>>>> Bob Hanson <[EMAIL PROTECTED]> 2/29/2008 6:09 AM >>> >By the way, Karl, I recommend NOT including the "sasurface" keyword in >your isosurface pocket command, or if you do, use "sasurface 0". When >you use sasurface just by itself it adds 1.2 Angstroms to the Van der >Waals radius. That's fine for an overall approximation of the molecular >surface, but it doesn't really give (in my opinion) the appropriate >sense of how large a cavity is. The real cavity size is better >represented by the Van der Waals surface, I think. > >Bob >
If I use cavity rather than sasurface as the keyword I obtain more realistic looking cavities. For clarity of my own thinking, does cavity give a Van der Waals surface? Karl >Karl Oberholser wrote: > >> Hi All, >> Up until about a month ago I successfully made surfaces from jvxl >> files that I copied from the console using the show command. Since >> that time the surfaces generated from the jvxl files are not the same >> as the original computed surface. The jvxl files made before that >> time still generate the correct surface. The link below contains two >> examples. >> >> http://www.messiah.edu/departments/chemistry/molscilab/jtat_ >080120/acetylcholinesterase/testing/chapter.htm >> >> Karl >> >> >>------------------------------------------------------------------------ >> >>------------------------------------------------------------------------- >>This SF.net email is sponsored by: Microsoft >>Defy all challenges. Microsoft(R) Visual Studio 2008. >>http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ >> >>------------------------------------------------------------------------ >> >>_______________________________________________ >>Jmol-users mailing list >>[email protected] >>https://lists.sourceforge.net/lists/listinfo/jmol-users >> >> > > >-- >Robert M. Hanson >Professor of Chemistry >St. Olaf College >Northfield, MN >http://www.stolaf.edu/people/hansonr > > >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 > > > >------------------------------------------------------------------------- >This SF.net email is sponsored by: Microsoft >Defy all challenges. Microsoft(R) Visual Studio 2008. >http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ >_______________________________________________ >Jmol-users mailing list >[email protected] >https://lists.sourceforge.net/lists/listinfo/jmol-users ------------------------------------------------------------------------- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
