The coordinates of the initial model 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 starting model is that derived from manual building into the experimental map obtained by MAD phasing.
cns_solve < generate_easy.inp > generate_easy.out [7 seconds]
There are two chain breaks in the initial model (the density was too poor to build these sections). In the PDB file these can be delimited by the use of a BREAK card:
ATOM 1499 C PHE 213 31.447 44.093 28.037 1.00 31.87 ATOM 1500 O PHE 213 32.494 44.700 27.777 1.00 31.87 BREAK ATOM 1501 OXT PHE 213 30.387 44.746 28.085 1.00 31.87 ATOM 1502 CB GLU 217 33.345 43.043 23.692 1.00 31.87 ATOM 1503 CG GLU 217 34.708 42.702 24.272 1.00 31.87
Alternatively, the generate_easy.inp task file will automatically identify chain breaks (on the basis of distance) and remove the peptide linkage at the break point. If the initial model is very poor, BREAK cards may be needed to ensure the correct topology is generated.
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).