Qun,
PyMOL doesn't (yet) have the ability to calculate Possion Boltzmann
electrostatic potentiallys. You'll need to use an external tool like GRASP
or APBS to perform that task.
If "spectrum b" doesn't produce the desired result, then there is
probably some strange B-value present on at least one of the atoms. Try
setting the range manually:
spectrum b, minimum=10, maximum=100
or
spectrum b, blue_red, minimum=10, maximum=100
Cheers,
Warren
--
mailto:war...@delsci.com
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154
Fax (650)-593-4020
> -----Original Message-----
> From: pymol-users-ad...@lists.sourceforge.net
> [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Qun Wan
> Sent: Tuesday, July 06, 2004 8:30 AM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] questions about electrostatics
>
> Hi,
> I want to show the electrostatics of my protein. However,
> when I click electrostatics from the Demo menu, the molecule
> shown in electrostatics is not what I want. Does any one know
> what is wrong?
> Meanwhile, I want to show my protein according to its
> B-factor. When I label it in color from the tool bar that
> says "by b-factor", the whole molecule is shown in blue, not
> colorful as I want: for example, the red means high b-factor,
> the blue means low b-factor, other colors are in the middel
> range. Anyones knows how to improve the color labelling?
>
> Thanks!
>
>
>
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