Hi Oliver,
Is it possible to use reference model restraints at the moment during real space refinement (in phenix.real_space_refine)? I can’t see it in the documentation.
no, sorry.
On a related note, would it be possible at some point to allow users to set d_max in the phenix.map_to_structure_factors utility?
It is possible in current Phenix: phenix.map_to_structure_factors map.ccp4 d_min=2 Note, d_min cannot be arbitrary as it needs to satisfy sampling requirements. No d_max though as I could not imagine a valid reason for cutting the low-res reflections. It's easy to add but I would like to understand why this is necessary before I do it. I think whether you get a box or a sphere with reflections is governed by the "box" keyword that is False by defalut (so that by default you get a sphere). Isn't it the case? Pavel