Re: MAD as a special case of MIR with anomalous

[Eleanor Dodson <ccp4@yorvic.york.ac.uk>]

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On Feb 22,  6:46pm, Edward Berry wrote:
> Subject: MAD as a special case of MIR with anomalous
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>
> Hello All,
> Does someone have a good answer for this question?
> ---------------------------------------------------
> If I phase a 4-wavelength MAD dataset using MLPHARE
> as described in its documentation, using one wavelength
> as both "native" and "derivative" and using the other three
> as "derivatives", with anomalous signal for all derivatives,
> am I justified in saying the structure was solved using
> the MAD method, or do I need to say it was solved
> "using MAD data treated as a special case of MIR
> with anomalous"?


 As I see it the "MAD" method applies to the data you collect - not to the
phasing method.. If you have used diffraction from a single crystal taken at
different wavelengths then you have carried out a MAD experiment. All the
phasing programs then use the observable differences to extract phases, in much
the same way as MIR differences are used. More sophisticated treatments will
assign the error estimates differently taking into account the fact that the
sites are the same for each set of measurements, but they all depend on the
observed differences!
 In fact all our MAD experiments are MAD data with initial phases as special
case of MIR, refined and extended by density modification. It is the density
modification which gives the real edge to MAD experiments; since the well
determined phases are distributed throughout the data set, and are just as good
at high resolution as at low resolution, unlike the MIR case, the DM procedures
usually do a brilliant job..

 >
> Never mind the semantics, or differences in the
> refinement method. Once positions and real & anomalous
> occupancies are refined for each site, is there a
> significant difference in the way phases are calculated,
> between MLPHARE and some specialized MAD phasing program?


 N0
>
> Does MLPHARE not use some information from the
> dataset that a MAD program would use?

No

 Eleanor Dodson

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Eleanor J.Dodson, Chemistry Department, University of York, U.K.
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