Re: [PyMOL] coordinate systems of pymol and povray

[Tsjerk W. <ts...@gm...>]

Hi Gabriela,

If you only want to get the molecule back in view and rotate/translate
it to your liking, you can use commands like:

#declare Protein = union { #include  "protein.inc" }
#declare Center = (min_extent(Protein)+max_extent(Protein))/2;
object { Protein translate -Center }

If you want to preserve the view you had in Pymol, you'll need
something more. For this purpose I wrote a set of POV-Ray macros,
which are attached. For this to work, you have to save the view from
get_view(). If you used the (better ;)) second version of make_pov
from the wiki, the view is already saved in the pov-ray file. Place
the macro file somewhere where POV-Ray can find it, and uncomment the
section in the .pov file starting with  "Uncomment the following
lines" :) Now, if you want to add objects to your scene that you have
defined based on the coordinates in the pdb file, you can use
something like:

// This draws a sphere of radius 1 at the origin of your .pdb coordinate system
sphere { 0, 1 SET_PYMOL_VIEW( PYMOL_VIEW )) }

For more extensive information, read the first section of the file. If
things are still unclear, feel free to contact me. And if you find
that you've managed to do really cool stuff with it, please let me
know :)


Hope it helps,

Tsjerk

On Wed, Feb 17, 2010 at 5:07 PM, Gabriela Schlau-Cohen
<gs...@ho...> wrote:
> Hi all,
>
> I am trying to load a pymol graphic into povray and then add on geometric
> objects.  I exported and loaded the molecular model from pymol successfully
> using the make_pov.py script from the wiki.  I can then copy and paste that
> file into povray to generate the molecules through povray.  Then, when I
> save the object in pymol to get the molecular coordinates, the coordinates
> are in a different system.
> Can someone tell me how to get the molecular coordinates and a povray file
> in the same coordinate system?
> Thanks,
> Gabriela
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-- 
Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist
Neuropharmacologist