Book excerpt: This book is a collection of notes and tutorial examples written by the author while he was learning molecules and related tools. Topics include understanding atoms, bonds and molecules; introduction of atomic isotopes and elements; introduction of proteins and amino acids; introduction of protein kinases; molecule SDF (Structure Data File) format; generating PNG pictures from molecule SDF files; installing RDkit as molecule tool; visualizing molecule structure in 3-D with PyMol; generating molecule movie with PyMol. Updated in 2023 (Version v1.26) with minor updates. For latest updates and free sample chapters, visit https://www.herongyang.com/Molecule.