Section 25.2.5.1.3. Representation of a map by free-atom models

An electron-density map can be used to create a free-atom atomic model, with equal atoms placed in regions of high density (Perrakis et al., 1997). To build this model, only the molecular weight of the protein is required, without any sequence information. In brief, a map covering a crystallographic asymmetric unit on a fine grid of about 0.25 Å is constructed. The model is slowly expanded from a random seed by the stepwise addition of atoms in significant electron density and at bonding distances from existing atoms. All atoms in this model and in all subsequent steps are considered to be of the same type. As ARP proceeds, the geometrical criteria remain the same, but the density threshold is gradually reduced, allowing positioning of atoms in lower-density areas of the map. The procedure continues until the number of atoms is about three times that expected. This number is then reduced to about n + 20% atoms by removing atoms in weak density. This method of map parameterization has the advantage that it puts atoms at protein-like distances while covering the whole volume of the protein.