1. One rigid body group per chain (default behavior):

   % phenix.refine data.hkl model.pdb strategy=rigid_body
   

2. Multiple groups (requires a basic knowledge of the PHENIX atom selection language, see below):

   % phenix.refine data.hkl model.pdb strategy=rigid_body \
     sites.rigid_body="chain A" sites.rigid_body="chain B"
   

   This will refine the chain A and chain B as two rigid bodies. The rest of the model will be kept fixed.

3. If there are many rigid groups to define, typing them in the command line may be a tedious exercise. In this case a better alternative is to create a parameter file rigid_body_selections containing the following lines:

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

   The command line will then be:

   % phenix.refine data.hkl model.pdb strategy=rigid_body \
     rigid_body_selections.params
   

   Files like this can be created, for example, by copy-and-paste from the complete list of parameters (phenix.refine --show-defaults=all).

And here (http://www.phenix-online.org/documentation/reference/refine_gui.html#refinement-settings) is some documentation for the GUI.

So "Modify selections for" (choose Rigid body from the dropdown menu) will let you define the selections, either with text (e.g. "chain A and resseq 1:100"), or by using the "View/Pick" GUI, where you can select atoms.

Hope this helps!

Best regards,

Folmer