This major menu is meant as an aid when solving a structure using Molecular Replacement. At present, two commands are available in the menu, but additional features are planned, and will appear in a future release. As usual, there is a setup command where different parameters can be defined. The idea of this menu is not to solve a Molecular Replacement problem, but to be able to quickly check solutions suggested by other programs.
The idea of Molecular Replacement is that you have an known structure that you are trying to replace in the data of the unknown structure. Structure factors are calculated from the coordinates of the known structure, generally in a cubic unit cell. If your known structure has not been placed in an orthogonal system (or higher) you have to be extremely careful, as the different programs use different conventions for transforming from fractional to orthogonal Å. X-PLOR, uses the same orthogonalization convention as O and PDB, but Merlot uses a different one.