Flexibility

By default:

• all residues that are present in Input structures but are not covered by Rigid bodies are represented as flexible beads. In this case, the representation resolution will be the highest resolution from struct_resolutions list in params.py.

• all residues that are present in the sequences but are not present in Input structures, will not be added

To add residues that are not present in the Input structures, but are present in the sequences, you can use add_missing parameter in params.py:

add_missing = True will add all missing residues

add_missing = <list of selectors> will add only selected residues. For example:

add_missing = [
    {
        "subunit": "Elp3",
        "resi_ranges": [[87, 92], [375, 390], [403, 406]]
    },
    {
        "subunit": "Elp1",
        "resi_ranges": [[1, 20]]
    }

]

If an input PDB structure does not fit as a rigid body, you can treat it somewhat flexibly by breaking it into smaller rigid bodies and defining Elastic network restraints to restrain original interfaces.