The third parameter is the selection used to compute pairwise distance. This is where biological prior knowledge can help identify the most important regions to look at. In the case of ADK, we used the distances between the core domain and the other two domains because we know this is the conformation change we are looking for. The same is true for the DDR1 case, where the DFG motif and the activation loop are highlighted. The case in RBD is where we know the least about its conformational diversity, so we used all C α atoms.