, there isn't really a way to do this directly, however
you can export a triangle mesh to one of the file formats in the File|Render
menu and extract the vertices that way if you like. In order to do that
an retain the coordinate system of the original molecule, you would also
need to set the molecule's view/rotate/centering transformation matrices
to identity before exporting. Let me know if you need more help with that.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Aug 06, 2013 at 01:05:11PM +0200, Axel Kohlmeyer wrote:
> On Tue, Aug 6, 2013 at 10:44 AM, Georgios Gerogiokas
> <G.Gerogiokas_at_sms.ed.ac.uk> wrote:
> > Hi all,
> >
> > I was wondering if anyone knows how to extract the
> > coordinates of the grid points in an isosurface created
> > at a particular isovalue, for instance from a dx file during
> > a vmd session.
>
> i dont' think this is possible directly, but there are some dusty
> corners in VMD that i have not looked into for a long time. what might
> work is to reset view and camera and everything to simple unit
> transformation and then output the isosurface to a render program and
> parse the resulting file.
>
> axel.
>
> >
> > Many thanks,
> > George
> >
> > --
> > The University of Edinburgh is a charitable body, registered in
> > Scotland, with registration number SC005336.
> >
> >
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> International Centre for Theoretical Physics, Trieste. Italy. 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/