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
