Re: [PyMOL] surface for oligosaccharide chains

[Robert C. <rob...@qu...>]

On Fri, 03 Jul 2009 16:18:10 +0200, Raluca Mihaela ANDREI <r.a...@sn...>
wrote:

> Hi!
> Can somebody tell me why I can't create surfaces for the 
> oligosaccharide chains?

By default, the surface and mesh commands ignore all atoms in HETATM records
in a PDB file.  You can change that with:

  set surface_mode, 1
  set mesh_mode, 1

That means, though, that *all* hetatm atoms will have a surface drawn.  If you
want to draw a surface for your oligosaccharide chains alone, then you can
copy them to a separate object and set the surface_mode flag just for that
object:

  set surface_mode, 0
  create saccharide, object & <selection>   
(fill in your residue selection for <selection>)

  set surface_mode, 1, saccharide


Hope that helps,
Rob

-- 
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor 
Botterell Hall Rm 644
Department of Biochemistry, Queen's University, 
Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821            Fax: 613-533-2497
<rob...@qu...>    http://pldserver1.biochem.queensu.ca/~rlc