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.