Hi Robbie,
I have been wondering how much information would be present in a
weighted CC1/2 with weights from the ML refinement program.
As I understand the concept behind paired refinement, one can use much
higher resolution data in refinement than you would expect from the
(classical) scaling statistics, because refinement programs down-weight
the outliers.
Maybe a weighted CC1/2 would be a convenient short cut the more time
consuming paired refinemement? How easily could the calculation of a
weighted CC1/2 be implemented in refmac? Refmac would have to merge the
data internally, but that's just a simple formula to implement.
Best,
Tim
On 07/02/2015 08:28 PM, Robbie Joosten wrote:
> 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:[log in to unmask]>
> Verzonden: 2-7-2015 20:12
> Aan: [log in to unmask]<mailto:[log in to unmask]>
> 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:[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] <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!
>>> >
>>>
>
--
--
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
phone: +49 (0)551 39 22149
GPG Key ID = A46BEE1A
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