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 <[log in to unmask]> 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
>
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