Extended Data Fig. 5: Water occupancy in the MD simulation of the HIV-1 CA tube.

a, Water occupancy map, averaged over 80 ns of the trajectory. For each frame in the trajectory, a binary mask is used to indicate the presence of water at every point in space. The average of these masks for a trajectory is the water occupancy map, and each point in the latter describes the fractional occupancy of water at a specific location. 3-D visualizations, isosurfaces, are generated according to the value at each point in the occupancy map and are shown at varying occupancy cutoffs. b, Histogram of dimer interfaces involved in water-mediated contacts, the latter determined by proximity of S149, E175 and W184 side chain atoms within 4.0 Å of the water occupancy map at the specified occupancy cutoff values. c, Illustration of a dimer interface with the side chains of S149, E175 and W184 in stick representation and an isosurface of the water occupancy map (red; > 0.70 fractional occupancy).