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
