Using Jmol

• The Student creates a set of 3D coordinates (CML, from digital repository)
• They upload the coordinate file to the Wiki
• The file name is wrapped with a Jmol Popup template:

  <jmol>
  <jmolAppletButton>
  <uploadedFileContents>FLAT.cml</uploadedFileContents>
  <text>Load Jmol of flat C=O molecule</text>
  <color>#FFFFFF</color>
  <size>600</size>
  <script>spin on;measure  1 2 3 4;</script>
  </jmolAppletButton>
  </jmol>

• Can make use of extensive Jmol scripting to illustrate a point
• Can display molecular vibrations (normal modes)
• Can display molecular surfaces (from .cube files)