Introduction to molecular visualization

Molecular visualization means looking at molecular models in order to explore and understand them. Molecular visualization does not necessarily involve molecular modeling, which means creating molecular models, or changing the composition or configurations of existing models. Here we will be dealing primarily with models of macromolecules (protein, DNA, RNA, or their complexes).

Obtaining Molecular ModelsObtaining Molecular Models

Methods for searching the Protein Data Bank for published empirical 3D models are explained here. Empirical models are those determined by experimentation, notably X-ray diffraction, solution nuclear magnetic resonance, or cryo-electron microscopy. Empirical models are far more reliable than theoretical models, but one must pay attention to the quality of an empirical model since some are more reliable than others.

Representations of Molecular ModelsRepresentations of Molecular Models

Molecular models can be represented (displayed, rendered) in various ways.

Atomic RepresentationsAtomic Representations

Atomic representations are illustrated in the page about Glycine. These show positions of atoms and covalent bonds. Such representations are too cluttered to be useful for visualizing peptides or protein chains.