What is “residue packing”, “repacking”, and so on?

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    • #2090

        The terms “residue packing”, “repacking”, “pack”, etc. appear all over rosetta documentation. What is their meaning?

      • #10670

          “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.

        • #10671

            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?

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