Dirk,
- 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.
I apology if what I wrote doesn't read clearly - this is exactly what
I'm saying: in this particular reply and across the whole discussion.
Note, I used the word "unfortunately" above. Anyway, saying it again:
What I mentioned is based on my (and not only my - see relevant papers)
observation running validation tools through the whole PDB and making
note of such manipulated structure. It is a matter of fact that there
are some intentionally or unintentionally manipulated models, it is very
bad, it is unfortunate and obviously I'm strictly against it. I'm
against it to a such a degree so even didn't bother to write a paper on
this matter, which I mentioned on this thread already:
J. Appl. Cryst. 2010, 43, 669-67.
Therefore it is important to have a model that you can use to reproduce
the reported statistics (for validation, at least), although having
Fcalc around wouldn't hurt.
Sorry again, if I wasn't clear in my previous reply.
All the best!
Pavel.
