This program reconstructs an all-atom protein model from a side chain centers with or without C-alpha coordinates. In the MMTSB Tool Set it is used by the package Molecule.pm. The input, either in a file given as the last command line argument or otherwise expected from standard input, has to be in a specific format as shown above. It consists of the residue number, residue name, side chain center coordinates, and C-alpha coordinates, if available, for each residue.
Options are available to request only a backbone reconstruction (-backonly), specify the location of the directory containing data files required by the program (-d), and to limit reconstruction to a subset of residues given with -l. In this case the rest of protein structure is taken from a reference PDB file.