[phenixbb] structures with problem loops / ligands

Kendall Nettles knettles at scripps.edu
Thu Apr 15 12:05:33 PDT 2010

Hi Pavel,
How about the ones I sent you? Amino acids 410-420. Here you have a  
couple of structures with the same problem, and the region contacts  
the ligands.
We are supposed to hear back from Nature Chemical Biology this week on  
the manuscript for those structures, so hopefully we will have to  
deposit them soon:)


On Apr 15, 2010, at 2:18 PM, "Pavel Afonine" <PAfonine at lbl.gov> wrote:

> Hi Everyone,
> I'm in search of a structure that has poor or nearly no density for  
> some
> relatively short loops or ligands. My search criteria are (which are
> flexible):
> - resolution 2-2.5A (slightly higher, slightly lower is ok);
> - structure is not large (~5000 atoms is absolute max., less is better
> so I can run tests quicker);
> - structure is nearly complete and correct - that is everything is  
> good
> about the structure (almost ready-to-PDB-deposit) apart from problem
> loops/ligands;
> - no data pathologies (twinning, severe incompleteness and the likes);
> - length of problem loops: from 1 to 10 residues;
> - no restrictions on data and model use (so the structure id may  
> appear
> in a future publication as an illustration, of course with all proper
> credits to the source);
> - it is desirable but not mandatory that a problem loop has some  
> importance.
> Please reply to me directly.
> Thanks in advance!
> Pavel.
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