[phenixbb] Double difference anomalous maps

Pavel Afonine pafonine at lbl.gov
Tue Nov 9 17:13:04 PST 2021

Hi Mark,

> I tried the "Isomorphous difference map” action and specified a file 
> for input 1 containing F1+, F1– at one wavelength, and the file input 
> 2 containing F2+,F2– at another wavelength. I selected the appropriate 
> Labels for the columns containing the anomalous data.  I then 
> specified in "Advanced Options” to *use anomalous differences instead 
> of amplitudes*.  Will this procedure use the following coefficients 
> for the difference Fourier?
> ( F1(+) – F1(–) ) – ( F2(+) – F2(–) ), alpha(calc)
> Can someone confirm if this is indeed what is calculated?

no, not quite.. Given two data sets, Fobs1 and Fobs2, and a phase source 
(eg., atomic model), it computes

(Fobs1-scale*Fobs2, Phase)

Fourier map. Both data sets are assumed to be collected from isomorphous 
crystals (same space groups, unit cells can deviate up to a small 

Phenix treats Fobs(+) and Fobs(-) as individual data points, so in the 
map above they will participate as, for example

(Fobs1(+)-scale*Fobs2(+), Phase)

(Fobs1(-)-scale*Fobs2(-), Phase)


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