Generation of a graph from a surface patch. Dots in the left circle in yellow are residues inside a surface patch. Generation of a graph starts at setting a default distance threshold of 6.5 Å. A graph can be generated from the surface patch by specifying the connection between pairs of vertices (residues) within the distance threshold. Such a graph is shown in the right circle where edges are colored in white. The CF value can be calculated from this graph. If the value is smaller (or greater) than the bottom (or top) bound of a pre-specified CF value, the distance threshold is increased (or decreased) by 0.01 and the corresponding graph is generated. New edges colored in red are added into the previous graph. This process can be repeated until the CF value falls into the specified range.