From: Ricardo O. S. Soares (rsoares_at_fcfrp.usp.br)
Date: Thu Jan 16 2014 - 07:55:14 CST

Hello John,

I see, there are indeed different ways to achieve those distinct colorings.
You're right, the built-in pymol contact potential gives false potential, and the optimal way to color by electrostatic surface, as I see, would be the use of APBS or other reliable Poisson-Boltzmann solver.

Thanks for your reply!

Ricardo.

---
Biological Chemistry and Physics
Faculty of Pharmaceutical Sciences at Ribeirão Preto
University of São Paulo - Brazil
----- Mensagem original -----

> De: "John Stone" <johns_at_ks.uiuc.edu>
> Para: "Ricardo O. S. Soares" <rsoares_at_fcfrp.usp.br>
> Cc: vmd-l_at_ks.uiuc.edu
> Enviadas: Terça-feira, 14 de Janeiro de 2014 13:43:03
> Assunto: Re: vmd-l: Display APBS on Solvent Accessible Surface

> Hi,
> I read the PyMol page you referenced, and I note that their coloring
> scheme is a false potential and is not based on the electrostatic
> field.
> If your goal is merely to have a strong coloring (e.g. solid red/blue
> with very little white/gray in between) you can achieve this in VMD
> by changing the "Color Scale Data Range" values in the "Trajectory"
> tab
> of the graphical representations window. If what you're after is to
> show the electrostatic coloring for a surface to the electrostatic
> potential
> other than the one that's actually being displayed on the screen
> (e.g.
> compute electrostatic field associated with vertices on a surface
> that's
> either 1.4A smaller or 1.4A larger due to the probe radius), then
> that
> is not something that VMD will allow you to do. You can only color by
> the actual potential associated with the location in space. Depending
> on
> which electrostatics solver has been used, the comments on the PyMol
> page
> you reference that relate to "artifacts and noise in the PB solver"
> may or may not be relevant.

> I don't think that coloring the SASA points makes much sense to me,
> if
> that were what you wanted, then you could get that directly from
> drawing
> an MSMS surface or Surf surface, and coloring by Volume.

> Cheers,
> John

> On Fri, Jan 10, 2014 at 12:42:05PM -0200, Ricardo O. S. Soares wrote:
> > Hello John and Josh,
> >
> > thank you for your inputs!
> >
> > I'm familiar with the surf representation+color by volume method,
> > in fact
> > that is the one I've been employing.
> > However the added 1.4 A radius from the solvent accessible surface
> > starting from the molecular surface does present changes in the
> > electrostatic profile, being them less intense (with more
> > pronounced
> > white/neutral regions).
> > If you take PyMol's APBS plugin as an example, under the
> > Visualization tab
> > you can check/uncheck the solvent acc. surf. box and see the
> > difference
> > (as briefly described here
> > http://www.pymolwiki.org/index.php/Protein_contact_potential).
> > In VMD I can simulate the same color pattern by setting the
> > representation
> > to VDW with added 1.4 radius, or more or less with surf rep. and a
> > larger
> > probe radius.
> > So Josh's suggestion of writing a script to color the SASA points
> > by
> > volume is what could come closer to what I need, however I was
> > hopping
> > there was a more direct way to do so with the surface/MSMS
> > representation.
> >
> > Thanks,
> >
> > ---
> > Biological Chemistry and Physics
> > Faculty of Pharmaceutical Sciences at RibeirA-L-o Preto
> > University of SA-L-o Paulo - Brazil
> >
> > ----------------------------------------------------------------------
> >
> > De: "Josh Vermaas" <vermaas2_at_illinois.edu>
> > Para: "Ricardo O. S. Soares" <rsoares_at_fcfrp.usp.br>, "VMD List"
> > <vmd-l_at_ks.uiuc.edu>
> > Enviadas: Quinta-feira, 9 de Janeiro de 2014 20:36:59
> > Assunto: Re: vmd-l: Display APBS on Solvent Accessible Surface
> >
> > Hi Ricardo,
> >
> > I'm not sure if this is what you want, but it sounds like you are
> > trying
> > to just color an approximation of the protein boundary by what is
> > loaded
> > into the volumetric data. What I do is just use the quicksurf
> > representation for my protein (which isn't quite SASA, but is close
> > enough), and then color by volume. I believe the displayed points
> > that
> > SASA can generate are just graphics objects, so if you are really
> > keen
> > you can write a script and color them all yourself, but I think
> > quicksurf + color by volume is close to what you want with much
> > less
> > fussing around.
> >
> > Good luck!
> > -Josh Vermaas
> >
> > On 01/09/2014 03:12 PM, Ricardo O. S. Soares wrote:
> >
> > Hello VMD users,
> >
> > I have an externally generated potential map (dx file) and I'd like
> > to
> > assign its MSMS representation to solvent accessible surface,
> > instead
> > of the default Connolly surface, but I can't figure a way to do
> > that.
> > (this is also cited here
> > http://ibicluster.uchicago.edu/roll-documentation/apbs/tutorial/index.html#ftn.id442044).
> >
> > I know one can calculate "measure sasa" and then draw the points,
> > but
> > I can't figure it out if its possible to assign these points the
> > colors of the electrostatic potential.
> >
> > Thanks,
> >
> > Ricardo.
> >
> > ---
> > Biological Chemistry and Physics
> > Faculty of Pharmaceutical Sciences at RibeirA-L-o Preto
> > University of SA-L-o Paulo - Brazil

> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/