<div dir="ltr"><div>Hi,<br><br></div>A bug seems to have slipped in, you are absolutely right. The 'delta selection' algorithm seems to need some tweaking. I'll have a look.<br><br>P<br></div><div class="gmail_extra">
<br><br><div class="gmail_quote">On 25 June 2013 15:37, Michael Thompson <span dir="ltr"><<a href="mailto:miket@chem.ucla.edu" target="_blank">miket@chem.ucla.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hello Developers,<br>
<br>
I would like to report a possible bug in newer versions of phenix.xtriage. I have noticed recently that I am getting some strange results for the results of the L-test when I run xtriage, as described below:<br>
<br>
My data show a strong non-crystallographic translation, described by the vector <uvw>=(1/3, 2/3, 1/2). This NCS translation is readily identified by xtriage. When Xtriage performs the L-test, the output states:<br>
<br>
<br>
�L test for acentric data<br>
<br>
�using difference vectors (dh,dk,dl) of the form:<br>
(2hp,2kp,2lp)<br>
� where hp, kp, and lp are random signed integers such that<br>
� 2 <= |dh| + |dk| + |dl| <= 8<br>
<br>
� Mean |L| � :0.504 �(untwinned: 0.500; perfect twin: 0.375)<br>
� Mean �L^2 �:0.340 �(untwinned: 0.333; perfect twin: 0.200)<br>
<br>
These results don't make sense, as the statistics show an "anti-twinned" effect, which should not happen with the L-test. It appears that xtriage is using reflections that do not have the same expected intensity values due to the NCS translation.<br>
<br>
The strange thing is that I have another xtriage logfile, which I produced in September of 2012 using the same input data, that indicates the reflections used for the L-test were chosen "using difference vectors (dh,dk,dl) of the form: (3hp,3kp,2lp)." This choice of reflections does account for proper parity, and I get results that are much more sensible (Mean |L|=0.394; Mean L^2=0.221).<br>
<br>
I am wondering why I am getting different results now than I did last September? Has something changed in the underlying code, or am I missing something silly? I do not have an easy way of determining which version of phenix I used when the L-test was conducted using sensible reflections (the xtriage logfile doesn't contain this info as far as I can tell), but the version that seems to choose reflections inappropriately is 1.8.2-1334.<br>
<br>
Thanks a lot for the help, and for phenix being awesome in general!<br>
<br>
Mike<br>
<br>
<br>
<br>
<br>
<br>
<br>
--<br>
Michael C. Thompson<br>
<br>
Graduate Student<br>
<br>
Biochemistry & Molecular Biology Division<br>
<br>
Department of Chemistry & Biochemistry<br>
<br>
University of California, Los Angeles<br>
<br>
<a href="mailto:miket@chem.ucla.edu">miket@chem.ucla.edu</a><br>
_______________________________________________<br>
phenixbb mailing list<br>
<a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br>
<a href="http://phenix-online.org/mailman/listinfo/phenixbb" target="_blank">http://phenix-online.org/mailman/listinfo/phenixbb</a><br>
</blockquote></div><br><br clear="all"><br>-- <br>-----------------------------------------------------------------<br>P.H. Zwart<br>Research Scientist<br>Berkeley Center for Structural Biology<br>Lawrence Berkeley National Laboratories<br>
1 Cyclotron Road, Berkeley, CA-94703, USA<br>Cell: 510 289 9246<br>BCSB:� � � <a href="http://bcsb.als.lbl.gov">http://bcsb.als.lbl.gov</a><br>PHENIX:�� <a href="http://www.phenix-online.org">http://www.phenix-online.org</a><br>
SASTBX:� <a href="http://sastbx.als.lbl.gov">http://sastbx.als.lbl.gov</a><br>-----------------------------------------------------------------
</div>