Hi Shawn,
As you can see when you select the generate electrostatic surface
within PyMol - Warren has stated that it is "unvalidated experimental
code" and the results should be viewed with skepticism. If you want
publishable electrostatics calculated using more realistic estimates of
dielectric constants then you should use eithe APBS, GRASp, or some
other Poisson Boltzman solver. Personally I wouldn't put figures
generated from PyMols internal electrostatics calculations any any
publication.
Scott
On Apr 10, 2005, at 9:29 AM, 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-
