Snehalathak: Created page with ''''Title of script''': '''Create and Edit Molecular models ''' '''Author: Snehalatha Kaliappan''' '''Keyword: 3D models of chemical structures, molecular visualization, video t…'

2013-12-20T05:04:54Z

Created page with ''''Title of script''': '''Create and Edit Molecular models ''' '''Author: Snehalatha Kaliappan''' '''Keyword: 3D models of chemical structures, molecular visualization, video t…'

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'''Title of script''': '''Create and Edit Molecular models '''

'''Author: Snehalatha Kaliappan'''

'''Keyword: 3D models of chemical structures, molecular visualization, video tutorial.'''

* '''Outline:- '''
* Substitute the hydrogen in molecular model with a functional group.
* Add and delete bonds
* Add and delete atoms
* Pop-up-menu (Contextual menu)

{| style="border-spacing:0;"
! <center>Visual Cue</center>
! <center>Narration</center>

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 1'''

'''Title Slide'''
| 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;"| Hello everyone.

Welcome to this tutorial on '''Create and Edit molecular models in''' '''Jmol Application.'''

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 2'''

'''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;"| In this tutorial, we will learn to,

* Substitute '''hydrogen '''atom in a molecular model with a functional group.
* Add and delete bonds.
* Add and delete atoms.
* and learn how to use the Pop-up menu also known as contextual menu.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 3'''

'''Pr-requisites'''
| 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;"| To follow this tutorial you should be familiar with,

* '''Jmol Application '''window and
* '''Modelkit '''function that is used to create molecular models

For relevant tutorials, please visit our website.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 4'''

'''System Requirement'''
| 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;"| To record this tutorial, I am using

* '''Ubuntu '''OS version. 12.04
* '''Jmol v'''ersion 12.2.2
* And '''Java '''version 7.

|-
| 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 '''“Dash Home”'''
| 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;"| To open the '''Jmol Application, '''click on '''Dash home'''.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Type “'''Jmol'''” in the search box.
| 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;"| Type '''Jmol''' in the search box.

|-
| 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 Jmol 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;"| Jmol icon appears on the screen

|-
| 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 Jmol 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 Jmol icon to open the Jmol application window.

|-
| 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 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;"| Let's begin with the model of '''Propane, '''which we had created earlier'''.'''

|-
| 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 Jmol panel

Click on “open a file” 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;"| To open the file, click on '''“Open a file”''' icon on 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 dialog box
| 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 dialog box appears on the screen.

|-
| 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 dialog box
| 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 folder where the required file is located.

|-
| 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 “desktop”.

Click on the “open” button
| 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;"| My file is located on the '''Desktop'''.

So, I will select '''Desktop '''and click on the '''Open '''button.

|-
| 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 “propane” file
| 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;"| Type the file name in the '''“File or URL” text box.'''

Then, click on the '''Open '''button.

|-
| 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 propane 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 Model of '''Propane''' appears on screen.

|-
| 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 propane 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;"| We can substitute '''hydrogens''' in the '''Propane''' with functional groups like:

'''hydroxy, amino, halogens '''like''' fluro, chloro, bromo''' and others.

|-
| 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 Modelkit menu

Click on the check box against oxygen 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;"| I want to add a '''hydroxy''' group to the '''Propane''' molecule, to convert it to '''Propanol'''.

Open the '''model kit '''menu. A list of functional groups is available here.

Check the box against '''oxygen '''atom.

|-
| 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 >> Click on the 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;"| Click on the '''hydrogen '''atom attached to the first carbon atom.

|-
| 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 Hydroxyl group

Cursor on the propanol 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;"| Observe that the '''hydrogen '''atom is replaced by '''hydroxy '''group. '''Oxygen atom''' is seen in red color here.

'''Propane '''in now converted to '''1-Propanol. '''

|-
| 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 propanol 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;"| Let's now try to convert 1-'''Propanol '''to '''2-chloro-1-propanol.'''

|-
| 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 check box against chloro 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;"| Select '''Chloro''' group from the '''model kit '''menu.

|-
| 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;"| Click on the '''hydrogen '''atom attached to the second '''carbon '''atom.

|-
| 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 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;"| We now have the model of''' 2-chloro-1-propanol'''. '''Chlorine '''is seen in green color.

You can do energy minimization and save the image as '''dot mol '''file.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide number 5'''

'''Assignment'''
| 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;"| Here is an assignment.

* Create models of the following molecules. '''3-bromo-1-butanol '''and '''2-amino-4-chloro-pentane''' 

* Do energy minimization and save the image in JPEG format.

To save the image in different file formats:

Use “Save current view as an image” icon in the Tool bar.

Your completed assignment should look as follows

|-
| 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 Jmol panel with 2-chloro-1-propanol 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;"| Now lets go back to the Jmol Application window.

'''Jmol Application '''also offers a '''Pop-up '''menu.

You can access the '''pop-up '''menu''' '''by two different methods.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Right click the mouse button.
| 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;"| Exit the '''model kit '''menu, if it is open.

Scroll down the '''model kit''' menu and click '''“exit model kit mode”.'''

To open the '''Pop-up '''menu, right-click the mouse button on the panel.

'''Pop-up '''menu 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;"| Scroll down the Pop-up 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;"| '''Pop-up '''menu offers many functions to modify the display of atoms.

It has a variety of selection and rendering options.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Scroll down the Pop-up 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;"| Most of the functions in this menu are duplicated in the menu 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 Pop-up 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;"| The items in the '''Pop-up '''menu are self-explanatory.

They don't need a detailed description.

|-
| 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 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;"| Click on the '''Jmol '''panel to exit the '''Pop-up '''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 “Jmol” logo.

| 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 second way to access the '''Pop-up '''menu is to click on the '''Jmol '''logo.

It is located at the bottom right corner of the '''Jmol '''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 2-chloro-1-propanol 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;"| Now let's see how to edit this molecule and convert it to '''Ethane '''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 hydroxyl group, chlorine group, carbon and hydrogen atoms.
| 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;"| For this, we will delete the '''hydroxy '''group, the '''chlorine''' group, the '''carbon''' and two '''hydrogen''' atoms.

|-
| 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 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;"| Open the '''model kit '''menu.

|-
| 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 box against “delete atom”.

Click on oxygen, chlorine and carbon.
| 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;"| Check the box against '''“delete atom”. '''

Click on the atoms you want to delete.

'''Oxygen, chlorine '''and the '''carbon '''atom.

|-
| 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 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;"| We have to add '''hydrogens '''to this molecule to create an '''ethane''' molecule.

|-
| 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 “add hydrogens” option from 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;"| Click on '''“add hydrogens”''' option from the '''model kit''' 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 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;"| Two '''hydrogen '''atoms are added to the molecule.

We now have the model of '''Ethane '''on the screen.

|-
| 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 ethane 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;"| Let's learn how to create '''alkenes '''and '''alkynes'''.

|-
| 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 modelkit menu.

Click on the “double” option in 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;"| To introduce a double bond in the molecule, open the '''model kit''' menu.

Check against “'''double'''” option.

|-
| 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 bond between two carbon atoms.
| 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;"| Place the cursor on the bond between two carbon atoms in the '''Ethane''' molecule.

|-
| 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 bond.
| 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;"| Red colored rings appear around the '''carbon''' atoms.

Click on the bond.

Observe that the single bond is converted to a double bond.

We have a model of '''Ethene''' 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 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;"| Now lets convert Ethene to Ethyne,

|-
| 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 modelkit menu.

Click on “triple”

Place the cursor on the double bond.

Click on the bond.
| 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 '''menu and select “'''triple'''” option.

Place the cursor on the double bond in the '''Ethene''' molecule and click on it.

|-
| 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 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 double bond is converted to a triple bond.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Point to the model.
| 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;"| This is the model of '''Ethyne.'''

|-
| 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 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;"| Do the energy minimization to get the most stable conformation and save.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 6'''

Summary
| 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;"| Let's summarize.

In this tutorial we have learnt to

* Substitute the '''hydrogen''' atom in '''alkanes''' with a functional group. 

* Add bonds to convert '''alkanes''' to '''alkenes''' and '''alkynes''' 

* Add and delete atoms and 

* Use the Pop-up-menu.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 7'''

Assignment
| 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;"| For the Assignment

# Create the models of '''2-fluoro-1,3-butadiene '''and''' 2-pentyne.''' 

# '''Use the Pop-up '''menu to change the display of the model to wireframe.

# Do energy minimization and save the image in '''PDF '''format.

Your completed assignment should look as follows

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 8'''

'''Acknowledgement '''
| 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;"| Watch the video available at this URL.

[http://spoken-tutorial.org/What 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

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 9'''

'''Acknowledgement '''
| 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 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

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide number 10'''

'''Acknowledgement '''
| 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;"| 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 http://spoken-tutorial.org/NMEICT-Intro] ]

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"|
| 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;"| This is Snehalatha from IIT Bombay signing off. Thank you for joining.

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-Create the models of '''2-fluoro-1,3-butadiene '''and''' 2-pentyne.'''
+* Create the models of '''2-fluoro-1,3-butadiene '''and''' 2-pentyne.'''
-Use the '''Pop-up''' menu to change the display of the model to wireframe.
+* Use the '''Pop-up''' menu to change the display of the model to '''wireframe'''.
-Do energy minimization and save the image in '''PDF '''format.
+* Do energy minimization and save the image in '''PDF''' format.
 Your completed assignment should look as follows

Jmol-Application/C2/Create-and-edit-molecular-models/English - Revision history

Madhurig at 13:04, 19 March 2025

Snehalathak at 11:28, 17 September 2019

Snehalathak at 11:26, 17 September 2019

Snehalathak: Created page with ''''Title of script''': '''Create and Edit Molecular models ''' '''Author: Snehalatha Kaliappan''' '''Keyword: 3D models of chemical structures, molecular visualization, video t…'