[phenixbb] polygon and membrane proteins

[Pavel Afonine]

Hi Pat,

thanks! The PDB codes seem to be there as well (at least it seems to be 
the case from a quick look).

Pavel.


On 4/6/10 2:20 PM, Patrick Loll wrote:
> I don't know how easy this would be to do, but...
>
> Steve White maintains a nice up-to-date database of membrane proteins 
> of known structure 
> (http://blanco.biomol.uci.edu/Membrane_Proteins_xtal.html). Since he 
> has tabulated all of the PDB IDs, it should be trivial for him to 
> supply just a list of the four-letter codes, which could be used as a 
> filter.
>
> Pat 
>
> On 6 Apr 2010, at 5:08 PM, Pavel Afonine wrote:
>
>> 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.
>>
>> Pavel.
>>
>>
>> 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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>
>
> ---------------------------------------------------------------------------------------
>
> Patrick J. Loll, Ph. D.  
>
> Professor of Biochemistry & Molecular Biology
>
> Director, Biochemistry Graduate Program
>
> Drexel University College of Medicine
>
> Room 10-102 New College Building
>
> 245 N. 15th St., Mailstop 497
>
> Philadelphia, PA  19102-1192  USA
>
>
> (215) 762-7706
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