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R-free and map calculations
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Can anyone enlighten me on the following two
It was mentioned in the literature that R-free,
a global indicator of the correctness of the model, is
calculated using a TEST set of reflections (between a
minimum of ~500 reflections to a maximum of ~2,000
reflections). Literature (Kleywegt & Jones (1997)
Methods in Enzymology, vol.277, 208-230) also suggests that
for a better model, it is WISE to include the TEST set of
reflections for map calculations.
My question is,
Incorporation of all reflections while calculating
a 2Fo-Fc/Fo-Fc or sigmaA style 2mFo-DFc/mFo-DFc maps won't
bias Rfree ?
So in case of a less complete data-set (say around 65%
overall completeness), one cannot then afford to omit those
TEST set of reflections for refinement/map calculation?
2: Simulated Annealing:-
Reports say that Simulated Annealing in Torsion angle
space (Torsion angle MD refinement?) decreases the number of
degrees of freedom (to N/3) as compared to that of Cartesian
coordinate space (=3N; where N=no. of atoms). Also, it was
mentioned that this method proves to have a LARGE value of
radius of convergence..
Can anyone please explain this in brief?
Bye and Regards,
| S.Ravichandran e-mail:- |
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