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:kell...@janelia.hhmi.org> > Verzonden: 2-7-2015 20:12 > Aan: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> > 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:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Dale > Tronrud > Sent: Thursday, July 02, 2015 1:46 PM > To: CCP4BB@JISCMAIL.AC.UK > 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: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! >>> > >>> > -- -- 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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