[Chimera-users] Chimera ESP values

Elaine Meng meng at cgl.ucsf.edu
Fri Feb 5 10:32:50 PST 2016


Hi Sarah,
Technically it can be done: you can choose the Coulombic option to “compute grid” and then use the “Values at Atom Positions” tool to get the grid values interpolated to atomic center locations.  That would give value per atom.  Then you could sum or average the atomic values with Attribute Calculator to get a single value per residue.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/density/density.html>
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/calculator/calculator.html>
Saving attribute values to a file:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#saving>

HOWEVER, it’s not really meaningful to evaluate ESP at the same atomic centers whose charges were used to calculate the ESP.  In general, people display ESP at the surface (not at the atom centers) as an indicator of how the molecule might interact with charges in other molecules like solvent, ligands, or other proteins that were not included in the calculation of the first molecule’s ESP.

The ESP becomes extremely high/low if you are right at the atomic center where the partial charge is modeled, like a singularity.  By default, we don’t even evaluate the ESP at the surface of the atomic sphere, but instead 1.4 Angstroms further out where the center of a “water” probe touching the atom might go.  That ESP value is then mapped to color which is shown back at the corresponding surface vertex. 

See also this previous post:
<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2013-December/009399.html>

You might as well just use AddH, Add Charge, and then just save the atomic charges to a file, but it will be no surprise that (disregarding chain termini) the atoms of Asp, Glu residues will sum to charge -1 and Lys, Arg will sum to charge +1. 

So the ESP values that might be of use are mapped to surface vertices, and there are several vertices per surface atom and zero vertices for atoms that aren’t at the surface.  It is not clear how you would combine that data into some single value for a residue.  You can see the values for surface positions upon mouseover by choosing the “compute grid” option in Coulombic, then closing the Coulombic tool and re-coloring the surface using that grid and the Surface Color tool which should automatically appear after the grid has been computed.  In Surface Color, click Options and then turn on the option to “Report value at mouse position” and then press Color.  The values and surface-point coordinates will be shown in the status line at the very bottom of the Chimera window as you move the mouse over the surface.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/surfcolor/surfcolor.html>

As far as I know, there is no option to save the ESP values at all the surface points into a file, however.

I hope this clarifies the situation,
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 Feb 4, 2016, at 10:29 AM, Sarah Keasey <keasey1 at umbc.edu> wrote:

> Hello,
> 
> I have generated structure images in Chimera and colored according to Coulomb ESP. I would like to export the ESP values so that I would have an ESP value for each residue in my protein. Is this possible?
> 
> Thanks in advance,
> 
> Sarah Keasey
> Ph.D. Candidate
> Biological Sciences
> University of Maryland Baltimore County
> 
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> Chimera-users at cgl.ucsf.edu
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