Hi Pavel,
Am 16.09.10 17:56, schrieb Pavel Afonine:
Hi Dirk,
so, wouldn't be the deposition of the final model's Fcalc, Phic (and
their weights) along with the final coordinates be the best solution?
The final Fcalc are our best model and can be used to reproduce the
final statistics (which would remove the sfcheck annoyance) and to
reproduce the final electron density maps, and the coordinates can be
used for what ever purpose they are needed, irrespective of adding
riding hydrogens or not.
it is a great idea and if you look in PDB deposited structure factors
there is a number of them (but certainly not the majority) that are
accompanied by Fcalc. However, a few things to keep in mind:
- Imagine a (not very uncommon, unfortunately) situation when someone
obtains the final model and Fcalc, and then, right before the PDB
deposition does a final check in Coot, and moves/removes a few atoms
(a few waters, or instance) here and there. Or may be does a
real-space fit of a residue. Or removes H, if present. Or renames a
ligand by request of PDB staff and accidentally change an atom
parameter(s). All this in turn will invalidate the R-factors and make
previously calculated Fcalc inconsistent with such a manipulated model.
So, the bottom-line is: having a model that you can use to reproduce
the reported statistics is important (for validation and database
sanity at least, if someones believe that such a minor things wouldn't
impair the biological interpretation - "ultimate goal of protein
structures").
but this is exactly what one shouldn't do: manipulate the structure
after the final refinement! And if you manipulate it for a good reason,
do a "last final" refinement after that, before depositing coordinates
and structure factors. Then, there will be no problems, as far as I can see.
Best regards,
Dirk
--
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Dirk Kostrewa
Gene Center Munich, A5.07
Department of Biochemistry
Ludwig-Maximilians-Universität München
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D-81377 Munich
Germany
Phone: +49-89-2180-76845
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