[phenixbb] automatically changed refinement parameters

Sara Züger szueger at bioc.uzh.ch
Mon Feb 1 03:18:54 PST 2010

Dear phenixbb,

I have some questions regarding refinement parameters:

When I run phenix v1.6 via the GUI, starting a fresh refinement session from
the main window (I do TLS+isotropic ADP refinement and 5 macrocycles,
otherwise everything default), I saw these non-default refinement settings
in the run, which I did not specify myself, but the program:

 adp_restraints {
    iso {
      use_u_local_only = True
      sphere_radius = 1.55
      distance_power = 0
      average_power = 0

In the documentation I found that when doing TLS+isotropic ADP refinement,
only Ulocal is restrained, so the first command makes sense.

But how is it with the sphere_radius, distance_power and average_power?
The default parameters are

sphere_radius= 5.0
distance_power= 1.69
average_power= 1.03

What do these parameters mean? What does it mean when these parameters have
changed (and why did they change)? And is it ok at all that they changed?
And would they have an influence if I modify the start model by setting
b_iso to a certain value and then refine "normally" with TLS+isotropic?

Another parameter that changed and I did not specify is:

Target_weights {
  wxu_scale = 2.72

Why did this happen, is it because few cycles before I included
optimize_weights? And why would this change the weights permanently? Does it
make sense?

Thank you for explaining me these things!


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