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From: Khaled Barakat (kbarakat_at_phys.ualberta.ca)
Date: Sun Jan 24 2010 - 15:31:59 CST

Thanks for your reply.

My probe radii were under my signature along with the SASA and SESA values that I got. They are: 2.5, 2.8, 3 and 4.25.

Thanks any way,
Khaled

> Hi,
> There's no need to re-post. If you're not getting any answers, it's
> either because the question is unclearly stated, or others don't know the
> answer. My own guess is that the behavior for response of SASA and SESA
> may depend on the specific values of probe radius that you're using. You
> didn't say what probe radii you are actually trying, so it's hard to give
> a general answer. For a probe radius near infinity, you'll get the area of
> a convex hull surrounding the structure. For a probe radius of zero, you'll
> get the surface area corresponding to the "union of balls". Presumably you
> are trying values that are close to the 1.4 A radius of a water molecule,
> but you haven't indicated to what degree you have increased the probe radius
> nor what your solute structure looks like. I think you may come up with your
> own explanation if you look very carefully at the MSMS surface that's
> generated for the probe radii you have selected. Failing this, you may
> want to discuss it with Michel Sanner, the primary author of MSMS, as it
> might be an unusual behavior of MSMS itself under your particular test
> circumstance. Do you get the same result with other SASA calculation tools?
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Sun, Jan 24, 2010 at 01:44:45PM -0700, Khaled Barakat wrote:
> > Hello,
> >
> > I am trying to calculate the solvent accessible/excluded surface area (SASA and SESA) using MSMS for different probe
> > radii. I noticed that the SASA increases with increasing the probe radius, while the SESA decreases. My question is:
> > Does these results make sense?! I was expecting opposite results ( i.e. the SASA decreases with increasing the probe
> > radius, because a larger solvent molecule will not be able to touch the surface of the protein as much as a smaller solvent
> > molecule).
> >
> > I will appreciate if someone can help me understand these results.
> >
> > Thanks in advance.
> > Khaled
> >
> > My numbers are:
> >
> > Radius SASA SESA
> > 2.5 7869.7254 5957.5241
> > 2.8 7936.7443 5832.3499
> > 3.0 7990.4262 5782.2308
> > 4.25 8535.3977 5491.1256
> >
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078