Hi all,
On Tue, Feb 22, 2011 at 8:00 AM, Schubert, Carsten [PRDUS] <
cschu...@its.jnj.com> wrote:
> Hi Wataru,
>
> in addition to what Jason mentioned: Have you tried to look at the
> potential mapped on the solvent accessible surface and display the
> molecular surface? If you display the potential like this the colors
> will be much more muted, on the other hand this is the setting you will
> find most often displayed in the literature.
>
I think this is likely the case. Due to a lot of feedback, the plugin
defaults changed to showing the solvent accessible surface a while ago (see
the checkboxes in the Molecular Surface section of the Visualization panel).
> Another option is to have a look at the charge distribution of your
> molecule in the actual PQR file. The potential distribution is dependent
> on the charging algorithm used. I would recommend using/looking into
> PDQ2PQR, which is available from the APBS website and compare this to
> the homegrown charging algorithm from PyMol or GRASP for that matter.
>
Many (most?) users of the plugin do indeed use PDB2PQR. It's worth noting
that the current version of the plugin allows you to specify command line
arguments to PDB2PQR (e.g. --ff=AMBER, etc. if you're interested in trying
out different force fields).
Cheers,
-Michael
>
> Hope I did not muddle the water too much
>
> Carsten
>
> > -----Original Message-----
> > From: Wataru Kagawa [mailto:wkag...@aoni.waseda.jp]
> > Sent: Monday, February 21, 2011 10:04 PM
> > To: pymol-users@lists.sourceforge.net
> > Subject: [PyMOL] Color scale changed in APBS?
> >
> > Dear PyMOL users:
> >
> > I recently used the APBS plugin (v1.3) to display the surface
> potential
> > of a protein. I noticed that the charged surfaces were much more
> > lightly colored, compared with the surface colors I have calculated in
> > the past (maybe a year ago?) on the same protein, using the same
> > softwares. The default settings and the same range (-10 kT to 10 kT)
> > were used in both cases. Has anyone experienced this?
> >
> > I would appreciate any help.
> >
> > Wataru
> >
> >
> >
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--
Michael Lerner, Ph.D.
IRTA Postdoctoral Fellow
Laboratory of Computational Biology NIH/NHLBI
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