Hi Błażej,

I have a ligand that I built into the polder map and I want to tell the
software "do not change the positions in space of these atoms". How can
I do that?
You can use reference_coordinate_restraints scope which is intended to keep the model in place. Note that they are restraints, so some deviation can still occur. Check available parameters here: https://phenix-online.org/documentation/reference/refinement.html , but you will need
enabled = True
selection = "your atom selection"
check https://phenix-online.org/documentation/reference/atom_selections.html for selection syntax.

Best regards,
Oleg Sobolev.
  
Also, side question: why there are three different(?) versions of
command line phenix.refine for every phenix installation? What is the
difference between them?

REMARK 6 I followed the online guide for "Refinement at high resolution"
on my 1,2~1,3A structure and the results were surprisingly nice, I'd say
potentially even better than usually used parameters in GUI (5 cycles
both).

Kind regards,
Blazej

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