[phenixbb] Dummy atoms

Nigel Moriarty nwmoriarty at lbl.gov
Thu Jul 29 11:27:33 PDT 2010 

Unfortunately, UND is undecane, but UNP and UNR are not specified yet.

On Thu, Jul 29, 2010 at 11:18 AM, Boaz Shaanan <bshaanan at bgu.ac.il> wrote:
> 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.
>> >>>>
>> >>>> _______________________________________________
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>> >>>> phenixbb at phenix-online.org
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>> >>>
>> >>> _______________________________________________
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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
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>> >> 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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>
> 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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>



-- 
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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