[phenixbb] picking Rfree set

David Garboczi dgarboczi at niaid.nih.gov
Tue Jan 22 09:48:41 PST 2008

So, for instance, when addition of a ligand to a P212121 cell (1 mol) 
changes the symmetry to P21 (almost same cell, but 2 mol), the 
selection of the Rfree set from the P21 data by phenix.refine will 
take the higher almost symmetry into account?


>btw3: the lattice symmetry is taken into account when choosing an free
>set in phenix.refine (unless specified otherwise). If all NCS
>rotational operators are approximately parallel to twin laws, you
>should be fine.
>2008/1/22, Ralf W. Grosse-Kunstleve <rwgk at cci.lbl.gov>:
>>  > Does phenix.refine take NCS into account when picking the Rfree set?
>>  > Thin shells, or other strategy...
>>  The short answer is no.
>>  We had long internal discussions about this without reaching a final
>>  conclusion. In the long run we may integrate alternative R-free set
>>  distributions in phenix.refine; in the meantime you have to use
>>  an external program (e.g. dataman or sftools).
>>  BTW 1: just to prove that we have thought about this subject, we have a
>>  simple tool for "visualizing" distributions of R-free flags:
>>    iotbx.r_free_flags_accumulation your.mtz
>>  It writes a file with x,y pairs which you can plot with e.g. Excel
>>  or any other 2D plotting program.
>>  BTW 2: The free reflections aren't as free as one may think. When
>>  using a maximum likelihood target (any program), the free reflections
>>  are used in the estimatation of the error model. This estimation
>>  becomes more tricky if the reflections are distributed in thin
>>  shells. I.e. if you go to thin shells you may in fact account to some
>>  degree for the NCS, but at the same time you compromise the error
>>  model estimation.
>>  Ralf
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David N. Garboczi, PhD
Phone: 301-496-4773
Investigator, Structural Biology Section (SBS)
Laboratory of Immunogenetics (LIG)
National Institute of Allergy and Infectious Diseases (NIAID)
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