On Tue, Apr 6, 2010 at 1:30 PM, Pascal Egea
I wonder if there would be a simple way to get the Polygon program implemented in Phenix to use only membrane protein deposited structures as the reference data set. I understand that the reference set is much smaller than the whole menagerie of available structures but it represents an homogenous class of protein (crystallized in detergent). Do you think that this would be meaningful and useful?
I think it is going to be limited by the relatively small sample size. Membrane proteins are only about 1% of the PDB, and the comparison of statistics in Polygon really needs to be filtered by resolution - which isn't going to leave many structures to compare with, especially at high resolution. -Nat