That depends on what you are trying to do. Maybe the best strategy is to use fuzzy logic, whereby a residue which has 30% of it's Gly-X-Gly ASA buried has the "surfaceness" of 0.7.
On Wed, 2010-11-03 at 09:55 -0400, Buz Barstow wrote: > Dear All, > > Thanks for your suggestions! I ended up using the areaimol program in ccp4. > > My next question: > > Given a list of accessible surface area, is there a generally accepted value > of ASA above which a residue classifies as a surface residue, while below > this number it is an interior residue? > > Thanks! and all the best, > > --Buz > > > On Nov 2, 2010, at 10:56 AM, Tim Gruene wrote: > > > Hello Buz, > > > > I do not know what you mean by 'linear map', but according to its manual, > > the > > ccp4-program "surface" writes a list of accessible are per atom per residue, > > which you could convert into the total fraction per residue with not too > > much > > effort. > > > > Is this what you are looking for? > > > > Cheers, Tim > > > > On Tue, Nov 02, 2010 at 10:36:56AM -0400, Buz Barstow wrote: > >> Dear All, > >> > >> I'm looking for a software program to produce, given a 3D atomic structure > >> of a molecule, a linear map showing the surface accessibility of residues > >> in a protein structure. > >> > >> Would any one know of a program that can produce this sort of map. > >> > >> Thanks! and all the best, > >> > >> --Buz > > > > -- > > -- > > Tim Gruene > > Institut fuer anorganische Chemie > > Tammannstr. 4 > > D-37077 Goettingen > > > > phone: +49 (0)551 39 22149 > > > > GPG Key ID = A46BEE1A > > -- Edwin Pozharski, PhD, Assistant Professor University of Maryland, Baltimore ---------------------------------------------- When the Way is forgotten duty and justice appear; Then knowledge and wisdom are born along with hypocrisy. When harmonious relationships dissolve then respect and devotion arise; When a nation falls to chaos then loyalty and patriotism are born. ------------------------------ / Lao Tse /
