5.6: Interactive Molecule and Protein - Reference Options
| Data-* Attribute | What it does | Example |
GLmol ? |
3Dmol ? |
JSmol ? |
|---|---|---|---|---|---|
| [required] id | Specifies Molecule using the syntax specified in Table2 |
data- data- |
Yes | Yes | Yes |
| height | Specifies Height |
data-height="100" data-height="80%" |
Yes | Yes | Yes |
| width | Specifies Width |
data-width="100" data-width="80%" |
Yes | Yes | px only |
| border | Shows colored border | data-border="true" | Yes | Yes | Yes |
| label | Shows colored label | data-label="true" | Yes |
Yes |
Shown by default |
| spin | Specifies if the molecule should spin | data-spin="true" | Yes | Yes | Not Recommended |
| multiple | Allows multiple molecules in a row | data-multiple="true" | Yes | Yes | Yes |
| orbital | Specifies an orbital to display using n, l, & m separated by spaces | data-orbital="4 1 1" | NO | NO | Yes |
| symmetry | When completed will allow JSmol to calculate symmetry of a molecule | [in development] | NO | NO | In Development |
| Prefix Character | Postfix | Example | Database |
|---|---|---|---|
| = | PDB ID | =2POR | RCSB PDB |
| == | RCSB ligand ID | ==HEM | RCSB PDB |
| $ | simple molecule name | $caffeine | NCI NIH |
| $ | SMILES | $CC/C=C/CC | NCI NIH |
| : | Pubchem CID | :1983 | Pubchem |
| : | InCHI |
:BSYNRYMUTXBXSQ-UHFFFAOYSA-N |
Pubchem |
| Data attribute name | Description | Choices |
|---|---|---|
| colormode | Sets the coloration of the main chain. |
[d] chainbow - makes the chain a rainbow * chain - colors each chain differently * b - colors by B factor * polarity - colors by polar/nonpolar * ss - colors by secondary structure |
| mainchain | Sets the display style of the main chain |
[d] thickRibbon * ribbon * strand * chain * cylinderHelix * tube * bonds * none |
| sidechains | Sets whether side chains will be visible. |
[d] false - will not show sidechains * true - will show sidechains |
| rough-beta | Sets if beta sheets should be rough (not smoothened). |
[d] false - will show smooth beta sheets * true - will show roughened beta sheets |
| hetatm-mode |
[d] ballAndStick2 * stick * line * icosahedron * sphere * ballAndStick |
|
| base-hetatm-mode | Sets the display style of Nucleic acid bases |
[d] line * stick * polygon * none |
| nonbonded |
[d] none * sphere * cross |
|
| projectionmode |
[d] perspective * orthoscopic |
|
| unitcell |
[d] false * true |
|
| bioassembly |
[d] false * true |
|
| crystalpacking |
[d] false * true |
|
| symmetry |
[d] false * true |
|
| speed | Set rotation speed |
[d] 5 * integer |