Re: [ccp4bb] metal ion coordination
Dear Faisal, When scrutinising such distances do be aware of the possibility of false precision in the estimates; see eg http://dx.doi.org/10.1107/S2052252513031485 Best wishes, John Prof John R Helliwell DSc On 17 Apr 2014, at 21:13, Faisal Tarique faisaltari...@gmail.com wrote: Dear all Can anybody please explain what is the classical metal ion coordination for Mg2+, Ca+ and Na+ with Oxygen atom and the average distance with these metal ions..does the distance vary with the type of metal ion and its coordination with oxygen atom..what is the best way to identify the correct metal ion in the electron density in the vicinity of negatively charged molecule mostly oxygen containing molecule..In one of my paper the reviewer has asked me to check whether the octahedrally coordinated Mg+ is Ca+ ion..and similarly raised doubt about the identity of the Na+ ion as well..his argument was based on metal ion to oxygen distance..I am attaching the figure with this mail..i request you to please shed some light on this area and help me in clearing some doubts regarding this. -- Regards Faisal School of Life Sciences JNU Fig3.tif
Re: [ccp4bb] Rmerge, Rmeas, I/sigma, Mn(I/sd)
Hi Roberto, for my taste the answers so far have not mentioned (or I did not understand them) that there is a distinction between indicators of the precision of merged data, and those for the precision of unmerged data. It is not possible to directly compare (or equate) indicators of one category with those of the other category. This would be like comparing apples to oranges, and is, in my experience, the biggest source of confusion in crystallographic statistics, _and_ not clearly explained in writing. The only way to do such a comparison numerically is to include a factor of sqrt(n) where n is the multiplicity - the ratio of the number of observations and the number of unique reflections. Indicators of precision of unmerged data are: [Rsym=Rmerge (which should be deprecated),] Rmeas and the I/sigma(I) of individual observations, as given in the first long table in XDS' CORRECT.LP which is fine-grained in resolution. Aimless also has this, but it is _not_ the quantity labeled Mn(I)/sd(Mn(I)). Indicators of precision of merged data are: CC1/2, Rpim and the I/sigma(I) of unique reflections after averaging, as given in the repeated (by DATA_RANGE) tables in XDS' CORRECT.LP. In aimless, the average signal/noise after averaging symmetry-related observations I/σ(I) is labelled Mn(I)/sd(Mn(I)). For both categories, there is not much difference in I/sigma(I) and I/sigma(I); in particular at high resolution, these are becoming equal. Thus, Rmerge ≈ 0.8/I/σ(I) can only hold for unmerged data (i.e. observations), not for merged data (unique reflections, after averaging over symmetry-related observations). HTH, Kay On Wed, 16 Apr 2014 17:09:28 +0200, Roberto Battistutta roberto.battistu...@unipd.it wrote: Hi, in the Rupp book the following relation is reported (on pag 415): Rmerge ≈ 0.8/I/σ(I) referring to a relation of the linear merging R-value with the signal-to-noise ratio. in a 2006 CCP4bb, Manfred Weiss reported: Rrim (or Rmeas) = 0.8*sd(i)/I so, First question: is it Rmerge or Rmeas (Rrim) that we are dealing with? Second question: at the denominator (of the Rupp way to write), it is the aimless Mn(I/sd) (usually indicated as the real signal-to-noise ratio) or the aimless I/sigma (very different from Mn(I/sd) with high redundancy)? Thank you very much for the clarification. Best, Roberto. Roberto Battistutta
[ccp4bb] ligand occupancy
Dear all I have a protein which is dimer having one ligand binding site in each monomer. I refined the crystal structure with ligand in both sites finally. I refined will full occupancy of 1 for ligands (same in both). But now i want to see is there any difference in the occupancy of both ligands in ligand binding sites of monomer A and B. Is there any way i can get any information about the occupancy of ligands in two monomers like one is binding more tightly than another so that i can get an idea about their differential binding contacts also. Thank you very much in advance. Regards Monica
Re: [ccp4bb] Validation reports for all X-ray structures in the PDB
Bonjour Philippe, The reports are based on the recommendations of the wwPDB X-ray validation task force - see http://www.wwpdb.org/workshop/2011/index.html and the report published by this task force at http://www.cell.com/structure/abstract/S0969-2126%2811%2900285-1 Of course, if you have specific suggestions for improvements, we'd be interested to hear from you - feel free to mail them to validat...@mail.wwpdb.org A stand-alone server already exists - see http://www.wwpdb.org/validation-servers.html - hope this turns your Good Friday into a Great Friday :-) Best wishes, --Gerard On Wed, 16 Apr 2014, Philippe BENAS wrote: Dear Gerard CD/DVD/Blue Ray (;-) ), Yes, these new reports are great although they should/will improve over time. Another point that would be also really helpful would be to have the opportunity to run the associated scripts either locally or on a remote server from the PDB, prior to the submission itself. Hence they should provide strong guidelines the crystallographers during their rebuilding/refinement stages. I know Phenix for instance has already some of these tools, but not all. Could the PDB provide something in that way for the everyday use of a poor X-ray crystallographer ? Best regards, Philippe Philippe BENAS, Ph.D. X-ray diffraction and computing facilities manager Laboratoire de Cristallographie et RMN Biologiques, UMR 8015 CNRS E-mails: philippe.be...@parisdescartes.fr, philippe_be...@yahoo.fr URLs: http://lcrbw.pharmacie.univ-paris5.fr/ , http://lcrbw.pharmacie.univ-paris5.fr/spip.php?article18 De : Gerard DVD Kleywegt ger...@xray.bmc.uu.se ? : CCP4BB@JISCMAIL.AC.UK Envoy? le : Mercredi 16 avril 2014 19h01 Objet : [ccp4bb] Validation reports for all X-ray structures in the PDB Hi all, You may not have noticed, but 19 March 2014 was VR Day - the day that new style wwPDB validation reports for all X-ray structures were made publicly available - see http://www.wwpdb.org/news/news_2014.html#18-March-2014 The validation-related files for individual X-ray PDB entries can be accessed through the web sites and ftp sites of the various wwPDB partners. Speaking for PDBe, if you go to the summary page of an X-ray PDB entry, for instance: http://pdbe.org/1cbs you will see the percentile sliders displayed in the PDBportfolio widget (http://pdbe.org/portfolio) on the right of the page. (Clicking the big white arrow will start a slideshow of images related to this entry.) The legend of the percentile-slider plot contains a direct link to the validation report (as a PDF file; in this case http://www.ebi.ac.uk/pdbe/entry-files/1cbs_validation.pdf). If you are not yet familiar with these new style validation reports, have a look here: http://www.wwpdb.org/validation-reports.html - in particular the user guide may be of interest: http://www.wwpdb.org/ValidationPDFNotes.html If you want to download the full report (which lists all outliers for many of the validation criteria, instead of just the worst 5 or the first 5), or a graphic image of the percentile-slider plot, or an XML file with all validation data in machine-readable form, go to the downloads page of any X-ray PDB entry, either through clicking the Downloads link in the menu on the left, or directly by going to a URL of the form: http://pdbe.org/1cbs/downloads The section labelled Validation of the table provides the relevant links. Note that sites that include PDBportfolio in their pages now automatically display the percentile-slider plot and download link as well! To see this in action, go to the EDS page (if any) of your favourite X-ray PDB entry, e.g.: http://eds.bmc.uu.se/cgi-bin/eds/uusfs?pdbCode=1cbs Please send any comments, questions or suggestions on the new style validation reports to validat...@mail.wwpdb.org Questions about PDBe-specific pages and services can be sent to pdbeh...@ebi.ac.uk --Gerard --- Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK ger...@ebi.ac.uk . pdbe.org Secretary: Pauline Haslam pdbe_ad...@ebi.ac.uk Best wishes, --Gerard ** Gerard J. Kleywegt http://xray.bmc.uu.se/gerard mailto:ger...@xray.bmc.uu.se ** The opinions in this message are fictional. Any similarity to actual opinions, living or dead, is purely coincidental. ** Little known gastromathematical curiosity: let z be the radius and a the thickness of a pizza. Then the volume of that pizza is equal to pi*z*z*a ! **
Re: [ccp4bb] Rmerge, Rmeas, I/sigma, Mn(I/sd)
[There is] a distinction between indicators of the precision of merged data, and those for the precision of unmerged data. Let's take a step back - definitions matter: (i) We have multiple observations of the same, already integrated h: the 'unmerged' data - most important data set which SHOULD BE deposited and rarely is. (ii) Now we weighted average those multiple instances of the same h, sans symmetry: 'merged' data - still useful to keep, particularly if one gets the metric symmetry/PG wrong (iii) Now we merge symmetry related data (generally keeping Friedels apart): 'unique' data (iv) both (ii) and (iii) are instances of 'merged' data. Is that correct? If so, let’s continue the thread (there is more to come...) or adjust the definitions. Best, BR
Re: [ccp4bb] Rmerge, Rmeas, I/sigma, Mn(I/sd)
On Fri, 18 Apr 2014 12:33:30 +0200, Bernhard Rupp hofkristall...@gmail.com wrote: [There is] a distinction between indicators of the precision of merged data, and those for the precision of unmerged data. Let's take a step back - definitions matter: (i) We have multiple observations of the same, already integrated h: the 'unmerged' data - most important data set which SHOULD BE deposited and rarely is. yes, fully agree. (ii) Now we weighted average those multiple instances of the same h, sans symmetry: 'merged' data - still useful to keep, particularly if one gets the metric symmetry/PG wrong (iii) Now we merge symmetry related data (generally keeping Friedels apart): 'unique' data (iv) both (ii) and (iii) are instances of 'merged' data. I don't quite understand the difference between (ii) and (iii). As soon as you take the weighted average, you merge the data, because you create one single estimate of the intensity I (and sigma(I)) of a unique reflection from several symmetry-related observations of that unique reflection. So, to me, 'taking the weighted average' and 'merging' are different words for the same procedure. best, Kay Is that correct? If so, let’s continue the thread (there is more to come...) or adjust the definitions. Best, BR
[ccp4bb] observed criterion sigma
Dear all I request you please tell me what is the value of Observed criterion sigma (F) and Observed criterion sigma (I) for any data processed by imosflm and scala ? -- Regards Faisal School of Life Sciences JNU
Re: [ccp4bb] Rmerge, Rmeas, I/sigma, Mn(I/sd)
(i) We have multiple observations of the same, already integrated h: the 'unmerged' data - most important data set which SHOULD BE deposited and rarely is. yes, fully agree. Perfect. I don't quite understand the difference between (ii) and (iii). As soon as you take the weighted average, you merge the data, because you create one single estimate of the intensity I (and sigma(I)) of a unique reflection from several symmetry-related observations of that unique reflection. So, to me, 'taking the weighted average' and 'merging' are different words for the same procedure. There is indeed no distinction between (ii) and (iii) form the merging point of view, I just wanted to point out the difference between just 'merged' and 'unique' data. We return to Kay's original post. Indicators of precision of *unmerged* data are: [Rsym=Rmerge (which should be deprecated),] - yes, and I want to iterate: Here is already where the notational confusion starts - 'unmerged' data (i) obviously contain multiple observations of a single reflection h, then how can any measure of their quality logically be called an Rsym (there is no sym in a single reflection) ? A Rsym is per definition of sym a measure producing merged data of type (iii) , although it is also AN Rmerge. Historically this seems to come from the original Arndt definition (c.f. Diederichs Karplus 1997) but it is illogical in the above context. The original definition of Rmerge also includes already the summation over a set of binned hkls. Along the same line, that the quality indicator for 'unmerged' data is their 'merging' R is also illogical - they have the same quality before they are merged. Not only as a statistic, even as a term Rmerge should be buried (i.e. finally BECOME a statistic). One primary statistic that is valid universally are the i/sigI. None of these Rs are robust statistics. Rmeas is an asymptotic target (penalizing you for small N) , and Rpim some form of standard error of the mean (rewarding you for large N). Choose wisely Because of its statistical defensibility (clear definition and the association with a confidence or significance level) CC1/2 is interesting and perhaps the only measure in addition to primary I/sigi needed - with the juicy bonus of having via CC*/work/free a traceable relation to the model quality. That, as Kay has pointed out in his papers, is more than you can say about any of these Rs. /anti_R_flame Thus, Rmerge � 0.8/I/s(I) can only hold for unmerged data (i.e. observations), not for merged data (unique reflections, after averaging over symmetry-related observations). True. I see that. Which is the reason why it is still close for the low redundancy data historically observed, but I think this will change rapidly with the PADs high redundancy becoming standard - another reason to bury Rmerge associates. Happy Easter, BR best, Kay Is that correct? If so, let�s continue the thread (there is more to come...) or adjust the definitions. Best, BR
Re: [ccp4bb] ligand occupancy
Hi Monica, Calculate the mean B-factor of all atoms that making interactions with each ligand in monomer A and B. Use those means values as B-factors for each ligand respectively. Adjust manually the occupancies, in order the B-factors for each ligand to stay after refinement close to the above values. In order to calculate occupancies more precisely, it would help to have the un-liganded structure and thus the location of the water molecules in each binding site. If you have the above information you could refine water molecules and ligands simultaneously in the binding site and get accurate refined occupancies. George From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Monica Mittal Sent: Friday, April 18, 2014 1:04 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] ligand occupancy Dear all I have a protein which is dimer having one ligand binding site in each monomer. I refined the crystal structure with ligand in both sites finally. I refined will full occupancy of 1 for ligands (same in both). But now i want to see is there any difference in the occupancy of both ligands in ligand binding sites of monomer A and B. Is there any way i can get any information about the occupancy of ligands in two monomers like one is binding more tightly than another so that i can get an idea about their differential binding contacts also. Thank you very much in advance. Regards Monica
Re: [ccp4bb] ligand occupancy
Hi Monica, You can refine the ligand occupancy in refmac as explained here: http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/refmac/refmac_keywords.html or in phenix, whichever program you're using. Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Monica Mittal [monica.mitta...@gmail.com] Sent: Friday, April 18, 2014 1:03 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] ligand occupancy Dear all I have a protein which is dimer having one ligand binding site in each monomer. I refined the crystal structure with ligand in both sites finally. I refined will full occupancy of 1 for ligands (same in both). But now i want to see is there any difference in the occupancy of both ligands in ligand binding sites of monomer A and B. Is there any way i can get any information about the occupancy of ligands in two monomers like one is binding more tightly than another so that i can get an idea about their differential binding contacts also. Thank you very much in advance. Regards Monica
Re: [ccp4bb] Rmerge, Rmeas, I/sigma, Mn(I/sd)
Roberto Battistutta wrote: Hi, in the Rupp book the following relation is reported (on pag 415): Rmerge ≈ 0.8/I/σ(I) referring to a relation of the linear merging R-value with the signal-to-noise ratio. in a 2006 CCP4bb, Manfred Weiss reported: Rrim (or Rmeas) = 0.8*sd(i)/I Bernhard Rupp wrote: 0.8*sd(i)/I = 0.8/(I/sd(i)) --- Yes, but in this context it is worth pointing out that I/σ(I) != 1/σ(I)/I especially if there is a wide range in values of I/σ(I), which would be narrower but still significant in the outer shells. ave(100, 10, 1) = 37 ave(0.01, 0.1, 1) = .37 = 1/(2.7) != 1/37 So while of course Rupp's equation is correct, if we try to apply it to average values, which we have to do to compare with Rmerge, it is no longer correct, so even at high multiplicity the two equations quoted in original post seem incompatible. (Unless I'm badly confused again) eab
Re: [ccp4bb] Rmerge, Rmeas, I/sigma, Mn(I/sd)
Hi Ed, your example seems to be designed to show that the average of reciprocal values is not the same as the reciprocal of an average value? If that is what you are alluding to, then please not that the (relatively narrow) Wilson distribution of intensities has the effect of making the relation I/σ(I) ~ 1/σ(I)/I work fairly well in practice. The relation Rmeas ≈ 0.8/I/σ(I) (where I refers to the intensity of unmerged, individual observations) is obviously not an exact one ... rather it depends on how the σ(I) are calculated (the error model) and some other things. But it should _not_ depend on the multiplicity, and it should hold fairly well at high resolution. Kay On Fri, 18 Apr 2014 10:12:10 -0400, Edward A. Berry ber...@upstate.edu wrote: Roberto Battistutta wrote: Hi, in the Rupp book the following relation is reported (on pag 415): Rmerge ≈ 0.8/I/σ(I) referring to a relation of the linear merging R-value with the signal-to-noise ratio. in a 2006 CCP4bb, Manfred Weiss reported: Rrim (or Rmeas) = 0.8*sd(i)/I Bernhard Rupp wrote: 0.8*sd(i)/I = 0.8/(I/sd(i)) --- Yes, but in this context it is worth pointing out that I/σ(I) != 1/σ(I)/I especially if there is a wide range in values of I/σ(I), which would be narrower but still significant in the outer shells. ave(100, 10, 1) = 37 ave(0.01, 0.1, 1) = .37 = 1/(2.7) != 1/37 So while of course Rupp's equation is correct, if we try to apply it to average values, which we have to do to compare with Rmerge, it is no longer correct, so even at high multiplicity the two equations quoted in original post seem incompatible. (Unless I'm badly confused again) eab
Re: [ccp4bb] crystallographic confusion
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 wrote: Hi everybody, since we seem to have a little Easter discussion about crystallographic statistics anyway, I would like to bring up one more topic. A recent email sent to me said: Another referee complained that the completeness in that bin was too low at 85% - my answer was that I consider the referee's assertion as indicating a (unfortunately not untypical case of) severe statistical confusion. Actually, there is no reason at all to discard a resolution shell just because it is not complete, and what would be a cutoff, if there were one? What constitutes too low? The benefit of including also incomplete resolution shells is that every reflection constitutes a restraint in refinement (and thus reduces overfitting), and contributes its little bit of detail to the electron density map. Some people may be mis-lead by a wrong understanding of the cats and ducks examples by Kevin Cowtan: omitting further data from maps makes Fourier ripples/artifacts worse, not better. The unfortunate consequence of the referee's opinion (and its enforcement and implementation in papers) is that the structures that result from the enforced re-refinement against truncated data are _worse_ than the original data that included the incomplete resolution shells. So could we as a community please abandon this inappropriate and un-justified practice - of course after proper discussion here? Kay
Re: [ccp4bb] crystallographic confusion
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 I see no problem with saying that the model was refined against every spot on the detector that the data reduction program said was observed (and I realize there is argument about this) but declare that the resolution of the model is a number based on the traditional criteria. This solution allows for the best possible model to be constructed and the buyer is still allowed to make quality judgements the same way as always. Dale Tronrud On 4/18/2014 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 wrote: Hi everybody, since we seem to have a little Easter discussion about crystallographic statistics anyway, I would like to bring up one more topic. A recent email sent to me said: Another referee complained that the completeness in that bin was too low at 85% - my answer was that I consider the referee's assertion as indicating a (unfortunately not untypical case of) severe statistical confusion. Actually, there is no reason at all to discard a resolution shell just because it is not complete, and what would be a cutoff, if there were one? What constitutes too low? The benefit of including also incomplete resolution shells is that every reflection constitutes a restraint in refinement (and thus reduces overfitting), and contributes its little bit of detail to the electron density map. Some people may be mis-lead by a wrong understanding of the cats and ducks examples by Kevin Cowtan: omitting further data from maps makes Fourier ripples/artifacts worse, not better. The unfortunate consequence of the referee's opinion (and its enforcement and implementation in papers) is that the structures that result from the enforced re-refinement against truncated data are _worse_ than the original data that included the incomplete resolution shells. So could we as a community please abandon this inappropriate and un-justified practice - of course after proper discussion here? Kay -BEGIN PGP SIGNATURE- Version: GnuPG v2.0.22 (MingW32) Comment: Using GnuPG with Thunderbird - http://www.enigmail.net/ iEYEARECAAYFAlNRz14ACgkQU5C0gGfAG138HwCfYbUXb5MgQvC/8iCftiuuP1pn H0AAn24ej2FSBxbNbndjnHoJ/xAKCitK =Xh7C -END PGP SIGNATURE-
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 la...@uic.edu 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 wrote: Hi everybody, since we seem to have a little Easter discussion about crystallographic statistics anyway, I would like to bring up one more topic. A recent email sent to me said: Another referee complained that the completeness in that bin was too low at 85% - my answer was that I consider the referee's assertion as indicating a (unfortunately not untypical case of) severe statistical confusion. Actually, there is no reason at all to discard a resolution shell just because it is not complete, and what would be a cutoff, if there were one? What constitutes too low? The benefit of including also incomplete resolution shells is that every reflection constitutes a restraint in refinement (and thus reduces overfitting), and contributes its little bit of detail to the electron density map. Some people may be mis-lead by a wrong understanding of the cats and ducks examples by Kevin Cowtan: omitting further data from maps makes Fourier ripples/artifacts worse, not better. The unfortunate consequence of the referee's opinion (and its enforcement and implementation in papers) is that the structures that result from the enforced re-refinement against truncated data are _worse_ than the original data that included the incomplete resolution shells. So could we as a community please abandon this inappropriate and un-justified practice - of course after proper discussion here? Kay
