[Chimera-users] ESP calculations

Tom Goddard goddard at sonic.net
Tue Jun 5 11:57:18 PDT 2012

Hi Elaine,

   You mentioned that the Surface Color dialog "report value at mouse 
position" wasn't working for a surface colored with Coulomb 
electrostatic coloring unless you pressed the Color button first to 
recolor the surface.  This is because the surface was in fact never 
colored with the Surface Color dialog.  Instead it was colored by the 
Coulombic Surface Coloring dialog.  The Surface Color dialog popped up 
because you used the Coulombic dialog with the option to "compute grid" 
and that Surface Color dialog pops up whenever a new electrostatics grid 
is created.  But the surface coloring didn't use that grid.  It instead 
directly computed the potential at the surface vertices from the 
charges.  So in fact if you color from the grid you might see a slightly 
different (less accurate) result.  At any rate this is the explanation 
of why you had to press the Color button on the Surface Color dialog to 
get the values on the surface reported.


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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