> > On Aug 18, 2006, at 9:24 PM, Bob Hanson wrote: > >> Frieda, what sort of surfaces are you particularly interested in >> displaying? >> >> Bob > > Solvent-accessible surfaces of macromolecules are what I am > accustomed to using vis Chime, hence what I am seeking to create. > However I have to admit that I am not aware of what the distinction > is between "isosurface" and solvent-accessible surface...
There are two subtle distinctions now being made in Jmol -- "Solvent-accessible" which means the probe center position when rolled around the molecule. This is: isosurface SAsurface 1.2 where 1.2 is the solvent probe radius. "solvent-excluded" or "molecular" which means the set of all points on the solvent sphere that touch the Van der Waals radius along with the portions of the solvent sphere that form "caveties" when the solvent sphere touches the molecule at more than one point. This is: isosurface solvent 1.2 Both are called isosurfaces because they represent the points in space that have the same measurement, in this case the same distance from the solvent probe (and as described above). "SAsurface" display is far faster than "solvent" and probably what you want. Sorry, earlier I forgot about the SAsurface option. Bob > > Frieda > > > >> >> Frieda Reichsman wrote: >> >>> Hi All, >>> >>> I am interested in fast rendering of surfaces for large molecules. It >>> seems that Bob Hanson has invented a file format for this purpose, >>> called JVXL. I have seem Angel Herraez's and Bob's test pages for >>> surfaces, but I am still puzzled as to how to get started in doing >>> this. >>> >>> To create a JVXL surface file in Jmol, do you first have to load a >>> CUBE file into Jmol? I have started to read a little about CUBE files >>> but am unfamiliar with them. How do you generate a CUBE file? >>> >>> Frieda >>> >>> /////////////////////////////////////////// >>> >>> >>> Frieda Reichsman, PhD >>> >>> Molecules in Motion >>> >>> Interactive Molecular Structures >>> >>> http://www.moleculesinmotion.com >>> >>> >>> /////////////////////////////////////////// >>> >>> >>> >>> --------------------------------------------------------------------- >>> --- >>> >>> --------------------------------------------------------------------- >>> ---- >>> Using Tomcat but need to do more? Need to support web services, >>> security? >>> Get stuff done quickly with pre-integrated technology to make your >>> job easier >>> Download IBM WebSphere Application Server v.1.0.1 based on Apache >>> Geronimo >>> http://sel.as-us.falkag.net/sel? >>> cmd=lnk&kid=120709&bid=263057&dat=121642 >>> >>> --------------------------------------------------------------------- >>> --- >>> >>> _______________________________________________ >>> Jmol-users mailing list >>> Jmol-users@lists.sourceforge.net >>> https://lists.sourceforge.net/lists/listinfo/jmol-users >>> >>> >> >> >> ---------------------------------------------------------------------- >> --- >> Using Tomcat but need to do more? Need to support web services, >> security? >> Get stuff done quickly with pre-integrated technology to make your >> job easier >> Download IBM WebSphere Application Server v.1.0.1 based on Apache >> Geronimo >> http://sel.as-us.falkag.net/sel? >> cmd=lnk&kid=120709&bid=263057&dat=121642 >> _______________________________________________ >> Jmol-users mailing list >> Jmol-users@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/jmol-users > > /////////////////////////////////////////// > > Frieda Reichsman, PhD > Molecules in Motion > Interactive Molecular Structures > http://www.moleculesinmotion.com > > /////////////////////////////////////////// > > > ------------------------------------------------------------------------- > Using Tomcat but need to do more? Need to support web services, security? > Get stuff done quickly with pre-integrated technology to make your job > easier > Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642_______________________________________________ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users > ------------------------------------------------------------------------- Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
