[PyMOL] vacuum electrostatics

[Scott C. <cl...@uc...>]

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-