Atomic force microscopy has recently provided highly precise measurements of mechanical properties of various viruses. However, molecular details underlying viral mechanics remain unresolved. Here we report atomic force microscopy nanoindentation experiments on T=4 hepatitis B virus (HBV) capsids combined with coarse-grained molecular dynamics simulations, which permit interpretation of experimental results at the molecular level. The force response of the indented capsid recorded in simulations agrees with experimental observations. In both experiment and simulation, irreversible capsid deformation is observed for deep indentations. Simulations show the irreversibility to be due to local bending and shifting of capsid proteins, rather than their global rearrangement. These results emphasize the viability of large capsid deformations without significant changes of the mutual positions of HBV capsid proteins, in contrast to the stiffer capsids of other viruses, which exhibit more extensive contacts between their capsid proteins than seen in the case of HBV. © 2009 by the Biophysical Society.