Hello Luca,

You can refer to this tutorial:

https://www.youtube.com/watch?v=qB8W_6yuw5k&ab_channel=PhenixTutorials

which exemplifies setting custom parameters in phenix.refine, but real-space-refine has exactly the same machinery.

Also you can prepare a .eff file with parameters you need to set and supply it as input file along with model and data files.

Best regards,

Oleg Sobolev.

On Wed, Aug 31, 2022 at 2:55 AM Luca Pellegrini <lp212@cam.ac.uk> wrote:

Hello,

Phenix.real_space_refine keeps pushing a residue out of density so I'd like to restrain it to its current position. Can you please let me know how to implement in the GUI the first example at point 14 at https://phenix-online.org/documentation/reference/real_space_refine.html#usage-examples?
phenix.real_space_refine model.pdb map.mtz \
reference_coordinate_restraints.enabled=true \
reference_coordinate_restraints.selection="chain A and resseq 12:21" \
reference_coordinate_restraints.sigma=0.05
Best wishes,
Luca

Luca Pellegrini, PhD

Department of Biochemistry
University of Cambridge
Cambridge CB2 1GA
UK
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