[phenixbb] possible Xtriage bug??

Peter Zwart PHZwart at lbl.gov
Tue Jun 25 16:19:12 PDT 2013


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.


On 25 June 2013 15:37, Michael Thompson <miket at chem.ucla.edu> wrote:

> Hello Developers,
> 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:
> 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:
>  L test for acentric data
>  using difference vectors (dh,dk,dl) of the form:
> (2hp,2kp,2lp)
>   where hp, kp, and lp are random signed integers such that
>   2 <= |dh| + |dk| + |dl| <= 8
>   Mean |L|   :0.504  (untwinned: 0.500; perfect twin: 0.375)
>   Mean  L^2  :0.340  (untwinned: 0.333; perfect twin: 0.200)
> 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.
> 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).
> 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.
> Thanks a lot for the help, and for phenix being awesome in general!
> Mike
> --
> Michael C. Thompson
> Graduate Student
> Biochemistry & Molecular Biology Division
> Department of Chemistry & Biochemistry
> University of California, Los Angeles
> miket at chem.ucla.edu
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P.H. Zwart
Research Scientist
Berkeley Center for Structural Biology
Lawrence Berkeley National Laboratories
1 Cyclotron Road, Berkeley, CA-94703, USA
Cell: 510 289 9246
BCSB:      http://bcsb.als.lbl.gov
PHENIX:   http://www.phenix-online.org
SASTBX:  http://sastbx.als.lbl.gov
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