Skip to main content
. 2023 Jan 1;79(Pt 1):50–65. doi: 10.1107/S2059798322011871

Figure 1.

Figure 1

MD–MX procedure to revise macromolecular crystal structures. In this procedure, an initial crystal structure S (top left) is used to prepare an MD simulation model, using ensemble refinement to generate a set of diverse conformations (the ensemble-refinement model, E; top center). Snapshots from the MD simulation (top right) are used to generate simulated data and MD ensemble visualizations (bottom right; protein density in purple and water density in cyan). The initial structure is refined against the simulated data, leading to a revised protein structure, M prot, and a new water network, M all (bottom center; densities on bottom right). The revised structure is refined against the experimental data to produce the initial MD-revised structure R i, and manual improvements are made guided by the MD density and snapshots, leading to a final MD-revised structure R f (bottom left; 2F o − F c density in blue at 1σ with traces of positive 3σ F o − F c density visible in green).