[phenixbb] automatically changed refinement parameters
PAfonine at lbl.gov
Tue Feb 2 11:43:16 PST 2010
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".
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
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:
> Then I would appreciate some explanation.
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