Similar orientation restraints

These restraints promote similar orientation between pairs of identical subunits, domains or residues.

They can be defined in the JSON configuration file like this:

{
    "type": "similar_orientation",
    "active": true,
    "name": "Ely5-Nup120_similar_orientation",
    "comment": "We assume Ely5 interacts in the same way with all copies of Nup120",
    "data": [
        [
            [
                {"subunit": "Nup120", "serie": "NR_1", "copies": [0]}, {"subunit": "Ely5", "serie": "NR_1", "copies": [0]}
            ],
            [
                {"subunit": "Nup120", "serie": "NR_2", "copies": [0]}, {"subunit": "Ely5", "serie": "NR_2", "copies": [0]}
            ]
        ]
    ],
    "weight": 10,
    "k": 1,
    "first_copy_only": true,
    "repr_resolution": 10
}

Parameters

type

Must be “similar_orientation”

active

true or false, whether the restraint should be created, you can set to false to save on loading time if you don’t need this restraint (even if it’s true, you still need to add it to a scoring function to have it an effect)

name

whatever name. Use this name to refer to this restraint in Parameter file when defining the scoring functions

comment

Optional comment, useful for documenting

data

A pair of pairs of Selectors between which the interaction restraints should be defined

weight

Weight of this restraint

first_copy_only

true or false, Apply only to the first molecule copy of each series?

repr_resolution

The resolution of representation to which this restraint should be applied

k

Spring constant for the harmonic potential, redundant to weight, ignore