Hello Ewen > I use Chime MEP surfaces for teaching basic ideas about molecular > polarity, but it's not a lightly-taken decision. > > I've converted my old Chime resources into Jmol ones now, except the > ones using MEP surfaces (and the dreaded Sculpt mode). Wanting to > push on with my Chime --> Jmol conversions, I have a newbie question for > Bob: What software would you use to calculate the MEP surface properly > from a mol (or other) file?
We've been recently trying to do this same thing. We found some solution in freeware Accelrys DS Visualizer, which can open the file (mol, pdb, whatever), calculate and show the MEP surface and export into MOL2 format, which keeps the calculated charges. However, sometimes the MEP coloring is not done by DSVis (don't know if it has to do with the original file or the program version). Also, it seems you need the latest 1.7 version to be able to export to MOL2 (1.5 won't offer this format). After that, Jmol will open the MOL2 and display the MEP either from the pop-up menu or from the equivalent isosurface command, something like isosurface molecular map mep I am still exploring other possibilities. For macromolecules, there is the pdb2pqr + APBS route --still I'm not getting successful results--. > PS Sorry if I missed it Bob, but did anything happen with lipophilic > potential colouring of surfaces? I think this is even more misterious than MEP; as far as I know, nobody says how it's calculated and, certainly, Jmol cannot do it now.. ------------------------------------------------------------------------- This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
