Difference between revisions of "Support for bond orders"
AngelHerraez (talk | contribs) (CML bond orders) |
AngelHerraez (talk | contribs) (more details on CML bond order) |
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* [[File_formats/Coordinates#MOL2_.28Sybyl.2C_Tripos.29|MOL2]] specifies bond order natively, using certain alphanumeric codes (see table below) | * [[File_formats/Coordinates#MOL2_.28Sybyl.2C_Tripos.29|MOL2]] specifies bond order natively, using certain alphanumeric codes (see table below) | ||
* [[File_formats/Coordinates#PDB|PDB]] can do double bonds using a trick: specify '''twice''' each [http://www.wwpdb.org/documentation/format23/sect10.html CONECT record], or put the second atom twice in the same record. | * [[File_formats/Coordinates#PDB|PDB]] can do double bonds using a trick: specify '''twice''' each [http://www.wwpdb.org/documentation/format23/sect10.html CONECT record], or put the second atom twice in the same record. | ||
| − | * CML specifies | + | * CML specifies bond order natively, using XML tags; Jmol implements single, double, triple, aromatic and 'partial12'. |
Jmol commands that assign bond order: | Jmol commands that assign bond order: | ||
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| || hBond <sup>a</sup> || -1 || n/a || n/a || hbond | | || hBond <sup>a</sup> || -1 || n/a || n/a || hbond | ||
|-align="center" | |-align="center" | ||
| − | | 0.5 || partial <sup>a</sup> || 0.5 || 8 <sup>d</sup> || n/a || partial01 | + | | 0.5 || partial <sup>a</sup> || 0.5 || 8 <sup>d</sup> || n/a || partial01 <sup>f</sup> |
|-align="center" | |-align="center" | ||
| 1 || single || 1 || 1 || 1 || 1 or S | | 1 || single || 1 || 1 || 1 || 1 or S | ||
| Line 31: | Line 31: | ||
| 2 || double || 2 || 2 || 2 || 2 or D | | 2 || double || 2 || 2 || 2 || 2 or D | ||
|-align="center" | |-align="center" | ||
| − | | 2.5 || partialTriple ? <sup>c</sup> || 2.5 or -2.5 <sup>b,c</sup> || n/a || n/a || partial23 | + | | 2.5 || partialTriple ? <sup>c</sup> || 2.5 or -2.5 <sup>b,c</sup> || n/a || n/a || partial23 <sup>f</sup> |
|-align="center" | |-align="center" | ||
| 3 || triple || 3 || 3 || 3 || 3 or T | | 3 || triple || 3 || 3 || 3 || 3 or T | ||
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(e) as documented at http://eugen.leitl.org/nesc/jumbo4.3/schemas/cmlAll/htmldocs/orderType.html | (e) as documented at http://eugen.leitl.org/nesc/jumbo4.3/schemas/cmlAll/htmldocs/orderType.html | ||
| − | (f) starting Jmol 11.7.32 | + | (f) not fully implemented; starting Jmol 11.7.32 only partial12 is implemented |
Revision as of 09:15, 19 June 2009
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, or put the second atom twice in the same record.
- CML specifies bond order natively, using XML tags; Jmol implements single, double, triple, aromatic and 'partial12'.
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 | bond code in CML file e |
|---|---|---|---|---|---|
| hBond a | -1 | n/a | n/a | hbond | |
| 0.5 | partial a | 0.5 | 8 d | n/a | partial01 f |
| 1 | single | 1 | 1 | 1 | 1 or S |
| 1.5 | partialDouble b | -1.5 | 5 | n/a | partial12 f |
| 1.5 | aromatic b | 1.5 | 4 | ar | A |
| 2 | double | 2 | 2 | 2 | 2 or D |
| 2.5 | partialTriple ? c | 2.5 or -2.5 b,c | n/a | n/a | partial23 f |
| 3 | triple | 3 | 3 | 3 | 3 or T |
| 4 | quadruple | 4 | n/a | 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; most versions of Jmol will render that as partial.
(e) as documented at http://eugen.leitl.org/nesc/jumbo4.3/schemas/cmlAll/htmldocs/orderType.html
(f) not fully implemented; starting Jmol 11.7.32 only partial12 is implemented
