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.

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 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 useful for looking at atomic detail, but become too cluttered to be useful for visualizing peptides or protein chains.

In FirstGlance in Jmol, you can isolate a small portion of a large structure, and then display it as sticks (Vines/Sticks in the Views tab). Or, rather than isolating it, which hides everything else, you can center it and then turn on slabbing.

SlabbingSlabbing

A useful way to see atomic details of a small part of a large macromolecular model is to center the moiety of interest, and then cut away the front and back portions of the molecule. This is called slabbing since one is, in effect, looking at a slab cut out of the larger model. Slabbing can be done using FirstGlance in Jmol: In the Views tab, use Center Atom, and then click the Slab button. Further instructions will appear automatically.

Simplified Schematic RepresentationsSimplified Schematic Representations

For large molecules such as proteins, DNA, RNA and their complexes, simplified representations such as backbone traces or ribbons/cartoons are very helpful in understanding structure. These representations are available under the representations tab in Proteopedia's Scene Authoring Tools.

Color Schemes for MacromoleculesColor Schemes for Macromolecules

A set of standard color schemes for macromolecules, called DRuMS, was released in 2000. These color schemes are offered on buttons in Proteopedia's Scene Authoring Tools. They derive in part from physical ball and stick models (called Corey-Pauling-Kolton or CPK models) that pre-dated computer visualization. Those early colors for chemical elements were incorporated into the color schemes built into early Molecular Visualization Software such as Kinemages, RasMol, and Chime. The CPK colors for elements were incorporated into the color schemes built into Jmol, the visualization engine used in Proteopedia.

See AlsoSee Also

• Help:Getting Started in Proteopedia
• Help:Contents -- a list of many Help pages in Proteopedia.
• History of Macromolecular Visualization
• Molecular Sculpture