[phenixbb] automatically changed refinement parameters

Pavel Afonine PAfonine at lbl.gov
Tue Feb 2 11:43:16 PST 2010

Hi Sara,

to answer your question, I'm copying you Ralf's reply to a similar 
inquiry from a few months ago:


We use "local sphere restraints".

  adp_restraints {
    iso {
      sphere_radius = 5.0
      distance_power = 1.69
      average_power = 1.03

The basic idea is to restrain each adp to the average of all its
neighbors within a sphere of a given radius (sphere_radius = 5). The
contribution to the refinement target function is:

                                   (u_i - u_j)**2
  1 / (r_ij ** distance_power) * ----------------------------------
                                  ((u_i + u_j)/2) ** average_power

These terms are computed over a double sum: loop over each atom, loop
over all neighbors of the atom. I'm not sure anymore how exactly we
arrived at distance_power = 1.69 and average_power = 1.03.
You can try different values for distance_power to change the
tightness of the restraints as a function of the distance of
a pair of atoms. The average_power links the tightness to the
absolute value of the adp; average_power=0 turns this feature off.

There are some remarks about this in the "ADP refinement" section in
this old newsletter article:


The formulas are a bit different (above is current), but the ideas
still apply.

In grouped b-factor mode the local sphere restraints are not used.


Please let me know if you have any questions!

On 2/2/10 2:13 AM, Sara Züger wrote:
> Hi Pavel,
> thanks for your answer!
> If there is an "easy" (and for you fast) way to clarify the parameters:
> Adp_restraints{
> iso{
> sphere_radius
> distance_power
> average_power
> }}
> Then I would appreciate some explanation.
> Sara

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