Difference between revisions of "Support for bond orders"
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| − | Jmol supports bond orders (i.e., different from single bonds). | + | Jmol supports bond orders (i.e., different from single bonds) and displays them as parallel, solid or dashed, cylinders. |
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| + | Visualization of non-single bonds can be supressed (all will show as single) if | ||
| + | <code>[http://chemapps.stolaf.edu/jmol/docs/#setbondstyles set showMultipleBonds off]</code> is issued at the console or from a script. | ||
File formats that specify bond order --and Jmol recognizes as such: | File formats that specify bond order --and Jmol recognizes as such: | ||
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Jmol commands that assign bond order: | Jmol commands that assign bond order: | ||
| − | * <code>[http://chemapps.stolaf.edu/jmol/docs/#connect connect]</code> accepts | + | * <code>[http://chemapps.stolaf.edu/jmol/docs/#connect connect]</code> accepts a parameter specifying bond type (see table below) |
| − | * <code>[http://chemapps.stolaf.edu/jmol/docs/#bond bondOrder]</code> (new in Jmol 11.3.x) accepts | + | * <code>[http://chemapps.stolaf.edu/jmol/docs/#bond bondOrder]</code> (new in Jmol 11.3.x) accepts a parameter specifying bond type (see table below) |
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Revision as of 15:22, 3 October 2007
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:
connectaccepts 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 [1] | n/a | n/a |
| 3 | triple | 3 | 3 |
| 4 | quadruple | n/a | n/a |
Note :
- ↑ starting Jmol 11.3.28
