Dear Randy, I could not agree more. Statistical methods for phasing and refinement must be better using the observed intensities and their esds than with (c)truncated F-values. In particular one should merge intensities, not truncated Fs!
To elaborate on Harry's comment, when SHELXL started refining only against intensities 22 years ago, I received many complaints from irate small molecule crystallographers whose papers had been rejected because the unweighted R-factors R2 (based on intensities) were too high. I even sent a letter to editors of the journals involved to explain why R-factors based on intensities are at least twice as high as those based on F, but to no avail. So I had to output R1 (the unweighted R-value based on F) even though the structure had been refined against intensitites, then everyone was happy. Do I correctly understand that you have developed new (better) maximum likelihood criteria for use with I rather than F? Best wishes, George On 12/02/2014 10:26 PM, Randy Read 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 t he 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 > -- Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-33021 or -33068 Fax. +49-551-39-22582
