So I guess there is never a case in crystallography in which our models predict the data to within the errors of data collection? I guess the situation might be similar to fitting a Michaelis-Menten curve, in which the fitted line often misses the error bars of the individual points, but gets the overall pattern right. In that case, though, I don't think we say that we are inadequately modelling the data. I guess there the error bars are actually too small (are underestimated.) Maybe our intensity errors are also underestimated?
JPK On Thu, Oct 28, 2010 at 9:50 AM, George M. Sheldrick <gshe...@shelx.uni-ac.gwdg.de> wrote: > > Not quite. I was trying to say that for good small molecule data, R1 is > usally significantly less than Rmerge, but never less than the precision > of the experimental data measured by 0.5*<sigmaI>/<I> = 0.5*Rsigma > (or the very similar 0.5*Rpim). > > George > > Prof. George M. Sheldrick FRS > Dept. Structural Chemistry, > University of Goettingen, > Tammannstr. 4, > D37077 Goettingen, Germany > Tel. +49-551-39-3021 or -3068 > Fax. +49-551-39-22582 > > > On Thu, 28 Oct 2010, Jacob Keller wrote: > >> So I guess a consequence of what you say is that since in cases where there >> is >> no solvent the R values are often better than the precision of the actual >> measurements (never true with macromolecular crystals involving solvent), >> perhaps our real problem might be modelling solvent? >> Alternatively/additionally, I wonder whether there also might be more >> variability molecule-to-molecule in proteins, which we may not model well >> either. >> >> JPK >> >> ----- Original Message ----- From: "George M. Sheldrick" >> <gshe...@shelx.uni-ac.gwdg.de> >> To: <CCP4BB@JISCMAIL.AC.UK> >> Sent: Thursday, October 28, 2010 4:05 AM >> Subject: Re: [ccp4bb] Against Method (R) >> >> >> > It is instructive to look at what happens for small molecules where >> > there is often no solvent to worry about. They are often refined >> > using SHELXL, which does indeed print out the weighted R-value based >> > on intensities (wR2), the conventional unweighted R-value R1 (based >> > on F) and <sigmaI>/<I>, which it calls R(sigma). For well-behaved >> > crystals R1 is in the range 1-5% and R(merge) (based on intensities) >> > is in the range 3-9%. As you suggest, 0.5*R(sigma) could be regarded >> > as the lower attainable limit for R1 and this is indeed the case in >> > practice (the factor 0.5 approximately converts from I to F). Rpim >> > gives similar results to R(sigma), both attempt to measure the >> > precision of the MERGED data, which are what one is refining against. >> > >> > George >> > >> > Prof. George M. Sheldrick FRS >> > Dept. Structural Chemistry, >> > University of Goettingen, >> > Tammannstr. 4, >> > D37077 Goettingen, Germany >> > Tel. +49-551-39-3021 or -3068 >> > Fax. +49-551-39-22582 >> > >> > >> > On Wed, 27 Oct 2010, Ed Pozharski wrote: >> > >> > > On Tue, 2010-10-26 at 21:16 +0100, Frank von Delft wrote: >> > > > the errors in our measurements apparently have no >> > > > bearing whatsoever on the errors in our models >> > > >> > > This would mean there is no point trying to get better crystals, right? >> > > Or am I also wrong to assume that the dataset with higher I/sigma in the >> > > highest resolution shell will give me a better model? >> > > >> > > On a related point - why is Rmerge considered to be the limiting value >> > > for the R? Isn't Rmerge a poorly defined measure itself that >> > > deteriorates at least in some circumstances (e.g. increased redundancy)? >> > > Specifically, shouldn't "ideal" R approximate 0.5*<sigmaI>/<I>? >> > > >> > > Cheers, >> > > >> > > Ed. >> > > >> > > >> > > >> > > -- >> > > "I'd jump in myself, if I weren't so good at whistling." >> > > Julian, King of Lemurs >> > > >> > > >> >> >> ******************************************* >> Jacob Pearson Keller >> Northwestern University >> Medical Scientist Training Program >> Dallos Laboratory >> F. Searle 1-240 >> 2240 Campus Drive >> Evanston IL 60208 >> lab: 847.491.2438 >> cel: 773.608.9185 >> email: j-kell...@northwestern.edu >> ******************************************* >> >> >
