I was probably using an old file. Karl Oberholser wrote:
> In 1mbo the molecular oxygen is part of the heme structure and is > therefore ignored along with the heme. > > >>> Bob Hanson <[EMAIL PROTECTED]> 5/20/2008 2:29 PM >>> > 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 > >[email protected] > >https://lists.sourceforge.net/lists/listinfo/jmol-users > > > > > > > -- > Robert M. Hanson > Professor of Chemis try > 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 > > -- 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
