The placement method has been described in:
Fleishman, SJ, Whitehead TA, et al. Science 332, 816-821. (2011) and JMB 413:1047
The objective of the placement methods is to help in the task of generating hot-spot based designs of protein binders. The starting point for all of them is a protein target (typically chain A), libraries of hot-spot residues, and a scaffold protein.
A few keywords used throughout the following section have special meaning and are briefly explained here.
Hotspot residue-libraries can be read once by the SetupHotspotConstraintsMover. In this mover you can decide how many hotspot residues will be kept in memory for a given run. This number of residues will be chosen randomly from the residues that were read. In this way, you can read arbitrarily large hotspot residue libraries, but each trajectory will only iterate over a smaller set.