[phenixbb] picking Rfree set
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.
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>phenixbb mailing list
>phenixbb at phenix-online.org
David N. Garboczi, PhD
Investigator, Structural Biology Section (SBS)
Laboratory of Immunogenetics (LIG)
National Institute of Allergy and Infectious Diseases (NIAID)
National Institutes of Health (NIH)
Twinbrook 2/Room 110
12441 Parklawn Drive
Rockville, Maryland 20852-1742
Email: dgarboczi at niaid.nih.gov
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