A local resolution map of the scaffold (left) was generated from focused refinement and overlaid on a low threshold globally refined map (white). The locally refined map of the scaffold maintains high-resolution features after the TPP riboswitch is embedded. Density for the TPP riboswitch is visible in the globally refined map at low threshold. A locally refined map of the TPP riboswitch (green) is shown on the right and overlaid on the same low threshold globally refined map (white) for clarity.
