I am trying to get isosurfaces with large probes in order to smooth out
small depressions. My goal is to select atoms that are truly near the
"outer" surface of a large structure, such as 2hil.
I am running into trouble because as the probe size gets larger, the
calculation begins to take a very long time, even at low resolution. For
example, calculation of an isosurface such as
isosurface s1 ignore {altconfigs or not target} resolution 0.20 solvent 12.0
takes about an hour on my fast MacBook Pro (only a few months old; 2.2
GHz Intel Core i7, 16 GB memory). But I have to play with the probe size
and resolution to get surfaces that don't wrap around to a channel in
the interior. And I have dozens of models to analyze. At this speed, it
becomes difficult to make usable progress.
Is there a faster way to generate such isosurfaces, or another way to
select atoms on the surface that exclude small pockets or crevices?
Thanks, Eric
------------------------------------------------------------------------------
Dive into the World of Parallel Programming The Go Parallel Website, sponsored
by Intel and developed in partnership with Slashdot Media, is your hub for all
things parallel software development, from weekly thought leadership blogs to
news, videos, case studies, tutorials and more. Take a look and join the
conversation now. http://goparallel.sourceforge.net/
_______________________________________________
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
