[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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