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: http://www.phenix-online.org/papers/ccp4_july_2005_afonine.pdf 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! Pavel. 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