<html>
<head>
<meta content="text/html; charset=windows-1252"
http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000000">
Hello Xiao,<br>
<br>
Xtriage estimates twin fraction, while phenix.refine refines it.
Therefore an estimated value may be different from refined one. By
how much different? That I would not dare to guess!<br>
<br>
Given that twining is present and you picked correct twin law the
value of twin fraction from phenix.refine is going to be more
accurate than its estimate from Xtriage.<br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 12/10/14 12:37 PM, Xiao Lei wrote:<br>
</div>
<blockquote
cite="mid:CABaNifzWmRm6EQephj_+CVj=bHmyrVFW1LTNeFgU6bbjX5pO-A@mail.gmail.com"
type="cite">
<div dir="ltr">Dear All,
<div><br>
</div>
<div>I have a x-ray dataset of a protein-DNA complex to 2.8 A
resolution with space group P312 checked by phenix xtriage for
twinning. The estimated twin fraction from the output of
xtriage is: 0.115 (Britton analysis); 0.119 (H test) and 0.022
(maximum likelihood method). However, the L-test graph in
xtriage shows my observed data almost perfectly overlay with
theoretical perfect twin data. In addition, when I tried to
use phenix to do refinement with twin law -h,-k,l, the log
file shows my twin fraction estimation is 0.49, which is very
high and much bigger than Britton analysis and H test
estimation.�</div>
<div><br>
</div>
<div>As far as my understanding is that if a twin fraction is
lower than 15%, I still have hope to solve the structure
(molecular replacement in this case) with reasonable R value,
but if the twin fraction is 0.49, which is almost a perfect
twin, which makes detwin impossible and refinement will stall
at high R values (in my case, R free start: 0.4199; R work
start: 0.4121; �and R free final: �0.4038 and R work final:
0.3640 after running phenix refinement with twin law -h, -k,
l).�</div>
<div><br>
</div>
<div>My question: �which twin fraction estimation is more
reliable? is my data almost perfectly twined?</div>
<div><br>
</div>
<div>I attached the graphs of L test, Britton analysis and twin
estimation from phenix xtriage and part of log file from
phenix refine here.</div>
<div><br>
</div>
<div>Many thanks in advance.</div>
<div><br>
</div>
<div>Xiao</div>
</div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
<pre wrap="">_______________________________________________
phenixbb mailing list
<a class="moz-txt-link-abbreviated" href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a>
<a class="moz-txt-link-freetext" href="http://phenix-online.org/mailman/listinfo/phenixbb">http://phenix-online.org/mailman/listinfo/phenixbb</a>
</pre>
</blockquote>
<br>
</body>
</html>