To achieve improved structures of cyclic peptides bound to mouse Pgp, the final drug-free mouse Pgp structure was first refined into the 4.4 Å QZ59-RRR and 4.35 Å QZ59-SSS datasets without drug (rigid body, TLS, NCS, group-, and individual- B-factors). Anomalous difference Fourier maps were then calculated (CNSv1.3) from model phases of the refined structures to pinpoint the location of the selenium atoms in the datasets. Regularized molecules of the RRR- and SSS-cyclic peptides were then manually docked into the structures (in both possible orientations), placing the selenium atoms in anomalous difference Fourier density. The docked structures were then subjected to another round of refinement using cyclic peptide parameter files with the exception that rigid body refinement was omitted. To examine the orientation of the drugs, refined structures were used to calculate Fo-Fc difference maps, and the vicinity of the drug was carefully inspected. As was originally discovered, the “upper” QZ59-SSS molecule was significantly disordered since Fo-Fc density was absent for two vertices of the triangular drug molecule. These atoms were subsequently removed from the final version of the structure.