Energy minimising structures in Rosetta/Pyrosetta is essential to avoid artifactual results. Say a mutation is introduced and in the protocol the neighbourhood is repacked: if the structure is not energy minimised properly the neighbourhood repacking step will spuriously reward the mutation a very negative ∆∆G. One worry is that the energy minimisation is not faithful to the crystal structure. This argument has two sides, on one the fudgey force fields in Rosetta do not truly model the chemical interactions while on the other crystal packing may be unnatural. Both points have merit. After all Rosetta does use implicit water, which do not behave like the stripped crystallographic waters and some residues may have non-standard protonations etc. But if one wants one can use a scorefunction that is weighted by the electron density map and here is how.
