Dear Jan,
an initial increase in Rfree usually means, that either, in case of
isomorphous crystal forms, the structure was refined before against a
different test set, or, in case of completely different crystal forms,
that you have a new test set. In both cases, Rwork and Rfree for the
initial model start at very similar values and "de-couple" during
refinement, resulting in decreasing Rwork and increasing Rfree values.
If you have similar resolution ranges, you should define your own
"standard" refinement protocol; for instance, rigid body -> TLS -> xyzB,
such that the rmsd in bond lengths converge at similar values, and then
compare the R-values afterwards.
This can be done with all modern refinement programs, such as REFMAC,
PHENIX, BUSTER and CNS.
Good luck,
Dirk.
Am 25.02.10 15:38, schrieb Jan Schoepe:
Dear all,
I do have a question about comparing Rfree and Rwork factors of
different refinement trials whereas I always started with the same pdb
file and structure factors (phasing by MR).
Means I had a protein structure which was (not just by me) refined
several times in different ways also with different programs and also
accordingly got different R factors for each finally refined structure.
Could anyone suggest if there is something like a "standard run" which
makes all these R factors (or "derivatives" since this run should
change the R factors) better comparable?
(E.g. it did not work for me to do a 1 cycle rigid body refinement in
refmac hoping that the R factors are measured well and the structure
does not change much. In fact, the R factors increased dramatically,
lets say Rfree from 30% to 40%.)
Many thanks for your suggestions!
Jan
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