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. K&K 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 > ******************************************* > >
