On Thu, 2 Jul 2015 00:15:58 +0100, Eric Karg <harvard...@yahoo.com> wrote:
>Hi all, > >I have a dataset processed in XDS to 2.3 A (based on CC1/2). I'm trying to do >"paired refinement" to determine the optimal resolution cutoff. Here is what I >get at different resolutions set in Phenix: > >Final Rfree/Rwork: >2.7—> 0.2498/0.2027 >2.6—> 0.2519/0.2009 >2.5—> 0.2567/0.2025 >2.4 —> 0.2481/0.2042 >2.3 —> 0.2493/0.2075 > >The geometry of all output structures are similar. > >1. What is the high resolution cutoff based on these data? I know that >Rfree/Rwork at different resolution should not be compared, but is there a >simple way to do the test as described in the K&D 2012 Science paper using >Phenix GUI? not, as far as I know, in a single step. Rather, you need to find out Rwork/Rfree of the 2.3A model, against the 2.4A data: if Rfree is better than 0.2481 (and Rfree-Rwork > 0.2481-0.2042), that would tell you that the reflections between 2.4 and 2.3 A improve the model. For consistency, I would then expect that a similar calculation involving the 2.3A model and the 2.5A data _also_ shows that the 2.3A model is superior than the 2.5A model. That would be two steps, but the second is of course not mandatory. If, on the other hand, Rfree of the 2.3A model is worse than 0.2481 against the 2.4A data, you should disregard 2.3A as a potential high-resolution cutoff. In that case, you would continue along the same lines, by using the 2.4A model, and investigating its Rwork/Rfree against the 2.5A data. > >2. For refining a structure at a lower resolution (lower than the initial >dataset), do I simply set the resolution limit in the refinement or I need to >reprocess the data starting from the images? Do I need to do anything with >Rfree flags? Based on the discussions on this forum I know I should deposit >the highest resolution dataset but my question is about the mtz file which >will be used for refinement. All you need "at a lower resolution" is Rwork/Rfree (of the higher-resolution model) _without_ positional or B-factor refinement. It is easiest to run (on the command line; don't know how to do it in the GUI) phenix.model_vs_data high_resolution=2.4 project.pdb project.mtz and finding the values of r_work_cutoff and r_free_cutoff in the output. These values are close (within 0.2%) to those you would obtain from a run of phenix.refine with xray_data.high_resolution=2.4 main.number_of_macro_cycles=0 . HTH, Kay > >Thank you very much for your help!
