[Chimera-users] Electrostatic potential values at each residue

Tom Goddard goddard at sonic.net
Tue Dec 3 19:19:32 PST 2013

Hi T.M.,

  I think you've left out details about what you have done -- how did you get this value_Coulombic_ESP attribute?  Did you use values at atom positions?  Did you use the "compute grid" option in the Coulombic Surface Coloring dialog?  I guess you did that.  And you say you use Attributes of Residues -- is that an average of the atom attribute obtained from the values at atom positions dialog?  I can't be sure what you've done, but here's a guess at what your problem is.  The Chimera Coulombic Surface Coloring dialog computes the potential at points 1.4 Angstroms out from the solvent excluded molecular surface and colors the surface points using that value.  If you instead use a potential value interpolated at the center of an atom, that will give a much different value -- in fact it should tend to give an extremely large value because if the atom is charged the potential at the atom center is infinite using the simple Coulomb calculation.  But because you are (I think) using a value interpolated from a grid you don't get an infinite value, just a very large value.  So I think your problem is you are not considering that the electrostatic potential varies rapidly in space and you are comparing colors using potential values at different positions in space.


On Dec 2, 2013, at 6:31 PM, Tatsuhito Matsuo wrote:

> Dear All,
> I'd like to get the electrostatic potential (ESP) values at each residue in a protein. I implemented the "Coulombic Surface Coloring", then get the distribution of ESP values at each residue by "Render/Select by Attribute" (Attributes of [residues], Select -> Attribute [value_Coulombic_ESP]). However, The surface plot and the ESP values obtained by "Render/Select by Attribute" do not coincide with each other. For example, there are some residues where the surface plot reports positive ESP values, while "Render/Select by Attribute" gives negative ones (e.g. VAL70 CG2 in the Chimera session file attached.). Could you teach me how to solve this discrepancy?
> Thank you very much in advance,
> T.M.
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