[phenixbb] Phenix.refine Restraints: replicating refmac external restaints

Pavel Afonine pafonine at lbl.gov
Wed Jan 18 10:28:33 PST 2017


Hi Elliot,

> Looking to generate restraints for phenix.refine that are 
> similiar/equivalent to external restraints in REFMAC. From over 
> viewing the documentation i feel the correct way to do this is to 
> generate bond restraints, i.e:
>
> Equivalent of:
>
> exte dist first chain A resi   38 atom  C   alte A second chain A 
> resi   38 atom  C   alte B value 0.0 sigma 0.02 type 1
>
> would be :

I don't know how restraints function in Refmac.

> refinment.geometry_restraints.edits {
>       bond {
>                             action = *add
>                             atom_selection_1 = chain A  and resid 38 
> and altloc A and name C
>                             atom_selection_2 = chain A  and resid 38 
> and altloc B and name C
>                             symmetry_operation = None
>                             distance_ideal = 0.0
>                             sigma = 0.02
>                             slack = None
>                 }
> }

This will define a bond between these two atoms by adding a term to the 
restraints:

(1/sigma**2)*(distance_model - distance_ideal)**2

Note, you can add as many of such bonds as you with. Also, using similar 
syntax you can add angles, planes, torsions, etc.

Just out curiosity and if it's not a secret: what are you trying to achieve?

Pavel

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