From: Mgr. Lubos Vrbka (lubos.vrbka_at_uochb.cas.cz)
Date: Mon Feb 28 2005 - 11:06:05 CST

dear John,

> Another method that likely has more merit,
> would be to calculate the solvent accessible surface area, and use that
> as your measure of "buried" or "surface" etc. You could run a script setting
> the user field for each residue with its SASA, and then use a selection like
> "user > 1.0" or something like that as a heuristic to determine which residues
> are exposed and which are not. One could even do this for all of the atoms
> invidually, but it would take a while to calculate. Try using the
> "user > 1.0" with a script like this one and let me know if that helps.
thank you for your quick reply. i tried your script that seems to work
nicely. however it seems that the value of 1.0 is way too small. for
most residues i get values >>50.

i want to compare surfaces of 2 different proteins, i.e. to know
protein 1 surface 50% arginine, 20% lysine, 5% glycine, ...
protein 2 surface 40% arginine, 40% lysine, 3% glycine, ...
is there some other easy way how to do that, or should i try to play
with the "SASA ball" diameter and "user" field threshold (with 1.4A and
threshold 150 it starts to look better)?

regards,
lubos

-- 
.....................................................
Mgr. Lubos Vrbka
Center for Biomolecules and Complex Molecular Systems
Institute of Organic Chemistry and Biochemistry
Academy of Sciences of the Czech Republic
Prague, Czech Republic
.....................................................