On Monday, May 09, 2011 12:50:48 pm Kenneth A. Satyshur wrote:
> YO!
>
> I am making thermal ellipsoid plots of a highly flexibile region of a
> chromophore using rastep and render from the raster3D package of Merritt el
> al.
> But I cannot control the orientation. It obscures the rest of the atoms in
> the
> plane of the molecule. Does anyone know a way to orientate molecules AND
> get a publication quality png file? ccp4mg only produces vague traces.
Simple thing to try first:
cat myatons.pdb | rastep -auto | render -size 900x900 > picture.png
The "-auto" option to rastep will orient the atoms so that they
are maximally spread out in the plane of the picture.
More general answer:
- Open the pdb file in a viewer of your choice
- Orient as you please
- Dump orientation matrix (exact button or command depends on the program)
- Copy the matrix into the header of the raster3d file fed to render
cheers,
Ethan
--
Ethan A Merritt
Biomolecular Structure Center, K-428 Health Sciences Bldg
University of Washington, Seattle 98195-7742
