The crystal structure describes the three-dimensional periodic arrangement of atoms, ions, or molecules in a crystal. The unit cell represents the simplest repeating unit of the crystal structure. It is a parallelepiped containing a certain spatial arrangement of atoms, ions, molecules, or molecular fragments. From the unit cell the crystal structure can be fully reconstructed via translations.
The visualization of a crystal structure can be reduced to the arrangement of atoms, ions, or molecules in the unit cell, with or without cell outlines. Structure elements extending beyond single unit cells, such as isolated molecular or polyhedral units as well as chain, net, or framework structures, can often be better understood by extending the structure representation into adjacent cells.
The space group of a crystal is a mathematical description of the symmetry inherent in the structure. The motif of the crystal structure is given by the asymmetric unit, a minimal subset of the unit cell contents. The unit cell contents can be fully reconstructed via the symmetry operations of the space group on the asymmetric unit. Visualization interfaces usually allow for switching between asymmetric unit and full structure representations.
Bonds between atoms or ions can be identified by characteristic short distances between them. They can be classified as covalent, ionic, hydrogen, or other bonds including hybrid forms. Bond angles can be deduced from the bond vectors in groups of atoms or ions. Bond distances and angles can be made available to the user in tabular form or interactively, by selecting pairs or groups of atoms or ions. In ball-and-stick models of crystal structures, balls represent atoms and sticks represent bonds.
Since organic chemists are particularly interested in molecular structures, it might be useful to be able to single out individual molecular units interactively from the drawing. Organic molecular units need to be given both as 2D structural formulae and full 3D molecular structures. Molecules on special-symmetry positions need to be reconstructed from the asymmetric unit. Protein crystallographers are interested in molecular structures of biological macromolecules, so that provisions need to be made to be able to represent molecular subunits as helices, sheets, or coils, respectively.
Crystal structure visualization can be integrated into a crystallographic database. Alternatively, the crystal structure data are exchanged between the database and the visualization software, preferably using the CIF format. Web-based crystallographic databases can integrate crystal structure visualization capability. Depending on the complexity of the structure, lighting, and 3D effects, crystal structure visualization can require a significant amount of processing power, which is why the actual visualization is typically run on the client.
Currently, web-integrated crystal structure visualization is based on Java applets from open-source projects such as Jmol. Web-integrated crystal structure visualization is tailored for examining crystal structures in web browsers, often supporting wide color spectra (up to 32 bit) and window size adaptation. However, web-generated crystal structure images are not always suitable for publishing due to issues such as resolution depth, color choice, grayscale contrast, or labeling (positioning, font type, font size).