Difference between revisions of "Jmol-Application/C2/Introduction-to-Jmol-Application/English"

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{| style="border-spacing:0;"
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{| style="border-spacing=1"
 
! <center>Visual Cue</center>
 
! <center>Visual Cue</center>
 
! <center>Narration</center>
 
! <center>Narration</center>
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How to:* Modify the size of '''Jmol''' panel.
+
How to:
 +
* Modify the size of '''Jmol''' panel.
 
* Create models of simple organic molecules.  
 
* Create models of simple organic molecules.  
 
* Build molecules by substituting '''hydrogen''' with a '''Methyl''' group.
 
* Build molecules by substituting '''hydrogen''' with a '''Methyl''' group.
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−
 
  
 
|-
 
|-
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'''Learning Objectives'''
 
'''Learning Objectives'''
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| We will also learn to:
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| We will also learn to:
−
 
  
 
* Minimize energy to get a stable conformation and
 
* Minimize energy to get a stable conformation and
 
* Save the image as '''.mol''' file.
 
* Save the image as '''.mol''' file.
−
 
−
 
  
 
|-
 
|-
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* High school Chemistry and  
 
* High school Chemistry and  
 
* Basic Organic Chemistry  
 
* Basic Organic Chemistry  
−
 
−
 
  
 
|-
 
|-
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'''About Jmol Application'''
 
'''About Jmol Application'''
−
 
−
 
  
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| About '''Jmol Application.'''
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| About '''Jmol Application.'''
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* Used to create and view 3 dimensional models of chemical structures. And also
 
* Used to create and view 3 dimensional models of chemical structures. And also
 
* Used to view secondary structures of '''proteins''' and '''macromolecules'''.
 
* Used to view secondary structures of '''proteins''' and '''macromolecules'''.
−
 
−
 
  
 
|-
 
|-
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|-
 
|-
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Ubuntu Desktop Screen
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Ubuntu Desktop Screen
−
 
−
 
  
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| I have already installed '''Jmol Application''' on my system using '''Ubuntu Software Center'''.
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| I have already installed '''Jmol Application''' on my system using '''Ubuntu Software Center'''.
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|-
 
|-
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on the “Open the modelkit” icon
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on the “Open the modelkit” icon
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Click on the “'''Open the modelkit” '''icon in the '''tool bar'''.
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Click on the “'''modelkit” '''icon in the '''tool bar'''.
  
 
|-
 
|-
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the methane molecule.
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the methane molecule.
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| A model of Methane appears on the panel.  
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| A model of '''Methane''' appears on the panel.  
  
 
|-
 
|-
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the modelkit menu
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the modelkit menu
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| A menu appears on the top-left corner of the Jmol panel.
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| A menu appears on the top-left corner of the '''Jmol panel'''.
  
 
|-
 
|-
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| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Features of this menu include ability to  
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Features of this menu include ability to  
  
−
* Easily add, delete ,drag atoms.
+
* Easily add, delete, drag atoms.
 
* Add functional groups.
 
* Add functional groups.
 
* Delete, add and rotate bonds.  
 
* Delete, add and rotate bonds.  
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|-
 
|-
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the Methane molecule.
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the Methane molecule.
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| The '''Modelkit''' function allows us to substitute a '''hydrogen''' '''atom''' with a '''methyl group'''.  
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| The '''Modelkit''' function allows us to substitute a '''Hydrogen''' '''atom''' with a '''Methyl group'''.  
  
 
|-
 
|-
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on Hydrogen atom of the Methane molecule
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on Hydrogen atom of the Methane molecule
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Bring the cursor to the hydrogen atom you want to substitute.
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Bring the cursor to the '''Hydrogen atom''' you want to substitute.
  
 
|-
 
|-
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on Hydrogen atom
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on Hydrogen atom
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| A '''red''' ring appears on that hydrogen atom.
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| A '''red''' ring appears on that '''Hydrogen atom'''.
  
 
Click on the atom.
 
Click on the atom.
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|-
 
|-
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the Methyl group
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the Methyl group
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| You will notice that a '''methyl''' group has been added.
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| You will notice that a '''Methyl''' group has been added.
  
 
|-
 
|-
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* About '''Jmol Application '''window.
 
* About '''Jmol Application '''window.
 
* Resize the '''Jmol panel.'''
 
* Resize the '''Jmol panel.'''
−
* Use the '''Modelkit''' function in the Tool bar to<br/> create 3D models of simple organic molecules like Methane, Ethane and Propane.  
+
* Use the '''Modelkit''' function in the Tool bar to create '''3D models''' of simple organic molecules like  
−
* Build molecules by substitution of '''hydrogen''' with '''Methyl group.'''
+
**Methane,  
 +
**Ethane and  
 +
**Propane.  
 +
* Build molecules by substitution of '''Hydrogen''' with '''Methyl group.'''
 
* Energy minimization to get a stable conformation.
 
* Energy minimization to get a stable conformation.
−
* And save the image as .mol file  
+
* And save the image as '''.mol''' file  
−
 
+
−
 
+
  
 
|-
 
|-
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−
* '''2-4 Dimethyl Pentane''' and '''3-Ethyl, 5-Methyl'''
+
* '''2-4 Dimethyl Pentane''' and '''3-Ethyl, 5-Methyl Heptane.'''
−
* '''Heptane.'''
+
 
* Minimize the energy to get a stable conformation.  
 
* Minimize the energy to get a stable conformation.  
 
* Save the image as '''.mol '''file.  
 
* Save the image as '''.mol '''file.  
−
* Rotate the model using the <br/> “rotate molecule” in tool bar  
+
* Rotate the model using '''rotate molecule''' option in the tool bar.
  
 
Your completed assignment should look as follows.
 
Your completed assignment should look as follows.

Latest revision as of 16:47, 1 September 2020

Visual Cue
Narration
Slide Number 1

Title Slide

Hello everyone.

Welcome to this tutorial on Introduction to Jmol Application.

Slide Number 2

Learning Objectives

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.
Slide Number 3

Learning Objectives

We will also learn to:
  • Minimize energy to get a stable conformation and
  • Save the image as .mol file.
Slide Number 4

Prerequisites

To follow this tutorial, you should have knowledge of
  • High school Chemistry and
  • Basic Organic Chemistry
Slide Number 5

System Requirement

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.

Slide Number 6

About Jmol Application

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.
Slide Number 7

Download and Installation

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.

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.


We will learn about these options in subsequent tutorials.

Cursor on the “Help” menu Help menu has a lot of useful information about Jmol Application.


It also has a user guide which contains the documentation.

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


Cursor on “open the modelkit” icon.

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


<Pause>

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”


Type 800 space 600>>click on OK button.

I need a window of size 800 by 600 pixels.


So I will type 800 space 600 and click on OK button.

Now the Jmol panel is resized to 800 by 600 pixels.

<Pause>

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
  • 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.

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


Click on the hydrogen atom.

Repeat the same step as before.


Click on the hydrogen atom to get a model of Propane.

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 folder where you want to save your file.

Click on the Desktop >> Open button I am choosing Desktop as the location for saving my file.


So, select Desktop and click on the Open button.

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.


<Pause>

Slide Number 8

Summary

Let's summarize.

In this tutorial we learnt :

  • About Jmol Application window.
  • Resize the Jmol panel.
  • Use the Modelkit function in the Tool bar to create 3D models of simple organic molecules like
    • Methane,
    • Ethane and
    • Propane.
  • Build molecules by substitution of Hydrogen with Methyl group.
  • Energy minimization to get a stable conformation.
  • And save the image as .mol file
Slide Number 9

Assignment

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 rotate molecule option in the tool bar.

Your completed assignment should look as follows.

Slide Number 10

Acknowledgement

Watch the video available at the following link.

http://spoken-tutorial.org/What_is_a_Spoken_ Tutorial

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

contact@spoken-tutorial.org

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.

Contributors and Content Editors

Madhurig, Nancyvarkey, Snehalathak

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