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Hi,<br>
<br>
it does not include ADP refinement by default. You can refine B by
adding "adp" to "run" keyword, as explained in documentation:<br>
<br>
<a class="moz-txt-link-freetext" href="https://www.phenix-online.org/version_docs/dev-2027/reference/real_space_refine.html">https://www.phenix-online.org/version_docs/dev-2027/reference/real_space_refine.html</a><br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 4/30/15 5:09 AM, Smith Liu wrote:<br>
</div>
<blockquote
cite="mid:43716530.2055a.14d0a3b287a.Coremail.smith_liu123@163.com"
type="cite">
<div
style="line-height:1.7;color:#000000;font-size:14px;font-family:Arial">
<div>Dear All,</div>
<div>�</div>
<div>By Phenix.real_space_refine if is very nic to fit a PDB
into an EM map, and we can get a fitted PDB. However no matter
what is the run strategy (default, morphing, local grid
search, etc), in the got PDB the B-factors for each atom in
the coordinates were always those from the original input PDB,
which may make the B-factors in refined PDB meaningless. As
finally we need to deposit the refined PDB and EM to the
database, will you please explain how to settle the B-factor
issues in the refined PDB related to Phenix.real_space_refine?</div>
<div>�</div>
<div>Smith<br>
</div>
</div>
</blockquote>
<br>
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