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Hi Jianghai,<br>
<br>
thanks for finding this: you find exotic problems, as always! Could you
please send us the files (after phenix.refine and after phenix.reduce)
so we can have a close look at this particular problem ? I can't
promise to look at it immediately, but it definitely will go into the
list. May be developers at Duke volunteer looking at this problem.<br>
<br>
Thanks!<br>
Pavel.<br>
<br>
<br>
On 8/6/2008 8:17 AM, Jianghai Zhu wrote:
<blockquote
cite="mid:24D55C29-C171-4465-8397-30587022B891@idi.harvard.edu"
type="cite">
<pre wrap="">Yes, I think the phenix group should figure that out :)
-- Jianghai
On Aug 6, 2008, at 5:12 AM, Pavel Afonine wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Hi Jianghai,
phenix.refine idealizes the geometry of hydrogen atoms using the
Monomer
Library definitions for ideal values (if riding model is used). I
presume that phenix.reduce uses some other values when adding H atoms.
So it is not too surprising that the geometries of H atoms are
different
after phenix.reduce and phenix.refine.
What is interesting though is why this has a significant impact on the
clash scores.
Pavel.
On 8/5/2008 1:38 PM, Jianghai Zhu wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Hi,
I used phenix.reduce to add riding hydrogens. After phenix.refine,
the structure got a good score from MolProbity. However, if I
stripped the riding hydrogens from the structure and let MolProbity
to
add hydrogens before the analysis, I got a much worse score,
especially the clash score. Does phenix.refine refine the hydrogen
positions?
-- Jianghai
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