[Chimera-users] Electrostatics potential of amino acid residues

[Elaine Meng]

Hi George,
In Chimera, the main possibilities are:

(A) side-by-side visualization by coloring molecular surfaces or showing isopotential contours (see Surface Color and Volume Viewer tools)
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfcolor/surfcolor.html>
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/framevolumeviewer.html>

(B) reporting values of superimposed ESP maps at some probe atom position(s) (see Values at Atom Positions)
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/density/density.html>

(C) calculating difference map of superimposed ESP maps (see command "vop subtract")
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html>

All of these require carefully superimposing the structures/maps (and for A, subsequently translating them apart without disrupting orientation). I suspect C might be swamped out by noise and not give a useful result, but I haven't tried it.

You might take a look at the PIPSA server mentioned earlier... I don't recall all of its capabilities.
<http://pipsa.eml.org/pipsa/>

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

P.S. your return address is not the same as the email you suggested I use, so I used both... however, please update your return address if that's what you want used

On Jan 13, 2012, at 10:20 AM, George Tzotzos wrote:

> Hi,
> Following this thread prompts me to ask the following question. Assume that one is dealing with highly homologous proteins, is there a way of telling the "fine" differences in the electrostatic potential of the residues encompassing the binding cavity (buried residues).
> Thanks in advance for any suggestions.
> George