Fig. 2
From: JED: a Java Essential Dynamics Program for comparative analysis of protein trajectories
Some cPCA results for the native protein. a The variance and cumulative variance of the first twenty principal components. b The reduced Q-matrix. c Projections of the trajectory onto the planes formed by (PC1 and PC2) and (PC2 and PC3). d The displacements along PC1 and PC2 are visualized and colored according to their RMSF for each residue using Pymol™. e The free energy surface associated with the first two principal components