Some PDB files represent two or more proteins, for example there are four proteins in one hemoglobin. At the end of each such protein there is a TER entry, indicating the termination of the protein. In other proteins, some residues are missing. Missing residues are indicated in the PDB file by a discontinuity in the residue number. When writing PDB formats using PDBOUT, information on the various proteins and on missing residues can be indicated by the START_RES(text) keyword. The format of the keyword is as follows:
START_RES[=](n1[ ,-][n2[ ,-][n3[ ,-]...]])
nn is the number of the first residue in a section of contiguous residues in the PDB file. If two contiguous sections are separated by missing residues, then the two nn are separated by a minus sign. If the two contiguous sections are on different proteins, then the two nn are separated by a single space.
Thus if a PDB file consists of two proteins, A and B, and A has residues 30 31 32 33 34 38 39 40, and B has residues 44 45 46 49 50 51 55 56 57, then the keyword would be:
START_RES(30-38 44-49-55) or START_RES=(30-38 44-49-55)
In the PDB file written by MOPAC, a "TER" line would be added after the last atom of protein A, residue 8 (residue 38 in the output), and before the first atom of protein B, residue 9 (residue 44 in the output) .
If the PDB file consists of one protein only, and there is a gap in the residue sequence, for example suppose the residue numbers were: 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, then the START_RES keyword would have two entries, e.g., START_RES(1-9), the first entry being the residue number of the first contiguous section.
See also CHAINS(text) to define chain-letters.