From: Frieda R. <fr...@ns...> - 2008-05-20 21:30:51
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Hi Thomas, cavity3 is the object ID in this case, just a name Karl is giving the isosurface so as to be able to refer to it in later commands... isosurface [object id] [construction/mapping parameters] [surface object]...etc. Frieda ////////////////////////////////////// Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com 413-253-2405 ////////////////////////////////////// On May 20, 2008, at 4:34 PM, Thomas Stout wrote: > > Sorry to burst in on this thread, but I found it interesting and > then the specification caught my eye: > > what does "cavity3" mean? I don't find that in the documentation > for the isosurface command (http://chemapps.stolaf.edu/jmol/docs/?ver=11.6#isosurface > ). According to this, "cavity" should take two arguments, "cr" and > "en", and so should look like: "cavity 1.2 10" (using the > defaults). Is "cavity3" shorthand for "cavity 3.0 10" ? > > Thanks! > -Tom > > > On Tue, May 20, 2008 at 11:29 AM, Bob Hanson <ha...@st...> > wrote: > Oh, also, you might want to add OXY ot that list and also try > experimenting with the probe radius after the CAVITY parameter. > Something like: > > isosurface cavity3 minset 500 pocket ignore (hem,solvent,oxy) color > yellow cavity 1.0 translucent > > Karl Oberholser wrote: > > > Hi All, > > When I use these two commands, select protein; isosurface cavity3 > > minset 500 pocket color yellow cavity translucent, with myoglobin > > (1mbo), I obtain two cavities. If I add ignore hem to give > isosurface > > cavity3 minset 500 pocket ignore hem color yellow cavity > translucent, > > I just obtain the cavity that is binding the heme. I would have > > expected to get the two other cavities along with the heme binding > > cavity. Am I missing something? > > > > 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 |