The recognition of molecular fragments in E maps and electron density maps

The advent of phase-determination computer programs like MULTAN has made the solution of many crystal structures a matter of routine. The next major step towards making the process completely automatic is to program the computer to recognize complete molecules and molecular fragments in E maps. Algorithms suitable for the machine interpretation of E maps are given. These include procedures for peak search, separation of peaks into bonded clusters, application of stereochemical criteria and comparison of the molecular fragments found with those expected. The algorithms are capable of giving alternative interpretations of the same map. Two methods of comparing molecular fragments found in E maps with the expected molecular structures are described. Both have been used successfully and examples of their use are presented. One of the methods can be programmed fairly easily in a completely general way and will be incorporated into MULTAN. The recognition of molecular fragments will allow the automatic use of a partial structure as a step in the determination of the complete structure.