My take on this- No one has been willing to specify a cutoff (and probably there is no rigorous way to mathematically define the cutoff) and say "If CC* (or CCfree or whatever) is below X then it will not improve your structure, if above X then it will". Probably depends among other things on how strong the lower resolution data is, how good the structure is without the added data. On the other hand in paired refinement, if adding the data improves the structure as measured by Rfree in a zone excluding the added data, then it is hard to deny that that data are worth including.
eab On 07/02/2015 12:52 PM, Keller, Jacob wrote:
Wasn’t all of this put to bed through the implementation of CC measures? JPK *From:*CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of *Robbie Joosten *Sent:* Thursday, July 02, 2015 12:46 PM *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* Re: [ccp4bb] paired refinement But it is not the R-free of the shell here. In paired refinement you take the R-free of the reflections outside the shell. Cheers, Robbie Sent with my Windows Phone ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ *Van: *Edward A. Berry <mailto:ber...@upstate.edu> *Verzonden: *2-7-2015 18:43 *Aan: *CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK> *Onderwerp: *Re: [ccp4bb] paired refinement Another criterion for cutoff, also requiring the structure to be solved, is the agreement between data and structure, e.g. Rfree or CCfree. I think it is very unlikely that you could get Rfree =.2493 in a shell which contains only noise. So I would suggest doing paired refinement to 2.2 and 2.1 A (if the data is available). On 07/01/2015 07:15 PM, Eric Karg 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? > > 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. > > Thank you very much for your help! >
