The terms "residue packing", "repacking", "pack", etc. appear all over rosetta documentation. What is their meaning?
"Rotamers", rotational isomers, are a consensus set of low-energy sidechain conformations. In other words, they're a set of possible sidechain configurations which captures the vast majority of physically likely positionings.
Packing is an algorithm which chooses a low-energy set of rotamers for a given backbone (where some of the rotamers might be fixed into specific positions). This lets one configuration of lysine become a different configuration of lysine.
Design uses the same algorithm as packing, more or less, except the chemical identity of the residues can change. This lets lysine become valine, etc.
Thanks. One more question. When a rosetta command does packing (in this case I am refering specifically toInterfaceAnalyzer, with the flag -pack_separated), it samples the entire sidechain conformational space? Or does it somehow respect the initial sidechain conformation in the input .pdb file?