The broad goal of the work has been to design, implement, and begin to use an extensible object oriented framework which represents biological macromolecules and which can be queried in efforts to better understand the biological significance of these complex molecules. Using this framework a variety of methods can be added (by us and others) with functionality ranging from simple verification of a single 3D coordinate set derived from X-ray crystallography or NMR studies, to a detailed interrogation of features common to a number of structures represented by one or more disparate experimental sets of data. Features of the current framework, which have been described in detail elsewhere, are summarized to define the context. This is followed by two examples of using the framework and a discussion of how it is being expanded.