Step 1. Global fluctuations (a & c) from hierarchical coarse-graining of the HK97 capsid (see right) identifies the  pentamers as the most mobile (red) regions.
 

Step 2.  Build a substructure (see above) centered around a pentamer (red) and repeat the calculations now with full residue detail for the substructure and a bath representing the effective interactions with other residues (gray). The substructure (right) is color coded according to the chains.

Step 3.  GNM using SIMPLE analysis of the given substructure (see right) gives the global dynamics of (a & b) prohead II and (c & d) Head II. The diagrams are color coded according to the residue mobilities in the global mode, from red (most mobile) to blue (almost rigid).