Re: [phenixbb] Local restraints

Hi Luca, Yes, it is for a disulphide in this example but it works for other atoms, too. Best wishes, Tomas On Tue, Mar 7, 2023 at 11:07 AM Luca Pellegrini wrote:

Hi Tomas,

Thank you for your help. Is this for restraining a disulphide bond? I am actually looking for a way to keep a side chain from moving during refinement.

Best wishes Luca

...

On 7 Mar 2023, at 11:00, Tomas Malinauskas wrote:

Hi Luca,

I typically create a file called restraints.eff containing something like

refinement { geometry_restraints.edits { bond { atom_selection_1 = (chain 'A' and (resid 101 and (name SG ))) atom_selection_2 = (chain 'A' and (resid 102 and (name SG ))) distance_ideal = 2.03 sigma = 0.1 slack = 0 } } }

and simply load this file via Phenix GUI. I am not sure if that is what Phenix developers recommend. I would be curious to know, too.

Best wishes, Tomas

On Tue, Mar 7, 2023 at 10:44 AM Luca Pellegrini wrote:

...

How can I freeze a set of atoms in phenix.real_space_refine? I've got an arginine side chain that is consistently misplaced during refinement, and I’d like to restrain its movement. I notice that refinement.geometry_restraints.edits.scale_restraints is not available anymore, is there another way?

Thanks, Luca

Luca Pellegrini, PhD Department of Biochemistry University of Cambridge Cambridge CB2 1GA UK

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