Hi Jacob, You need unmerged data to calculate cc1/2. That's not the sort of data you get from the PDB. But anyway, we have a fairly simple automated test that we can use on a case-by-case basis. I would argue that that is nicer than a empirical cut-off that may or may not be correct for you case.
Cheers, Robbie Sent with my Windows Phone ________________________________ Van: Keller, Jacob<mailto:kell...@janelia.hhmi.org> Verzonden: 2-7-2015 20:12 Aan: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> Onderwerp: Re: [ccp4bb] paired refinement Well, in that case, one could simply look at the plot of CC1/2 versus resolution and see the step up to one, conclude something was off. I wonder whether PDB REDO was able to get some empirically-determined values for CC1/2 cutoffs by comparing paired refinement versus CC1/2 versus other parameters? JPK -----Original Message----- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Dale Tronrud Sent: Thursday, July 02, 2015 1:46 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] paired refinement While I was puzzling over an entry in the PDB some years ago (since obsoleted) I noticed that all the high resolution amplitudes were equal to 11.0! This was before CC1/2 but for this structure it would have been equal to one, and yet the outer data were useless. A practical test like paired refinement can't be fooled in this way. Dale Tronrud On 7/2/2015 10:25 AM, Edward A. Berry wrote: > 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! >> > >>
