Main page Jmol  TUTORIAL
 

Jmol applets can be a lot of fun, but you need to learn a little about their operation and menus to take the full advantage of the molecular information they contain.  Jmol is Java-based program that is completely and safely executed on your computer, independently of the operating system, as long as you have Java installed and your browser is Java-script enabled.  You may learn much more about the applet and even download your own (desktop) version at Jmol website or Jmol wiki pages.

Here are two Jmol applets for illustration purposes. One represent a small molecule (8 atoms), while the other shows a relatively large protein-DNA complex (1762 atoms) .

propenal (acrolein) Protein - DNA complex (1D66)
Here you can play with a molecule of a simple conjugated aldehyde. The file contains structural data, vibrational data, and some details of electronic structure. For now you just want to get comfortable with the applet. Follow instructions on this page to get a flavor of what can be visualized. What you see here is an X-ray crystal structure of a complex between GAL4 (yeast transcriptional activator) with 17-base pair DNA sequence.  It is a synthetic construct that illustrated protein-DNA interactions and gives us an opportunity to explore Jmol display capabilities for large bio-molecules.

Basic Operations

Start with some basic mouse manipulations. After some practice open the menu and stop the spinning (Spin -> Off). Then, practice some measurements. Approximately, how many times is the protein-DNA complex longer than acrolein?

  left mouse button middle mice button (when available) right mouse button
rotate around X, Y      
rotate around Z hold Shift  and  hold Shift  and 
zoom hold Shift  and  
 

or use mouse wheel

move along X, Y (translate) double click, hold down on the second click, and double-click, hold down on the second click and  Ctrl and
 

you may click on a molecule or anywhere with the applet

restore and center hold Shift and double click double click  
 

you must click with the applet but away from the molecule

open menu Ctrl and click   click
    = press and drag in any direction   = press and drag horizontally   = press and drag vertically
       
measurements atom id hover over the atom ( a tooltip will show  identification)  
  select starting atom double click as a pointer is moved a red rubberband extends from the origin until the pointer hovers over another atom at which point a provisional distance measurement is displayed
  second atom double click the measurement line is set and the distance is shown
    single click the provisional angle measurement is displayed with second rubberband when the pointer hovers over another (third) atom
  third atom double click the angle measurement is set and displayed
    single click the provisional dihedral angle (torsional angle) measurement is displayed with another rubberband when the pointer hovers over another (fourth) atom
  fourth atom single or double click the dihedral angle measurement is set

Menu Options:

Menu (see above) provides many other option for visualizing molecular information.  Information available depends on the file being served to the applet and may vary from just basic geometry to sophisticated aspects of electronic structures. In most cases the choices are self-explanatory. We summarize here the options that may be of particular interest to students of organic chemistry.  Not all option are always available (it depends on what we offer in the file) and on rare occasions we may remove the menu altogether for simplicity. Do not be afraid to try on your own. If you get "lost" just reload the page.

Main

1o sub-level

1o sub-level

Comments

Style Schemes CPK Spacefill various molecular representations, especially applicable to organic molecules; explore on the structure of acrolein (on the left)
Ball and Stick
Sticks
Wireframe
Structures Backbone various molecular representations, especially applicable to large bimolecules such as proteins or nucleic acids; explore these options on the complex on the right
Cartoon
Cartoon Rockets
Ribbons
Rockets
Strands
Trace
model     shows number of "models" included in the file; usually these are different models of the same molecule, showing different properties

In the example of acrolein we have 19 models, (1.1) show electronic structure details such as molecular orbitals or electrostatic potential map (check them under surfaces) and 18 others (1.2-1.9) showing molecular vibrations (select one or more for fun).
Console     opens Java console for scripting (see Jmol website for details)

For acrolein, make sure that model 1.1 is selected (model menu). Open console and type in the lower frame one of the following (without quotation marks) and then press enter  (or press "Run" button):  "set showMultipleBonds on", "set showMultipleBonds off",  "mo homo", "mo lumo",  "mo lumo (-1)" "mo next"
 
Show     opens Java console and shows menu-requested details
Surfaces Van der Waals   shows "true" volumes of molecules
Molecular Electrostatic Potentials   shows electrostatic potential mapped on the van der Waals surface
Molecular Orbitals   shows MOs (if available in the file)

 

 
Technical Last updated 08/07/12 Copyright 1997-2013
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