Bob Hanson schrieb: > The trick to updating the menu is to use the frame command. If you only > have one frame, just add this: > > frame 0 > > and the menu will be updated to enable isosurface mapping of MEP > > Bob > > frame Reinhold Stoermann wrote: > > >> Hello to all, >> >> I just joined this list, because I currently try to convert a website >> > >from using the old MDL Chime to jmol. > >> (jmol 11.2.14). >> >> The molecules are represented by a bunch of PDB files, where the columns >> 61-66 usually holding the temperature factor have been filled instead >> with partial charges of the atoms which where computed with MOPAC. >> >> This arrangement made it possible in Chime to generate an isosurface >> with a coloring scheme according to the partial charges. >> >> If I laod the same pdb files in jmol, the menu option >> >> Surfaces -> Molecular Electrostatic Potential >> >> is not accessible, and a script using the command >> >> color atoms temperature >> >> gives an image of red an blue atom colorings bearing no relation to the >> "temperature factors" (which are actually partial charges). Even if I >> change some of the these values in the pdb file by hand, this has no >> effect on the given coloration of the manipulated atoms. >> >> Maybe Jmol does not support this trick to visualize molecular >> electrostatic potentials from pdb files? >> >> So if I have to convert the pdb files to some other format, what would >> it be? >> (I still need the pdb columns for the "residue name" to be conserved in >> that other format, because some other coloration scheme depends on that.) >> >> >> Dr. Reinhold Störmann >> Bioorganic Chemistry >> Center for Environmental Research & Technology (UFT) >> Leobener Str. >> D-28359 Bremen >> >> >> ------------------------------------------------------------------------- >> 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 >> >> >> > > > Thanks alot for providing the nice trick. It really works.
Dr. Reinhold Störmann Bioorganic Chemistry Center for Environmental Research & Technology (UFT) Leobener Str. D-28359 Bremen ------------------------------------------------------------------------- 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
