VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jan 14 2014 - 09:43:03 CST

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/