Just a quick question/comment,<br><br>I may remember this incorrectly but isn't the best wxu_scale=1.81 when you use TLS? Older versions of phenix.refine changed it automatically when you applied TLS IIRC but now it only goes to 1.81 if I use the optimize_wxu option.<br>
Am I remembering correctly or is my headache screwing with me?<br><br>Sincerely,<br>Morten<br><br><div class="gmail_quote">2009/1/26 Pavel Afonine <span dir="ltr"><<a href="mailto:pafonine@lbl.gov">pafonine@lbl.gov</a>></span><br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Hi Scott,<br>
<div class="im"><br>
> In general should one optimize wxc and wxu ONLY as a final polishing<br>
> step or can this be done earlier in the refinement and then the<br>
> optimized values used for subsequent rounds of refinement?<br>
<br>
</div>Optimizing weights is time consuming: depending on the data and model<br>
size it can take from many minutes to hours, and this is the only reason<br>
for suggesting it as a final step.<br>
<br>
However if it runs quickly or/and you are not in rush, you can do it all<br>
the time: then it will always make sure that the weights are "optimal"<br>
(in terms of giving the best Rfree). Note, that most of the time you<br>
don't really need it since the automatically determined weights are<br>
pretty good (most of the time).<br>
<br>
The optimal weight found after running phenix.refine with<br>
optimize_wxc=true (or/and optimize_wxu=true) may substantially vary<br>
between structure determination stages or even between refinement<br>
macro-cycles within one refinement run. This is why it is not generally<br>
advised to use the same weights (determined at the beginning) all the<br>
time, although technically you can: just pick up the best wxc_scale from<br>
the log file and specify it for the next run.<br>
<br>
Please let me know if you have any questions!<br>
<font color="#888888"><br>
Pavel.<br>
</font><div><div></div><div class="h5"><br>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>Morten K Gr�ftehauge<br>PhD student<br>Department of Molecular Biology<br>Gustav Wieds Vej 10 C<br>8000 Aarhus C - Denmark<br>Phone: +45 89 42 52 61<br>Fax: +45 86 12 31 78<br>
<a href="http://www.bioxray.dk">www.bioxray.dk</a><br><br><br>