[phenixbb] polygon and membrane proteins

Pavel Afonine PAfonine at lbl.gov
Tue Apr 6 14:08:09 PDT 2010

Hi Pascal,

what are the selection criteria that can be used to identify those 
structures in PDB? Any specif keywords in PDB file header? Can it be 
done (such a selection) in a robust way (with minimum guesses and 
resulting errors)?

If you can formulate these selection criteria, then I will be able to 
add it to a future version.


On 4/6/10 1:30 PM, Pascal Egea wrote:
> Dear Developers,
> 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?
> Thanks in advance,
> -- 
> Pascal F. Egea, PhD
> Assistant Professor
> UCLA, David Geffen School of Medicine
> Department of Biological Chemistry
> 314 Biomedical Sciences Research Building
> office (310)-983-3515
> lab (310)-983-3516
> email pegea at mednet.ucla.edu <mailto:pegea at mednet.ucla.edu>
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