Re: [PyMOL] [Pymol] Set scale of vacuum electrostatic potential

Hi Victor,

You should never use the build-in "generate vacuum electrostatic potential"
function for any real analysis. The theoretically correct approach is to
use the Poisson-Boltzman equation (as implemented for example in the APBS
plugin). Other approaches like generalized Born models or SASA methods can
be justified for things like Molecular Dynamics, i.e. when you need to
compute the electrostatic energy contributions very often (at expense of
reducing the accuracy of your computations).
Could you provide an example of your "white" molecules? I would like to see
if I can reproduce your observation.


Cheers,
Osvaldo.



On Sun, Jul 26, 2015 at 3:48 AM, Victor Xiao <vic...@gm...> wrote:

> Dear All,
>
> First, I am trying to compare surface electrostatic potential among
> several members from a protein family. I was able to use build-in function
> in pymol (generate vacuum electrostatic potential). However, the range of
> potential for each molecule is automatically set up and they are different.
> (e.g, one could be -5 to 5 and another one could be -10 to 10, so the color
> scales between these two molecule are not comparable. A -5 potential will
> be compeletely red in the first molecule, but is only light red in the
> second molecule). Can I set the potential to the same range in order to
> compare?
>
> Second, a off-topic question, I also tried to use APBS calculation. By
> this way I was able to render most of molecules in red-white-blue scale,
> but a few of molecules are completely white. I couldn't find where the
> problem is.
>
>
> Any comment or suggestion will be appreciated. Thank you very much!
>
> Best,
> Xiao
>
>
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