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.
