> (& while I'm at it, freeR has nothing to do with model bias (which is
> largely imaginary anyway, only a problem with low resolution molecular
> replacement))
>
> Phil
Phil, I understand what you're saying but 'model bias' in this context
has a wider meaning than just failing to rebuild the chain correctly
from an MR model at low resolution, and using this wider meaning Rfree
has everything to do with model bias. For example, if I refine a high
res structure with 1 Ang data using an isotropic-only B-factor model,
then Rfree (& Rwork) will almost certainly be higher than you would
expect using the optimal parameterisation of 3 xyz's + 6 ADPs per atom
with the appropriate restraints (whatever the optimum happens to be).
Bias is defined as 'difference from expectation', so the isotropic model
is almost certainly biased, as reflected in the higher-than-expected
Rwork & Rfree. I'm well aware that bias by itself is not necessarily a
bad thing particularly when a biased estimator happens to have the least
error (difference from the truth), but I doubt one can claim that in
this example.
Cheers
-- Ian
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