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:ccp...@jiscmail.ac.uk] On Behalf Of Charles
> W. Carter, Jr
> Sent: 06 January 2011 09:52
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] Fwd: [ccp4bb] FW: [ccp4bb] Resolution and distance
> accuracies
>
>
>
>
>
>
>
> Begin forwarded message:
>
>
>
>
>
> From: "Charles W. Carter, Jr" <car...@med.unc.edu>
>
> Date: January 6, 2011 10:51:20 AM GMT+01:00
>
> To: Gerard Bricogne <g...@globalphasing.com>
>
> 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: brun...@stanford.edu
>
> Phone: +1 650-736-1031
>
> Fax: +1 650-745-1463
>
>
>
>
> --
>
> ===============================================================
> * *
> * Gerard Bricogne g...@globalphasing.com *
> * *
> * Global Phasing Ltd. *
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