[Chimera-users] (no subject)

[Cédric Govaerts]

Hi there,

I want to compute accessible surface area for the backbone, as I want to
compare the predicted amide deuteration between two conformations of a
protein (I have PDBs for both). I tried with VADAR but the results are
puzzling, I suspect they are not correct (the more open structure gets a
lower score).

Is there a way I can do something like that in Chimera ?

In other word I need to compute how exposed to the solvent are the backbone
atoms (in fact just the NH) and get a table for every position.
Cannot seem to find a simple way to do that with Chimera...

Thanks again for your help

Cedric


Cedric Govaerts, Ph.D.
Structure et Fonction des Membranes Biologiques (SFMB)
Universite Libre de Bruxelles
Boulevard du Triomphe - CP 206/2
B-1050 Bruxelles (Belgium)
Tel:  +32-2-650.53.77
Fax: +32-2-650.53.82