<span class="Apple-style-span" style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; background-color: rgba(255, 255, 255, 0.917969); ">Sorry I'm chiming in a bit late here, but I think its worthwhile to point out that hydrogen atoms are highly influenced by (and affect!) prior chemical forces - primarily electrostatics/polarization and van der Waals. Given the difficulty in refining hydrogen atoms against the scattering data alone, I would argue a rigorous model for electrostatics/vdw terms in the prior is essential. This also makes it a moot point of having to decide how to refine hydrogen atoms and dealing with tricky cases (like rotatable degrees of freedom or water molecules). There is technology available to do this already and some publications on its importance in the refinement process, for those that are interested.</span><div>
<font class="Apple-style-span" color="#222222" face="arial, sans-serif"><br></font></div><div><font class="Apple-style-span" color="#222222" face="arial, sans-serif">Regards,</font></div><div><font class="Apple-style-span" color="#222222" face="arial, sans-serif">Tim<br>
</font><br><div class="gmail_quote">On Mon, Nov 14, 2011 at 6:27 PM, Pavel Afonine <span dir="ltr"><<a href="mailto:pafonine@lbl.gov">pafonine@lbl.gov</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
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Hi Damian,<div class="im"><br>
<br>
<blockquote type="cite">
<pre>This question was motivated by discussions of whether or not to deposit riding hydrogens in the PDB, </pre>
</blockquote>
<br></div>
this was discussed so many times on both ccp4bb and phenixbb... So,
very briefly, I do not know any single reason (and can't even
imagine one) why one may want to remove hydrogens before PDB
deposition. Most of reasons why hydrogen atoms should not be removed
are listed in:<br>
<br>
<span style="color:rgb(0, 0, 0);font-family:verdana,helvetica,arial,sans-serif;font-size:14px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;display:inline ! important;float:none">phenix.model_vs_data: a high-level tool for the calculation
of crystallographic model and data statistics. P.V. Afonine, R.W.
Grosse-Kunstleve, V.B. Chen, J.J. Headd, N.W. Moriarty, J.S.
Richardson, D.C. Richardson, A. Urzhumtsev, P.H. Zwart, P.D. Adams
J. Appl. Cryst. 43, 677-685 (2010).</span> <br>
<br>
and lots of hints here:<br>
<br>
Joint X-ray and neutron refinement with phenix.refine. P.V. Afonine,
M. Mustyakimov, R.W. Grosse-Kunstleve, N.W. Moriarty, P. Langan, and
P.D. Adams Acta Cryst. D66, 1153-1163 (2010).<div class="im"><br>
<br>
<blockquote type="cite">
<pre>So in the context of Phenix and Fcalc, do the positions of the riding hydrogens matter? </pre>
</blockquote>
<br></div>
Yes, positions matter. As well as B-factors and occupancies. Note,
B-factors of H are inherited from parent atoms with some multiplier
that ranges from 1 to 1.5 (see SHELXL manual for details).<div class="im"><br>
<br>
<blockquote type="cite">
<pre>And if they don't, does this mean that when an input model has zero hydrogens, Phenix is still trying in some way to account for the unmodeled/invisible hydrogens that we know are in there?
</pre>
</blockquote>
<br></div>
No, if there are no H atoms in input PDB file, phenix.refine will
not try to account for missing H in any way.<span class="HOEnZb"><font color="#888888"><br>
<br>
Pavel<br>
<br>
</font></span></div>
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