Thank you for your help Thomas, Using your settings I get a lot of "partial surfaces"
Showing the surface around the Pocket selection like this: show surface, protein within 0.5 of pocket_selection worked well but I still see a piece of surface that I really don't want to show up. I guess I can take it out in photoshop but that just seems wrong. I have attached it. -Yarrow > 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 > ------------------------------------------------------------------------------ Everyone hates slow websites. So do we. > Make your web apps faster with AppDynamics > Download AppDynamics Lite for free today: > http://p.sf.net/sfu/appdyn_d2d_feb > _______________________________________________ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697
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