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
<kostr...@genzentrum.lmu.de> 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: kostr...@genzentrum.lmu.de
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: kostr...@genzentrum.lmu.de
WWW: www.genzentrum.lmu.de
*******************************************************
