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:[log in to unmask]] On Behalf Of Dale Tronrud
Sent: Thursday, July 02, 2015 1:46 PM
To: [log in to unmask]
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:[log in to unmask]] *On Behalf
>> Of *Robbie Joosten
>> *Sent:* Thursday, July 02, 2015 12:46 PM
>> *To:* [log in to unmask]
>> *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
>>
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>>
>> *Van: *Edward A. Berry <mailto:[log in to unmask]>
>> *Verzonden: *‎2-‎7-‎2015 18:43
>> *Aan: [log in to unmask]">*[log in to unmask] <mailto:[log in to unmask]>
>> *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!
>>  >
>>