Hey Björn,
The mesh will be in Pymol camera coordinates, not in PDB coordinates.
You'll have to take the object_matrix (cmd.get_object_matrix) and
apply it to the protein to convert it to the same space if you are to
use it outside of Pymol.
Hope it helps,
Tsjerk
On Mon, Aug 22, 2011 at 8:12 PM, björn
<bjoern-oliver.goh...@student.uni-tuebingen.de> wrote:
> Hey,
>
> I have a little problem to get the points/coordinates of a mesh.
> I know he command:
> open("pymol.mesh","w").write( cmd.get_povray()[1] )
>
> But when I run this command, the coordinates of these spheres are not
> equal to these of the mesh.
>
> For example, if a generate the mesh for a protein and run this command, the
> coordinates of the generated spheres are shifted by an axis I think.
>
> So my question is, is there a function where I can get the coordinates of the
> SES-mesh in an easier way??
> Or do sombody know what my fault is, by running the above command?
>
> Thanks in advance,
> Björn
>
>
>
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--
Tsjerk A. Wassenaar, Ph.D.
post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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