Hi Joe,
Below are some notes regarding our ADP restraints. At your resolution the defaults may be too tight.
The choice of scattering table shouldn't matter, except for small runtime differences. (You can find some notes here:
http://cci.lbl.gov/publications/download/iucrcompcomm_jan2004.pdf
section 4.)
Ralf

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.

From: Joseph Noel <[email protected]>
To: [email protected]
Sent: Sun, December 19, 2010 12:58:43 PM
Subject: [phenixbb] ADP restraints - distance power, average power, etc

Hi All,

I am refining a very well ordered structure at 1.45 A and find that after doing just about everything including optimization of weights, etc that there are still areas of positive density residing over S atoms of Met, backbone atoms, etc. I have added hydrogens and used them during refinement as well. The maps are of a high quality and Free R factors are quite good, ~ 17%. Is there anything that can be played with more such as values used in the ADP restraints window to try and achieve a difference map with far fewer areas of significant positive density (all greater then or equal to 4 sigma)?

I am not sure exactly what effect the values of distance power, average power, etc will have on refinement. The other option I was thinking of was the scattering table options. I have other structures of this protein that extend to about 1.2.

Thanks!

Joe

___________________________________________________________
Joseph P. Noel, Ph.D.
Investigator, Howard Hughes Medical Institute
Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics
The Salk Institute for Biological Studies
10010 North Torrey Pines Road
La Jolla, CA 92037 USA

Phone: (858) 453-4100 extension 1442
Cell: (858) 349-4700
Fax: (858) 597-0855
E-mail: [email protected]

Web Site (Salk): http://www.salk.edu/faculty/faculty_details.php?id=37
Web Site (HHMI): http://hhmi.org/research/investigators/noel.html
___________________________________________________________