On Thu, 2 Jul 2015 13:25:07 -0400, Edward A. Berry <ber...@upstate.edu> 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".
the electron microscopy community uses a similar measure ("FSC", Fourier Shell
Correlation) as CC1/2. They follow their "Gold Standard" if they cut their data
at FSC=0.143 . Mathematically, CC1/2=0.143 is equivalent to CC*=0.5 . So
researchers of that community _do_ specify a cutoff, and by calling it "Gold
Standard" they cast it in stone. Very helpful because probably no reviewer ever
calls a "Gold Standard" into question.
> Probably depends
>among other things on how strong the lower resolution data is, how good the
>structure is without the added data.
the latter point is crucial: a structure that is good can "make use of"
higher-resolution data than a structure that is not properly refined. That is
different from the situation in electron microscopy, where the phases are
obtained experimentally. This is why an X-ray structure at an early stage of
iterative refinement/fitting may possibly not be improved by the weak
high-resolution data , and why the paired refinement should be done during the
"end game" of refinement. But as long as CC1/2 is statistically significant it
may improve a very good model even if CC*<0.5 (see Bublitz et al IUCrJ 2,
409-420 (2015) for an example).
To find out how close the structure to the data is, it helps to compare CCwork
and CC*.
An arbitrary cutoff (like CC*=0.5) is thus not sensible in all situations; it
may serve as a rule of thumb though since the difference in resolution limit is
not large anyway: CC*=0.5 and CC*=0.3 usually differ by (say) 0.1A only.
>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.
Absolutely. Much better than to believe in rules of thumb.
best,
Kay
>
>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!
>> >
>>
