[phenixbb] Dummy atoms

Boaz Shaanan bshaanan at bgu.ac.il
Thu Jul 29 11:18:49 PDT 2010


UNP - for unknown peptides, UND- for DNA, UNR for RNA, UNL- for ligands and UNK for things that we don't know that we don't know (quoting D. Ramsfeld).

           Boaz

----- Original Message -----
From: Phil Evans <pre at mrc-lmb.cam.ac.uk>
Date: Thursday, July 29, 2010 2:29
Subject: Re: [phenixbb] Dummy atoms
To: PHENIX user mailing list <phenixbb at phenix-online.org>

> 
> I was thinking of the case (which we have had) where we could 
> place the peptide plausibly (eg in a helix) but not identify the 
> side chain. Maybe there should be different UNK-likes, for 
> unknown amino-acid, unknown nucleotide, unknown thing
> 
> Phil
> 
> On 28 Jul 2010, at 23:34, Pavel Afonine wrote:
> 
> > I agree with Phil about UNK - it seems to be good indeed to 
> call unknown (undefined) residue as it appears on the map rather 
> than call ALA something that in fact is TYR, and then later on 
> getting confused about the mismatch between actual sequence and 
> the one derived from PDB file. This is actually what I get 
> confused all the time looking at results of model building 
> programs, because the first thing I always do is I compare the
> real actual sequence with the one derived from PDB file - just
> to validate the result of model building.
> > 
> > However, I agree with Tom too about loosing identity in cases 
> where we really do know what to expect: polypeptide or rna/dna.
> > 
> > Hm... interesting situation -:)
> > 
> > I guess UNK is may be still better, ONLY IF you go one level 
> deeper and look at atom names (or make sure you do that 
> consistently). Say you name a "residue" as UNK and name 
> corresponding atoms within this residue as CA, N, C, O (kind of 
> peptide pattern) - then you have a chance to guess what it is. 
> Of course how you then know where you place those CA,N,C and O...
> > 
> > Pavel.
> > 
> > 
> > 
> > On 7/28/10 3:19 PM, Tom Terwilliger 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.
> >>>> 
> >>>> _______________________________________________
> >>>> phenixbb mailing list
> >>>> phenixbb at phenix-online.org
> >>>> http://phenix-online.org/mailman/listinfo/phenixbb
> >>> 
> >>> _______________________________________________
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> >> 
> >> 
> >> 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>> 
> >> 
> >> 
> >> 
> >> 
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> > 
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Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel
Phone: 972-8-647-2220 ; Fax: 646-1710
Skype: boaz.shaanan‎
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