Display Protein Structure with 3Dmol.js

Q

How to display a protein structure with 3Dmol.js?

✍: FYIcenter.com

A

You can follow these steps to display a protein structure by loading an online PDB file.

1. Get URL of the online PDB file:

https://files.rcsb.org/download/1YCR.pdb

2. Create an HTML file, View-PDB-Online.html, with the following code. The PDB file loaded with an AJAX call.

<html><head>
<script src="/3Dmol-min.js"></script>
<style>
.mol-container {width: 400px; height: 400px; position: relative;}
</style>
</head>
<body>
  <div id="container-01" class="mol-container"></div>
<script>
$(function() {
  let element = $('#container-01');
  let config = { backgroundColor: 'grey' };
  let viewer = $3Dmol.createViewer( element, config );

  let pdbUri = 'https://files.rcsb.org/download/1YCR.pdb';
  jQuery.ajax( pdbUri, { 
    success: function(data) {
      let v = viewer;
      v.addModel( data, "pdb" );                       /* load data */
      v.setStyle({}, {cartoon: {color: 'spectrum'}});  /* style all atoms */
      v.zoomTo();                                      /* set camera */
      v.render();                                      /* render scene */
    },
    error: function(hdr, status, err) {
      console.error( "Failed to load PDB " + pdbUri + ": " + err );
    },
  });

});
</script>
</body></html>

3. View the HTML document through your Web server: http://localhost/Display-Molecule.html. You see the protein structure displayed. You can room in and rotate it with your mouse.

3Dmol.js Example - Display Protein PDB File
3Dmol.js Example - Display Protein PDB File

 

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2022-12-26, 399🔥, 0💬