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