1. Crystal structure description
Asym.part
Dictionary
Description of
Monomers
atoms
Links
modifications
chain
monomer
atom

2. Atomic model description in PDB
Default pointers in PDB file
ATOM C LEU A ATOM O LEU A ATOM N ILE A ATOM CA ILE A ATOM CB ILE A
Pointer to link description
Pointer to monomer description
Pointer to atom description

3. Refmac Dictionary Describes all amino acids All nucleic acids
Common sugars
Many organic and inorganic compounds
Links and modifications
There are tools to deal with dictionary
Dictionary format is mmCIF

5. Example of peptide link
Add notes
Link formalism allows to join monomers together
Link describes in details the result of chemical reaction

6. Example of a modification
Add notes
Modification formalism allows to change a monomer
Modification describes in details the result of chemical reaction

7. Thank you very much