[phenixbb] Fix coordinates of one single residue

Oleg Sobolev osobolev at lbl.gov
Thu Oct 27 09:31:44 PDT 2016

Hi Anna-Carin,

According to documentation (

Refinement with minimization (selected part of model):
% phenix.refine data.hkl model.pdb strategy=individual_sites \
sites.individual="chain A"
This will refine the coordinates of atoms in chain A only.

In your case selection would look more like sites.individual='not (chain A
and resid 123)' given you want to exclude residue with number 123 in chain
In GUI (latest version), go to "Refinement settings" tab, button "Select
Atoms", "Refinement Strategy" tab and put the selection there.

Hope this helps,

Best regards,
Oleg Sobolev.

On Thu, Oct 27, 2016 at 8:52 AM, ancacarl <AnnaCarin.Carlsson at colostate.edu>

> Hi,
> I'm working on the refinement of a protein mutated with an unnatural
> amino acid that is present as two rotamers. Whenever I do refinements, one
> of the rotamers moves away from the electron density map. I therefore would
> like to
> fix the coordinates for this amino acid only while continuing the
> refinement of the rest of the protein. Is there a way in Phenix to do
> this?  Any advice is welcome.
> Best regards,
> Anna-Carin
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