automodel.nonstd_restraints() -- add restraints on ligands

nonstd_restraints(aln)

This routine adds restraints to keep residues that have no defined topology (generally BLK residues, used to transfer ligands directly from templates, as described in Section 2.2.1) in a reasonable conformation. You can override this method if you need to change these restraints.

By default, four sets of restraints are built:

• 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 also excluded from the nonbonded list.
• Residue-protein atom distances are 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.
• Residue-protein ${C}_\alpha$ 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.