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CCP4BB  September 2010

CCP4BB September 2010

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Subject:

Re: Deposition of riding H: R-factor is overrated

From:

Ethan Merritt <[log in to unmask]>

Reply-To:

Ethan Merritt <[log in to unmask]>

Date:

Thu, 16 Sep 2010 09:20:53 -0700

Content-Type:

Text/Plain

Parts/Attachments:

Parts/Attachments

Text/Plain (71 lines)

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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