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

Elaine Meng meng at cgl.ucsf.edu
Wed Jan 26 13:29:27 PST 2011

Hi Boaz,
By default, the ESP coloring will get the values projected 1.4 A out from the molecular surface and use them for the coloring on the surface -- thus it shows what values would be experienced by the centers of any atoms interacting directly with the surface rather than the surfaces of those atoms .  The ESP values right at the molecular surface are generally too high and vary too rapidly, which is why this "surface offset" is done (shown if you click the Options button in the tool).

I believe either map, if calculated with reasonable parameters, should be appropriate for this use.  One thing to doublecheck is that the atomic charges for calculating the ESP got assigned correctly for the APBS or DelPhi calculation.  For example, if you had hydrogens but their names weren't recognized by that program, you could have a protein with a giant negative charge.

Now, when you ask how to get the surface at the interface, I'm guessing that your current problem is that the surface encloses both subunits together instead of each one separately.  You could get separate surfaces for the separate chains by using the command "split" to make the chains different models, or by leaving them in the same model but using "surfcat" to indicate they should be treated as separate groups for surface purposes.

I hope this helps,
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jan 26, 2011, at 12:44 PM, Boaz Shaanan wrote:

> Hi
> 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

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