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11.5: Interactive Molecule and Protein - Reference Options

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    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

    This page titled 11.5: Interactive Molecule and Protein - Reference Options was last modified on Tue, 23 Jul 2024 01:45:26 GMT and is shared under a CC BY-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.