Difference between revisions of "Support for bond orders"

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Note &dagger;: starting Jmol 11.3.28
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Note : <references />

Revision as of 15:00, 3 October 2007

Jmol supports bond orders (i.e., different from single bonds).

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

  • MOL
  • PDB can do it using a trick: specify twice each CONNECT record for a double bond.

Jmol commands that assign bond order:

  • connect accepts parameters (see table below)
  • bondOrder (new in Jmol 11.3.x) accepts parameters (see table below)

Visualization of non-single bonds can be supressed (all will show as single) if set showMultipleBonds off is issued.

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

Note :

  1. starting Jmol 11.3.28