[cctbxbb] E value calculation

Petrus Zwart phzwart at lbl.gov
Thu Sep 3 08:46:08 PDT 2020

Hi All,

There is a method in the miller module:


check out this function and related:

normalize(reflections_per_bin=150, eps_fac=None)
  Compute E-values: E = (F/eps**0.5) / rms of (F/eps**0.5) This is ‘Karle’
approach, that is not using overall B from Wilson plot.

Also, check out this tutorial:


"This means we are ready to calculate quasi-normalized structure factors by
computing f_sq / <f_sq/epsilon> in resolution bins:

all_e_values = miller_array.quasi_normalize_structure_factors().sort(by_value="data")

This statement performs two steps at once. First, the
quasi_normalize_structure_factors() method creates a new
cctbx.miller.array instance
with the same unit cell, space group, anomalous flag and Miller indices as
the input miller_array, but with a new data array containing the normalized
structure factors. The sort() method is used immediately on this
intermediate instance to sort the E-values by magnitude. By default, the
data are sorted in descending order (largest first, smallest last). This is
exactly what we want here. To convince yourself it is correct, insert


On Thu, Sep 3, 2020 at 8:37 AM Pavel Afonine <pafonine at lbl.gov> wrote:

> Hello AC Research,
> > I am trying to find how to perform the E value calculation using
> > CCTBX. I am unable to find the method in the documentation. Can
> > someone assist me, please?
> I might be wrong but I don't think cctbx has a ready-to-use function to
> calculate E values. However, it should be easy to make one using
> existing tools. If you tell me your definition of E-values I might be
> able to help with the script.
> Pavel
> _______________________________________________
> cctbxbb mailing list
> cctbxbb at phenix-online.org
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P.H. Zwart
Staff Scientist
Molecular Biophysics and Integrated Bioimaging &
Center for Advanced Mathematics for Energy Research Applications
Lawrence Berkeley National Laboratories
1 Cyclotron Road, Berkeley, CA-94703, USA
Cell: 510 289 9246

PHENIX:   http://www.phenix-online.org
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