Warren, I've used Varshney's surface code (written at UNC)
for many years now. There are some legal statements but I
checked with UNC and they told me they didn't care who used
copied or modified the code, so I consider it public domain
at this point. I would be happy to send you a copy. It is
C-code that can actually run in parallel and is quite fast.
The surface is the true solvent contact surface (piecewise
spheres and tori). It has a couple minor problems that are solvable:
1. poor/degenerate triangulation in a few places
2. needs better dynamic memory management
I would be happy to send you a copy of the code.
Sorry I have not time to work with PyMol yet,
perhaps someday.
Richard Gillilan
MacCHESS
"DeLano, Warren" wrote:
> 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,
> > 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=1"
>
> Cheers,
> Warren
>
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