Ligand compatibility with SEWING is in its early stages, but is currently supported via the RosettaScripts interface via a Ligands subtag to any SEWING mover. If the Ligands tag is not provided, any ligand in the input structure will be stripped from the structure and ignored during the alignment/design process. Using this tag ensures that the SEWING Assembly will be aware of the ligand atoms and that any residue contacts with the ligand will be preserved throughout the SEWING protocol. However, to verify that there won't be any clashes with the ligand during the assembly process, you need to provide a LigandClashRequirement.
The Ligands tag takes a list of Ligand subtags. The Ligand tag has several options: