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.

Version History

• 2.3.0 new implementation, works correctly with gaps
• 1.8.4 feature removed
• <= 1.8.2 feature broken for various use cases (e.g. gaps)
• <= 1.5.0.4 feature broken for HETATM polymer residues (e.g. MSE)

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)

See Also

• pdb_conect_nodup
• pdb_conect_all