RE: [PyMOL] About Surface

[DeLano, W. <wa...@su...>]

Now, on to Alan's specific questions:

> 	I'm particularly interested in how pymol generate surface (a
> internal algorithm?) and how to compare it to vdW, solvent,=20
> Connolly and
> MSMS surfaces.

PyMOL's surfacing algorithm is just something I cooked up over a weekend
a couple years back.  It is brute-force: 1. surface the atoms, 2.
surface waters in contact with those atoms, and 3. merge the result into
a continuous surface and try to cover up any glitches.  If a better (ie.
faster) surfacing algorithm ever enters the public domain/BSD-licecnse
software pool, then I would love to include it as an alternative.

To get a better surface, select "Maximum Quality" from the "Display"
menu, a go get a cup of coffee while you wait : ).  You may need extra
RAM too...

To make it transparent, "set transparency=3D1"

Cheers,
Warren