chapter  21
20 Pages

◾ Working with 3D Structure Data

Learning goal: You can use Biopython to work with macromole-cular 3D structures. 21.1 IN THIS CHAPTER YOU WILL LEARN

• How to parse PDB les with Biopython

• How to access chains, residues, and atoms

• How to superimpose structures onto corresponding residues

e PDB format is the most popular le format for 3D coordinates of macromolecules in structural bioinformatics. In Chapter 10, you learned how to extract information from a PDB le writing your own scripts. You may have thought that it is a pretty dicult task, which is true. Once you are capable of writing a PDB parser by yourself (i.e., without using Biopython), you can claim you have become a good programmer! However, PDB les contain a lot more than just coordinates. In particular, if you want to fully represent the structure of atoms, residues, chains, etc., you need to write a lot more code. Fortunately, the Biopython developers have done that for you.