Ewen, I think Angel covers it pretty well. Thank you, Angel. The file formats from which Jmol currently reads partial charge information include:
Chem3D XML (http://www.cambridgesoft.com/) CML (http://www.xml-cml.org/) CSF (Sygress, formerly CAChe, by Fujitsu, http://www.cachesoftware.com/cache/) Gaussian output files (http://www.gaussian.com/) Ghemical molecular mechanics files (http://www.uku.fi/~thassine/ghemical/) HIN (Hyperchem native format, http://www.hyper.com) MOL2 (Trypos, http://www.tripos.com/index.php?family=modules,SimplePage,,,&page=sup_mol2&s=0) MOPAC7 (http://sourceforge.net/projects/mopac7/) NWChem (http://www.emsl.pnl.gov/docs/nwchem/nwchem.html) PQR (http://pdb2pqr.sourceforge.net/, upcoming 11.1.30) QChem (http://www.q-chem.com/) Spartan Smol (Wavefunction, http://www.wavefun.com) If we are not reading partial charge information that is present in a file type you are using, just ask for it. Bob Angel Herraez wrote: >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 > > ------------------------------------------------------------------------- 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
