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Hi all, If I am not wrong, the Karplus & Diederich paper suggests that data is generally meaningful upto CC1/2 value of 0.20 but they suggest a paired refinement technique ( pretty easy to perform) to actually decide on the resolution at which to cut the data. This will be the most prudent thing to do I guess and not follow any arbitrary value, as each data-set is different. But the fact remains that even where I/sigma(I) falls to 0.5 useful information remains which will improve the quality of the maps, and when discarded just leads us a bit further away from truth. However, as always, Dr Diederich and Karplus will be the best persons to comment on that ( as they have already done in the paper :) ) best, Arka Chakraborty p.s. Aimless seems to suggest a resolution limit bases on CC1/2=0.5 criterion ( which I guess is done to be on the safe side- Dr. Phil Evans can explain if there are other or an entirely different reason to it! ). But if we want to squeeze the most from our data-set, I guess we need to push a bit further sometimes :) On Wed, Aug 28, 2013 at 9:21 AM, Bernhard Rupp <[log in to unmask]>wrote: > *>*Based on the simulations I've done the data should be "cut" at CC1/2 = > 0. Seriously. Problem is figuring out where it hits zero. **** > > ** ** > > But the real objective is – where do data stop making an improvement to > the model. The categorical statement that all data is good**** > > is simply not true in practice. It is probably specific to each data set & > refinement, and as long as we do not always run paired refinement ala KD** > ** > > or similar in order to find out where that point is, the yearning for a > simple number will not stop (although I believe automation will make the KD > approach or similar eventually routine). **** > > ** ** > > >As for the "resolution of the structure" I'd say call that where |Fo-Fc| > (error in the map) becomes comparable to Sigma(Fo). This is I/Sigma = 2.5 > if Rcryst is 20%. That is: |Fo-Fc| / Fo = 0.2, which implies |Io-Ic|/Io = > 0.4 or Io/|Io-Ic| = Io/sigma(Io) = 2.5.**** > > ** ** > > Makes sense to me...**** > > ** ** > > As long as it is understood that this ‘model resolution value’ derived via > your argument from I/sigI is not the same as a <I/sigI> data cutoff (and > that Rcryst and Rmerge have nothing in common)….**** > > ** ** > > -James Holton**** > > MAD Scientist**** > > ** ** > > Best, BR**** > > ** ** > > ** ** > > > On Aug 27, 2013, at 5:29 PM, Jim Pflugrath <[log in to unmask]> > wrote:**** > > I have to ask flamingly: So what about CC1/2 and CC*? **** > > ** ** > > Did we not replace an arbitrary resolution cut-off based on a value of > Rmerge with an arbitrary resolution cut-off based on a value of Rmeas > already? And now we are going to replace that with an arbitrary resolution > cut-off based on a value of CC* or is it CC1/2?**** > > ** ** > > I am asked often: What value of CC1/2 should I cut my resolution at? > What should I tell my students? I've got a course coming up and I am sure > they will ask me again.**** > > ** ** > > Jim**** > > ** ** > ------------------------------ > > *From:* CCP4 bulletin board [[log in to unmask]] on behalf of Arka > Chakraborty [[log in to unmask]] > *Sent:* Tuesday, August 27, 2013 7:45 AM > *To:* [log in to unmask] > *Subject:* Re: [ccp4bb] Resolution, R factors and data quality**** > > Hi all,**** > > does this not again bring up the still prevailing adherence to R factors > and not a shift to correlation coefficients ( CC1/2 and CC*) ? (as Dr. > Phil Evans has indicated).?**** > > The way we look at data quality ( by "we" I mean the end users ) needs to > be altered, I guess.**** > > best,**** > > ** ** > > Arka Chakraborty**** > > ** ** > > On Tue, Aug 27, 2013 at 9:50 AM, Phil Evans <[log in to unmask]> wrote: > **** > > The question you should ask yourself is "why would omitting data improve > my model?" > > Phil**** > > -- *Arka Chakraborty* *ibmb (Institut de Biologia Molecular de Barcelona)** **BARCELONA, SPAIN** *