[Chimera-users] electrostatic potential in active site at an interface

Boaz Shaanan bshaanan at bgu.ac.il
Wed Jan 26 12:44:31 PST 2011


I need your advice on the following: I have an active site which is located at the interface between two subunits. The cofactor in the active site makes interactions with residues from the two subunits. I have a few mutants and would like to display their effect on the electrostatic potential around the cofactor in order to explain changes in the activity of the enzyme.  I have a electrostatic potential calculated both in apbs (.px) and delphi (.phi) on the basis of whole dimer structure. My first question is whether those potential maps are relevant for displaying in chimera the potential in an inner part of the protein or should I calculate the potential over the interface region that I'd like to be displayed. If the latter is correct my second question how do I get a surface (molecular or accessible) depiction of this region. I tried several options in chimera (following some examples in the gallery) but none seems to be doing it right. I probably miss something. I would be grateful for any clues on how to go about this.

 Thanks for your help,


Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Phone: 972-8-647-2220 ; Fax: 646-1710
Skype: boaz.shaanan‎
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