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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