One pure PyMOL-based approach is to use the surface_carve settings as follows:
load $TUT/1hpv.pdb, tmp extract lig, organic extract prot, polymer delete tmp set surface_carve_cutoff, 4.5 set surface_carve_selection, lig set surface_carve_normal_cutoff, -0.1 show surface, prot within 8 of lig set two_sided_lighting set transparency, 0.5 show sticks, lig orient lig This approach culls away any triangle more than 4.5 angstroms away from all ligand atoms and any triangle not facing at least one ligand atom. It tends to produce a fairly clean pocket representation. Also worth trying (after the above): set surface_color, white set surface_type, 2 unset ray_shadows Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:[email protected] ________________________________ From: [email protected] [mailto:[email protected]] On Behalf Of Thomas S. Leyh, Ph. D. Sent: Tuesday, May 27, 2008 1:53 PM To: [email protected] Subject: [PyMOL] interior protein-surfaces From time to time I find it valuable to view the suface of a ligand-binding pocket looking out from the surface's interior. This is accomplished in a variety of ways - principally, zooming and clipping. It would be wonderful to be able to represent just the "skin" of the active site wrapping around the ligands, like a sac - this seems quite difficult to achieve. A related problem is that ray-ing a surface that has been clipped yields a collection of odd surface regions that represent poorly the non-ray-ed version - it is as if the resolution of the ray it too gross to capture the clipping edges. Advice appreciated. Thanks, Tom Leyh
