We use electron microcopy and image analysis to investigate the structure of biological macromolecules consisting of protein subunits and cofactors. Electron microscope images are combined to produce maps corresponding to 3-dimensional density distributions. The ultimate goal of this work is to understand the biological function at the atomic level. 3-dimensional maps generated in MRC or Imagic format are converted into native AVS format using our input module mrcin. They are then visualised as surface models using the isosurface module. We proceed to generate 3-dimensional models based on the underlying atomic backbone, or if more appropriate, an assembly of simple geometrical objects. Atomic models consist of pdb coordinate files. These can be positioned within the geometrical space of the 3-dimensional map in a wireframe representation using our pdb_cylinders module. A number of examples of these and related applications will be shown.