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
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