Hi,
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.
P
On 25 June 2013 15:37, Michael Thompson
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
[email protected] _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
-- ----------------------------------------------------------------- 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 -----------------------------------------------------------------