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
> Email: brun...@stanford.edu
> Phone: +1 650-736-1031
> Fax: +1 650-745-1463
>
--
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