Thanks Bob. If I understand correctly, this means that Jmol is calculating the surface MEP based on the values in the file, which do not represent absolute MEP but rather, are partial charges. And that means that when Jmol calculates the surface MEP for only part of the amino acid (the side chain), the absence of the 'backbone' atoms greatly influences the calculation of the potential over the side chain, yes? And so the absence of those atoms is creating the effect I'm seeing of diminishing the potential on the charged side chain, and magnifying it a bit on the uncharged side chain?
This leads to another question, would it be possible to show a partial surface? That is, 'build' the surface for the entire amino acid, but only display only the surface over the side chain. I imagine this would be a feature request, would it be feasible to do this? Frieda On Aug 5, 2008, at 12:11 PM, Bob Hanson wrote: > if you are mapping MEP data, remember that a MEP calculation is > being done that converts charge on atoms to potential at some distance > (on the surface) from a bunch of atoms, collectively. This value falls > off with distance. So that's probably why your numbers are low. They > aren't just charges, and really they are just approximations of > electron > potential, as well. If you want to map the charges themselves, you > will > need to use "map property partialcharge". But that will look somewhat > blotchy, I suspsect. > > I'm sure you have the color range/absolute business correct. > > > Bob > >> Am I misunderstanding what "color range/absolute x.xxx y.yyy" should >> be doing? Is there a way to get the coloring for "color range all" >> but >> only show the surface for the side chains? >> >> Frieda >> >> >> ////////////////////////////////////// >> >> Frieda Reichsman, PhD >> Molecules in Motion >> Interactive Molecular Structures >> http://www.moleculesinmotion.com >> 413-253-2405 >> >> ////////////////////////////////////// >> >> >> >> >> >> ------------------------------------------------------------------------- >> This SF.Net email is sponsored by the Moblin Your Move Developer's >> challenge >> Build the coolest Linux based applications with Moblin SDK & win >> great prizes >> Grand prize is a trip for two to an Open Source event anywhere in >> the world >> http://moblin-contest.org/redirect.php?banner_id=100&url=/ >> _______________________________________________ >> Jmol-users mailing list >> Jmol-users@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/jmol-users >> >> > > > -- > Robert M. Hanson > Professor of Chemistry > St. Olaf College > Northfield, MN > http://www.stolaf.edu/people/hansonr > > > If nature does not answer first what we want, > it is better to take what answer we get. > > -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 > > > > ------------------------------------------------------------------------- > This SF.Net email is sponsored by the Moblin Your Move Developer's > challenge > Build the coolest Linux based applications with Moblin SDK & win > great prizes > Grand prize is a trip for two to an Open Source event anywhere in > the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > _______________________________________________ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
