Although the fundamental steps in Fourier-based image analysis of electron micrographs of helical structures have not changed significantly since the techniques were developed 30 years ago, there have been developments which aid both the analysis itself and the interpretation of results. Increases in computational resources have allowed the automation of many of the repetitive steps in image processing. We describe here a set of computer programs which have been developed at Brandeis University over the past 10 or more years. These programs, referred to as the Brandeis Helical Package, are designed to operate independently of each other with a simple and more uniform protocol for the flow of information between them. The programs are now easier to understand and to use and therefore represent a good tool for the analysis of helical structures. (C) 1996 Academic Press, Inc.