I am replying since your question did not get addressed in the past, but know that I am not intimately familiar with PyMOL code or python.  I do have a thought, though, if using a grid approximation would work.  I have done some work with using MRC density map format in pymol, partly in anticipation of the v1.4 improvements that will come (I wanted to link to them, but can't find it...).  There is a 3D grid described by these files, usually encoding density information.  I have edited (or created) these maps to encode other types of data.  You could use them to record the potential value at each point in the grid.  Then the comparison of your two (or more) equal volume structures is just comparing grid points with the same [x,y,z] triple.

On Tue, Mar 15, 2011 at 3:39 PM, Matteo Pendleton <znfinger@gmail.com> wrote:
I posed this question some while back and thought I'd submit it again as my question wasn't answered completely. 

Is it possible to have APBS spit out a list of values for points on the surface? I'd like to be able to quantitatively compare surface electrostatics of volumetrically identical proteins. I've been able to export a mesh of points on the solvent accessible surface but would also like to have electrostatic potential values at those points.


Matt Pendleton

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Michael Zimmermann
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