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.

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