Hello everyone,Welcome to this tutorial on Introduction to Jmol Application.
In this tutorial, I will briefly explain about
Jmol Application window and some basic operations.
We will learn about:
Menu bar, Tool bar and 'Jmol' panel
How to modify the size of Jmol panel
Create models of simple organic molecules.
Build molecules by substituting hydrogen with a Methyl group.
We will also learn
to Minimize energy to get a stable conformation
and Save the image as '.mol' file.
To follow this tutorial, you should have knowledge of:
High school Chemistry and Basic Organic Chemistry.
To record this tutorial, I am using:
Ubuntu Operating System version. 12.04
Jmol version 12.2.2
and Java version 7.
Please note-for Jmol Application to run smoothly, you should have Java installed on your system.
About Jmol Application-
It is: * A free and open source Molecular Viewer.
Used to create and view 3 dimensional models of chemical structures.
And also used to view secondary structures of proteins and macromolecules.
Information regarding download and installation-
For Ubuntu OS, installation of Jmol is done using Ubuntu Software Center.
Please follow this tutorial in the Linux series on our website: www.spoken-tutorial.org
For installation on Windows, Mac OS and Android devices, please visit: www.jmol.sourceforge.net
and follow the instructions given on the web page to install.
I have already installed Jmol Application on my system using Ubuntu Software Center.
To open the Jmol Application, click on Dash home.
Type Jmol in the search box.
Jmol icon appears on the screen.
Click on the Jmol icon to open the Jmol Application window.
Jmol Application window has a Menu bar at the top.
Below the Menu bar, there is a Tool bar.
Here is the Display area which is referred to as Jmol panel.
In the menu bar, there are various options like- File, Edit, Display etc.
Each of these have various sub-options as well.
Tools menu has tools to measure distances between atoms, apart from other options.
We will learn about these options in subsequent tutorials.
Help menu has a lot of useful information about Jmol Application.
It also has a User Guide which contains the documentation.
Tool bar has a number of menu icons.
The menu icons execute certain functions quickly; for e.g.- Open, Save, Export, Print etc.
Here is a set of icons- to rotate, select a set of atoms, measure distances etc.
“ modelkit” icon is used to create and edit molecular models.
The Jmol panel can be resized according to our requirement.
Take the cursor to any corner of the window till it changes to an arrow indicator.
Now, resize the window by dragging diagonally upwards or downwards.
Display menu in the Menu bar can also be used to change the size of the panel.
Click on Display menu and select Resize option.
A dialog-box opens where we can specify the width and height dimensions, in pixels.
I need a window of size 800 by 600 pixels.
So, I will type 800 space 600 and click on the OK button.
Now the Jmol panel is resized to 800 by 600 pixels.
Let's now proceed to create models of some simple organic molecules.
Modelkit allows us to build and modify models with energy minimization.
Click on the “modelkit” icon in the tool bar.
A model of Methane appears on the panel.
A menu appears on the top-left corner of the Jmol panel.
Features of this menu include ability to * Easily add, delete, drag atoms
Add functional groups
Delete, add and rotate bonds
add hydrogens, minimize and save files etc.
To use a particular feature on the menu, click on the check-box provided.
The Modelkit function allows us to substitute a hydrogen atom with a Methyl group.
Bring the cursor to the hydrogen atom, you want to substitute.
A red ring appears on that hydrogen atom.
Click on the atom.
You will notice that a Methyl group has been added.
Methane molecule is now converted to Ethane.
Repeat the same step as before.
Click on the hydrogen atom to get a model of Propane.
Energy minimization on this molecule will give us the most stable conformation.
To do Energy minimization-
Scroll down the options in the Modelkit menu.
Click on the option minimize.
We now have the model of the most stable conformation of Propane molecule.
To save this structure as a '.mol' file, open the Modelkit menu.
Scroll down the menu and click on save file option.
A Save dialog-box appears on the screen.
Click on the folder where you want to save your file.
I am choosing Desktop as the location for saving my file.
So, select Desktop and click on the Open button.
Go to the File Name and type propane in the text-box.
Click on Files of Type and select MOL option.
Now, click on the Save button at the bottom right of the dialog-box.
3D model of Propane will be saved as '.mol' file on the Desktop.
To exit Jmol: click on the File menu and select Exit option to exit the program.
Let's summarize.In this tutorial, we learnt :
About Jmol Application window.
To resize the Jmol panel.
To use the Modelkit function in the Tool bar to create 3D models of simple organic molecules like Methane, Ethane and Propane.
Build molecule by substitution of hydrogen with methyl group.
Energy minimization to get a stable conformation.
And save the image as .mol file.
Using the Jmol Modelkit function, make models of the following molecules:
2-4 Dimethyl Pentane and 3-Ethyl, 5-Methyl Heptane.
Minimize the energy to get a stable conformation.
Save the image as .mol file.
Rotate the model using the rotate molecule in the tool bar.
Your completed assignment should look as follows.
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