Displaying orbitals

Once the molecule file is fully loaded the image at right will become live. At that time the "activate 3-D" icon will disappear.

How to Display Orbitals

The display at right is from the file ethane-staggered-3-21G.log. To follow along you can use the applet at right or download the file and open it in a copy of the Jmol application.

Load the file into the Jmol application (already done if you are using the applet at right).
Advance to the last "frame" because the quantum software puts the optimized orbital information in the last "frame". Use the pull-down menu in the Jmol application (Tools > Animate > Once) or the pop-up menu in both the application and the applet (right mouse button, control click on a one button mouse, > Model > select the last one, bottom choice).
Start the molecule spinning. Use the pop-up menu in both the application and the applet. (right mouse button > Spin > On). This should give you an animated molecule that looks like what you get by clicking on the button below.

Display your first orbital. In the application or the applet use the pop-up menu (right mouse button > Surfaces > Molecular Orbitals > 1..25 > #3 - 1.013). This will display the third orbital with an energy of -1.013 Hartrees. Your display should look like the one created by clicking on the button below.

Display the two HOMOs (Highest Occupied Molecular Orbitals). These are the degenerate orbitals number 8 and 9. Use the pop-up menu (right mouse button > Surfaces > Molecular Orbitals > 1..25 > #8 - 0.4773) and (right mouse button > Surfaces > Molecular Orbitals > 1..25 > #8 - 0.4773). The two buttons below will display these two orbitals as you should have.

Display the LUMO (Lowest Unoccupied Molecular Orbital). This is orbital number 10. Use the pop-up menu (right mouse button > Surfaces > Molecular Orbitals > 1..25 > #10 0.274). The button below will generate the display you should have.

Many more options for orbital display are available by using the commands "mo" and "isosurface" in the scripting window. A brief tutorial on using commands in the script window may be found here. Detailed documentation on scripting may be found here

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You may look at any of these intermediate views again by clicking on the appropriate button.

Based on template by A. Herráez as modified by J. Gutow

Page skeleton and JavaScript generated by export to web function using Jmol 14.1.7 2014-01-22 20:25: on Jan 24, 2014.

Using directory /Users/gutow/Desktop/How to Display Orbitals
  adding JmolPopIn.js
  ...jmolApplet0
      ...adding Staggered_Ethane.png
copying and unzipping jsmol.zip directory into /Users/gutow/Desktop/How to Display Orbitals
      ...copying
file:/Users/gutow/Documents/Web Pages/Jmol_Web_Page_Maker/How-To/Make a ScriptButton Page/ethane-staggered-3-21G.log
         to
/Users/gutow/Desktop/How to Display Orbitals/ethane-staggered-3-21G.log
      ...adding Staggered_Ethane.spt
  ...jmolApplet1
      ...adding Spin_On.png
copying and unzipping jsmol.zip directory into /Users/gutow/Desktop/How to Display Orbitals
      ...adding Spin_On.spt
  ...jmolApplet2
      ...adding Molecular_Orbital_3.png
copying and unzipping jsmol.zip directory into /Users/gutow/Desktop/How to Display Orbitals
      ...adding Molecular_Orbital_3.spt
  ...jmolApplet3
      ...adding HOMO_1__MO8_.png
copying and unzipping jsmol.zip directory into /Users/gutow/Desktop/How to Display Orbitals
      ...adding HOMO_1__MO8_.spt
  ...jmolApplet4
      ...adding HOMO_2__MO9_.png
copying and unzipping jsmol.zip directory into /Users/gutow/Desktop/How to Display Orbitals
      ...adding HOMO_2__MO9_.spt
  ...jmolApplet5
      ...adding LUMO__MO_10_.png
copying and unzipping jsmol.zip directory into /Users/gutow/Desktop/How to Display Orbitals
      ...adding LUMO__MO_10_.spt

This will be the viewer still of jmol image

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