Given the 677 compounds tested and the proximity to the TSAR values, I think that's an odd comment. It's an approximation, true, but for the drop in computational cost I find the accuracy astounding.
Thanks for the isosurface command I requested. 2009/9/2 Robert Hanson <[email protected]>: > 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 :-) >>> > >>> > >>> >>> >>> ------------------------------------------------------------------------------ >>> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 >>> 30-Day >>> trial. Simplify your report design, integration and deployment - and >>> focus on >>> what you do best, core application coding. Discover what's new with >>> Crystal Reports now. http://p.sf.net/sfu/bobj-july >>> _______________________________________________ >>> Jmol-users mailing list >>> [email protected] >>> https://lists.sourceforge.net/lists/listinfo/jmol-users >> >> >> >> -- >> 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 > ------------------------------------------------------------------------------ Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
