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Hi Filip,<br>
<br>
<blockquote
cite="mid:83950325.4242331.1432665765628.JavaMail.yahoo@mail.yahoo.com"
type="cite">
<div style="color:#000; background-color:#fff;
font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial,
Lucida Grande, sans-serif;font-size:12px"><o:p class="" style="">�</o:p>I
am currently refining a 1.75A structure and wanted to use
the riding hydrogen model in pehnix.refine. From what I found in
the manual and
previous discussions on the mailing list and if I understand
well, using riding
Hs is advised for every resolution and<span
style="mso-spacerun:yes" class="">�</span>the way of doing
this in phenix.refine is not
Refmac-like but instead I should 1) put Hs using ReadySet, 2)
select the
�riding� option for Hs and 3) use the PDB containing the H
coordinates for
deposition, even though they were not individually refined. In
this case their
contribution to scattering is also taken into account (which
makes sense),
which is a different way of treating riding Hs compared to
Refmac, if I
understand well. </div>
</blockquote>
<br>
I don't know how Refmac handles H so I cannot comment on this; the
rest I think is more or less accurate. Note, "riding" option is used
by default (unless it is neutron data).<br>
<br>
Also, for some more details and illustration on how H contribute to
overall scattering and R-factors in different cases have a look at
"On contribution of hydrogen atoms to X-ray scattering" article
here:<br>
<br>
<a class="moz-txt-link-freetext" href="https://www.phenix-online.org/newsletter/">https://www.phenix-online.org/newsletter/</a><br>
<br>
<blockquote
cite="mid:83950325.4242331.1432665765628.JavaMail.yahoo@mail.yahoo.com"
type="cite">
<div style="color:#000; background-color:#fff;
font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial,
Lucida Grande, sans-serif;font-size:12px"><o:p class="" style=""></o:p><o:p
class="" style=""></o:p>
<div class="" style="" id="yui_3_16_0_1_1432516382475_118259">Would
it be possible to comment on this and in case I got things
wrong, correct?</div>
</div>
</blockquote>
<br>
Perhaps one more thing we did not mention yet is that it's best to
use H towards the end when the model of the crystal structure is
reasonably good.<br>
<br>
<blockquote
cite="mid:83950325.4242331.1432665765628.JavaMail.yahoo@mail.yahoo.com"
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<div class="" style="" id="yui_3_16_0_1_1432516382475_118258">In
fact for my structure, after<span
style="mso-bidi-font-family:"Lucida Sans""
class="" id="yui_3_16_0_1_1432516382475_118307"> adding the
Hs prior to refinement using ReadySet and using the
riding option, I actually got Rfree dropping by 1% (from
19.5 to 18.5) and better clash score (~0.5 according to
Molprobity).</span><br>
</div>
</div>
</blockquote>
<br>
This is well expected and in line with the illustrations in the
article I referred to above.<br>
<br>
All the best,<br>
Pavel<br>
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