Dear Daniel,

- Is it possible to restrain the position of certain parts of the model (i.e. "freeze" them so that they move at all) to do focused refinement of subdomains or loops?

Although it is not currently possible to completely "freeze" some atoms (exclude them from coordinate refinement) in phenix.real_space_refine, you can try reference coordinate restraints described in #14 in documentation here:

https://www.phenix-online.org/documentation/reference/real_space_refine.html

to restrain certain atoms to their initial position. Depending on sigma you provide these restraints could be more or less strict (use smaller sigma to make them stronger).

- In the instructions it says that you can do both NCS constraints and restraints. How you do the latter? I can only do the former by default or by defining ncs_constraints=True and give a NCS definition file.

I'm afraid it is mistake in the instructions. I believe that presently NCS torsion restraints are not available in phenix.real_space_refine.

- When I do a run with run=rigid_body, some rigid body groups move in to each other and overlap. Is there no collision detection using this algorithm? If I do a run=minimization_global, things work a bit better in this regard, but is not really what I want (at this stage). Am I doing something wrong? Here is the run command and the rigid body definition file:

Hopefully, Pavel will be able to answer this question.

Best regards,

Oleg Sobolev.