Elastic network restraints

Elastic network restraints allow to flexibly restrain input orientations between subunits, domains or residues.

The input orientations are as read from the input PDB files, regardless whether the particles are in the same or different PDB files.

The elastic network can be defined in the JSON configuration file like this:

{
    "active": true,
    "type": "elastic_network",
    "name": "Nup107_Nup132_elastic_network1",
    "repr_resolution": 10,
    "distance_threshold": 15,
    "random_fraction": 1.0,
    "within_molecule": false,
    "k" : 1,
    "weight": 100,
    "first_copy_only": true,
    "optimized_components": [
        {
            "name": "Nup132", "subunit": "Nup132", "serie": "NR_1",
            "resi_ranges": [
                [
                    459,
                    1162
                ]
            ]
        },
        {
            "name": "Nup107", "subunit": "Nup107", "serie": "NR_1",
            "resi_ranges": [
                [
                    581,
                    813
                ]
            ]
        }
    ]
}

This example will create elastic network between the specified residue ranges of Nup132 and Nup107 subunits.

Parameters

type

Must be “elastic_network”

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

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

optimized_components

A list of Selectors defining molecules or parts to which this restraint should be applied to.

distance_threshold

Residue pairs within this distance threshold will be included in the elastic network

random_fraction

A fraction of distances below the thresholds to be randomly selected for creating the elastic network, default: 1.0 (all distances)

within_molecule

If set to true, only distances within the same subunit will be added to the elastic network

elastic_network_source

Optional list of Selectors PDB files and residue ranges that should serve as a source of distances for the elastic restraints. For example:

{
    "active": false,
    "type": "elastic_network",
    "name": "elastic_network_3-4",
    "repr_resolution": 1,
    "distance_threshold": 5,
    "random_fraction": 1.0,
    "within_molecule": true,
    "k": 1,
    "weight": 1,
    "optimized_components": [
        {
            "subunit": "ProteinA",
            "copies": [
                0
            ]
        },
        {
            "subunit": "ProteinA",
            "copies": [
                0
            ]
        }
    ],
    "elastic_network_source": [
        {
            "filename": "proteinA.pdb",
            "chain_id": "A",
            "resi_ranges": [
                [
                    403,
                    501
                ]
            ]
        },
        {
            "filename": "proteinA.pdb",
            "chain_id": "A",
            "resi_ranges": [
                [
                    509,
                    606
                ]
            ]
        }
    ]