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Pdb use ter records
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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.
Example
get pdb_use_ter_records # return current value of pdb_use_ter_records
set pdb_use_ter_records, 0
PYMOL API
cmd.set('pdb_use_ter_records', 0)