Dear Chimera folks, I've been looking into making Difference Distance Matrix Plots (a la Richards & Kundrot, Proteins 1988) to evaluate domain movements between two models. Chimera's RR Distance plots get most of the way there and since they start from sequence alignments do a nice job handling different patches of missing residues between the two models. In addition to plotting Avg and Std Distances would it be possible to compute the differences between RR distances of two structures. Or if you don't want to implement this function in the RR Distance GUI, at least some sort of python script that could access the distance matrices from the RR Distance function and direct that to some sort of output either with matplotlib or the data as text to plot with another program. Thanks for considering it, Ed