Dear Kay, You are right. I had forgotten the normalization part of the CC calculation.
Dale On 7/3/2015 12:01 AM, Kay Diederichs wrote: > Hi Dale, > > On Thu, 2 Jul 2015 10:45:45 -0700, Dale Tronrud <de...@daletronrud.com> wrote: > >> 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. > > no, the correlation coefficient between data that are exactly the same (which > you imply) is (mathematically) undefined. Most implementations would either > crash with a divide-by-zero error, or (if they catch the problem) give a > correlation of zero. The latter is sensible because the correlation is > invariant to adding an offset to one (or both) of the variables that are > compared. > > (You know all of this, and) I just want to point out that this is not a valid > example where CC1/2 would be 1. > > best, > > Kay > >> 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! >>>> > >>>>
