11.5: Interactive Molecule and Protein - Reference Options
- Page ID
- 483765
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\(\newcommand{\avec}{\mathbf a}\) \(\newcommand{\bvec}{\mathbf b}\) \(\newcommand{\cvec}{\mathbf c}\) \(\newcommand{\dvec}{\mathbf d}\) \(\newcommand{\dtil}{\widetilde{\mathbf d}}\) \(\newcommand{\evec}{\mathbf e}\) \(\newcommand{\fvec}{\mathbf f}\) \(\newcommand{\nvec}{\mathbf n}\) \(\newcommand{\pvec}{\mathbf p}\) \(\newcommand{\qvec}{\mathbf q}\) \(\newcommand{\svec}{\mathbf s}\) \(\newcommand{\tvec}{\mathbf t}\) \(\newcommand{\uvec}{\mathbf u}\) \(\newcommand{\vvec}{\mathbf v}\) \(\newcommand{\wvec}{\mathbf w}\) \(\newcommand{\xvec}{\mathbf x}\) \(\newcommand{\yvec}{\mathbf y}\) \(\newcommand{\zvec}{\mathbf z}\) \(\newcommand{\rvec}{\mathbf r}\) \(\newcommand{\mvec}{\mathbf m}\) \(\newcommand{\zerovec}{\mathbf 0}\) \(\newcommand{\onevec}{\mathbf 1}\) \(\newcommand{\real}{\mathbb R}\) \(\newcommand{\twovec}[2]{\left[\begin{array}{r}#1 \\ #2 \end{array}\right]}\) \(\newcommand{\ctwovec}[2]{\left[\begin{array}{c}#1 \\ #2 \end{array}\right]}\) \(\newcommand{\threevec}[3]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \end{array}\right]}\) \(\newcommand{\cthreevec}[3]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \end{array}\right]}\) \(\newcommand{\fourvec}[4]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \\ #4 \end{array}\right]}\) \(\newcommand{\cfourvec}[4]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \\ #4 \end{array}\right]}\) \(\newcommand{\fivevec}[5]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \\ #4 \\ #5 \\ \end{array}\right]}\) \(\newcommand{\cfivevec}[5]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \\ #4 \\ #5 \\ \end{array}\right]}\) \(\newcommand{\mattwo}[4]{\left[\begin{array}{rr}#1 \amp #2 \\ #3 \amp #4 \\ \end{array}\right]}\) \(\newcommand{\laspan}[1]{\text{Span}\{#1\}}\) \(\newcommand{\bcal}{\cal B}\) \(\newcommand{\ccal}{\cal C}\) \(\newcommand{\scal}{\cal S}\) \(\newcommand{\wcal}{\cal W}\) \(\newcommand{\ecal}{\cal E}\) \(\newcommand{\coords}[2]{\left\{#1\right\}_{#2}}\) \(\newcommand{\gray}[1]{\color{gray}{#1}}\) \(\newcommand{\lgray}[1]{\color{lightgray}{#1}}\) \(\newcommand{\rank}{\operatorname{rank}}\) \(\newcommand{\row}{\text{Row}}\) \(\newcommand{\col}{\text{Col}}\) \(\renewcommand{\row}{\text{Row}}\) \(\newcommand{\nul}{\text{Nul}}\) \(\newcommand{\var}{\text{Var}}\) \(\newcommand{\corr}{\text{corr}}\) \(\newcommand{\len}[1]{\left|#1\right|}\) \(\newcommand{\bbar}{\overline{\bvec}}\) \(\newcommand{\bhat}{\widehat{\bvec}}\) \(\newcommand{\bperp}{\bvec^\perp}\) \(\newcommand{\xhat}{\widehat{\xvec}}\) \(\newcommand{\vhat}{\widehat{\vvec}}\) \(\newcommand{\uhat}{\widehat{\uvec}}\) \(\newcommand{\what}{\widehat{\wvec}}\) \(\newcommand{\Sighat}{\widehat{\Sigma}}\) \(\newcommand{\lt}{<}\) \(\newcommand{\gt}{>}\) \(\newcommand{\amp}{&}\) \(\definecolor{fillinmathshade}{gray}{0.9}\)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 |