[phenixbb] high resolution refinement with phenix.refine

Pavel Afonine PAfonine at lbl.gov
Tue Jan 22 15:46:24 PST 2008

Dear phenix.refine users:

responding to Vijayalakshmi Janakiraman's questions about refinement at 
high resolution with phenix.refine, I finally documented this 
functionality of phenix.refine and supplied it with a small example.

This paragraph (see attached HTML file) will be available as part of 
phenix.refine documentation in the next release of PHENIX and CCI Apps.

*Important:* writing this text I assumed that the latest version of 
phenix.refine is used (currently, it is one from CCI Apps: 
/2008_01_09_2058/ , http://www.phenix-online.org/download/).


>> I have a high resolution structure with NADP as ligand bound to it.
>> I was using CNS to start with. Somehow the Rfree was always very
>> high. But when I tried  with default options of data=  and model=,
>> in phenix.refine with the whole data and the intial rigid body
>> refined coordinates from CNS, the Rfactors came down to 31%. I have
>> now decided to do refinements with phenix.refine.
>> Do you suggest  any protocol for refinement of structure at this high
>> resolution starting from initial rigid body refinements?
>> Since I would like to handle alternate conformations in the final
>> steps. I am wondering if the 2007 July version could handle
>> refinements of alternate conformations.
>> Thanks,
>> Viji
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