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.

{@lang xml} <script src="http://3Dmol.csb.pitt.edu/build/3Dmol-min.js"></script> </head>    
         <div style="height: 400px; width: 400px; position: relative;" class='viewer_3Dmoljs' data-pdb='2POR' data-backgroundcolor='0xffffff' data-style='stick'></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-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-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.

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

    {@lang xml} 
          <div style="height: 400px; width: 400px; position: relative;" class='viewer_3Dmoljs' data-pdb='1YCR' data-backgroundcolor='0xffffff' 
          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.