column headers: PHI, PSI, OMEGA and CHI1. All torsion angles are reported in degrees. Torsion angles are a very useful indicator of the stereochemistry and the stereochemical quality of a protein structure, with most high-quality proteins exhibiting a relatively tight clustering of phi/psi angles and relatively little deviation in the omega angles. Determination of Beta Turns Beta turns are another type of “short” or local secondary structure that is distinct from the more common helices, beta sheets or random coils. Beta turns are reasonably abundant (15%) and very important secondary structures in proteins. In particular, beta turns play a critical role in defining the topology of proteins. They also likely play a role in initiating early packing events during the protein folding process. In VADAR beta turns are identified under the BTURN header using standard Roman numeral notation (I = type I, II = type II, etc.). In VADAR, beta turns are identified using a combination of different pieces of information including hydrogen bond data, the location of previously identified secondary structures and the value of their local dihedral angles. In VADAR the classification and nomenclature used for beta turns follows the definitions proposed by Wilmot and Thornton. Calculation of Amino Acid Residue Volume Because of the van der Waals force, atoms occupy space, which prevents other atoms from passing through each other. This 3D space or volume is called the excluded volume. Excluded volume is defined as the volume occupied by an atom or residue as determined by its atomic radii and its nearest neighbors. Excluded volume it is typically given in units of cubic Angstroms. In VADAR the excluded volume for each amino acid residue is listed under two different column headers: RES VOL (residue volume) and FRAC VOL (fractional volume). Residue volume is presented in cubic Angstraoms and calculated using the Vornoi polyhedra algorithm that was first introduced by Dr. Frederic Richards. In VADAR the number listed under the RES VOL header corresponds to the excluded volume (in cubic Angstroms) while the value under the FRAC VOL header corresponds to the fractional volume (which ranges from 0 to 1.0 or more). If a protein is efficiently packed, all of its residues should have fractional volumes close to 1.0 (+/- 0.1). In certain circumstances, if an amino acid residue is located in an interior cavity (or it has been placed improperly through poor refinement) it could have a