that first one is doing an implicit IGNORE(solvent). Since you are adding the IGNORE explicitly in the second case, it is no longer automatically ignoring solvent. Use:
isosurface cavity3 minset 500 pocket ignore (hem,solvent) color yellow cavity translucent Bob 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 >[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
