Connectivity restraints

Connectivity restraints are used to restrain distance between:

  • consecutive single-residue beads (e.g. when representation resolution of 1 is used)

  • two consecutive domains of a single protein separated by a linker of non-modelled/missing residues

The restraint is implemented as a harmonic distance restraint with a target distance equal to:

  • 3.8 Angstrom for single-residue beads

  • distance proportional to the number of missing residues between connected consecutive domains

The connectivity restraints are defined in the Parameter file automatically. If you want to use them, add conn_restraints to the scoring functions (see Parameter file).

Parameters (to be defined in the Parameter file):

connectivity_restraint_weight

Connectivity restraint weight, default: 1.0

max_conn_gap

Number of missing residues of the missing atomic region above which the restraint will not be added, default: None

connectivity_restraint_k

Connectivity restraint spring constant k., default: 10.0

conn_reweight_fn

A function that accepts the following parameters: mol - PMI molecule object next_resi_idx - residue of the next rigid body or bead prev_resi_idx - residue of the previous rigid body or bead connectivity_restraint_weight - default weight passed to add_connectivity_restraints, default: None

conn_first_copy_only

Whether to add the restraints only for the first copy of the molecule (useful for symmetrical assemblies), default: False

ca_ca_connectivity_scale

Scale the average CA-CA distance of 3.8 to account for that it is unlikely that the linker is fully stretched, default: 0.526 (count 2A per peptide bond), default: 0.526 Use 1.0 for no scaling at all.