Michael, I've cc'd the list with my response.
"Correct" VDW radii are only in version 0.78 and beyond -- they were important for the sculpting feature. Before, PyMOL was using a set that was about 5% too large (they were originally taken from another popular graphics program...). Here are the values for key atoms in the current set. C 1.7 N 1.55 O 1.52 H 1.2 S 1.80 Cl 1.75 Br 1.85 F 1.47 I 1.98 P 1.80 After loading a molecule, you can use the alter command to provide your own vdw radii. A solvent accessible dot surface (only) can be had with set dot_mode=1 show dots Want more dots? Set dot_density to 3. There's no equivalent yet for solid or mesh surfaces. Electrostics are in progress -- no public announcements yet. Warren -- mailto:war...@sunesis.com Warren L. DeLano, Ph.D. > From: michaelw [mailto:micha...@well.ox.ac.uk] > I need to confirm that PyMOL is using vanderWaals distances > for generation of > surfaces. Also, has anyone written surface charge or solvent > accessible > surface functions for PyMOL yet? > > PyMOL is excellent! > > CHEERS! > > Michael >
