Whenever you visualize a protein structure using PyMOL or Chimera , have you ever wondered what’s really inside the file ? Nowadays, I am getting into informatics, and hope that this series helps beginners like me to get into it. Today, let's explore the PDB and CIF file formats , and their differences, Let's start by going to RCSB PDB and searching for 5GZA , a kinase enzyme that interacts with mannose sugar. Click the download tab and select PDB and CIF file formats. Exploring the PDB File Format To visualize the contents of a PDB file , open it in VS Code (or any text editor—though I personally dislike Notepad!). PDB files contain structured information with well-defined column formats . The first few sections include: HEADER, TITLE, COMPND → Metadata about the protein SOURCE, AUTHOR → Experimental details ATOM & HETATM → Atomic coordinates and ligands CONECT → Connectivity (bonds between atoms) The most useful part is the ATOM section , which contains 3D atomic ...