Crystal structure description

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Presentation transcript:

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

Atomic model description in PDB Default pointers in PDB file . . . . . . ATOM 7 C LEU A 5 37.584 4.085 ATOM 8 O LEU A 5 36.548 3.447 ATOM 9 N ILE A 6 37.887 5.098 ATOM 10 CA ILE A 6 37.032 5.447 ATOM 11 CB ILE A 6 37.835 6.276 . . . . . . Pointer to link description Pointer to monomer description Pointer to atom description

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

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

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

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