[phenixbb] Dummy atoms

Nigel Moriarty nwmoriarty at lbl.gov
Wed Jul 28 16:41:10 PDT 2010


Folks

I think that UNK is an unknown residue, UNL is an unknown ligand, UNX
is an unknown atom or ion and UPL is "UNKNOWN BRANCHED FRAGMENT OF
PHOSPHOLIPID".  Some of these have atoms in the chemical components
entry (which is strange) and some don't.  Naturally, the user has to
make the decision to use the correct one ...

Nigel

On Wed, Jul 28, 2010 at 3:19 PM, Tom Terwilliger <terwilliger at lanl.gov> wrote:
> 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.
> -Tom T
> 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
>
> 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.
>
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> Thomas C. Terwilliger
> Mail Stop M888
> Los Alamos National Laboratory
> Los Alamos, NM 87545
>
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-- 
Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov



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