[Chimera-users] Electrostatics potential of amino acid residues

George Tzotzos gtzotzos at me.com
Fri Jan 13 10:48:31 PST 2012

Many thanks Elaine, much appreciated



On Jan 13, 2012, at 7:43 PM, Elaine Meng wrote:

> 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

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