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 >>> Email: brun...@stanford.edu >>> Phone: +1 650-736-1031 >>> Fax: +1 650-745-1463 >>> >> >> -- >> >> =============================================================== >> * * >> * Gerard Bricogne g...@globalphasing.com * >> * * >> * Global Phasing Ltd. * >> * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * >> * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 * >> * * >> =============================================================== >
