Figure 1.

(a) Input data defined by the user: the reference structure (green), the model (red), the center atom of the sphere, vector of radii, level of accuracy—positions of all atoms or only the selected atom type of a particular nucleotide will be considered. (b) The sphere is built based on a selected atom of every residue from the reference structure; the radius can be set by the user (e.g. 6 Å—left, 18 Å—right picture). (c) The reference structure atoms for the selected sphere are recognized, corresponding atoms from the model are identified, both sets are superimposed, and RMSD is calculated. (d) Spheres are built based on a selected type of atom for every nucleotide in the reference structure, and the process from (c) is repeated (reference structure: RNA Puzzles Problem 3, model: Dokholyan_model_2 (23)).