Examples for Molecular Structure Generation

The general strategy for setting up the molecular structure for a combination of proteins, water, substrates, ligands, and/or nucleic acids is:

1. Split the original coordinate file into several files containing the segments. A segment is defined as a protein with one continuous polypeptide chain, a continuous protein chain, a substrate, a cofactor, a ligand, all water molecules combined, or a single nucleic acid strand.
2. Generate each segment separately.
3. If necessary, apply appropriate patches to establish covalent links between segments or within segments, such as disulfide bridges.