| Slide Number 1
| Hello everyone.
Welcome to this tutorial on Introduction to Jmol Application.
| Slide Number 2
| In this tutorial, I will briefly explain about:
Jmol Application window and some basic operations.
Menu Bar, Tool bar, and Jmol panel.
| Slide Number 3
| We will also learn to:
| Slide Number 4
| To follow this tutorial, you should have knowledge of
| Slide Number 5
| To record this tutorial I am using:
For Jmol Application to run smoothly, you should have Java installed on your system.
| Slide Number 6
About Jmol Application
| About Jmol Application.
| Slide Number 7
Download and Installation
| Information regarding Download and Installation
|Ubuntu Desktop Screen||I have already installed Jmol Application on my system using Ubuntu Software Center.|
|Click on “Dash Home”||To open the Jmol Application, click on Dash home.|
|Type “Jmol” in the search box.||Type Jmol in the search box.|
|Place Cursor on Jmol icon.||Jmol icon appears on the screen.|
|Click on Jmol icon.||Click on the Jmol icon to open the Jmol Application window.|
|Cursor on Top menu bar.||Jmol Application window has a menu bar at the top.|
|Cursor on tool bar||Below the Menu bar there is a Tool bar.|
| Cursor on the Display area
||Here is the Display area, which is referred to as Jmol panel.|
|Cursor on the top menu bar and point as per narration.||In the menu bar, there are various options like File, Edit, Display, etc.|
|Click on the “file” menu||Each of these have various sub-options as well.|
|Cursor on “tool” menu|| Tools menu has tools to measure distances between atoms, apart from other options.
|Cursor on the “Help” menu|| Help menu has a lot of useful information about Jmol Application.
| Cursor on the tool bar.
Move the cursor on, load, save, export and print icons of tool bar.
| Tool bar has a number of menu icons.
The menu icons execute certain functions quickly; for eg open, save, export, print etc.
| Hover the mouse on “rotate, select a set of atoms and measurements” icons
|| Here is a set of icons to rotate, select a set of atoms, measure distances, etc.
|Cursor on the Jmol panel.||The Jmol panel can be resized, according to our requirement.|
|Move the Cursor to the top-right corner.||Take the cursor to any corner of the window till it changes into an arrow indicator.|
|Drag diagonally upwards and downwards.||Now resize the window by dragging diagonally upwards or downwards.|
|Click on the display menu on the top menu bar||Display menu in the menu bar can also be used to change the size of the panel.|
|Scroll down to resize button at the bottom of the menu.||Click on Display menu and select Resize option.|
|Cursor on the “Resize window”||A dialog box opens, where we can specify the width and height dimensions, in pixels.|
| Cursor on the “Resize window”
|| I need a window of size 800 by 600 pixels.
| Now the Jmol panel is resized to 800 by 600 pixels.
| Cursor on the Jmol panel
||Let's now proceed to create models of some simple organic molecules.|
|Cursor on the “Open the modelkit” icon||Modelkit allows us to build and modify models with energy minimization.|
|Click on the “Open the modelkit” icon||Click on the “modelkit” icon in the tool bar.|
|Cursor on the methane molecule.||A model of Methane appears on the panel.|
|Cursor on the modelkit menu||A menu appears on the top-left corner of the Jmol panel.|
|Scroll down the “Modelkit” menu|| Features of this menu include ability to
To use a particular feature on the menu, click on the check box provided.
|Cursor on the Methane molecule.||The Modelkit function allows us to substitute a Hydrogen atom with a Methyl group.|
|Cursor on Hydrogen atom of the Methane molecule||Bring the cursor to the Hydrogen atom you want to substitute.|
|Click on Hydrogen atom|| A red ring appears on that Hydrogen atom.
Click on the atom.
|Cursor on the Methyl group||You will notice that a Methyl group has been added.|
|Cursor on the ethane molecule||Methane molecule is now converted to Ethane.|
| Cursor on Hydrogen atom
|| Repeat the same step as before.
|Cursor on the propane molecule||Energy minimization on this molecule will give us the most stable conformation.|
|Cursor on the “Open the Modelkit menu|| To do Energy minimization:
Scroll down the options in the Modelkit menu.
|Click on “minimize”||Click on the option minimize.|
|Cursor on the propane molecule||We now have the model of the most stable conformation of Propane molecule.|
|Cursor on Jmol panel.||To save this structure as a .mol file, open the Modelkit menu.|
| Scroll down the Modelkit menu
Click on “save file” option
|Scroll down the menu and click on save file option.|
| A Save dialog box appears on the screen.
|Click on the Desktop >> Open button|| I am choosing Desktop as the location for saving my file.
|Click on File Name >> type Propane||Go to the File Name and type Propane in the text box.|
|Click on Files of Type >> select MOL (*.mol)option.||Click on Files of Type and select MOL option.|
|Click on “save” tab||Now, click on the Save button at the bottom right of the dialog box.|
|Jmol panel||3D model of Propane will be saved as .mol file on the Desktop.|
|Click on File menu >> select Exit option|| To exit Jmol, click on File menu and select Exit option, to exit the program.
| Slide Number 8
| Let's summarize.
In this tutorial we learnt :
| Slide Number 9
| Using the Jmol Modelkit function, make models of the following molecules:
Your completed assignment should look as follows.
| Slide Number 10
| Watch the video available at the following link.
It summarizes the Spoken Tutorial project.
If you do not have good bandwidth, you can download and watch it.
|Slide Number 11|| The Spoken Tutorial Project Team:
Conducts workshops using spoken tutorials.
Gives certificates to those who pass an on-line test .
For more details, please write to
|Slide number 12|| Spoken Tutorial Project is a part of the Talk to a Teacher project
It is supported by the National Mission on Education through ICT, MHRD, Government of India
More information on this Mission is available at this link http://spoken-tutorial.org/NMEICT-Intro ]
|This is Snehalatha from IIT Bombay signing off. Thank you for joining.|