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
>

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