Difference between revisions of "Support for bond orders"
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File formats that specify bond order --and Jmol recognizes as such: | File formats that specify bond order --and Jmol recognizes as such: | ||
| − | * [[File_formats#.28MDL.29_MOL_and_SD|MOL]] | + | * [[File_formats#.28MDL.29_MOL_and_SD|MOL]] specifies bond order natively, using certain numeric codes (see table below) |
| − | * [[File_formats#PDB|PDB]] can do it using a trick: specify twice each | + | * [[File_formats#.28Sybyl.29_MOL2|MOL2]] specifies bond order natively, using certain alphanumeric codes (see table below) |
| + | * [[File_formats#PDB|PDB]] can do it using a trick: specify '''twice''' each [http://www.wwpdb.org/documentation/format23/sect10.html CONECT record] for a double bond. | ||
Jmol commands that assign bond order: | Jmol commands that assign bond order: | ||
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{| border="1" cellpadding="5" cellspacing="0" | {| border="1" cellpadding="5" cellspacing="0" | ||
|-align="center" | |-align="center" | ||
| − | ! bond order !! Jmol syntax !! bond | + | ! bond order !! Jmol syntax !! bond code in MOL file !! bond code in MOL2 file |
|-align="center" | |-align="center" | ||
| − | | 0.5 || hBond || n/a | + | | 0.5 || hBond || n/a || n/a |
|-align="center" | |-align="center" | ||
| − | | 0.5 || partial || 8 | + | | 0.5 || partial || 8 || n/a |
|-align="center" | |-align="center" | ||
| − | | 1 || single || 1 | + | | 1 || single || 1 || 1 |
|-align="center" | |-align="center" | ||
| − | | 1.5 || partialDouble || 5 | + | | 1.5 || partialDouble || 5 || n/a |
|-align="center" | |-align="center" | ||
| − | | 1.5 || aromatic || 4 | + | | 1.5 || aromatic || 4 || ar |
|-align="center" | |-align="center" | ||
| − | | 2 || double || 2 | + | | 2 || double || 2 || 2 |
|-align="center" | |-align="center" | ||
| − | | 2.5 || partialTriple <ref>starting Jmol 11.3.28</ref> || n/a | + | | 2.5 || partialTriple <ref>starting Jmol 11.3.28</ref> || n/a || n/a |
|-align="center" | |-align="center" | ||
| − | | 3 || triple || 3 | + | | 3 || triple || 3 || 3 |
|-align="center" | |-align="center" | ||
| − | | 4 || quadruple || n/a | + | | 4 || quadruple || n/a || n/a |
|} | |} | ||
Note : <references /> | Note : <references /> | ||
Revision as of 15:15, 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 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 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 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
