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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">There are a number of twinning tests, and if they indicate a ~>5% twin fraction, the convention is to use twin refinement. Refining twin fractions then gives
a more accurate estimate of the true fraction.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">I think your hypothetical about not helping anything besides R might not really happen in practice—has it happened to you, or do you know of such a case? In
any case, if you know something is there in your data (twinning, waters, chloride ions, etc) why not model it if you have reasonable evidence that it’s there?<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">JPK<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> phenixbb-bounces@phenix-online.org [mailto:phenixbb-bounces@phenix-online.org]
<b>On Behalf Of </b>wtempel<br>
<b>Sent:</b> Wednesday, December 16, 2015 3:21 PM<br>
<b>To:</b> PHENIX user mailing list<br>
<b>Subject:</b> [phenixbb] Fwd: ML with Twinning?<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p>Hello,<br>
please allow me to use this prompt for my twinning-related question.<br>
A recent version of xtriage prints this warning:<o:p></o:p></p>
<blockquote style="border:none;border-left:solid #DDDDDD 3.0pt;padding:0in 0in 0in 12.0pt;margin-left:0in;margin-top:.2in;margin-right:0in;margin-bottom:.2in;quotes:none">
<p style="margin:0px!important"><span style="color:#777777">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.<o:p></o:p></span></p>
</blockquote>
<p style="margin: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<o:p></o:p></p>
<p style="margin: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><o:p></o:p></p>
<p style="margin:0px!important">Hi Jacob,<o:p></o:p></p>
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<p class="MsoNormal" style="margin:0px!important">Is Phenix able yet to use the ML target function with twinned data?<o:p></o:p></p>
</blockquote>
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<p style="margin:0px!important">no.<o:p></o:p></p>
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<p class="MsoNormal" style="margin:0px!important">Is it in the works?<o:p></o:p></p>
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<p style="margin:0px!important">There are formulas written out:<o:p></o:p></p>
<p style="margin:0px!important">“Maximum likelihood refinement for twinned structures”:<o:p></o:p></p>
<p style="margin:0px!important"><a href="http://phenix-online.org/newsletter/CCN_2011_01.pdf">http://phenix-online.org/newsletter/CCN_2011_01.pdf</a><o:p></o:p></p>
<p style="margin:0px!important">some one needs to code it.<o:p></o:p></p>
<p style="margin:0px!important">Pavel<o:p></o:p></p>
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<p style="margin:0px!important">phenixbb mailing list<br>
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Unsubscribe: <a href="mailto:phenixbb-leave@phenix-online.org">phenixbb-leave@phenix-online.org</a><o:p></o:p></p>
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