Designed to automate paired comparisons of protein tertiary structures in order to obtain the distance values needed to construct a matrix that can be used to generate structural similarity trees. Designed to automate paired comparisons of protein tertiary structures in order to obtain the distance values needed to construct a matrix that can be used to generate structural similarity trees. The scripts make use of the tools included in UCSF Chimera to make the alignments and extract the number of aligned residues and the RMSD between each pair of structures.