[phenixbb] phenix.refine command lane xyz restrains

Oleg Sobolev osobolev at lbl.gov
Wed Aug 24 08:51:21 PDT 2022

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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