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. Author manuscript; available in PMC: 2015 Dec 5.
Published in final edited form as: J Comput Chem. 2014 Sep 27;35(31):2245–2255. doi: 10.1002/jcc.23743

Figure 1.

Figure 1

The default clustering scheme used in GneimoSim is shown for an alanine-tyrosine-alanine section of a protein. Sections of a single color represent a rigid cluster whose atoms move together as a single unit. The gray rods and arrows represent hinges connecting two clusters.