A Case Study: Molecules, Atoms, and PDB Files

Molecular graphic visualization tools allow for interactive exploration of molecular structures. Most read PDB-formatted files, which we describe in Multiline Records. For example, Jmol (in the following graphic) is a Java-based open source 3D viewer for these structures.

images/oop/ammonia.png

In a molecular visualizer, every atom, molecule, bond, and so on has a location in 3D space, usually defined as a vector, which is an arrow from the origin to where the structure is. All of these structures can be rotated and translated.

A vector is usually represented by x, y, and z coordinates that specify how far along the ...

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