Dear Ed, Thankyou for this. Indeed I have not pushed into the domain of <I/sigI> as low as 0.4 or CC1/2 as low as 0.012. So, I do not have an answer to your query at these extremes. But I concede I am duly corrected by your example and indeed my email did not tabulate specifically how far one could investigate the plateau of DPI and certainly I was not considering such an extreme as you have investigated. Best wishes, Yours sincerely, John
Prof John R Helliwell DSc On 15 Jun 2013, at 15:31, Ed Pozharski <epozh...@umaryland.edu> wrote: > On 06/14/2013 07:00 AM, John R Helliwell wrote: >> Alternatively, at poorer resolutions than that, you can monitor if the >> Cruickshank-Blow Diffraction Precision Index (DPI) improves or not as more >> data are steadily added to your model refinements. > Dear John, > > unfortunately the behavior of DPIfree is less than satisfactory here - in a > couple of cases I looked at it just steadily improves with resolution. > Example I have in front of me right now takes resolution down from 2.0A to > 1.55A, and DPIfree goes down from ~0.17A to 0.09A at almost constant pace > (slows down from 0.021 A/0.1A to 0.017 A/0.1A around 1.75A). > > Notice that in this specific case I/sigI at 1.55A is ~0.4 and CC(1/2)~0.012 > (even this non-repentant big-endian couldn't argue there is good signal > there). > > DPIfree is essentially proportional to Rfree * d^(2.5) (this is assuming > that No~1/d^3, Na and completeness do not change). To keep up with > resolution changes, Rfree would have to go up ~1.9 times, and obviously that > is not going to happen no matter how much weak data I throw in. > > The maximum-likelihood e.s.u. reported by Refmac makes more sense in this > particular case as it clearly slows down big time around 1.77A (see > https://plus.google.com/photos/113111298819619451614/albums/5889708830403779217). > Coincidentally, Rfree also starts going up rapidly around the same > resolution. If anyone is curious what's I/sigI is at the "breaking point" > it's ~1.5 and CC(1/2)~0.6. And to bash Rmerge a little more, it's 112%. > > So there are two questions I am very much interested in here. > > a) Why is DPIfree so bad at this? Can we even believe it given it's erratic > behavior in this scenario? > > b) I would normally set up a simple data mining project to see how common > this ML_esu behavior is, but there is no easily accessible source of data > processed to beyond I/sigI=2, let alone I/sigI=1 (are structural genomics > folks reading this and do they maybe have such data to mine?). I can look > into all of my own datasets, but that would be a biased selection of several > crystal forms. Perhaps others have looked into this too, and what are your > observations? Or maybe you have a dataset processed way beyond I/sigI=1 and > are willing to either share it with me together with a final model or run > refinement at a bunch of different resolutions and report the result (I can > provide bash scripts as needed). > > Cheers, > > Ed. > > -- > Oh, suddenly throwing a giraffe into a volcano to make water is crazy? > Julian, King of Lemurs >
