Skip to main content
Library homepage
 
Chemistry LibreTexts

5.6: Interactive Molecule and Protein - Reference Options

  • Page ID
    97416
  • \( \newcommand{\vecs}[1]{\overset { \scriptstyle \rightharpoonup} {\mathbf{#1}} } \) \( \newcommand{\vecd}[1]{\overset{-\!-\!\rightharpoonup}{\vphantom{a}\smash {#1}}} \)\(\newcommand{\id}{\mathrm{id}}\) \( \newcommand{\Span}{\mathrm{span}}\) \( \newcommand{\kernel}{\mathrm{null}\,}\) \( \newcommand{\range}{\mathrm{range}\,}\) \( \newcommand{\RealPart}{\mathrm{Re}}\) \( \newcommand{\ImaginaryPart}{\mathrm{Im}}\) \( \newcommand{\Argument}{\mathrm{Arg}}\) \( \newcommand{\norm}[1]{\| #1 \|}\) \( \newcommand{\inner}[2]{\langle #1, #2 \rangle}\) \( \newcommand{\Span}{\mathrm{span}}\) \(\newcommand{\id}{\mathrm{id}}\) \( \newcommand{\Span}{\mathrm{span}}\) \( \newcommand{\kernel}{\mathrm{null}\,}\) \( \newcommand{\range}{\mathrm{range}\,}\) \( \newcommand{\RealPart}{\mathrm{Re}}\) \( \newcommand{\ImaginaryPart}{\mathrm{Im}}\) \( \newcommand{\Argument}{\mathrm{Arg}}\) \( \newcommand{\norm}[1]{\| #1 \|}\) \( \newcommand{\inner}[2]{\langle #1, #2 \rangle}\) \( \newcommand{\Span}{\mathrm{span}}\)\(\newcommand{\AA}{\unicode[.8,0]{x212B}}\)

    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
    Table 2: Data-id reference table
    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
    Table 3: GLmol specific data-attributes
    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


    5.6: Interactive Molecule and Protein - Reference Options is shared under a CC BY 1.3 license and was authored, remixed, and/or curated by LibreTexts.

    • Was this article helpful?