Support for bond orders

Jmol supports bond orders (i.e., different from single bonds) and displays them as parallel, solid or dashed, cylinders.

Visualization of non-single bonds can be supressed (all will show as single) if set showMultipleBonds off is issued at the console or from a script.

File formats that specify bond order --and Jmol recognizes as such:

• MOL specifies bond order natively, using certain numeric codes (see table below)
• MOL2 specifies bond order natively, using certain alphanumeric codes (see table below)
• PDB can do it using a trick: specify twice each CONECT record for a double bond.

Jmol commands that assign bond order:

• connect accepts a parameter specifying bond type (see table below)
• bondOrder (new in Jmol 11.3.x) accepts a parameter specifying bond type (see table below)

bond order	Jmol syntax	bond code in MOL file	bond code in MOL2 file
0.5	hBond	n/a	n/a
0.5	partial	8	n/a
1	single	1	1
1.5	partialDouble	5	n/a
1.5	aromatic	4	ar
2	double	2	2
2.5	partialTriple	n/a	n/a
3	triple	3	3
4	quadruple	n/a	n/a

Note :

Contributors

AngelHerraez, NicolasVervelle