Figure 5.

The coordinates of the C1′ atom can be accurately determined after locating the sugar center. (a) The Cartesian coordinate system defined using the locations of the sugar center, 3′ phosphate and 5′ phosphate (see §3). (b) Plots showing all C1′ atoms from the RNA05 data set relative to their respective sugar center, using the axes shown in (a) with sugar puckers as indicated. The top plot shows the C1′ coordinates in the x and y axes, while the bottom plot shows the x and z axes. The mean C1′ location is shown as a yellow diamond in both plots. During backbone tracing, RCrane places new C1′ atoms using this mean location.