Hiya,
I have used rigid body refinement in phenix.refine as suggested:

refinement.refine.sites {
  rigid_body = chain A
  rigid_body = chain B
}

If I have a multidomain protein like kinases, or G proteins which have flexible switches, how can I define the region within a given chain?

Best, Partha

--
MRC National Institute for Medical Research
Division of Molecular Structure
The Ridgeway, NW7 1AA, UK
Email: pchakra@nimr.mrc.ac.uk
Phone: + 44 208 816 2515