Convergence example. Top panels: The minimum dissimilarity scores obtained at different iterations subtracted from the true dissimilarity score. Bottom panels: The difference between predicted and true transforms at those iterations where minimum dissimilarity scores are obtained. Left, subtomogram alignments based on the real space constrained dissimilarity score (RCS). Right, alignment based on the Fourier space constrained dissimilarity score (FCS). Shown is the performance for subtomograms with SNR 0.5, tilt angle range ±60°. The method was tested with rotation angle seeds sampled at angle interval 60°.