[phenixbb] WAS: changing TLS groups mid refinement

Peter Zwart PHZwart at lbl.gov
Mon May 17 20:02:44 PDT 2010

Hi Phil,

Can you redo the exercise but get your intensities like this:

phenix.reflection_file_converter mysca.sca --massage-intensities
--write_mtz_amplitudes  --mtz_root_label=FM  \

You did use the common set of miller indices for R value computation, right?



2010/5/17 Pavel Afonine <PAfonine at lbl.gov>:
> Dear Phil,
>> Can we turn the argument on its head ?
> well, it depends what you call "head" -:)
>> Short version:
>> phenix.refine throws out 2896 reflections of 48895, including 11% of the
>> data in the outermost shell, compared to using TRUNCATE to prep my data.
>>  Using the common data subset the structure has a decreased R-free of 0.8%
>> if you refine against the truncate=yes PDB file with the common subset of
>> data.
>> 0.8% at a 24% R-free (24.0 vs 24.8) is pretty significant IMHO.
> You cannot compare the R-factors that were computed using different sets of
> reflections. Therefore the above comparison is not valid, obviously. Same
> applies to your "Longer version". Let's compare apples with apples.
> Comparing R-factors in this case does not tell that one refinement is better
> or worse than the other one. It just doesn't tell anything because the
> R-factor is not a good measure when you deal with two different datasets
> (datasets containing different amount of reflections).
> Pavel.
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P.H. Zwart
Beamline Scientist
Berkeley Center for Structural Biology
Lawrence Berkeley National Laboratories
1 Cyclotron Road, Berkeley, CA-94703, USA
Cell: 510 289 9246
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