VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Sun Jan 24 2010 - 15:47:28 CST

Hi,
  Have you tried computing the SASA with a different tool yet?
(e.g. "measure sasa" in VMD?) I'd still advise _looking_ at the
resulting MSMS surfaces very carefully to see what you are getting
out of the MSMS parameters and structure you're testing.

If you ask me, a probe radius of 4.25 is pretty huge and is rapidly
heading towards the convex hull case I mentioned earlier. This may
be causing MSMS problems and it may not be a valid result.

I just loaded a random PDB and made two overlapping MSMS surface
representations, one using the probe radius of 4.25 A, and another
with a probe radius of 2.5 A. I made the surface for the 4.25 A
probe radius transparent so I could easily see the difference in
the resulting surfaces. From what I see for the protein I loaded,
I would also expect that the SASA would decrease, even for the 4.25 A
values you're giving, but without seeing the surfaces you're getting
out of MSMS, it's hard to say for sure. Is MSMS computing some area
associated with some internal cavities in one case but not the other?

Again, I recommend checking with another tool since these seem to be
unusual results.

Cheers,
  John

On Sun, Jan 24, 2010 at 02:31:59PM -0700, Khaled Barakat wrote:
> 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
>
>
>
> 

-- 
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