[phenixbb] Dummy atoms

Pavel Afonine pafonine at lbl.gov
Wed Jul 28 11:12:55 PDT 2010

  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


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!

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