In order to display a molecule, RasMol needs a data file called an atomic coordinate file. This data file specifies the position of every atom in the molecule, as cartesian coordinates X, Y, and Z.
Three-dimensional structures can be predicted for many small molecules, but must be determined empirically for macromolecules. The most common method for determining structure is X-ray diffraction analysis of a crystal. Nuclear magnetic resonance (NMR) can also be used. Some structures are available only as theoretical models, often based on related molecules for which empirical structures have been determined.
There are several "standard" formats for atomic coordinate files. One of the most common is the Protein Data Bank or PDB format. Others which RasMol can display are listed in the technical introduction.