Hi Randy, I can see all good reasons for using intensities! What about maps and R-factors? I guess you still need F to compute them (I realize you can compute R(I) but this is not what people are used to do in general), and if that's the case then I->F is still inevitable (at least for some purposes).
Thanks, Pavel On Tue, Dec 2, 2014 at 1:26 PM, Randy Read <rj...@cam.ac.uk> wrote: > Dear Mohamed, > > At the moment, a lot of programs require amplitudes, but I believe that > they should all eventually be updated to use intensities. In fact, we’re > in the end stages of a large project to switch Phaser from using amplitudes > to using intensities. There are a number of reasons why, in principle, > it’s better to work in terms of intensities. One is that it’s perfectly > reasonable to have a negative observed intensity, which can come from > subtracting a background estimate with measurement errors from a very weak > peak with its own measurement errors. That, of course, is where the French > and Wilson algorithm comes in, allowing an amplitude to be estimated > without simply taking a square root. However, the problem with the French > and Wilson algorithm is that it loses information, i.e. you can’t > reconstruct the intensity and its standard deviation. What you get out of > French & Wilson depends on the estimate of the expected intensity for a > reflection, which is typically taken from the mean in the resolution shell > but should vary with direction for crystals suffering from anisotropic > diffraction and should be modulated for crystals with translational > non-crystallographic symmetry. > > Another reason it’s better to work in terms of intensities is that it’s > reasonable to assume that the measurement errors for intensities are > Gaussian, but then less reasonable to assume that for amplitudes > (particularly with the problem that amplitudes can’t be negative). > > For now, you need amplitudes for a lot of purposes and then the French & > Wilson algorithm is useful. But what I would strongly recommend is that > you hang on to the intensities and you make sure that the intensities are > deposited at the PDB. It’s a pity that many PDB depositions only have > amplitudes that have been through French & Wilson, so that new procedures > based on intensities won’t be able to be applied with their full power. > > Best wishes, > > Randy Read > > ----- > Randy J. Read > Department of Haematology, University of Cambridge > Cambridge Institute for Medical Research Tel: +44 1223 336500 > Wellcome Trust/MRC Building Fax: +44 1223 336827 > Hills Road > E-mail: rj...@cam.ac.uk > Cambridge CB2 0XY, U.K. > www-structmed.cimr.cam.ac.uk > > On 1 Dec 2014, at 20:49, Mohamed Noor <mohamed.n...@staffmail.ul.ie> > wrote: > > > Dear crystallographers > > > > Is there any reason for using one data type over the other? Are there > any errors associated with the French and Wilson I-to-F conversion step? > > > > Thanks. > > Mohamed >
