Dont forget all the "atomic resolution" 3Å structures! ________________________________________ From: Pavel Afonine [pafon...@gmail.com] Sent: Thursday, January 06, 2011 6:23 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Fwd: [ccp4bb] FW: [ccp4bb] Resolution and distance accuracies
Hi, creative language, you say... ha-ha. Go through this: A number of publications define ultrahigh or subatomic resolution in the range of 1.0–0.5A (Lecomte et al., 2008; Petrova et al., 2006; Howard et al., 2004; Guillot et al., 2008; Housset et al., 2000). Right? When you see ultra-high resolution, you can arbitrary pick any number from 1 to 0.5A, and call it "ultra-high resolution", just arbitrarily. What happens at lower resolution end is somewhat a bigger mess simply because there is no such eye-catching names, so "super-resolution" looks just fine to me - just to fill the gap, unless you know which numbers you mean. And to know these numbers you probably need to carefully read this paper. Not necessarily it will give you the numbers, but definitely the ideas to think about: Acta Cryst. (2009). D65, 1283-1291 On the use of logarithmic scales for analysis of diffraction data A. Urzhumtsev, P. V. Afonine and P. D. Adams Good luck! Pavel. On Thu, Jan 6, 2011 at 2:48 PM, Gerard Bricogne <g...@globalphasing.com<mailto:g...@globalphasing.com>> wrote: 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:CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>] On Behalf Of > Charles W. Carter, Jr > Sent: 06 January 2011 09:52 > To: CCP4BB@JISCMAIL.AC.UK<mailto: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<mailto:car...@med.unc.edu>> > > Date: January 6, 2011 10:51:20 AM GMT+01:00 > > To: Gerard Bricogne <g...@globalphasing.com<mailto: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<mailto: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 * > * * > =============================================================== >
