Pymol should draw the molecular surface (or Connolly surface) by default. If you want the solvent accessible surface, turn on the option "solvent accessible" under Setting/Surface.
Yong -----Original Message----- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Edward A. Berry Sent: Friday, May 15, 2015 3:08 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Two kinds of solvent-accessible-surface ? If I remember correctly, there are two different ways to calculate a surface by rolling a ball over it, and i think that I want a program to calculate the non-conventional one. As I understand, the ASA is defined as the surface traced out by the _center_ of the rolling sphere, i.e. one radius above the vdw surface. The justification being that an atom (i.e. it's center coordinates) can't get any closer to the surface than that. The second type of surface is defined by the closest approach of the _surface_ of the rolling sphere, i.e. it would be the vdw radius of the (protein) but not descending into cracks between atoms where the rolling ball won't fit. For making models of a multisubunit protein, and wanting to be able to assemble the separately-made subunits so that they make intermolecular vdw contacts, the second kind of surface would be desirable, as otherwise atoms won't be able to get their surfaces closer than twice the sphere radius. Is that an option that can be chosen in pymol or such? Thanks, eab
