Supplemental Material

This document provides Supplementary Material for the manuscript "Analysis of Mapping Atomic Models to Coarse-grained Resolution" by Katherine M. Kidder and W. G. Noid. Section I describes the inverses and pseudo-inverses of congruent ma- trices. Section II analyzes the Hessian matrix, h, of the linear models considered in the main text. In particular, Section IIC derives the determinant identity presented in Eq. (61) of the main text. Finally, Section III demonstrates that the 2-site rep- resentation, MQ, that maximizes Q aligns nicely with the lowest frequency normal mode of the Gaussian Network model (GNM) for actin.