[Chimera-users] finding residues with large effects on local electrostatic potential

Elaine Meng meng at cgl.ucsf.edu
Wed Jun 1 16:16:39 PDT 2016

Hi Deniz,
No need to apologize, that’s why we have an address for questions.  :-)

I am guessing you were coloring by electrostatic potential and want to figure out which residues are having large effects in some places.  The question is not that simple because electrostatic interactions are long-range, meaning that the potential at a point is based on many atoms in many residues, including those farther away.  

However, the largest contributions at a surface point will generally be from the residues with net positive or negative charges that are not too far away.

In other words, if you see a blue patch, you could then try to figure out positively charged residues are near it, or if a red patch, which negatively charged residues are near it.  The problem in Chimera that you may be having is that when you put the mouse over the surface, the surface is blocking the atoms, so it does not tell you what residue is under that surface. 

One way to try to figure it out is to temporarily hide the surface (Favorites… Model Panel, uncheck the “Shown” button for the surface), then click back into the main window *without moving the structure* and put the mouse over the same area to see what residues are there, using the pop-up balloons with residue information.  You would probably want to show all the sidechain atoms first (e.g. command: display protein), and maybe select residues that are known to be positive (or negative) to help guide yourself to the right place.

Command: select :lys,arg,his
(… the ones likely to contribute to positive patches…)

Command: select :asp,glu
(… the ones likely to contribute to negative patches…)

You can keep turning the surface on and off with the checkbox in the Model panel.  This is interactive guessing and may not be that easy.  Just keep in mind that you can’t say that some patch is all from one or two residues, only that they have significant contributions.

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 Jun 1, 2016, at 3:44 PM, Deniz Simsek Buck <simsekd at stanford.edu> wrote:

> Hi Elaine,
> I am sorry for bothering you. But, I need urgent help.
> If I tell chimera to find the surface charge, negative and positive, and if I want to know which residues are responsible for this charge, what do I do?
> thank you so much,
> deniz

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