<div dir="ltr"><div class="markdown-here-wrapper" style=""><p style="margin:1.2em 0px!important">Hello,<br>please allow me to use this prompt for my twinning-related question.<br>A recent version of xtriage prints this warning:</p>
<blockquote style="margin:1.2em 0px;border-left-width:4px;border-left-style:solid;border-left-color:rgb(221,221,221);padding:0px 1em;color:rgb(119,119,119);quotes:none">
<p style="margin:1.2em 0px!important">It might be worthwhile carrying out refinement with a twin specific target function.<br>Please note however that R-factors from twinned refinement cannot be directly<br>compared to R-factors without twinning, as they will always be lower when a<br>twin law is used.  You should also use caution when interpreting the maps from<br>refinement, as they will have significantly more model bias.</p>
</blockquote>
<p style="margin:1.2em 0px!important">Consider a case where specification of a twin law produces a “significant” reduction in the residuals, say between 5 and 10%-points. Maps have not revealed any additional features or model errors. Model geometry (such as fraction of residues in favored regions of the Ramachandran plot) has not improved. Should I specify the twin target during refinement?<br>How do my colleagues decide when to use twin refinement?<br>Best regards.<br>Wolfram Tempel</p>
<p style="margin:1.2em 0px!important">————— Forwarded message —————<br>From: Pavel Afonine <a href="http://mailto:pafonine@lbl.gov">pafonine@lbl.gov</a><br>Date: Wed, Dec 16, 2015 at 2:06 PM<br>Subject: Re: [phenixbb] ML with Twinning?<br>To: “Keller, Jacob” <a href="http://mailto:kellerj@janelia.hhmi.org">kellerj@janelia.hhmi.org</a>, “<a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a>” <a href="http://mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a></p>
<p style="margin:1.2em 0px!important">Hi Jacob,</p>
<p style="margin:1.2em 0px!important"></p><div class="markdown-here-exclude"><p></p><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
Is Phenix able yet to use the ML target function with twinned data?<br>
</blockquote><p></p></div><p style="margin:1.2em 0px!important"></p>
<p style="margin:1.2em 0px!important"> no.</p>
<p style="margin:1.2em 0px!important"></p><div class="markdown-here-exclude"><p></p><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
Is it in the works?<br>
</blockquote><p></p></div><p style="margin:1.2em 0px!important"></p>
<p style="margin:1.2em 0px!important"> There are formulas written out:</p>
<p style="margin:1.2em 0px!important"> “Maximum likelihood refinement for twinned structures”:</p>
<p style="margin:1.2em 0px!important"> <a href="http://phenix-online.org/newsletter/CCN_2011_01.pdf">http://phenix-online.org/newsletter/CCN_2011_01.pdf</a></p>
<p style="margin:1.2em 0px!important"> some one needs to code it.</p>
<p style="margin:1.2em 0px!important"> Pavel</p>
<hr>
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