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.

• What to Do about Unknown Atoms
• A Standard Protein Structure
• How to Set Up Unusual Geometries
• A Protein Structure with Water or Ligands
• A Protein Structure with a Cofactor or Substrate
• A Protein Structure with a Metal Cluster
• A Nucleic Acid Structure
• Virus Structures or Structures with Many Identical Units