VMD-L Mailing List

From: Ricardo O. S. Soares (rsoares_at_fcfrp.usp.br)
Date: Fri Jan 10 2014 - 08:42:05 CST

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 elec trostatic 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 Ribeirão Preto
University of São Paulo - Brazil
----- Mensagem original -----

> 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 Ribeirão Preto
>
> > University of São Paulo - Brazil
>