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").
- To reproduce typically the most used electron density maps, such as
2mFo-DFc and mFo-DFc, you would also need to deposit coefficients m and
D, or, alternatively, have a program and free-R flags handy to compute m
and D yourself.
- Requiring Fcalc, you would have to make sure that this is actually the
total structure factors Fmodel = scales*(Fcalc_atoms + F_bulk_solvent)
with all other appropriate scales included. Although, this is easy to do
by computing the R-factor and comparing it with the reported number.
All the best!
Pavel.
|