[Chimera-users] ESP calculations

[Elaine Meng]

Hi Nikolay,
You can generate a grid of values with the "Compute grid" option of Coulombic Surface Coloring (or corresponding option of the "coulombic" command).  The grid is a volume data set, and when it is generated the Volume Viewer  and Surface Color dialogs will automatically appear. 

<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/coulombic/coulombic.html>
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/coulombic/coulombic.html#volume>

You can save the grid to a file with the FIle menu of Volume Viewer.
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/framevolumeviewer.html>

As for the values at each point of the surface, I don't know of a way to write these all to a file, but in Surface Color if you click the Options button and then turn on the option to "Report value at mouse position" it will report the values in the status line at the bottom of the Chimera window when you click into the graphics window and then mouse over the surface. I just noticed that to make this work it is necessary to recolor the surface first by clicking the Color button on this dialog, which may be a bug, but that's the workaround!
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfcolor/surfcolor.html>

If you have the grid file saved you can reopen it in Chimera later and use it in Surface Color without rerunning the ESP calculation.

However, keep in mind that Coulombic ESP is more for qualitative purposes of visualization or making comparisons between related structures than for absolute quantitative accuracy.  For example, you could easily make all the ESP values half as large simply by doubling the dielectric constant used in their calculation, as shown in the equation in the Coulombic Surface Coloring manual page.

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 May 21, 2012, at 8:05 AM, Nikolay Igorovich Rodionov wrote:

> Hi all,
> I was wondering if there was a way to get an output data file regarding ESP coloring and calculations based on Coulomb’s law. The visualization is great but I would also like to quantify the data.
> Thank you,
> Nikolay Rodionov