OK, I did find that bug. Eric, if your isosurface suddenly disappears, let
me know. I will upload the changes. But I am at the ACS meeting right now.
On Mon, Mar 23, 2015 at 6:46 AM, Robert Hanson <hans...@stolaf.edu> wrote:
> The algorithm is what it is, right? The MSMS solvent surface algorithm (
> http://mgl.scripps.edu/people/sanner/html/msms_home.html) is
> computationally expensive because it involves checking all pairs of atoms
> for edges, then, with those, checking all triples for faces where a solvent
> probe might settle. Jmol does its best to do this rapidly -- it uses "3D
> binary trees" to very rapidly identify potentially close atoms rather than
> just looping through all possible atoms. It's this last phase, though, that
> is a killer, because it requires checking each triple for blocking atoms
> within the probe radius that would hinder that settling. With a large probe
> radius, that ends up checking an enormous number of atoms.
>
> I was able to make it more efficient by incrementally excluding interior
> atoms:
>
> isosurface s solvent 2.0;
> select within(2.1, $s)
> isosurface s solvent 4.0;
> select within(2.1, $s)
> isosurface s solvent 8.0;
> select within(2.1, $s)
> isosurface s solvent 10.0;
> select within(2.1, $s)
>
> So you might want to try that.
>
> But, interestingly, when I went to 12.0, the solvent disappeared. I'm not
> sure why that happened.
>
>
> Bob
>
>
--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
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
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