Dirk
Personally I wouldn't make use of the deposited Fcalcs, I would insist
on having the refined model, not only for the reasons Pavel gave, but
also because it's never clear which mathematical model was used to
produce the deposited Fcalcs. There are 2 problem areas (at least 2 I
can think of right now!):
1. Do the deposited Fcalcs include bulk solvent? Depending on which
Fcalc column was chosen from Refmac (either FC/PHIC or
FC_ALL/PHIC_ALL), either they won't or they will resp., but the CIF
header doesn't provide that information!
2. Do the deposited Fcalcs include the effect of co-ordinate errors?
In other words, is the column labelled 'FC' or 'FC_ALL' actually
D*Fcalc (as it is in Refmac), but I've no idea what other programs do.
If the deposited CIF file is the one produced from Refmac then one
can assume that FC = D*Fcalc, but you can't be sure that that's
actually what the user did!
Cheers
-- Ian
On Fri, Sep 17, 2010 at 10:20 AM, Dirk Kostrewa
<[log in to unmask]> wrote:
> Hi Pavel,
>
>
> Am 16.09.10 17:56, schrieb Pavel Afonine:
>>
>> 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").
>
> but this is exactly what one shouldn't do: manipulate the structure after
> the final refinement! And if you manipulate it for a good reason, do a "last
> final" refinement after that, before depositing coordinates and structure
> factors. Then, there will be no problems, as far as I can see.
>
> Best regards,
>
> Dirk
>
> --
>
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> Dirk Kostrewa
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> Department of Biochemistry
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