UNK residues have another valid use where you can see
peptide but not assign a sequence register. A poly-Ala
model in that case is better labelled UNK than ALA, since
it isn't ALA
Phil
On 28 Jul 2010, at 19:12, Pavel Afonine wrote:
Dear Ed,
I think it is very important to
be able to include unknown atoms
in a deposited pdb file (with
echoing the caveat about flooding
the structure with UNK's to
lower the R-factor).
yes, as I wrote in original reply,
including these atoms may improve the map and in turn
may reveal or improve some its other important
(biologically) places. The only point is: please define
these dummy atoms properly, providing all the
information, such as scattering element type that you or
your program used for such an approximation.
For one thing, these structures
are produced not just for structure-factor
calculation and validation. Many
of the end users will never even
bother to do a structure factor
calculation.
The ability to reproduce the
R-factor is not only for someones pleasure but for the
validation purposes at least. If I've got a PDB file for
which I can't compute the R-factors (and, by the way,
even the map too), then I don't need the deposited Fobs
too, unless I'm going to re-determine the structure from
scratch.
It important for the
depositor to be able to refer to
an unknown but likely significant
ligand and for the reader to be
able to go and look at that position
(ideally surrounded by electron
density).
Sure, it is important.
For another thing, the structure
factor calculation will give exactly
the same result whether the
dummy atoms are omitted or are flagged
with zero occupancy or atom-type
X to be ignored in sf calculation.
If you look in PDB you will find
that very often the occupancies are not set up to 1.
Plus, as I mentioned, often the B-factors for these
atoms are set to some funny numbers (looks like they
were refined).
Are we sure that these programs
were ignoring these dummies in Fcalc calculations? If so
how the B-factor were refined, or they were made up?
Again, if it is defined properly,
for example, like this:
ATOM 1959 O DUM A 1
-8.762 8.060 25.324 1.00 31.23 O
or
ATOM 1959 O UNK A 1
-8.762 8.060 25.324 1.00 31.23 O
then it is absolutely OK to have
such entries, because it is completely defined and can
be used in any calculations without any unnecessary
guesswork. But if you start masking things with X or
blanks then I (and the software I write) will start
asking all these nasty questions...
All the best!
Pavel.
_______________________________________________
phenixbb mailing list
phenixbb@phenix-online.org
http://phenix-online.org/mailman/listinfo/phenixbb
_______________________________________________
phenixbb mailing list
phenixbb@phenix-online.org
http://phenix-online.org/mailman/listinfo/phenixbb