By default, the residue sequence will be that supplied by the data set. To re-calculate residues, use RESIDUES; that will ignore the residue names supplied by the data set, and re-calculate them using the topology of the system.
If the data set includes comments (lines that start with an asterisk (*), see example), these will be printed in the PDB format. This is very useful in preserving the integrity of the PDB file.
If residues are missing, or if multiple proteins are present, keyword START_RES(text) should be used to indicate this. By default, each chain, or section of chain, will be given a different letter, starting with "A". This can cause problems, particularly if a chain has a gap in it, because, by default, MOPAC would give the two chain sections different letters. Chain letters can be explicitly assigned by using CHAIN(text). These keywords are automatically generated when a PDB file is read in and a MOPAC data set generated.
If hydrogen atoms have been added, these can be put in their correct place in the PDB file by using RESEQ.
If either 0SCF or RESEQ. is present, the PDB file written will not contain any non-PDB text, i.e. it will only contain PDB data. This means that all information regarding optimization flags, reaction paths, etc., will be lost.