It is necessary to delete atoms you don't want included in the calculation before initiating the calculation. Undisplaying atoms or surface does not make a difference - the atoms are still there, just undisplayed. Later, you could open the electrostatic potential map with the original full structure, if you wanted to display parts that had been deleted for the potential calculation.

The "Electrostatic Surface Coloring" tool does get a potential value at each surface point in order to do the coloring, but the values are not available from the user interface. The "Values at Atom Positions" tool could be used to get the potential at the positions of atoms, but not the surface. If you knew particular coordinates you wanted to look at, you could make a PDB file with fake atoms at those positions and use the latter tool. However, if you really did want all the surface point values, I must defer to others who know python and the under-the-hood details.

On Aug 6, 2006, at 11:36 PM, Nihshanka Debroy wrote:

Hi everyone,

I have a couple of questions about the electrostatic potentials generated in Chimera using the Delphi Controller. If I have a protein with 5 chains A,B,C,D,E, and I choose to show the surfaces of all chains except C (but keep the wireframe of chain C's atoms) and then run Delphi using the DelphiController, does that mean that the potential surface generated is in the absence of chain C (which is what I want)? I'm trying to generate the potential surface without taking into account chain C, but would like to see C's wire frame for analysis purposes.

Also, is there a way to get the actual potential values at each surface coordinate?

Thanks a lot for the help.

Sincerely,

Nihshanka
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-----

Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu

UCSF Computer Graphics Lab and Babbitt Lab

Department of Pharmaceutical Chemistry

University of California, San Francisco

http://www.cgl.ucsf.edu/home/meng/index.html