Difference between revisions of "Support for bond orders"
AngelHerraez (talk | contribs) (code (8) for partial bond in MOL is not read by Jmol 11.5.46) |
AngelHerraez (talk | contribs) |
||
| Line 16: | Line 16: | ||
{| border="1" cellpadding="5" cellspacing="0" | {| border="1" cellpadding="5" cellspacing="0" | ||
|-align="center" | |-align="center" | ||
| − | ! bond order !! Jmol syntax in connect and bondOrder !! Jmol syntax in bondOrder !! bond code in MOL file !! bond code in MOL2 file | + | ! bond order !! Jmol syntax in <code>connect</code> and <code>bondOrder</code> !! Jmol syntax in <code>bondOrder</code> !! bond code in MOL file !! bond code in MOL2 file |
|-align="center" | |-align="center" | ||
| || hBond <sup>a</sup> || -1 || n/a || n/a | | || hBond <sup>a</sup> || -1 || n/a || n/a | ||
|-align="center" | |-align="center" | ||
| − | | 0.5 || partial <sup>a</sup> || 0.5 || 8 <sup>d</sup> || n/a | + | | 0.5 || partial <sup>a</sup> || 0.5 || 8 ? <sup>d</sup> || n/a |
|-align="center" | |-align="center" | ||
| 1 || single || 1 || 1 || 1 | | 1 || single || 1 || 1 || 1 | ||
| Line 45: | Line 45: | ||
(c) starting Jmol 11.3.28 | (c) starting Jmol 11.3.28 | ||
| − | (d) | + | (d) type 8 is defined as "any" in MOL format; rendering varies across Jmol versions (none, partial, partially double) |
Revision as of 12:25, 12 July 2008
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 double bonds using a trick: specify twice each CONECT record.
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 in connect and bondOrder |
Jmol syntax in bondOrder |
bond code in MOL file | bond code in MOL2 file |
|---|---|---|---|---|
| hBond a | -1 | n/a | n/a | |
| 0.5 | partial a | 0.5 | 8 ? d | n/a |
| 1 | single | 1 | 1 | 1 |
| 1.5 | partialDouble b | -1.5 | 5 | n/a |
| 1.5 | aromatic b | 1.5 | 4 | ar |
| 2 | double | 2 | 2 | 2 |
| 2.5 | partialTriple ? c | 2.5 or -2.5 b,c | n/a | n/a |
| 3 | triple | 3 | 3 | 3 |
| 4 | quadruple | 4 | n/a | n/a |
Notes:
(a) "hBond" and "partial" are both dashed, but they have different patterns, and newly created hydrogen bonds are only thin lines (wireframe style).
(b) "partialDouble" and "aromatic" are identical except for which side of the bond is represented by a dashed line. Same applies to "2.5" and "-2.5".
(c) starting Jmol 11.3.28
(d) type 8 is defined as "any" in MOL format; rendering varies across Jmol versions (none, partial, partially double)
