Dear Ian,
Am 17.09.10 12:30, schrieb Ian Tickle:
> 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!):
yes, as I said, I would also like to deposit the Fcalc along with the
model. And that final model should not be touched after the last
refinement cycle, anymore.
> 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!
Oh, goodness, I see: even here, we would need clear rules what the
calculated structure factors are, which weights are were, which bulk
solvent correction was applied ... a maze, too!
But could future programs really re-calculate the same structure factors
from the deposited model? Because of the expected development of more
advanced methods and algorithms, I have my doubts ... *sigh*
Cheers,
Dirk.
> 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
>>
>> --
>>
>> *******************************************************
>> Dirk Kostrewa
>> Gene Center Munich, A5.07
>> Department of Biochemistry
>> Ludwig-Maximilians-Universität München
>> Feodor-Lynen-Str. 25
>> D-81377 Munich
>> Germany
>> Phone: +49-89-2180-76845
>> Fax: +49-89-2180-76999
>> E-mail: [log in to unmask]
>> WWW: www.genzentrum.lmu.de
>> *******************************************************
>>
--
*******************************************************
Dirk Kostrewa
Gene Center Munich, A5.07
Department of Biochemistry
Ludwig-Maximilians-Universität München
Feodor-Lynen-Str. 25
D-81377 Munich
Germany
Phone: +49-89-2180-76845
Fax: +49-89-2180-76999
E-mail: [log in to unmask]
WWW: www.genzentrum.lmu.de
*******************************************************
|