Pairwise alignment of protein complexes. (a) Dissimilarity score matrices for subtomogram classification. The matrix elements representing the same complexes are in consecutive order. (Top row) Dissimilarity score matrix based on the initial subtomogram orientations before alignment for (left column) RCS score and (right column) FCS score. (Bottom row) RCS and FCS score matrices after subtomogram alignments. The alignment is performed at a sampling with 60° rotation angle intervals. (b) Density maps of complexes generated after averaging of the aligned subtomograms in the same class. (Left column) isosurface of the density distribution in single subtomogram for each complex. (Middle and right columns) isosurface of the resulting density maps generated by averaging the 20 subtomograms aligned with the RCS and FCS scores, respectively.