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
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