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Dear phenix.refine users:<br>
<br>
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.<br>
<br>
This paragraph (see attached HTML file) will be available as part of
phenix.refine documentation in the next release of PHENIX and CCI Apps.
<br>
<br>
*Important:* writing this text I assumed that the latest version of
phenix.refine is used (currently, it is one from CCI Apps: <i>2008_01_09_2058</i>
, <a class="moz-txt-link-freetext" href="http://www.phenix-online.org/download/">http://www.phenix-online.org/download/</a>).<br>
<br>
Cheers,<br>
Pavel.<br>
<br>
<br>
<blockquote cite="mid:6.2.5.6.2.20080122083035.031456f8@lanl.gov"
type="cite">
<blockquote type="cite">I have a high resolution structure with NADP
as ligand bound to it.
<br>
I was using CNS to start with. Somehow the Rfree was always very
<br>
high. But when I tried with default options of data= and model=,
<br>
in phenix.refine with the whole data and the intial rigid body
<br>
refined coordinates from CNS, the Rfactors came down to 31%. I have
<br>
now decided to do refinements with phenix.refine.
<br>
Do you suggest any protocol for refinement of structure at this high
<br>
resolution starting from initial rigid body refinements?
<br>
Since I would like to handle alternate conformations in the final
<br>
steps. I am wondering if the 2007 July version could handle
<br>
refinements of alternate conformations.
<br>
Thanks,
<br>
Viji
<br>
</blockquote>
</blockquote>
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