The secondary structure definitions consolidated in the previous step are used to calculate loops, understood as coiled-coil regions and their flanking regular secondary structures, in the insert and the scaffold proteins. Here loops may be added and/or deleted and the geometries of loops may be compared. It is especially helpful to assess how geometrically similar loops are. Very different loops may be compared but are not advisable to graft latter down the workflow. The four loop-defining internal parameters are calculated on the fly and the visual representation of the parameters are shown under the alignment with values of those internal parameters. The compared loops may be focused-in and visualized on the left side in the protein “3D Viewer”.