[Chimera-users] Partial Charge and Electrostatic Potential Maps

Elaine Meng meng at cgl.ucsf.edu
Thu May 10 15:42:31 PDT 2012

Hi Nikolay,
Again I don't have the greatest solution... maybe others have better ideas.

Your options for ESP map calculation are
(A) use a separate program like APBS, UHBD, or DelPhi  for continuum electrostatic (Poisson-Boltzmann) calculations
(B) if Coulombic ESP is OK, in Chimera use Coulombic Surface Coloring or "coulombic" command, turning on the option to create a map (grid) file. Unfortunately the way this tool works right now, it won't run unless you already have a surface.  However...

Each Coulombic calculation uses only the atoms enclosed in a molecular surface.  Maybe by default your assembly is enclosed in one giant surface, but you can instead specify a separate surface for each chain.  One easy way is to use the command "split" to make separate chain models from your assembly before showing molecular surface.   Or if you want to divide the structure some other way not based on chain ID, you can use the command "surfcat" to define surface categories (mutually exclusive sets of atoms, each of which would be enclosed in their own surface).

You could also try tinkering with surface calculation parameters (such as larger probe radius, lower vertex density, see New Surfaces category of Preferences) since it doesn't matter how ugly the surface is if you only care about the output grid file.

If partial charge (not ESP) is good enough, then after running AddH and Add Charge (or reading in a PQS file or Mol2 file that includes charges), you can just color atoms by their partial charge values using Render by Attribute or command "rangecolor".

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 May 10, 2012, at 3:05 PM, Nikolay Igorovich Rodionov wrote:

> Hi Everyone,
>                 I was wondering if there is a way to create a maps of partial charge and electrostatic potential that I could then overlay on top of a similar structure. The biological assembly I am working with is too large for good surface calculations so I would like to overlay these maps on the surface of a condensed structure that only includes the regions I am concentrating on.
> Thank you,
> Nikolay Rodionov

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