[phenixbb] Dummy atoms
terwilliger at lanl.gov
Wed Jul 28 15:19:03 PDT 2010
One disadvantage of using UNK is that it is often a loss of
information. For example in the case Phil mentions...we do think that
we have a polypeptide. By labelling protein residues UNK we no longer
distinguish them from DNA, or depending on HETATM vs ATOM
identification, from ligands.
On Jul 28, 2010, at 4:01 PM, Phil Evans wrote:
> 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
> 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
>>> For one thing, these structures are produced not just for
>>> 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
>>> 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
>> 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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Thomas C. Terwilliger
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Los Alamos National Laboratory
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