The coordinates of the search model (the known structure) must be converted to a format suitable for use in CNS. This is done with the CNS task file generate_easy.inp. In this example the homologous structure is that of the same protein in a different crystal form.
cns_solve < generate_easy.inp > generate_easy.out [7 seconds]
There are two files generated: a PDB file and an MTF file (this contains the molecular topology information which describes to covalent topology of the molecule).