[Chimera-users] ESP calculations

Eric Pettersen pett at cgl.ucsf.edu
Mon May 21 11:57:23 PDT 2012

Also, if you compute a volume, you can use the "Values at Atom  
Positions" tool to, um, get the values at atom positions (say, a  
ligand), if that's relevant to what you're doing.


On May 21, 2012, at 9:09 AM, Elaine Meng wrote:

> 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
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