The overall procedure has three reequired steps: converting the density map to rectangular coordinates, positioning the molecule, and clustering the final positions. The main input is the electron density map in Xplor format. The first step is the conversion of the map to rectangular coordinates by the program Map2Grid (see section 4). The main output file from Map2Grid is the density grid file. The actual positioning is performed by the program Blob (see section 6) which uses the density grid file to calculate a quick score. The output of Blob is a file containing a list of final positions of the molecule being positioned. The final step is the clustering of these final positions by the program Hits (see section 7). The overall process is controlled by a parameter file which will be discussed in section 3.
The procedure can be somewhat more complicated when a flexible molecule is being positioned in the binding site of a protein. In particular the program GridsRUs will create electrostatic and atomic affinity grids so that intermolecular interactions can be included as part of Blob's score. In this case the molecule needs some special formatting code. Some auxiliary programs have been written (see section 2) to help but some steps are left up to the user. For example, adding hydrogens and charges must be done by an outside program.