Electron microscopy and image processing are powerful tools for investigating different conformational states of enzymes. It is not always possible to isolate these often unstable intermediates as single species. As a result electron micrographs show a snapshot of enzymes in various conformational. states. We describe here how to recognize that the imaged particles have different conformations and how to obtain for each species a three-dimensional model using single-particle image processing. We investigated the ATP synthase from chloroplasts, which has a molecular mass of about 550 kDa. It is a membrane-bound enzyme and consists of two segments, a membrane-embedded hydrophobic F-0 part and a hydrophilic F-0 part. Analysis of the particle images indicated that the molecules were in two different conformations. For both conformations three-dimensional models were calculated, which showed that the structures differed mainly in the tilt of the F-0 part with respect to the F-1 part.