Shawn Milano wrote:
Hi,
I want to show an electrostatic surface of my protein for publication. In
Pymol, I believe I can use generate-vacuum electrostatics. However, I am not
quite sure what the difference is between absolute and relative protein
surface potential. Could you help me with this? Second, I have a question
about the slider that appears after the surface is calculated. What do the
numbers represent, and what is changing as you slide to the left and right.
I want to use the figure for publication and make sure I understand how to
explain it properly.
Thanks,
Shawn-
Dear Shawn,
as the word implies, "relative potential" means that you are looking
only at the differences in electrostatic potential between different
parts of the protein,
as in "a is more positive than b". Absolute potential refers to the
absolute values calculated at a given point, irrespective of other
regions. Since what matters is the
derivative (gradient) of the potential, and not the potential itself,
the zero value is fixed by convention, but you want to make sure you
use a consistent convention when
comparing different calculations. In any case, and as Scott as pointed
out, it is not a good idea to estimate molecular potentials for proteins
with a vacuum model -
you can get very large errors due to neglecting the low-dielectric
behavior of the protein interior. Definitely use something like APBS,
Grasp, Delphi, MEAD or other
Poisson-Boltzmann package which generates electrostatic potential grids
in a format that can be read in PyMOL. Also note that both relative and
absolute potentials may be deeply affected by the model you use to
represent the charges in your molecular system.
Best regards,
Paulo
