Hierarchical natural move Monte Carlo refines flexible RNA structures into cryo-EM densities

HNMMC refined models of the complete MS2 gRNA. (A) The ensemble of 20 refined models colored according to the genes in the schematic diagram at the bottom (MP: maturation protein, CP: coat protein, Rep: replicase, Lys: lysis protein). The lysis gene is not colored on the ribbon models due to the overlap with the genes for the coat protein and the replicase. (B) The conformational variation among the 20 refined models at each nucleotide colored by the average C4′ RMSD among the 20 models. The color scale from white to red denotes low to high RMSD.