Hi Dale,
On Thu, 2 Jul 2015 10:45:45 -0700, Dale Tronrud <[log in to unmask]> 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:[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
>>>
>>> ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
> ---
>>>
>>>
>>> *Van: *Edward A. Berry <mailto:[log in to unmask]>
>>> *Verzonden: *2-7-2015 18:43
>>> *Aan: *[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!
>>> >
>>>
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