[phenixbb] Anomalous or not?

Francis Reyes Francis.Reyes at colorado.edu
Thu Jul 10 07:38:48 PDT 2014

Hi Tim

So from the XDS docs, the estimates of the sigmas are performed by the CORRECT step in the following way:

"The residual scatter in intensity of symmetry-equivalent reflections is used to estimate their standard deviations. Here, the initial estimate v0(I) (obtained from the INTEGRATE step) for the variance of the reflection intensity I is replaced by v(I)=a*(v0(I)+b*I^2). The two constants a and b are chosen to minimize discrepancies between v(I) and the variance estimated from sample statistics of symmetry related reflections. Based on the more realistic error estimates for the intensities, outliers are recognized by comparison with other symmetry-equivalent reflections. These outliers are included in the main output file XDS_ASCII.HKL in which they are marked by a negative sign attached to the estimated standard deviations of their intensity...."

SCALA/AIMLESS have a completely different way of estimating the sigmas. 

"After scaling, the error estimates can be improved by comparing the observed scatter between observations and the estimated standard deviation, making them equal on average. If the standard deviations 􏰇(Ihl) are correct, then the normalized deviations 􏰂hl = (Ihl - hIh0 i)/􏰇(Ihl) (where hIh0 i is averaged over all observations of reflection h excluding the lth observation) should be distributed with a mean 0.0 and stan- dard deviation 1.0. A simple correction to give improved error estimates is 􏰇0(Ihl) = Sdfac[􏰇2(Ihl) + (Sdadd ghlhIhi)2]1/2. "

And are the two models for estimating the sigmas compatible? 


On Jul 10, 2014, at 9:22 AM, Tim Gruene <tg at SHELX.UNI-AC.GWDG.DE> wrote:

> The CORRECT step scales your data. It appears that autoxds will call
> aimless or scala to scale your data again. This is little harmful for
> the intensities, but corrupts the sigma values because the error model
> is applied twice and thus it is harmful for phasing using the
> anomalous signal because this relies on proper sigma values.

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