[Chimera-users] electrostatic surface calculation

Ursula Schulze-Gahmen uschulze-gahmen at lbl.gov
Wed Oct 2 14:51:29 PDT 2013

I calculated the coulombic surface and the electrostatic surface for my
molecule. They show a significant difference in the shape of a small
surface area. For the electrostatic surface, I converted the pdb file into
a pqr file using the pdb2pqr called from chimera. Then I ran APBS also from
within Chimera. When I display this surface it exhibits a strong protrusion
in an area where there is no side chain. This protrusion is not present in
the Coulombic surface. Any idea where this is coming from?



Ursula Schulze-Gahmen, Ph.D.
Assistant Researcher
UC Berkeley, QB3
356 Stanley Hall #3220
Berkeley, CA 94720-3220
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