<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<meta content="text/html;charset=ISO-8859-1" http-equiv="Content-Type">
</head>
<body bgcolor="#ffffff" text="#000000">
Hi Joe,<br>
<br>
could you send me the log file (from the refinement run giving the best
Rw/Rf) for some quick diagnostics ? Please send the files to my email
(and not to the list).<br>
<br>
If you send model and data I will have a closer look.<br>
<br>
Pavel.<br>
<br>
<br>
On 6/7/10 6:52 PM, Joseph Brock wrote:
<blockquote cite="mid:SNT120-W63BC30F5E2A713ED090E369BD60@phx.gbl"
type="cite">
<style><!--
.hmmessage P
{
margin:0px;
padding:0px
}
body.hmmessage
{
font-size: 10pt;
font-family:Verdana
}
--></style>Dear
Phenix users,<br>
<br>
I am currently using version 1.6.1-353 and I'm working on a 1.7A
structure that has refined quite well using
Individual_sites+individual_adp(isotropic)+occupanices+TLS: Final
R-work = 0.1776, R-free = 0.2262<br>
<br>
However, I noticed that the average B-factor reported by polygon with
these settings was quite high ( < 0.1 of other structures with a
similar resolution).<br>
<br>
Discovering I could not change the value of wxu_scale when using
individual_adp+TLS, I went about trying to reduce the average B using
the method described here:<br>
<br>
<a class="moz-txt-link-freetext" href="http://phenix-online.org/pipermail/phenixbb/2007-September/000511.html">http://phenix-online.org/pipermail/phenixbb/2007-September/000511.html</a><br>
<br>
However, I still can't seem to reduce the average B-factor. I've just
done a refinement with the following non-default (extreme) target
weight settings:<br>
<br>
target_weights {<br>
wxc_scale = 1.5<br>
fix_wxc = 2<br>
fix_wxu = 0.1<br>
(wxu_scale = 1)<br>
<br>
But if anything, reducing wxu to such low values makes the avergae
B-even higher while concuretnly making the gap between R-values much
worse:<br>
<br>
Final R-work = 0.1602, R-free = 0.2457<br>
<br>
This suggests to me that I'm obviously over fitting the data but I'm at
a loss on how to proceed. Should i just accept that the automatic
scaling used for Phenix TLS wxu is doing a good job and that my
structure actually does have an unusually high avergae B? <br>
<br>
I'm fitting two ligands into density, which is at several places
ambiguous, so I would like the most unbiased difference density
possible.<br>
<br>
Many thanks in advance,<br>
<br>
Joe. <br>
<br>
<br>
<hr>Find it at CarPoint.com.au <a moz-do-not-send="true"
href="http://clk.atdmt.com/NMN/go/206222968/direct/01/" target="_new">New,
Used, Demo, Dealer or Private?</a>
<pre wrap="">
<hr size="4" width="90%">
_______________________________________________
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>
</body>
</html>