Re: [ccp4bb] crystallographic confusion [SEC=UNCLASSIFIED]
There are three places in a pdb file where resolution is defined. Unfortunately by current conventions I believe they are all required to show the same value. If one of them could be redefined to be "effective resolution", with a comment to explain how that was arrived at, it would take the pressure off of resolution cuttoff to serve double duty as the principal indicator of quality. I guess you can entitle your paper "2.2 A structure of XYZ" even if the pdb file shows the resolution to be 1.92 with 22% completeness in the last shell, which could appease some reviewers but make problems with others. eab DUFF, Anthony wrote: I thought... we had a definition for reportable resolution: The resolution at which = 2, and completeness > 50% This reported resolution is not to be confused with data cutoff. We give the software all the scaled and merged data and let it down-weight the weak data. At the edge, we might happily have Rmerge=50%, multiplicity = 1.1, = 1. The resolution of the edge data should not be reported as the resolution of the data. This reportable resolution is actually useful in refinement. Very very roughly, you are done when the R-factor equals reportable resolution divided by 10. 25% for 2.5A data. 15% for 1.5A data. Anthony Duff -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Tom Peat Sent: Saturday, 19 April 2014 6:03 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] crystallographic confusion As has been alluded to, people (and not just crystallographers) are looking for a simple number to indicate the quality of a structure. Unfortunately this doesn't exist, but it doesn't keep people from wanting such a number. Most crystallographers (I think) now agree that throwing data away is a bad idea and will make maps worse. The real question is not whether to throw data away, but what to call the resolution of a map/ structure. A structure that has been refined with data that is ~90% complete at 3.6 Angstrom resolution but that has 2% completeness at 2.8 Angstrom would be considered to be ? (Just to pull one instance from the PDB). If we as crystallographers could agree to some definition as to what our arbitrary resolution number is, life would probably be easier for the non-crystallographers (as well as for the crystallographers in some instances- particularly in the process of reviewing papers). cheers, tom Tom Peat Biophysics Group CSIRO, CMSE 343 Royal Parade Parkville, VIC, 3052 +613 9662 7304 +614 57 539 419 tom.p...@csiro.au From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of William G. Scott [wgsc...@ucsc.edu] Sent: Saturday, April 19, 2014 11:41 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] crystallographic confusion Dear Arnon et al: My understanding of the Shannon/Nyquist sampling theorem is admittedly extremely rudimentary, but I think aliasing can result if an arbitrary brick-wall resolution cut-off to the data is applied. So let's say there are real data are to 2.0 Å resolution. Applying the 2.2 Å cutoff will result in aliasing artifacts in the electron density map corresponding to an outer shell reciprocal space volume equal but opposite to the cut out data. The alternative, which is to process and keep all the measured reflections, should help to minimize this. An effective resolution can be calculated and quoted. This becomes a significant problem with nucleic acids and their complexes, which often diffract with significant anisotropy. The idea that 85% completeness in the outer shell should dictate its rejection seems rather surprising and arbitrary. The aliasing artifacts in that case would probably be significant. The map image quality, after all, is what we are after, not beautiful Table 1 statistics. Bill William G. Scott Professor Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA University of California at Santa Cruz Santa Cruz, California 95064 USA http://scottlab.ucsc.edu/scottlab/ On Apr 18, 2014, at 5:22 PM, Lavie, Arnon wrote: Dear Kay. Arguably, the resolution of a structure is the most important number to look at; it is definitely the first to be examined, and often the only one examined by non-structural biologists. Since this number conveys so much concerning the quality/reliability of the the structure, it is not surprising that we need to get this one parameter right. Let us examine a hypothetical situation, in which a data set at the 2.2-2.0 resolution shell has 20% completeness. Is this a 2.0 A resolution structure? While you make a sound argument that including that data may result in a better refined model (more observations, more restraints), I would not consider that model the same quality as one refined against a data set that has >90% completeness at that resolution shell. As I see it, there are two issues here: one, is whether to inclu
Re: [ccp4bb] crystallographic confusion [SEC=UNCLASSIFIED]
I thought... we had a definition for reportable resolution: The resolution at which = 2, and completeness > 50% This reported resolution is not to be confused with data cutoff. We give the software all the scaled and merged data and let it down-weight the weak data. At the edge, we might happily have Rmerge=50%, multiplicity = 1.1, = 1. The resolution of the edge data should not be reported as the resolution of the data. This reportable resolution is actually useful in refinement. Very very roughly, you are done when the R-factor equals reportable resolution divided by 10. 25% for 2.5A data. 15% for 1.5A data. Anthony Duff -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Tom Peat Sent: Saturday, 19 April 2014 6:03 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] crystallographic confusion As has been alluded to, people (and not just crystallographers) are looking for a simple number to indicate the quality of a structure. Unfortunately this doesn't exist, but it doesn't keep people from wanting such a number. Most crystallographers (I think) now agree that throwing data away is a bad idea and will make maps worse. The real question is not whether to throw data away, but what to call the resolution of a map/ structure. A structure that has been refined with data that is ~90% complete at 3.6 Angstrom resolution but that has 2% completeness at 2.8 Angstrom would be considered to be ? (Just to pull one instance from the PDB). If we as crystallographers could agree to some definition as to what our arbitrary resolution number is, life would probably be easier for the non-crystallographers (as well as for the crystallographers in some instances- particularly in the process of reviewing papers). cheers, tom Tom Peat Biophysics Group CSIRO, CMSE 343 Royal Parade Parkville, VIC, 3052 +613 9662 7304 +614 57 539 419 tom.p...@csiro.au From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of William G. Scott [wgsc...@ucsc.edu] Sent: Saturday, April 19, 2014 11:41 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] crystallographic confusion Dear Arnon et al: My understanding of the Shannon/Nyquist sampling theorem is admittedly extremely rudimentary, but I think aliasing can result if an arbitrary brick-wall resolution cut-off to the data is applied. So let's say there are real data are to 2.0 Å resolution. Applying the 2.2 Å cutoff will result in aliasing artifacts in the electron density map corresponding to an outer shell reciprocal space volume equal but opposite to the cut out data. The alternative, which is to process and keep all the measured reflections, should help to minimize this. An effective resolution can be calculated and quoted. This becomes a significant problem with nucleic acids and their complexes, which often diffract with significant anisotropy. The idea that 85% completeness in the outer shell should dictate its rejection seems rather surprising and arbitrary. The aliasing artifacts in that case would probably be significant. The map image quality, after all, is what we are after, not beautiful Table 1 statistics. Bill William G. Scott Professor Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA University of California at Santa Cruz Santa Cruz, California 95064 USA http://scottlab.ucsc.edu/scottlab/ On Apr 18, 2014, at 5:22 PM, Lavie, Arnon wrote: > Dear Kay. > > Arguably, the resolution of a structure is the most important number > to look at; it is definitely the first to be examined, and often the > only one examined by non-structural biologists. > > Since this number conveys so much concerning the quality/reliability > of the the structure, it is not surprising that we need to get this > one parameter right. > > Let us examine a hypothetical situation, in which a data set at the > 2.2-2.0 resolution shell has 20% completeness. Is this a 2.0 A > resolution structure? While you make a sound argument that including > that data may result in a better refined model (more observations, > more restraints), I would not consider that model the same quality as > one refined against a data set that has >90% completeness at that resolution > shell. > > As I see it, there are two issues here: one, is whether to include > such data in refinement? I am not sure if low completeness > (especially if not > random) can be detrimental to a correct model, but I will let other > weigh in on that. > > The second question is where to declare the resolution limit of a > particular data set? To my mind, here high completeness (the term "high" > needs a precise definition) better describes the true resolution limit > of the diffraction, and with this what I can conclude about the > quality of the refined model. > > My two cents. > > Arnon Lavie > > On Fri, April 18, 2014 6:51 pm, Kay Diederichs wro
