Pdb use ter records
When a molecule (e.g. a protein molecule) is saved in pdb format by PyMOL, a line of TER record is inserted wherever the residue id is not sequential. To suppress this feature, set pdb_use_ter_records value to 0 before saving protein molecules.
get pdb_use_ter_records # return current value of pdb_use_ter_records set pdb_use_ter_records, 0 import cmd cmd.set(name='pdb_use_ter_records', value=0) # same effect