From: Yarrow M. <ama...@uc...> - 2013-03-03 17:35:12
|
Hello, Does anyone know how to visualize a surface within a given radius from a ligand binding site? In chimera you can limit the display surface within 0-X angstrom of a ligand. This allows you to see the surface surrounding the ligand without the rest of the protein. I guess you could create a new selection of residues around a ligand and show this surface but I wondered if there are any other ways of doing this. -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697 |
From: Thomas H. <tho...@sc...> - 2013-03-03 18:14:52
|
Hi Yarrow, should be as simple as: PyMOL> hide surface PyMOL> show surface, (organic around 8.0) PyMOL> set transparency, 0.3 PyMOL> set two_sided_lighting See also: http://pymolwiki.org/index.php/Selection_Algebra Hope that helps. Cheers, Thomas Yarrow Madrona wrote, On 03/03/13 18:34: > Hello, > > Does anyone know how to visualize a surface within a given radius from a > ligand binding site? In chimera you can limit the display surface within > 0-X angstrom of a ligand. This allows you to see the surface surrounding > the ligand without the rest of the protein. > > I guess you could create a new selection of residues around a ligand and > show this surface but I wondered if there are any other ways of doing > this. -- Thomas Holder PyMOL Developer Schrödinger Contractor |