[phenixbb] Dummy atoms

Tom Terwilliger 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.
-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.
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb

Thomas C. Terwilliger
Mail Stop M888
Los Alamos National Laboratory
Los Alamos, NM 87545

Tel:  505-667-0072                 email: terwilliger at LANL.gov
Fax: 505-665-3024                 SOLVE web site: http://solve.lanl.gov
PHENIX web site: http:www.phenix-online.org
ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu
TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB
CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20100728/171b9a90/attachment-0003.htm>

More information about the phenixbb mailing list