Knowledge about the assembled structures of the secondary elements in proteins is essential to understanding protein folding and functionality. In particular, the analysis of helix geometry is required to study helix packing with the rest of the protein and formation of super secondary structures, such as, coiled coils and helix bundles, formed by packing of two or more helices. Here we present an improved computational method, QHELIX, for the calculation of the orientation angles between helices. Since a large number of helices are known to be in curved shapes, an appropriate definition of helical axes is a prerequisite for calculating the orientation angle between helices. The present method provides a quantitative measure on the irregularity of helical shape, resulting in discriminating irregular-shaped helices from helices with an ideal geometry in a large-scale analysis of helix geometry. It is also capable of straightforwardly assigning the direction of orientation angles in a consistent way. These improvements will find applications in finding a new insight on the assembly of protein secondary structure.