This step of the pipeline aims to confirm the initial assumptions about the possible pairs of insert and candidate loops for transferring the desired function from the insert to the scaffold protein. Here we compare the geometry of loops. It is especially helpful to compare similar loops. Very different loops may be compared but not grafted latter down the workflow. The four loop-defining internal coordinates are calculated on the fly and the visualization of the comparison is shown under the alignment with values of the internal coordinates and their visual representation shown. The compared loops may be visualised on the left side in the protein “3D Viewer” visualisation area.