Re: [Jmol-developers] surfaces... volume too?

[Robert H. <ha...@st...>]

Yes, Miguel was the mastermind behind the original isosurface command and
Marching Cubes and as well a very nice implementation of "Gouraud shading".
As I recall Marching Cubes had just come off patent and was finally
available for general use. This was a hugely important contribution to Jmol,
and also associated with that, Miguel introduced the use of geodesic
surfaces. Miguel also introduced pmesh. I have to admit that the
isosurface/Marching Cubes code is virtually unrecognizable now from that
original coding, but that was definitely a key starting point. Many thanks
to Miguel for this.

My contribution was to refine and expand it:

-- adding "true" molecular surface calculations, solving the "stitching"
problem
-- introducing surface mapping of data
-- adding a variety of other surface types including cavities, molecular
orbitals, atomic orbitals, lcaoCartoons, generic functions, and such
-- making the code work "progressively" -- not requiring the actual
generation of a full cube of data and saving hugely on memory
-- introducing JVXL compression of surfaces created with Marching Cubes,
making rapid transmission of surface information over the web possible
-- creating "Marching Squares" for planar slices
-- planar and surface contour line representations
-- more aesthetic mesh rendering, with selectively hidden triangle lines
-- grouped/associated normals for cleaner lighting
-- a variety of readers for different data sources

I've been thinking that we really should still do a publication on this.
There's some good stuff there.

By the way, I just added "noncovalent interactions" (NCI) surfaces. No
documentation on this yet, because I JUST got it working, but it's kind of
interesting. See http://www.ch.ic.ac.uk/rzepa/blog/?p=2230 (which now needs
some revision regarding Jmol, Henry!) or
http://www.ncbi.nlm.nih.gov/pubmed/21516178

Anyway, Egon, yes, the isosurface volume and area work great. I still don't
quite understand why that works so well, but it is some very nice
fundamental 3D geometry that makes it work. There must be a nice little
proof of this somewhere. The algorithm for it is only about 10 lines long!


Bob





-- 
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900