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Revision as of 03:22, 16 September 2014
Overview
The pdb_conect_nodup setting in pymol controls if duplicated connectivity record (CONECT) in saved PDB is used to stored bond order.
This is an unofficial PDB feature to store bond order and is supported by several applications that read PDB files, but may break PDB file loading in other applications which don't support it. PyMOL always wrote duplicated connect records (pdb_conect_nodup=0) and the setting allows you to switch that off (pdb_conect_nodup=1).
Syntax
get pdb_conect_nodup # get current value
set pdb_conect_nodup, 1 # no CONECT duplication is used to store bond order
Notes
- PyMOL user mailing list discussion on pdb_conect_nodup: http://sourceforge.net/p/pymol/mailman/message/32735483/
- Jmol support for bond order: http://wiki.jmol.org/index.php/Support_for_bond_orders
- Aromatic bonds are stored using four duplication of the same CONECT records, as specified in, for example, MOL format. See http://wiki.jmol.org/index.php/Support_for_bond_orders