Re: [Jmol-users] [Fwd: thoughts on surface rendering]

[Frieda Reichsman]

On Oct 7, 2006, at 8:18 AM, Bob Hanson wrote: This email describes how Jmol renders molecular surfaces and their  derivative, "solvent accessible surfaces" and how Jmol produces a slice  through the data. Wow. Oblique slabbing. Fantastic. And the planar surface slices are just too cool. It actually makes me want to write yet another protein secondary structure tutorial, just to use these features - and that's saying a lot. OK, as I was reading CCW, I was very impressed that they had considered the idea of cavities. We can look inside our Jmol surfaces using slab, and I just recently added a colorScheme I call "sets" that allows you to color the surface triangles based on which connected set of triangles it is in. This turns out to be very pretty. When I use the example page http://www.stolaf.edu/academics/chemapps/jmol/docs/examples-11/new.htm the link for the "sets" colorscheme: isosurface ignore(solvent) molecular colorscheme "sets"  turns the entire surface a sort of aqua green color. I don't get it - is that what "sets" is supposed to do? Frieda /////////////////////////////////////////// Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com ///////////////////////////////////////////

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