Figure 25.2.8.4 

All-atom contact dots being used in O for model rebuilding during refinement of a Trp tRNA synthetase at 2.3 Å resolution (courtesy of Charles W. Carter, University of North Carolina, Chapel Hill). The Met side-chain density is fairly round and accommodates the original fitting reasonably, but the contact dots show serious clashes (red spikes in the left panel). Rebuilding relieved all clashes (right panel), with equal or better fit to the map and to rotamer preferences. In this case, the electron density can be contoured lower to show a small but definite bulge in the direction of the rebuilt methyl.