[phenixbb] phenix.refine command lane xyz restrains

Błażej Bagiński baginskiblazej at gmail.com
Tue Aug 23 16:09:18 PDT 2022

Dear Phenix community,
lately I started toying with the terminal version of our favourite 
refinement software (on kubuntu linux).
I'm refining a structure with a ligand that is not in the refmac 
database (.cif file needed), and I couldn't find anything on how to 
implement xyz coordinates restraints for the procedure. In other words, 
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?

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 

Kind regards,

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