The most powerful fashion to use noncrystallographic symmetry is to reduce the number of parameters in your model with constraints. The correspondence of the separate images of the molecule is assumed to be perfect and the model does not allow any variation between copies. Basically the number of parameters in the model decreases by the number of images in the asymmetric unit.
When using noncrystallographic constraints your coordinate file will contain only a single copy of each molecule. This copy is called the prototype. You must supply the transformations which will be applied to the atoms in the prototype to generate each individual molecule: reconstructing the asymmetric unit.
Refinement of a model with constrained ncs is somewhat more complicated than basic refinement. This complications arrises because the coordinate file does not contain all the atoms in the asymmetric unit of the crystal. To proceed you must generate a TNT coordinate file containing only the unique atoms, and an ``ncs" file containing the ncs operators which generate the rest of the atoms. The easiest way to do this is to start with a PDB file containing all atoms in the asymmetric unit. After using from_pdb to convert this data to TNT's format edit the TNT control file to add the proper CLUSTER statements. You can then use the gather command to determine the ncs operators and average the redundant atomic positions. gather writes two files: gathered.cor, which contains the coordinates, and gathered.ncs, which contains the operators. It would be best to rename these files to something more memorable.
You are now nearly ready to start constrained refinement. The remaining step is to create a refinement script. In all other cases you can run TNT refinement using one of the scripts supplied in $tntbin. When running constrained ncs refinement you must customize the refinement script to your project. Make a copy of $refroot/tnt/doc/tnt_cycle_cons_ncs. Inside this file certain locations are marked where you must make changes.
Once these changes have been made you can start your refinement. Type the command ``tnt 1 30 pcg tnt_cycle_cons_ncs" and away you go.