View source for Jmol-Application/C2/Create-and-edit-molecular-models/English-timed

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

'''Author: Snehalatha Kaliappan'''

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

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|'''Time'''
|'''Narration'''

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|00:01
| Hello everyone.
Welcome to this tutorial on '''Create and Edit molecular models in''' '''Jmol Application.'''

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| 00:09
| In this tutorial, we will learn to,

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| 00:12
| * Substitute '''hydrogen '''atom in a molecular model with a functional group.

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| 00:17
| * Add and delete bonds.

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| 00:20
| * Add and delete atoms.

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| 00:23
| * and learn how to use the Pop-up menu also known as contextual menu. 

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| 00:29
| To follow this tutorial you should be familiar with,

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| 00:32
| * '''Jmol Application '''window and

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| 00:36
| * '''Modelkit''' function that is used to create molecular models

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| 00:41
| For relevant tutorials, please visit our website. 

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| 00:46
| To record this tutorial, I am using

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|00:49 
| * '''Ubuntu '''OS version. 12.04

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| 00:53
| * '''Jmol''' version 12.2.2

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| 00:57
| * And '''Java '''version 7.

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| 01:00
| To open the '''Jmol Application''', click on '''Dash home'''. 

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|01:05
| Type '''Jmol''' in the search box.

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| 01:08
| '''Jmol''' icon appears on the screen

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| 01:11
| Click on the '''Jmol''' icon to open the Jmol application window.

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| 01:17
| Let's begin with the model of '''Propane, '''which we had created earlier'''.'''

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| 01:22
| To open the file, click on '''“Open file”''' icon on the tool bar.

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| 01:27
|A dialog box appears on the screen.

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| 01:30
| Click on the folder where the required file is located.

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| 01:34
| My file is located on the '''Desktop'''.

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| 01:37
| So, I will select '''Desktop''' and click on the '''Open''' button.

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| 01:43
| Type the file name in the '''“File or URL” text box.'''

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| 01:48
| Then, click on the '''Open '''button.

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| 01:51
| The Model of '''Propane''' appears on screen.

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| 01:55
| We can substitute '''hydrogens''' in the '''Propane''' with functional groups like:

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| 01:59
| '''hydroxy, amino, halogens '''like''' fluro, chloro, bromo''' and others.

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| 02:07
| I want to add a '''hydroxy''' group to the '''Propane''' molecule, to convert it to '''Propanol'''.

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| 02:13
| Open the '''model kit '''menu. A list of functional groups is available here.

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| 02:20
| Check the box against '''oxygen '''atom.

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| 02:23
| Click on the '''hydrogen '''atom attached to the first carbon atom.

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| 02:28
| Observe that the '''hydrogen '''atom is replaced by '''hydroxy '''group. '''Oxygen atom''' is seen in red color here.

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| 02:37
| '''Propane '''is now converted to '''1-Propanol. '''

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| 02:41
| Let's now try to convert 1-'''Propanol '''to '''2-chloro-1-propanol.'''

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| 02:47
| Select '''Chloro''' group from the '''model kit '''menu.

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|02:51
| Click on the '''hydrogen '''atom attached to the second '''carbon '''atom. 

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| 02:57
| We now have the model of''' 2-chloro-1-propanol'''. '''Chlorine '''is seen in green color here.

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|03:04 
| You can do energy minimization and save the image as '''dot mol '''file.

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| 03:10
| Here is an assignment.

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| 03:11
| * Create models of the following molecules.'''3-bromo-1-butanol '''and '''2-amino-4-chloro-pentane'''

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| 03:20
| * Do energy minimization and save the image in JPEG format.

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| 03:25
| To save the image in different file formats:

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| 03:28
| Use “Save current view as an image” icon in the Tool bar.

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| 03:33
| Your completed assignment should look as follows

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| 03:40
| Now lets go back to the Jmol Application window.

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| 03:45
| '''Jmol Application '''also offers a '''Pop-up '''menu.

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| 03:50
| You can access the '''pop-up '''menu''' '''by two different methods.

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| 03:55
| Exit the '''model kit '''menu, if it is open. 

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| 03:59
| Scroll down the '''model kit''' menu and click '''“exit model kit mode”.'''

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| 04:04
| To open the '''Pop-up '''menu, right-click the mouse button on the panel. 

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| 04:09
| '''Pop-up '''menu appears on the panel.

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| 04:12
| '''Pop-up '''menu offers many functions to modify the display of atoms.

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| 04:18
| It has a variety of selection and rendering options.

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| 04:22
| Most of the functions in this menu are duplicated in the menu bar.

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| 04:28
| The items in the '''Pop-up '''menu are self-explanatory.

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| 04:32
| They don't need a detailed description.

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| 04:35
| Click on the '''Jmol '''panel to exit the '''Pop-up '''menu.

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| 04:39
| The second way to access the '''Pop-up '''menu is to click on the '''Jmol '''logo.

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| 04:44
| It is located at the bottom right corner of the '''Jmol '''panel. 

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| 04:49
| Now let's see how to edit this molecule and convert it to '''Ethane '''molecule.

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| 04:55
| For this, we will delete the '''hydroxy '''group, the '''chlorine''' group, the '''carbon''' and two '''hydrogen''' atoms. 

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| 05:05
| Open the '''model kit '''menu.

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| 05:08
|Check the box against '''“delete atom”. '''

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| 05:12
| Click on the atoms you want to delete. 

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| 05:15
| '''Oxygen, chlorine '''and the '''carbon '''atom.

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| 05:21
|We have to add '''hydrogens '''to this molecule to create an '''ethane''' molecule.

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|05:26
| Click on '''“add hydrogens”''' option from the '''model kit''' menu.

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| 05:32
| Two '''hydrogen '''atoms are added to the molecule.

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| 05:36
| We now have the model of '''Ethane '''on the screen.

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| 05:40
| Let's learn how to create '''alkenes '''and '''alkynes'''. 

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| 05:45
| To introduce a double bond in the molecule, open the '''model kit''' menu.

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| 05:50
| Check against “'''double'''” option.

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| 05:53
| Place the cursor on the bond between two carbon atoms in the '''Ethane''' molecule.

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| 05:58
| Red colored rings appear around the '''carbon''' atoms. 

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| 06:01
| Click on the bond.

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| 06:05
| Observe that the single bond is converted to a double bond.

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| 06:09
| We have a model of '''Ethene''' on the panel.

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| 06:13
| Now lets convert Ethene to Ethyne, 

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| 06:16
| Click on the '''modelkit '''menu and check against “'''triple'''” option. 

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| 06:21
| Place the cursor on the double bond in the '''Ethene''' molecule and click on it.

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| 06:28
| The double bond is converted to a triple bond.

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| 06:31
| This is the model of '''Ethyne.'''

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|  06:34
| Do the energy minimization to get the most stable conformation and save. 

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| 06:40
| Let's summarize.

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| 06:41
| In this tutorial we have learnt to

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| 06:43
| * Substitute the '''hydrogen''' atom in '''alkanes''' with a functional group.

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| 06:48
| * Add bonds to convert '''alkanes''' to '''alkenes''' and '''alkynes'''

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| 06:52
| * Add and delete atoms and

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| 06:54
| * Use the Pop-up-menu.

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| 06:58
| For the Assignment

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| 06:59
| # Create the models of  '''2-fluoro-1,3-butadiene '''and''' 2-pentyne.'''

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| 07:06
| # '''Use the Pop-up '''menu to change the display of the model to wireframe.

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| 07:10
| # Do energy minimization and save the image in '''PDF '''format.

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| 07:16
| Your completed assignment should look as follows

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| 07:24
| Watch the video available at this URL.
 [http://spoken-tutorial.org/What http://spoken-tutorial.org/What]_is_a_Spoken_ Tutorial

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| 07:27
| It summarizes the Spoken Tutorial project

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| 07:31
| If you do not have good bandwidth, you can download and watch it 

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| 07:36
| The Spoken Tutorial Project Team: 

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| 07:38
| Conducts workshops using spoken tutorials

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| 07:41
| Gives certificates to those who pass an on-line test 

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| 07:45
| For more details, please write to contact@spoken-tutorial.org 

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| 07:52
| Spoken Tutorial Project is a part of the Talk to a Teacher project 

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| 07:57
| It is supported by the National Mission on Education through ICT, MHRD, Government of India

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| 08:04
| More information on this Mission is available at the following  link [http://spoken-tutorial.org/NMEICT-Intro http://spoken-tutorial.org/NMEICT-Intro] ] 

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| 08:08
| This is Snehalatha from IIT Bombay signing off. Thank you for joining. 

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