Swap chemical elements , atom positions, residue side-chains and entire objects. Create individual atoms , or residues, build loops (including the loop database) or entire proteins, extending them at the C-terminus , possibly adding missing oxygens and protection caps. To prepare a molecular dynamics simulation, clean the structures. When looking at oligomers, duplicate objects, use the BIOMT transformations in the PDB file to create the biological oligomeric state or add the crystal symmetry related copies .