Menu
▾
▴
Re: [Jmol-users] Surfaces from jvxl files
|
From: Bob H. <ha...@st...> - 2008-03-11 17:05:52
|
Karl Oberholser wrote: >>>>>Bob Hanson <ha...@st...> 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? > > Yes, I think it defaults to that. >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 >>>Jmo...@li... >>>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 >>Jmo...@li... >>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 >Jmo...@li... >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 |