Rigid bodies

By default, rigid bodies will be defined automatically based on the specifications in the PDB files Input structures. If you want to define rigid bodies differently to your PDB files, you can do it in a separate rigid_bodies block at the top level of the JSON configuration file.

Warning

For rigid_bodies to have an effect, you have to set add_rigid_bodies = False in the Parameter file

The specification is the same as for PDB files:

{
    "rigid_bodies": [
        {
            "components": [
                "list of selectors"
            ]
        },
        {
            "components": [
                "list of selectors"
            ]
        },

        "and so on"
    ]
}

You can also use the foreach_serie and foreach_copy keywords here:

{
    "rigid_bodies": [
        {
            "foreach_serie": true,
            "foreach_copy": true,
            "components": [
                "list of selectors"
            ]
        },
        {
            "foreach_serie": true,
            "foreach_copy": true,
            "components": [
                "list of selectors"
            ]
        },

        "and so on"
    ]
}

An example:

{
    "rigid_bodies": [
        {
            "foreach_serie": true,
            "foreach_copy": true,
            "components": [
                { "name": "Elp1_1", "subunit": "Elp1", "domain": "propeller1"}
            ]
        },
        {
            "foreach_serie": true,
            "foreach_copy": true,
            "components": [
                { "name": "Elp1_1", "subunit": "Elp1", "domain": "propeller2"}
            ]
        },
        {
            "foreach_serie": true,
            "components": [
                { "name": "Elp1_1", "subunit": "Elp1", "domain": "CTD", "copies": [0, 1]}
            ],
            "freeze": true
        },
        {
            "foreach_serie": true,
            "foreach_copy": true,
            "components": [
                { "name": "Elp2_1", "subunit": "Elp2",
                    "resi_ranges": [
                        [1, 239],
                        [257, 788]
                    ]
                }
            ]
        },
        {
            "foreach_serie": true,
            "foreach_copy": true,
            "components": [
                { "name": "Elp3_4", "subunit": "Elp3", "domain": "helix4"}
            ]
        },
        {
            "foreach_serie": true,
            "foreach_copy": true,
            "components": [
                { "name": "Elp3_5", "subunit": "Elp3", "domain": "struct"}
            ]
        },
        {
            "foreach_serie": true,
            "foreach_copy": true,
            "components": [
                { "name": "Elp3_6", "subunit": "Elp3", "domain": "flex_helix"}
            ]
        }
    ]
}