So I read that JOC article... I think both their methods are crap. Jmol
should be doing a much better job because it is the ACTUAL area, not some
(gross) approximation.
Bob
On Wed, Sep 2, 2009 at 10:58 AM, Robert Hanson <[email protected]> wrote:
> 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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>
>
>
> --
> 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
>
--
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
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