Using Jmol 11.8:
isosurface volume sasurface 0
should do it. You might have to increase the resolution for good results:
isosurface resolution 10 volume sasurface 0
keep increasing the number until you are satisfied.
I'll also check that reference. Maybe we can implement that.
Bob
On Wed, Sep 2, 2009 at 10:10 AM, N David Brown <[email protected]>wrote:
> Ok, thanks for the info, Angel :o)
>
> Bob, clarification please?
>
> I've just found an intriguing paper indeed, "Fast calculation of van
> der Waals volume as a sum of atomic bond contributions and its
> application to drug compounds" by Zhao, Abraham and Zissimos (J. Org.
> Chem. 2003, 68, 7368-7373). They describe a method of calculating the
> vdW volume using utterly trivial maths - so simple they actually test
> it in an Excel spreadsheet! Incredibly it seems to work to a high
> accuracy; examples they provide show deviation from the MacroModel
> calc'd value (the long but accurate calculation method) of at most ~19
> Angstroms. Very happy they've discovered this!
>
> David
>
>
>
> 2009/9/2 Angel Herráez <[email protected]>:
> > David, I remebmer reading of a recent feature in Jmol that offers the
> > volume inside an isosurface. Maybe that can be extended or matched to
> > a vdW surface (there are many options in the isosurface command)
> >
> > Surely Bob will tell you, but you can follow that line --and let us
> > know :-)
> >
> >
>
>
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