Figure 5. Essential dynamics of the capsid.

(a–f) Views of the first mode from PCA, which comprises only 6% of total variance, illustrate the striking complexity and intrinsic asymmetry of capsid dynamics. PCA calculation based on Cα trace of 50,000 conformations sampled over 1 µs of simulation. Mode representation shown as a porcupine plot projected onto a polyhedral surface with pentamers highlighted in red; eigenvalue scaling increased by five for visual clarity.

Figure 5—figure supplement 1. Scree plot for PCA modes.

Scree plot showing percent contribution to total variance for the first 100 modes determined by PCA of the capsid.