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
.
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
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