[phenixbb] polygon and membrane proteins

Nathaniel Echols nechols at lbl.gov
Tue Apr 6 14:42:15 PDT 2010

On Tue, Apr 6, 2010 at 1:30 PM, Pascal Egea <pascal at msg.ucsf.edu> wrote:

> 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

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