Scott, > From: Scott Classen [mailto:clas...@uclink.berkeley.edu] > > Hello fellow PyMOLers, > Is the surface in PyMOL a solvent accessible surface or > a molecular > surface? It looks like a solvent accessible surface to me. Is > there any > way to change the radius of the water probe that is used to > create the > surface?
PyMOL's default surface is a water contact surface (approximates a Connolly surface). >I noticed that there are a few surface settings, but I can't > figure out what effects they are having on the displayed surface. Can > anybody shed light on these commands? What are their default > settings? You can use the settings editor to get the default (except if you're using the native OSX version on a mac). > What are the high and low values they can take? > > surface_best > surface_normal > surface_proximity > surface_quality These settings haven't yet been documented, but they will be in an upcoming version of the manual. > I would like to create a fairly tight molecular surface and I just > can't figure it out. ANy help would be appreciated. show surface set surface_quality=1 set solvent_radius=0.8 rebuild WARNING: PyMOL may crash if solvent_radius is too low. If it does, try incrementing it by 0.1 until it stabilizes. Cheers, Warren
