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How can there be nothing "wrong" with something that is unphysical? Intensities cannot be negative. How could you measure a negative number of photons? You can only have a Gaussian distribution around I=0 if you are using an incorrect, unphysical statistical model. As I understand it, the physics predicts that intensities from diffraction should be gamma distributed (i.e., the square of a Gaussian variate), which makes sense as the gamma distribution assigns probability 0 to negative values. On Jun 20, 2013, at 1:00 PM, Bernard D Santarsiero <[log in to unmask]> wrote: > There's absolutely nothing "wrong" with negative intensities. They are measurements of intensities that are near zero, and some will be negative, and others positive. The distribution around I=0 can still be Gaussian, and you have true esd's. With F's you used a derived esd since they can't be formally generated from the sigma's on I, and are very much undetermined for small intensities and small F's. > > Small molecule crystallographers routinely refine on F^2 and use all of the data, even if the F^2's are negative. > > Bernie > > On Jun 20, 2013, at 11:49 AM, Douglas Theobald 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 <[log in to unmask]> 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:[log in to unmask]] 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 <[log in to unmask]<mailto:[log in to unmask]>> 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 <[log in to unmask]<mailto:[log in to unmask]>> 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 >>> >>> >>> >>> >>> >>> >>> >>> >>> >> >