The commands described in this node are used to construct and manipulate the PSF, the central data structure in CONGEN. The PSF is comprised of lists giving every bond, bond angle, torsion angle, and improper torsion angle as well as information needed to generate the hydrogen bonds and the non-bonded list. It is essential for the calculation of the energy of the system. A separate data structure deals with symmetric images of the atoms (see Images).
There exists one other command for manipulating the PSF, the SPLICE command, see Splice Command. The SPLICE command can change the sequence of PSF and shuffle the coordinates so that the CONGEN command, see Conformational Search, which can be used to find conformations for the new amino acids.
There is an order with which commands to generate and manipulate the PSF must be given. First, segments in the PSF must be generated one at a time. Prior to generating any segments, one must first have read a residue topology file, see Residue Topology Files. To generate one segment, one must first read in a sequence using the READ command, see Read Sequence. Then, the GENERATE command must be given. RTF's may be changed as needed; however, the SPLICE command will only work correctly when only one RTF is used to build the entire structure.
Once a segment is generated, it may be manipulated. It may be edited using the EDIT command. Cystine bridges may be added using the DISULFIDE command. A histidine heme crosslink may be added using the PATCH HEME command.