Introduction to molecular visualization
From Proteopedia
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).
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Obtaining 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.
Empirical models are available for only a small fraction of all proteins, probably <10%. If an empirical model is not available, the next best thing would be a homology model. About one third of all proteins can be reliably homology modeled, but homology models have more uncertainties than do empirical models.
Representations of Molecular Models
Molecular models can be represented (displayed, rendered) in various ways.
Atomic 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.
