Frieda, you hit on just what I happened to be working on today. How convenient! The problem is those water molecules. Yes, we need a new option. This is to ignore a certain set of atoms, in this case the water molecules. Here you go, just uploaded:
isosurface ignore(solvent) sasurface This tells Jmol you don't want the surface around the water molecules. Check out http://www.stolaf.edu/academics/chemapps/jmol/docs/examples-11/new.htm (tomorrow -- right now I can't compile the applet because of changes made earlier today, but I have it working on my machine) Bob Frieda Reichsman wrote: > > On Aug 20, 2006, at 4:38 PM, [EMAIL PROTECTED] > <mailto:[EMAIL PROTECTED]> wrote: > >> >> "Solvent-accessible" which means the probe center position when rolled >> >> around the molecule. This is: >> >> >> isosurface SAsurface 1.2 >> > > I am trying the command as shown above and I am getting only very > partial surfaces on e.g., 1mbo.pdb (myoglobin) and on other pdb files > as well. Is there something more to it than just opening the file, > selecting protein, and issuing the command? > > Thanks, > 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
