[Chimera-users] areaSAS calculation intuition detail
dziemian at ucalgary.ca
Tue Feb 20 11:47:05 PST 2018
I have read as much as I can about SASA calculations but I'm still missing something.
I've been enlightened on the difference between solvent-excluded surface (SES) and solvent-accessible (SAS) - particularly from this post: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2010-September/005532.html
>From my understanding, the SES is calculated via the 'rolling sphere' method, where the radius of the probe contacts the VDW surface of individual atoms. This used to be my understanding of SAS, as other descriptions have explained it this way, but I now realize this is incorrect. The SES is also what is shown when one enables the surface representation.
Now, I read the description of how SAS is calculated at: https://www.cgl.ucsf.edu/chimera/data/sasa-nov2013/sasa.html which more or less makes sense to me. Basically, the radius of the probe is the 'limit of what is seen' from the perspective of the probe center when it overlaps with the VDW of molecule atoms.
In this regard, is it true that the SAS probe 'penetrates' the SES surface representation, so greater probe radii observe a greater SAS, with respect to residues. Conversely, larger probe radii observe a reduced SES, with respect to residues. This is my understanding based on my calculations in Chimera.
The missing intuition is that I do not understand what the 'limit of penetration', so to speak, is for the SAS probe. E.g. given a protein and its surface, is the probe center limited by the surface but it's radius penetrates/overlaps the surface and the residues within? There must be some sort of limit for the probe center, I imagine, otherwise it would penetrate within the protein molecule and 'see' everything.
I hope my question and explanations are clear. It's rather difficult to describe without a visual aid.
P.S. these sort of calculations are a dream with Chimera!
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