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
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