DireX is a program to refine protein (or RNA) structures into density maps obtained from X-ray crystallography or electron microscopy.

The only two things that you need as input is a starting PDB file ('input.pdb') that holds the initial coordinates of the protein(s) and a density map ('density.mrc') in either MRC or ASCII-XPLOR file format.

DireX runs on the command line and a basic program call looks like this:

direx -pdb input.pdb -f refine.par -map density.mrc -op out

The -op option defines the name of the output PDB files that are written during the refinement. A number and '.pdb' is attached to the name. Other command line arguments are described here. The file refine.par contains a definition of several run parameters. A template parameter file containing all available parameters (set to default values) can be generated with:

direx -of all.par

In the parameter file you define the resolution, the number of iterations, choice and behaviour of additional restraints, etc. See here for a list of all parameters.

In general, it is a good idea to prepare the protein for the refinement calculation by adding missing atoms, removing multiple configurations, and finally minimizing the structure to ensure that all bond lengths and angles are reasonable and to resolve any atom overlaps. Note that DireX takes the input structure as is, it is not performing any minimizations or regularizations.