where <main.pdb> is your main pdb file (the one which went through generate.inp) and <alt_conformer.pdb> is a file containing the co-ordinates of your multiple conformers. Output is directed to stdout. This program is most effective when used in conjunction with Gerard's aconio program which splits a CNS pdb file with multiple conformations into several files (one for the main conformer and additional files for the alternates). These files may then be loaded into O as different molecules. As such, when finished with manual refinement one needs only sam_atom_out a few different files (one for the main conformer and one or more for the alternate conformers) in order to be ready for CNS refinement (well, you still have to split the main file for generate, but this is still easier than manually re-typing co-ordinates!). Example:
$ fixmultocc main.pdb alternate_conf.pdb > main_correct_coords.pdb