We present a sensitive analysis technique to explore the configurational space of non-stationary systems. With it, we discuss the pattern of large-scale molecular shape transitions observed during the computer-simulated unfolding of charged in vacuo lysozyme. Using a statistical treatment for the charge distribution among residues, we have estimated the value of the critical total charge that unleashes rapid unfolding in vacuo. Analyses of the molecular dynamics trajectories in a space of molecular shape descriptors indicate a transition between quasi-native folds and denatured conformers. At the critical charge, we find an intermediate regime of persistent partly unfolded structures. This behaviour is compatible with experimental observations of lysozyme ions in the gas phase. Our results indicate that then is a subtle balance between the unfolding tendency of the Coulomb repulsion and the tendency to implode associated with the in vacuo boundary conditions.