Dear Gerard
Yes I had seen this paper before but forgot about it (was probably in my subconscious). Wladek also mentioned this to me and I was in the process of acknowledging this when your email arrived.
The paper by Wladek and co-authors covers much (and more) of what has been said on the bulletin board including acknowledging the benefits of the procedure described in Schroeder et. al. It refers to the super-resolution in light microscopy and the paper by Stelzer, E. H. (2002). Nature (London), 417, 806-807. Stelzer suggests that super-resolution in some light microscopy methods is also a misleading term as it might not meet the criteria for distinguishing features separated by a certain distance. However, I am not sure this is correct as the excitation/de-excitation mechanism in STED (for example) leads to intrinsically sharp profiles for the remaining fluorescence.
Until persuaded otherwise my present view is
- The procedure in Schroeder et. al. is a useful development
- The use of the term super-resolution is misleading in this context
- The use of the term super-resolution for some excitation based light microscopy methods is probably justified
And of course your reference to Monsieur Jourdain lead me to finding some very amusing Moliere quotes.
Best Regards
Colin
> -----Original Message-----
> From: Gerard Bricogne [mailto:[log in to unmask]]
> Sent: 06 January 2011 22:48
> To: Nave, Colin (DLSLtd,RAL,DIA)
> Cc: [log in to unmask]
> Subject: Re: [ccp4bb] Fwd: [ccp4bb] FW: [ccp4bb] Resolution and
> distanceaccuracies
>
> Dear Colin,
>
> Wladek Minor has just drawn my attention to the following recent
> paper:
>
> Acta Cryst. (2010). D66, 1041.1042
>
> (that I must admit to having failed to notice) also expressing
> reservations
> about some uses of "creative language".
>
>
> With best wishes,
>
> Gerard.
>
> --
> On Thu, Jan 06, 2011 at 11:13:41AM -0000, Colin Nave wrote:
> > I too think the phrase super-resolution is rather misleading, in
> particular the analogy with light microscopy methods. Super-resolution
> in these latter cases is achieved via different physical phenomena
> (think excitations not waves).
> >
> >
> >
> > Would one claim super-resolution when refining the relative positions
> of the carbon atoms in benzene given the constraints of 6 fold symmetry
> and a carbon carbon distance of 1.39 angstroms?
> >
> >
> >
> > What would Moliere think?
> >
> >
> >
> > However, to quote from the DEN paper
> >
> > "Our approach is a major advance over conventional modeling of low
> resolution X-ray diffraction data by fitting rigid bodies since it
> accounts for deformations of the models while at the same time using a
> minimal set of variables (the single-bond torsion angles)"
> >
> >
> >
> > Overall this seems a reasonable claim.
> >
> > Colin
> >
> >
> >
> > From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of
> Charles W. Carter, Jr
> > Sent: 06 January 2011 09:52
> > To: [log in to unmask]
> > Subject: [ccp4bb] Fwd: [ccp4bb] FW: [ccp4bb] Resolution and distance
> accuracies
> >
> >
> >
> >
> >
> >
> >
> > Begin forwarded message:
> >
> >
> >
> >
> >
> > From: "Charles W. Carter, Jr" <[log in to unmask]>
> >
> > Date: January 6, 2011 10:51:20 AM GMT+01:00
> >
> > To: Gerard Bricogne <[log in to unmask]>
> >
> > Subject: Re: [ccp4bb] FW: [ccp4bb] Resolution and distance accuracies
> >
> >
> >
> > I echo Gérard's thought.
> >
> >
> >
> > Pascal Retailleau did a relevant experiment published in Acta D:
> >
> >
> >
> > Retailleau, et al., (2001) High-resolution experimental phases for
> tryptophanyl-tRNA synthetase
> >
> > (TrpRS) complexed with tryptophanyl-5'AMP, Acta Cryst, D57, 1595-1608
> >
> >
> >
> > He determined three independent sets of experimental phases for two
> different 1.7 Å selenomethionine structures (SAD) plus a 1.6 Å native
> (MIRAS) and refined the structures independently. The rmsd between the
> two SeMet structures was 0.25 Å, whereas that between the two SAD
> structures and the native structure was 0.39 Å, sufficient to
> demonstrate significant differences between the SeMet and native
> proteins. This experimental variance is a quite considerable indication
> of the magnitude of coordinate errors.
> >
> >
> >
> > Thus, as Gérard, who also was an author on that work together with
> Bob Sweet, points out, we're delighted to discover we have been
> achieving super-resolution to use Axel's neologism!
> >
> >
> >
> > Charlie
> >
> >
> >
> >
> >
> >
> >
> > On Jan 6, 2011, at 10:13 AM, Gerard Bricogne wrote:
> >
> >
> >
> >
> >
> > Dear Axel,
> >
> > On Sun, Dec 26, 2010 at 01:15:44PM -0800, Axel Brunger wrote:
> >
> >
> >
> > We defined "super-resolution" in our DEN paper as
> >
> > achieving coordinate accuracy better than the resolution
> >
> > limit d_min of the diffraction data. We proposed this
> >
> > definition in analogy to its use wide-spread use in optical
> microscopy:
> >
> > "super-resolution" methods such as STORM, PALM, and STED achieve
> >
> > accuracy of positions of fluorescent labels significantly better
> than the
> >
> > diffraction limit (in some cases, sub-nanometer accuracy -
> >
> > Pertsinidis, Zhang, Chu, Nature 466, 647-651, 2010).
> >
> >
> > In that case, all crystallographers doing stereochemically
> restrained
> > refinement will now have become aware, to their great delight, that
> they
> > have been unknowingly achieving "super-resolution" all the time, from
> the
> > grand old days of Bob Diamond's real-space refinement program - just
> like
> > Monsieur Jourdain found out that he had been speaking in prose all
> his life
> > without realising it.
> >
> > I guess that "super-resolution" is a sexier keyword in the mind
> of
> > editors of Nature that "restrained crystallographic refinement" :-))
> !
> >
> >
> > With best wishes for the New Year,
> >
> > Gerard.
> >
> > --
> >
> >
> >
> > We found DEN to be useful to move some atoms into correct
> >
> > positions in cases where electron density maps are difficult or
> >
> > impossible to interpret at low resolution. By default, DEN is
> >
> > active during the first torsion angle molecular dynamics stages,
> >
> > but then turned off during the last two stages. In addition, the
> >
> > DEN network is deformable. Thus, DEN is very different from
> >
> > "secondary structure" restraints or point restraints to reference
> >
> > models which are "on" all the time. Rather, DEN steers or
> >
> > guides the torsion angle conformational search process during
> >
> > refinement.
> >
> >
> >
> > Cheers,
> >
> > Axel
> >
> >
> >
> >
> >
> >
> >
> > On Dec 24, 2010, at 2:14 PM, Bernhard Rupp (Hofkristallrat a.D.)
> wrote:
> >
> >
> >
> > I find the "super-resolution" claims in this paper a
> bit of a conjuring
> >
> > trick.
> >
> >
> >
> > I think it is understood that information cannot come from
> nothing. You
> >
> > cannot cheat in basic physics. Interestingly, I had the
> same discussion with
> >
> > bioinformatics colleagues a short time ago. The problem is
> the same and
> >
> > seems of a semantic nature. They are using prior
> information of some sort
> >
> > (undisclosed) to successfully improve maps and they
> suggested to call this
> >
> > 'resolution increase'. I had the same objection and said
> that in
> >
> > crystallography resolution is a relatively hard term
> defined by the degree
> >
> > to which experimental observations are available, and as
> crystallographers
> >
> > we won't like that claim at all.
> >
> >
> >
> > On the other side it is uncontested that as long as the
> model fits
> >
> > (crossvalidation-) data better when prior information is
> used, something
> >
> > useful has been achieved - again with all the caveats of
> weights and bias
> >
> > etc admitted.
> >
> >
> >
> > However, how to entice non-experts to actually use new
> methods is another
> >
> > thing, and here the semantics come in. In essence, if at
> the end it results
> >
> > in better structures, how much of the unfortunately but
> undeniably necessary
> >
> > salesmanship is just right or acceptable? Within
> contemporary social
> >
> > constraints (aka Zeitgeist) that remains pretty much an
> infinitely debatable
> >
> > matter..
> >
> >
> >
> > Merry Christmas, BR
> >
> > -----------------------------------------------------------
> ---------------
> >
> > Dear Bernhard,
> >
> >
> >
> > I must say that I find the "super-resolution" claims in
> this paper a
> >
> > bit of a conjuring trick. If the final refined model has
> greater accuracy
> >
> > than one would expect from the resolution of the data it
> has been refined
> >
> > against, it is because that extra accuracy has been lifted
> from the higher
> >
> > resolution data that were used to refine the structure on
> the basis of which
> >
> > the elastic network restraints were created.
> >
> >
> >
> > Should we then say that we achieve super-resolution
> whenever we refine
> >
> > a macromolecular structure using Engh & Huber restraints,
> because these
> >
> > enable us to achieve distance accuracies comparable with
> those in the small
> >
> > molecules structures in the Cambridge Structural Database?
> >
> >
> >
> > Perhaps I have missed an essential point of this paper.
> >
> >
> >
> >
> >
> > With best wishes,
> >
> >
> >
> > Gerard.
> >
> >
> >
> > Axel T. Brunger
> >
> > Investigator, Howard Hughes Medical Institute
> >
> > Professor of Molecular and Cellular Physiology
> >
> > Stanford University
> >
> >
> >
> > Web: http://atbweb.stanford.edu <http://atbweb.stanford.edu/>
> >
> > Email: [log in to unmask]
> >
> > Phone: +1 650-736-1031
> >
> > Fax: +1 650-745-1463
> >
> >
> >
> >
> > --
> >
> > ===============================================================
> > * *
> > * Gerard Bricogne [log in to unmask] *
> > * *
> > * Global Phasing Ltd. *
> > * Sheraton House, Castle Park Tel: +44-(0)1223-353033 *
> > * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 *
> > * *
> > ===============================================================
> >
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