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. Author manuscript; available in PMC: 2011 Sep 1.
Published in final edited form as: J Phys Chem B. 2010 Aug 12;114(31):10039–10048. doi: 10.1021/jp1057308

Figure 2.

Figure 2

Coarse-graining for RNA scattering. (left) Cartoon representation of the 3D structure of valine transfer RNA (tRNA; PDB entry 2K4C), colored from blue at the 5′ end to red at the 3′ end. (right) The 3D structure is coarse-grained into the two-particle representation, where the backbone particles are large blue spheres, and the sidechain in red. In addition, explicit water molecules are placed surrounding the RNA molecule and shown as small blue dots.