Hi Pavel,
Thanks, it is clear now.
I have a last concern, though. Does phenix impose minimal values to
the refined ADPs? I guess it does not, for I have found nothing like
that in the documentation. But, if it does so, are they imposed to the
individual B-factors or the B-overall is also taken into account? In
the former case you might have problems with the refinement in a case
as the one I described in my previous e-mail (coming from a model with
artificially low, 'residual' B-factors).
Cheers,
Miguel
Le 4 févr. 09 à 18:23, Pavel Afonine a écrit :
Hi Miguel,
Right, but why this happens only in the final bss step ? Why not in
the first one?
It's arbitrary: one can do it every macro-cycle as well. The main
idea is to have a total B-factor in ATOM records written out to a
PDB file.
I have noticed the behaviour described by José when I refine in
phenix a model previously refined in refmac5 _with_ TLS, so the
ADPs in the model are actually 'residual' ADPs of refmac5 TLS
refinement. In these cases, during the refinement in phenix, the
ADPs seem to be kept at very low values all throughout until they
abruptly go to the higher, more reasonable values, after the final
bulk solvent correction step. There may be a good reason for this
behaviour, but I don't see it. I would appreciate if you could
elaborate.
Like I said, it is arbitrary. You can store the overall B-factor in
overall anisotropic scale matrix (B_overall) or in individual atomic
B-factors; in both cases the total model structure factor
Fmodel = scale_overall * exp(-h*B_overall*ht) * (Fcalc + k_sol *
exp(-B_sol*s^2) * Fmask)
will remain the same.
Pavel.
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Miguel Ortiz Lombardía
Architecture et Fonction des Macromolécules Biologiques
UMR6098 ( CNRS, U. de Provence, U. de la Méditerranée )
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