The prior knowledge about Is is not merely that they are >= 0, it's more than that: we know they have an (approximate) Wilson distribution. AFAICS incorporating that information at the integration stage would be almost equivalent to the F&W procedure. In fact it would probably not be as good since the experimental estimates of I do have an (approximate) Gaussian distribution, being the difference of 2 Poisson distributions with large means (or at least >~ 10). The corrected Is, being the best estimates of the true Is would as you point out not have a Gaussian distribution, and some of the assumptions made in averaging equivalent reflections would not be valid. You could still use the corrected Is instead of the experimental Is in refinement but I suspect it would not make any difference to the results (except you would get lower R factors!).
-- Ian On 20 June 2013 17:49, Douglas Theobald <dtheob...@brandeis.edu> wrote: > Seems to me that the negative Is should be dealt with early on, in the > integration step. Why exactly do integration programs report negative Is > to begin with? > > > On Jun 20, 2013, at 12:45 PM, Dom Bellini <dom.bell...@diamond.ac.uk> > wrote: > > > Wouldnt be possible to take advantage of negative Is to > extrapolate/estimate the decay of scattering background (kind of Wilson > plot of background scattering) to flat out the background and push all the > Is to positive values? > > > > More of a question rather than a suggestion ... > > > > D > > > > > > > > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of > Ian Tickle > > Sent: 20 June 2013 17:34 > > To: ccp4bb > > Subject: Re: [ccp4bb] ctruncate bug? > > > > Yes higher R factors is the usual reason people don't like I-based > refinement! > > > > Anyway, refining against Is doesn't solve the problem, it only postpones > it: you still need the Fs for maps! (though errors in Fs may be less > critical then). > > -- Ian > > > > On 20 June 2013 17:20, Dale Tronrud <det...@uoxray.uoregon.edu<mailto: > det...@uoxray.uoregon.edu>> wrote: > > If you are refining against F's you have to find some way to avoid > > calculating the square root of a negative number. That is why people > > have historically rejected negative I's and why Truncate and cTruncate > > were invented. > > > > When refining against I, the calculation of (Iobs - Icalc)^2 couldn't > > care less if Iobs happens to be negative. > > > > As for why people still refine against F... When I was distributing > > a refinement package it could refine against I but no one wanted to do > > that. The "R values" ended up higher, but they were looking at R > > values calculated from F's. Of course the F based R values are lower > > when you refine against F's, that means nothing. > > > > If we could get the PDB to report both the F and I based R values > > for all models maybe we could get a start toward moving to intensity > > refinement. > > > > Dale Tronrud > > > > > > On 06/20/2013 09:06 AM, Douglas Theobald wrote: > > Just trying to understand the basic issues here. How could refining > directly against intensities solve the fundamental problem of negative > intensity values? > > > > > > On Jun 20, 2013, at 11:34 AM, Bernhard Rupp <hofkristall...@gmail.com > <mailto:hofkristall...@gmail.com>> wrote: > > As a maybe better alternative, we should (once again) consider to refine > against intensities (and I guess George Sheldrick would agree here). > > > > I have a simple question - what exactly, short of some sort of historic > inertia (or memory lapse), is the reason NOT to refine against intensities? > > > > Best, BR > > > > > > > > > > -- > > > > This e-mail and any attachments may contain confidential, copyright and > or privileged material, and are for the use of the intended addressee only. > If you are not the intended addressee or an authorised recipient of the > addressee please notify us of receipt by returning the e-mail and do not > use, copy, retain, distribute or disclose the information in or attached to > the e-mail. > > > > Any opinions expressed within this e-mail are those of the individual > and not necessarily of Diamond Light Source Ltd. > > > > Diamond Light Source Ltd. cannot guarantee that this e-mail or any > attachments are free from viruses and we cannot accept liability for any > damage which you may sustain as a result of software viruses which may be > transmitted in or with the message. > > > > Diamond Light Source Limited (company no. 4375679). Registered in > England and Wales with its registered office at Diamond House, Harwell > Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom > > > > > > > > > > > > > > > > > > >
