Figure 1

Calculation of the truly local score. This figure explains how the truly-local score is calculated for a single residue in a pairwise comparison (using the default parameters for the program). Previously, a user-provided alignment allows establishing which residues and atoms of one structure are equivalent to which ones in the other. A) On each structure to be compared, a sphere is considered around the alpha carbon atom (red) of the residues corresponding to the alignment position whose truly-local score will be calculated. Two lists including all the backbone atoms falling inside each sphere are prepared (atoms which belong to one list are rendered blue, while the atoms which belong to the other are rendered green). B) Lists are compared to find equivalent atoms. The atoms that were inside one or another sphere are now rendered as balls. The color of atom pairs whose members were one of them inside one sphere and the other outside has been changed to yellow, and these pairs are dismissed from the comparison. C) The remaining atom pairs (whose members were both inside their respective sphere) are taken as a group of fixed points. Then, the alpha carbon atoms being the former centers of the spheres are superposed, and the system is rotated until the root mean square of the atom pair distances reaches a minimum. This minimum value is the score for the residue considered. All the process is iterated for each residue along the sequence. Variations and alternatives on the procedure are discussed in the main text.