ignore_pdb_segi (boolean, default: off) controls whether or not the PDB segment identifier is ignored.
pdb_conect_all (boolean, default: off) controls whether or not PDB files are written out with CONECT records for all atoms/.
pdb_conect_nodup (boolean, default: off) if off, encode bond orders by duplicating CONECT records when writing PDB files (new in PyMOL 1.6.1).
pdb_discrete_chains (integer, default: -1) controls whether or not bonds are allowed between chains within a PDB file.
pdb_echo_tags (string, default: HEADER, TITLE, COMPND) controls which tags in the PDB file are echoed to the output.
pdb_hetatm_guess_valences (bool, default: on) If true, PyMOL will guess the valences on HETATMs.
pdb_hetatm_sort (boolean, default: off) controls whether HETATMs are segregated.
pdb_honor_model_number (boolean, default: off) controls whether or not PDB MODEL numbers are used as state indices.
pdb_ignore_conect (bool, default: off) If true, PyMOL ignores CONECT records from PDB files. This causes PyMOL to use structural knowledge to bond atoms. See also connect_mode.
pdb_insertions_go_first (boolean, default: off) controls how insertion residues are sorted.
pdb_insure_orthogonal (boolean, default: on) controls whether or not suspicious PDB SCALEn matrices are ignored.
pdb_literal_names (boolean, default: off) controls whether or not names are preserved literally.
pdb_no_end_record (boolean, default: off) controls whether or not an END record is omitted.
pdb_reformat_names_mode (integer: 0-4, default: 0) affects how and whether or not PDB names are reformatted in order to attempt to meet alternate conventions.
pdb_retain_ids (boolean, default: off) controls whether or not PDB files are written out with their original identifier numbers preserved intact.
pdb_standard_order (boolean, default: on) controls whether or not PDB atoms are sorted using the standard conventions.
pdb_truncate_residue_name (boolean, default: off) controls whether or not PDB residue names are truncated to three letters only.
pdb_unbond_cations (boolean, default: on) controls whether or not cations within bonding distances are left unbound during automatically bond detection.
pdb_use_ter_records (boolean, default: on) controls whether or not TER records are written.
pqr_no_chain_id (boolean, default: on) controls whether or not PQR files are written without chain identifiers.