[Chimera-users] Electrostatics potential of amino acid residues

[Elaine Meng]

Hi Ankush,
If you want to show the electrostatic potential by coloring the molecular surface in Chimera, please see this recent post for two possible ways:
<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2012-January/007058.html>

See also this tutorial:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/surfprop.html>

For plotting, you would need to use some other program.  Also, it is unclear what would be on the X-axis and Y-axis of this plot, since the potential varies in 3D space.  There is not a single potential value per residue or anything like that.

For comparing electrostatics of proteins, you might be interested in this web server:
<http://pipsa.eml.org/pipsa/>

I hope this helps,
Elaine
-----
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 13, 2012, at 9:05 AM, Ankush Sharma wrote:

> Regards all,
> i wanted to calculate the calculate the Electrostatics potential associated with a specific part of the protein and differentiate from the other part of protein. How can it Possible . is there any method apart from MD to plot a graph of both to diffrentiate Quantitatively the The Potential
> Thanks in advance 
> Ankush Sharma