Embedding a 3Dmol Viewer

A viewer can be automatically instantiated by simply assigning the class viewer_3Dmoljs to a div.
The viewer will be styled according to the containing div, so be sure to set a height and width.
The code below is all that is needed to create the displayed viewer.

<script src="https://3Dmol.org/build/3Dmol-min.js"></script>     
<script src="https://3Dmol.org/build/3Dmol.ui-min.js"></script>     

<div style="height: 400px; width: 400px; position: relative;" class='viewer_3Dmoljs' data-pdb='2POR' data-backgroundcolor='0xffffff' data-style='stick' data-ui='true'></div>       

The contents of the viewer can be set and manipulated through the use of data- tags, as shown above. Supported tags include:

  • data-pdb The value describes a PDB ID to be loaded into the viewer.
  • data-cid The value describes a PubChem compound id to be loaded into the viewer.
  • data-href The value is a URL to a molecular data file.
  • data-element The value is the id of an HTML element on the current page that has molecular data embedded in it.
  • data-type The value is the file format (default pdb; can be pdb, sdf, xyz, mol2, or cube).
  • data-backgroundcolor The background color (default black).
  • data-backgroundalpha The background alpha (default opaque: 1.0).
  • data-select The value is an AtomSpec selection specification.
  • data-style The value is a style specification.
  • data-surface A surface style specification.
  • data-labelres A residue label style specification.
  • data-zoomto An AtomSpec selection specification to zoom to.
  • data-spin If set will spin the model using $3Dmol.GLViewer#spin. Can specify axis and speed (e.g. data-spin='axis:z;speed:10')
  • data-ui If set will show the UI for the viewer.

Multiple selections, styles, residue labels, and surfaces can be provided by appending a suffix
each tag.

For example:

         <div style="height: 400px; width: 400px; position: relative;" class='viewer_3Dmoljs' data-pdb='1YCR' 
         data-select1='chain:A' data-style1='cartoon:color=spectrum' data-surface1='opacity:.7;color:white' data-select2='chain:B' data-style2='stick'></div>       

Once created, the 3Dmol viewer can be accessed using the id of the container div in $3Dmol.viewers.