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/).

Cheers,
Pavel.

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