This method is called automatically by automodel after it generates
the standard protein restraints. It adds restraints to keep non-standard
residues (anything treated
as a HETATM or BLK residue, such as ligands or metal ions) in a reasonable
conformation. You can override this method if you need to change these
By default, four sets of restraints are built:
- For each residue that has no defined topology (generally BLK residues,
used to transfer ligands directly from templates, as described in
Section 2.2.1), intra-residue distances are all
constrained to their template values. This causes each residue to
behave as a rigid body.
- Inter-residue distances are constrained to template values if these are
7Å or less. This has the effect of preserving multiple-HETATM
structures such as DNA chains. If the distances are 2.3Å or less they
are assumed to be bonds and so are restrained more strongly and also
excluded from the nonbonded list.
- Residue-protein atom distances are strongly constrained to template
values (and excluded from the nonbonded list) if these are 2.3Å or
less. This preserves chemical bonds between ligands and the protein.
distances are constrained to template values if
these are 10Å or less and are not already bonded by the previous
restraints. This preserves the ligand position.