[ccp4bb] Fwd: [ccp4bb] Death of Rmerge
Alas, how many lines like the following from a recent Science paper (PMID: 22605777), probably reviewer-incited, could have been avoided! Here, we present three high-resolution crystal structures of the Thermus thermophilus (Tth) 70S ribosome in complex withRMF, HPF, or YfiA that were refined by using data extending to 3.0 Å (I/sI = 1), 3.1 Å (I/sI = 1), and 2.75 Å (I/sI = 1) resolution, respectively. The resolutions at which I/sI = 2 are 3.2 Å, 3.4 Å, and 2.9 Å, respectively. JPK On Thu, May 31, 2012 at 1:59 PM, Edward A. Berry ber...@upstate.edu wrote: Yes! I want a copy of this program RESCUT. REMARK 200 R SYM FOR SHELL (I) : 1.21700 I noticed structure 3RKO reported Rmerge in the last shell greater than 1, suggesting the police who were defending R-merge were fighting a losing battle. And this provides a lot of ammunition to those they are fighting. Jacob Keller wrote: Dear Crystallographers, in case you have not heard, it would appear that the Rmerge statistic has died as of the publication of PMID: 22628654. Ding Dong...? JPK -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu *** -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu *** -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu ***
Re: [ccp4bb] Fwd: [ccp4bb] Death of Rmerge
On 05/31/12 12:07, Jacob Keller wrote: Alas, how many lines like the following from a recent Science paper (PMID: 22605777), probably reviewer-incited, could have been avoided! Here, we present three high-resolution crystal structures of the Thermus thermophilus (Tth) 70S ribosome in complex withRMF, HPF, or YfiA that were refined by using data extending to 3.0 Å (I/sI = 1), 3.1 Å (I/sI = 1), and 2.75 Å (I/sI = 1) resolution, respectively. The resolutions at which I/sI = 2 are 3.2 Å, 3.4 Å, and 2.9 Å, respectively. I don't see how you can avoid something like this. With the new, higher, resolution limits for data (which are good things) people will tend to assume that a 2.6 A resolution model will have roughly the same quality as a 2.6 A resolution model from five years ago when the old criteria were used. KK show that the weak high resolution data contain useful information but certainly not as much information as the data with stronger intensity. The resolution limit of the data set has been such an important indicator of the quality of the resulting model (rightly or wrongly) that it often is included in the title of the paper itself. Despite the fact that we now want to include more, weak, data than before we need to continue to have a quality indicator that readers can use to assess the models they are reading about. While cumbersome, one solution is to state what the resolution limit would have been had the old criteria been used, as was done in the paper you quote. This simply gives the reader a measure they can compare to their previous experiences. Now would be a good time to break with tradition and institute a new measure of quality of diffraction data sets. I believe several have been proposed over the years, but have simply not caught on. SFCHECK produces an optical resolution. Could this be used in the title of papers? I don't believe it is sensitive to the cutoff resolution and it produces values that are consistent with what the readers are used to. With this solution people could include whatever noisy data they want and not be guilty of overstating the quality of their model. Dale Tronrud JPK On Thu, May 31, 2012 at 1:59 PM, Edward A. Berry ber...@upstate.edu wrote: Yes! I want a copy of this program RESCUT. REMARK 200 R SYM FOR SHELL(I) : 1.21700 I noticed structure 3RKO reported Rmerge in the last shell greater than 1, suggesting the police who were defending R-merge were fighting a losing battle. And this provides a lot of ammunition to those they are fighting. Jacob Keller wrote: Dear Crystallographers, in case you have not heard, it would appear that the Rmerge statistic has died as of the publication of PMID: 22628654. Ding Dong...? JPK -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu *** -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu ***
Re: [ccp4bb] Fwd: [ccp4bb] Death of Rmerge
Good idea, but how to get it to catch on without publishing in Science? JPK On Thu, May 31, 2012 at 4:21 PM, Dale Tronrud det...@uoxray.uoregon.edu wrote: On 05/31/12 12:07, Jacob Keller wrote: Alas, how many lines like the following from a recent Science paper (PMID: 22605777), probably reviewer-incited, could have been avoided! Here, we present three high-resolution crystal structures of the Thermus thermophilus (Tth) 70S ribosome in complex withRMF, HPF, or YfiA that were refined by using data extending to 3.0 Å (I/sI = 1), 3.1 Å (I/sI = 1), and 2.75 Å (I/sI = 1) resolution, respectively. The resolutions at which I/sI = 2 are 3.2 Å, 3.4 Å, and 2.9 Å, respectively. I don't see how you can avoid something like this. With the new, higher, resolution limits for data (which are good things) people will tend to assume that a 2.6 A resolution model will have roughly the same quality as a 2.6 A resolution model from five years ago when the old criteria were used. KK show that the weak high resolution data contain useful information but certainly not as much information as the data with stronger intensity. The resolution limit of the data set has been such an important indicator of the quality of the resulting model (rightly or wrongly) that it often is included in the title of the paper itself. Despite the fact that we now want to include more, weak, data than before we need to continue to have a quality indicator that readers can use to assess the models they are reading about. While cumbersome, one solution is to state what the resolution limit would have been had the old criteria been used, as was done in the paper you quote. This simply gives the reader a measure they can compare to their previous experiences. Now would be a good time to break with tradition and institute a new measure of quality of diffraction data sets. I believe several have been proposed over the years, but have simply not caught on. SFCHECK produces an optical resolution. Could this be used in the title of papers? I don't believe it is sensitive to the cutoff resolution and it produces values that are consistent with what the readers are used to. With this solution people could include whatever noisy data they want and not be guilty of overstating the quality of their model. Dale Tronrud JPK On Thu, May 31, 2012 at 1:59 PM, Edward A. Berry ber...@upstate.edu wrote: Yes! I want a copy of this program RESCUT. REMARK 200 R SYM FOR SHELL (I) : 1.21700 I noticed structure 3RKO reported Rmerge in the last shell greater than 1, suggesting the police who were defending R-merge were fighting a losing battle. And this provides a lot of ammunition to those they are fighting. Jacob Keller wrote: Dear Crystallographers, in case you have not heard, it would appear that the Rmerge statistic has died as of the publication of PMID: 22628654. Ding Dong...? JPK -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu *** -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu *** -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu ***
Re: [ccp4bb] Fwd: [ccp4bb] Death of Rmerge
On Thursday, May 31, 2012 02:21:45 pm Dale Tronrud wrote: The resolution limit of the data set has been such an important indicator of the quality of the resulting model (rightly or wrongly) that it often is included in the title of the paper itself. Despite the fact that we now want to include more, weak, data than before we need to continue to have a quality indicator that readers can use to assess the models they are reading about. While cumbersome, one solution is to state what the resolution limit would have been had the old criteria been used, as was done in the paper you quote. This simply gives the reader a measure they can compare to their previous experiences. [\me dons flame suit] To the extent that reporting the resolution is simply a stand-in for reporting the quality of the model, we would do better to cut to the chase. For instance, if you map the Molprobity green/yellow/red model quality scoring onto good/mediocre/poor then you can title your paper Crystal Structure of Fabulous Protein Foo at Mediocre Quality [\me removes flame suit from back, and tongue from cheek] More seriously, I don't think it's entirely true that the resolution is reported as an indicator of quality in the sense that the model is well-refined. There are things you can expect to learn from a 2Å structure that you are unlikely to learn from a 5Å structure, even if equal care has been given to both experiments, so it makes sense for the title to give the potential reader an idea which of the two cases is presented. But for this purpose it isn't going to matter whether 2Å is really 1.8Å or 2.2Å. Now would be a good time to break with tradition and institute a new measure of quality of diffraction data sets. I believe several have been proposed over the years, but have simply not caught on. SFCHECK produces an optical resolution. Could this be used in the title of papers? I don't believe it is sensitive to the cutoff resolution and it produces values that are consistent with what the readers are used to. With this solution people could include whatever noisy data they want and not be guilty of overstating the quality of their model. We should also encourage people not to confuse the quality of the data with the quality of the model. Ethan -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg University of Washington, Seattle 98195-7742
Re: [ccp4bb] Fwd: [ccp4bb] Death of Rmerge
There are things you can expect to learn from a 2Å structure that you are unlikely to learn from a 5Å structure, even if equal care has been given to both experiments, so it makes sense for the title to give the potential reader an idea which of the two cases is presented. But for this purpose it isn't going to matter whether 2Å is really 1.8Å or 2.2Å. What should the title say when a crystal diffracts to, lets say, 3 A in one direction and 4-5 A in others? Alex Aleshin, Sanford-Burnham Medical Research Institute 10901 North Torrey Pines Road La Jolla, California 92037 On May 31, 2012, at 2:50 PM, Ethan Merritt wrote: On Thursday, May 31, 2012 02:21:45 pm Dale Tronrud wrote: The resolution limit of the data set has been such an important indicator of the quality of the resulting model (rightly or wrongly) that it often is included in the title of the paper itself. Despite the fact that we now want to include more, weak, data than before we need to continue to have a quality indicator that readers can use to assess the models they are reading about. While cumbersome, one solution is to state what the resolution limit would have been had the old criteria been used, as was done in the paper you quote. This simply gives the reader a measure they can compare to their previous experiences. [\me dons flame suit] To the extent that reporting the resolution is simply a stand-in for reporting the quality of the model, we would do better to cut to the chase. For instance, if you map the Molprobity green/yellow/red model quality scoring onto good/mediocre/poor then you can title your paper Crystal Structure of Fabulous Protein Foo at Mediocre Quality [\me removes flame suit from back, and tongue from cheek] More seriously, I don't think it's entirely true that the resolution is reported as an indicator of quality in the sense that the model is well-refined. There are things you can expect to learn from a 2Å structure that you are unlikely to learn from a 5Å structure, even if equal care has been given to both experiments, so it makes sense for the title to give the potential reader an idea which of the two cases is presented. But for this purpose it isn't going to matter whether 2Å is really 1.8Å or 2.2Å. Now would be a good time to break with tradition and institute a new measure of quality of diffraction data sets. I believe several have been proposed over the years, but have simply not caught on. SFCHECK produces an optical resolution. Could this be used in the title of papers? I don't believe it is sensitive to the cutoff resolution and it produces values that are consistent with what the readers are used to. With this solution people could include whatever noisy data they want and not be guilty of overstating the quality of their model. We should also encourage people not to confuse the quality of the data with the quality of the model. Ethan -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg University of Washington, Seattle 98195-7742
Re: [ccp4bb] Fwd: [ccp4bb] Death of Rmerge
In the meantime we could follow Phoebe Rice's example and put the resolution at I/sigma=2 in REMARK 2 resolution of structure but put the actual bleeding-edge resolution we used in the reduction and refinement statistics (At least if the PDB will allow us to have different values in these three places) And cite the REM 2 value in the article. eab PS - I believe optical resolution actually gives significantly more optimistic numbers for resolution than extending from I/sigma=2 to 0.5. The resolution we are used to is the d-spacing of the Fourier components, which is theoretically larger than the microscopist's definition of resolution (how close objects can be and still give separate maxima with a minimum between). Miller, Mitchell D. wrote: All three numbers (high resolution limit in remark 2, remark 3 and Remark 200) are supposed to be consistent and are defined as the highest resolution reflection used. http://mmcif.rcsb.org/dictionaries/mmcif_pdbx_v40.dic/Items/_reflns.d_resolution_high.html http://mmcif.rcsb.org/dictionaries/mmcif_pdbx_v40.dic/Items/_refine.ls_d_res_high.html Looking at the PDB specification, it shows that there is an option to add a free text comment to the remark 2 resolution -- Additional explanatory text may be included starting with the third line of the REMARK 2 record. For example, depositors may wish to qualify the resolution value provided due to unusual experimental conditions. http://www.wwpdb.org/documentation/format33/remarks1.html On Wed, Apr 25, 2012 at 12:23 AM, Phoebe Ricepr...@uchicago.edu wrote: I just noticed that the PDB has changed the stated resolution for one of my old structures! It was refined against a very anisotropic data set that extended to 2.2 in the best direction only. When depositing I called the resolution 2.5 as a rough average of resolution in all 3 directions, but now PDB is advertising it as 2.2, which is misleading. I'm afraid I may not have paid enough attention to the fine print on this issue - is the PDB now automatically advertising the resolution of a structure as that of the outermost flyspeck used in refinement, regardless of more cautious assertions by the authors? If so, I object! Dale Tronrud wrote: On 05/31/12 12:07, Jacob Keller wrote: Alas, how many lines like the following from a recent Science paper (PMID: 22605777), probably reviewer-incited, could have been avoided! Here, we present three high-resolution crystal structures of the Thermus thermophilus (Tth) 70S ribosome in complex withRMF, HPF, or YfiA that were refined by using data extending to 3.0 Å (I/sI = 1), 3.1 Å (I/sI = 1), and 2.75 Å (I/sI = 1) resolution, respectively. The resolutions at which I/sI = 2 are 3.2 Å, 3.4 Å, and 2.9 Å, respectively. I don't see how you can avoid something like this. With the new, higher, resolution limits for data (which are good things) people will tend to assume that a 2.6 A resolution model will have roughly the same quality as a 2.6 A resolution model from five years ago when the old criteria were used. KK show that the weak high resolution data contain useful information but certainly not as much information as the data with stronger intensity. The resolution limit of the data set has been such an important indicator of the quality of the resulting model (rightly or wrongly) that it often is included in the title of the paper itself. Despite the fact that we now want to include more, weak, data than before we need to continue to have a quality indicator that readers can use to assess the models they are reading about. While cumbersome, one solution is to state what the resolution limit would have been had the old criteria been used, as was done in the paper you quote. This simply gives the reader a measure they can compare to their previous experiences. Now would be a good time to break with tradition and institute a new measure of quality of diffraction data sets. I believe several have been proposed over the years, but have simply not caught on. SFCHECK produces an optical resolution. Could this be used in the title of papers? I don't believe it is sensitive to the cutoff resolution and it produces values that are consistent with what the readers are used to. With this solution people could include whatever noisy data they want and not be guilty of overstating the quality of their model. Dale Tronrud JPK On Thu, May 31, 2012 at 1:59 PM, Edward A. Berryber...@upstate.edu wrote: Yes! I want a copy of this program RESCUT. REMARK 200 R SYM FOR SHELL(I) : 1.21700 I noticed structure 3RKO reported Rmerge in the last shell greater than 1, suggesting the police who were defending R-merge were fighting a losing battle. And this provides a lot of ammunition to those they are fighting. Jacob Keller wrote: Dear Crystallographers, in case you have not heard, it would appear that the Rmerge statistic has died as of the publication of PMID: 22628654. Ding Dong...?
