Hi Massimo, I think the reason buried solvent accessible area is usually reported is because it is probably better correlated with the solvation energy, how much energy is related to the water / protein interface, then solvent excluded area. This makes some sense to me because the SAS surface is where the “probe” sphere representing a water molecule is centered so it roughly says how many spheres or water molecules you can pack against the protein. This is all just my guess. The only case where I have read literature on this topic is studies that try to identify biologically meaningful protein-protein interfaces in X-ray crystal structures by measuring buried areas. A sanity check on your buried area values (after checking that they are positive) is try changing the probe radius by a small bit and see if you get just a small change in buried area. This will cause different surfaces to be computed but should result in a small area change if the calculation is correct. The default probe radius is 1.4 Angstroms, so try “measure buried #0 #1 probe 1.45”. Tom
On Mar 11, 2015, at 3:48 PM, ms wrote:
Hi Tom,
Thanks for your reply.
On 11/03/15 23:18, Tom Goddard wrote:
I think buried solvent accessible area (SAS) is most often used when buried areas are reported.
OK, thanks. Any justification in the literature for that, just to be on the safe side?
Negative values of buried SAS are impossible, that would be a bug, probably a failure of the surface calculation,
OK.
and if you see a case of that could you send me a Chimera session that demostrates it?
I will do it tomorrow.
Unfortunately with erratic surface calculation (which does not always report when it goes awry) you cannot be certain the numbers are correct.
Understood. If so, is there any sanity check I can do to see if a calculation has more or less chances of being meaningful?
thanks, Massimo
-- Massimo Sandal, Ph.D. http://devicerandom.org