 |
 |
On Thursday 16 September 2010 01:25:12 am Dirk Kostrewa wrote: > > > 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. I believe that deposition of Fc Phic FOM should be required. Certainly it should be the recommended practice. Strangely, I can find no statement of either policy or recommended practice on the PDB FAQ or deposition site. On Thursday 16 September 2010 08:56:46 am Pavel Afonine wrote: > > - 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. Pavel: You yourself have railed against any such post-refinement model-mangling. Yet now you make it sound like such model-mangling is the norm. Do you have any evidence that this kind of bad practice is common? Note that it's really easy in the ccp4i interface to simply re-run your final refinement cycle and update the deposition materials following such a tweak to the model. Just substitute in the name of your tweaked file for the previous XYZIN and hit the "delete/archive" files button before running the replacement through. Maybe it's more cumbersome in phenix? > - 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. You are making this all sound much more complicated than it needs to be. Just use CAD to merge the output *.mtz file from your final refinement with the original file of observed intensities, convert the merged file to cif [*], and pack it off as part of the deposition. [*] In fact you can just deposit the merged *.mtz file without conversion. But I don't trust the auto-conversion script at the PDB to correctly interpret the mtz column labels. Better to do it yourself and take a quick look at the top of the cif file to confirm that the right columns are present. Ethan -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg University of Washington, Seattle 98195-7742