[PyMOL] Mutagenesis on apo structure and/or complex with adduct atoms removed?

[Colin D. <Col...@uw...>]

A single residue change in the enzyme active site confers resistant to inhibitor (adduct). Structures of apo enzyme and complexed with adduct available. Should I do the mutagenesis on the apo or on the complex after removal of the adduct atoms and relaxing the structure? When I align the apo structure with the complex or the adduct-removed structure the RMSD values are 0.47 and 0.52, respectively.