Difference between revisions of "Jmol-Application/C2/Create-and-edit-molecular-models/English-timed"

From Script | Spoken-Tutorial
Jump to: navigation, search
 
(2 intermediate revisions by 2 users not shown)
Line 1: Line 1:
−
'''Title of script''': '''Create and Edit Molecular models '''
 
−
 
−
'''Author: Snehalatha Kaliappan'''
 
−
 
−
'''Keyword: 3D models of chemical structures, molecular visualization, video tutorial.'''
 
−
 
 
{| border =1
 
{| border =1
 
|'''Time'''
 
|'''Time'''
Line 11: Line 5:
 
|-
 
|-
 
|00:01
 
|00:01
−
| Hello everyone.
+
|Hello everyone.Welcome to this tutorial on '''Create and Edit molecular models''' in '''Jmol Application.'''
−
Welcome to this tutorial on '''Create and Edit molecular models''' in '''Jmol Application.'''
+
  
 
|-
 
|-
−
| 00:09
+
|00:09
−
| In this tutorial, we will learn to:
+
|In this tutorial, we will learn to:
  
 
|-
 
|-
−
| 00:12
+
|00:12
−
| * Substitute '''hydrogen '''atom in a molecular model with a '''functional group'''
+
|Substitute '''hydrogen '''atom in a molecular model with a '''functional group'''.
  
 
|-
 
|-
−
| 00:17
+
|00:17
−
| * Add and delete '''bond'''s
+
|Add and delete '''bonds'''
  
 
|-
 
|-
−
| 00:20
+
|00:20
−
| * Add and delete atoms and
+
|Add and delete atoms and
  
 
|-
 
|-
−
| 00:23
+
|00:23
−
| * learn how to use the '''Pop-up menu''', also known as contextual menu.  
+
|learn how to use the '''Pop-up menu''', also known as contextual menu.  
  
 
|-
 
|-
−
| 00:29
+
|00:29
−
| To follow this tutorial, you should be familiar with-
+
|To follow this tutorial, you should be familiar with-
  
 
|-
 
|-
−
| 00:32
+
|00:32
−
| * '''Jmol Application '''window and
+
|'''Jmol Application '''window and
  
 
|-
 
|-
−
| 00:36
+
|00:36
−
| * '''Modelkit''' function that is used to create molecular models.
+
|'''Modelkit''' function that is used to create molecular models.
  
 
|-
 
|-
−
| 00:41
+
|00:41
−
| For relevant tutorials, please visit our website.  
+
|For relevant tutorials, please visit our website.  
  
 
|-
 
|-
−
| 00:46
+
|00:46
−
| To record this tutorial, I am using:
+
|To record this tutorial, I am using:
  
 
|-
 
|-
 
|00:49  
 
|00:49  
−
| * '''Ubuntu '''OS version '''12.04'''
+
|'''Ubuntu '''OS version '''12.04'''
  
 
|-
 
|-
−
| 00:53
+
|00:53
−
| * '''Jmol''' version '''12.2.2'''
+
|'''Jmol''' version '''12.2.2'''
  
 
|-
 
|-
−
| 00:57
+
|00:57
−
| * And '''Java '''version '''7'''.
+
|And '''Java '''version '''7'''.
  
 
|-
 
|-
−
| 01:00
+
|01:00
−
| To open the '''Jmol Application''', click on '''Dash home'''.  
+
|To open the '''Jmol Application''', click on '''Dash home'''.  
  
 
|-
 
|-
 
|01:05
 
|01:05
−
| Type '''Jmol''' in the '''search box'''.
+
|Type '''Jmol''' in the '''search box'''.
  
 
|-
 
|-
−
| 01:08
+
|01:08
−
| '''Jmol''' icon appears on the '''screen'''.
+
|'''Jmol''' icon appears on the '''screen'''.
  
 
|-
 
|-
−
| 01:11
+
|01:11
−
| Click on the '''Jmol''' icon to open the '''Jmol application window'''.
+
|Click on the '''Jmol''' icon to open the '''Jmol application window'''.
  
 
|-
 
|-
−
| 01:17
+
|01:17
−
| Let's begin with the model of '''Propane '''which we had created earlier.
+
|Let's begin with the model of '''Propane '''which we had created earlier.
  
 
|-
 
|-
−
| 01:22
+
|01:22
−
| To open the file, click on '''“Open file”''' icon on the tool bar.
+
|To open the file, click on '''“Open file”''' icon on the tool bar.
  
 
|-
 
|-
−
| 01:27
+
|01:27
 
|A dialog-box appears on the screen.
 
|A dialog-box appears on the screen.
  
 
|-
 
|-
−
| 01:30
+
|01:30
−
| Click on the folder where the required file is located.
+
|Click on the folder where the required file is located.
  
 
|-
 
|-
−
| 01:34
+
|01:34
−
| My file is located on the '''Desktop'''.
+
|My file is located on the '''Desktop'''.
  
 
|-
 
|-
−
| 01:37
+
|01:37
−
| So, I will select '''Desktop''' and click on the '''Open''' button.
+
|So, I will select '''Desktop''' and click on the '''Open''' button.
  
 
|-
 
|-
−
| 01:43
+
|01:43
−
| Type the file name in the '''“File or URL” text box.'''
+
|Type the file name in the '''“File or URL” text box.'''
  
 
|-
 
|-
−
| 01:48
+
|01:48
−
| Then, click on the '''Open '''button.
+
|Then, click on the '''Open '''button.
  
 
|-
 
|-
−
| 01:51
+
|01:51
−
| The Model of '''Propane''' appears on the screen.
+
|The Model of '''Propane''' appears on the screen.
  
 
|-
 
|-
−
| 01:55
+
|01:55
−
| We can substitute '''hydrogens''' in the '''Propane''' with functional groups like:
+
|We can substitute '''hydrogens''' in the '''Propane''' with functional groups like:
  
 
|-
 
|-
−
| 01:59
+
|01:59
−
| '''hydroxy, amino, halogens '''like''' fluro, chloro, bromo''' and others.
+
|'''hydroxy, amino, halogens '''like''' fluro, chloro, bromo''' and others.
  
 
|-
 
|-
−
| 02:07
+
|02:07
−
| I want to add a '''hydroxy''' group to the '''Propane''' molecule to convert it to '''Propanol'''.
+
|I want to add a '''hydroxy''' group to the '''Propane''' molecule to convert it to '''Propanol'''.
  
 
|-
 
|-
−
| 02:13
+
|02:13
−
| Open the '''model kit '''menu. A list of functional groups is available here.
+
|Open the '''model kit '''menu. A list of functional groups is available here.
  
 
|-
 
|-
−
| 02:20
+
|02:20
−
| Check the box against '''oxygen '''atom.
+
|Check the box against '''oxygen '''atom.
  
 
|-
 
|-
−
| 02:23
+
|02:23
−
| Click on the '''hydrogen '''atom attached to the first '''carbon''' atom.
+
|Click on the '''hydrogen '''atom attached to the first '''carbon''' atom.
  
 
|-
 
|-
−
| 02:28
+
|02:28
−
| Observe that the '''hydrogen '''atom is replaced by '''hydroxy '''group. '''Oxygen''' atom is seen in red color here.
+
|Observe that the '''hydrogen '''atom is replaced by '''hydroxy '''group. '''Oxygen''' atom is seen in red color here.
  
 
|-
 
|-
−
| 02:37
+
|02:37
−
| '''Propane '''is now converted to '''1-Propanol. '''
+
|'''Propane '''is now converted to '''1-Propanol. '''
  
 
|-
 
|-
−
| 02:41
+
|02:41
−
| Let's now try to convert '''1-Propanol '''to '''2-chloro-1-propanol.'''
+
|Let's now try to convert '''1-Propanol '''to '''2-chloro-1-propanol.'''
  
 
|-
 
|-
−
| 02:47
+
|02:47
−
| Select '''Chloro''' group from the '''model kit '''menu.
+
|Select '''Chloro''' group from the '''model kit '''menu.
  
 
|-
 
|-
 
|02:51
 
|02:51
−
| Click on the '''hydrogen '''atom attached to the second '''carbon '''atom.  
+
|Click on the '''hydrogen '''atom attached to the second '''carbon '''atom.  
  
 
|-
 
|-
−
| 02:57
+
|02:57
−
| We now have the model of''' 2-chloro-1-propanol'''. '''Chlorine '''is seen in green color here.
+
|We now have the model of''' 2-chloro-1-propanol'''. '''Chlorine '''is seen in green color here.
  
 
|-
 
|-
 
|03:04  
 
|03:04  
−
| You can do energy minimization and '''save''' the '''image''' as '''dot mol '''file.
+
|You can do energy minimization and '''save''' the '''image''' as '''dot mol '''file.
  
 
|-
 
|-
−
| 03:10
+
|03:10
−
| Here is an assignment-
+
|Here is an assignment-Create models of the following molecules:'''3-bromo-1-butanol '''and '''2-amino-4-chloro-pentane'''.
  
 
|-
 
|-
−
| 03:11
+
|03:20
−
| * Create models of the following molecules:
+
|Do energy minimization and '''save''' the image in '''JPEG''' format.
−
'''3-bromo-1-butanol '''and
+
−
'''2-amino-4-chloro-pentane'''.
+
  
 
|-
 
|-
−
| 03:20
+
|03:25
−
| * Do energy minimization and '''save''' the image in '''JPEG''' format.
+
|To save the image in different file formats,
  
 
|-
 
|-
−
| 03:25
+
|03:28
−
| To save the image in different file formats,
+
|use “Save current view as an image” icon in the Tool bar.
  
 
|-
 
|-
−
| 03:28
+
|03:33
−
| use “Save current view as an image” icon in the Tool bar.
+
|Your completed assignment should look as follows.
  
 
|-
 
|-
−
| 03:33
+
|03:40
−
| Your completed assignment should look as follows.
+
|Now, let's go back to the '''Jmol Application''' window.
  
 
|-
 
|-
−
| 03:40
+
|03:45
−
| Now, let's go back to the '''Jmol Application''' window.
+
|'''Jmol Application '''also offers a '''Pop-up '''menu.
  
 
|-
 
|-
−
| 03:45
+
|03:50
−
| '''Jmol Application '''also offers a '''Pop-up '''menu.
+
|You can access the pop-up menu by two different methods.
  
 
|-
 
|-
−
| 03:50
+
|03:55
−
| You can access the pop-up menu by two different methods.
+
|Exit the '''model kit '''menu, if it is open.  
  
 
|-
 
|-
−
| 03:55
+
|03:59
−
| Exit the '''model kit '''menu, if it is open.  
+
|Scroll down the '''model kit''' menu and click '''“Exit model kit mode”.'''
  
 
|-
 
|-
−
| 03:59
+
|04:04
−
| 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.
  
 
|-
 
|-
−
| 04:04
+
|04:09
−
| To open the '''Pop-up '''menu, right-click the '''mouse''' button on the panel.  
+
|'''Pop-up '''menu appears on the panel.
  
 
|-
 
|-
−
| 04:09
+
|04:12
−
| '''Pop-up '''menu appears on the panel.
+
|'''Pop-up '''menu offers many functions to modify the display of atoms.
  
 
|-
 
|-
−
| 04:12
+
|04:18
−
| '''Pop-up '''menu offers many functions to modify the display of atoms.
+
|It has a variety of selection and rendering options.
  
 
|-
 
|-
−
| 04:18
+
|04:22
−
| It has a variety of selection and rendering options.
+
|Most of the functions in this menu are duplicated in the menu bar.
  
 
|-
 
|-
−
| 04:22
+
|04:28
−
| Most of the functions in this menu are duplicated in the menu bar.
+
|The items in the '''Pop-up '''menu are self-explanatory.
  
 
|-
 
|-
−
| 04:28
+
|04:32
−
| The items in the '''Pop-up '''menu are self-explanatory.
+
|They don't need a detailed description.
  
 
|-
 
|-
−
| 04:32
+
|04:35
−
| They don't need a detailed description.
+
|Click on the '''Jmol '''panel to exit the '''Pop-up '''menu.
  
 
|-
 
|-
−
| 04:35
+
|04:39
−
| Click on the '''Jmol '''panel to exit the '''Pop-up '''menu.
+
|The second way to access the '''Pop-up '''menu is to click on the '''Jmol '''logo.
  
 
|-
 
|-
−
| 04:39
+
|04:44
−
| 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.  
  
 
|-
 
|-
−
| 04:44
+
|04:49
−
| It is located at the bottom right corner of the '''Jmol '''panel.  
+
|Now, let's see how to '''edit''' this molecule and convert it to '''Ethane '''molecule.
  
 
|-
 
|-
−
| 04:49
+
|04:55
−
| Now, let's see how to '''edit''' this molecule and convert it to '''Ethane '''molecule.
+
|For this, we will delete the '''hydroxy '''group, the '''chlorine''' group, the '''carbon''' and two '''hydrogen''' atoms.  
  
 
|-
 
|-
−
| 04:55
+
|05:05
−
| For this, we will delete the '''hydroxy '''group, the '''chlorine''' group, the '''carbon''' and two '''hydrogen''' atoms.  
+
|Open the '''model kit '''menu.
  
 
|-
 
|-
−
| 05:05
+
|05:08
−
| Open the '''model kit '''menu.
+
−
 
+
−
|-
+
−
| 05:08
+
 
|Check the box against '''“delete atom”. '''
 
|Check the box against '''“delete atom”. '''
  
 
|-
 
|-
−
| 05:12
+
|05:12
−
| Click on the atoms you want to delete-  
+
|Click on the atoms you want to delete-  
  
 
|-
 
|-
−
| 05:15
+
|05:15
−
| '''Oxygen, chlorine '''and the '''carbon '''atom.
+
|'''Oxygen, chlorine '''and the '''carbon '''atom.
  
 
|-
 
|-
−
| 05:21
+
|05:21
 
|We have to add '''hydrogens '''to this molecule, to create an '''ethane''' molecule.
 
|We have to add '''hydrogens '''to this molecule, to create an '''ethane''' molecule.
  
 
|-
 
|-
 
|05:26
 
|05:26
−
| Click on '''“add hydrogens”''' option from the '''model kit''' menu.
+
|Click on '''“add hydrogens”''' option from the '''model kit''' menu.
  
 
|-
 
|-
−
| 05:32
+
|05:32
−
| Two '''hydrogen '''atoms are added to the molecule.
+
|Two '''hydrogen '''atoms are added to the molecule.
  
 
|-
 
|-
−
| 05:36
+
|05:36
−
| We now have the model of '''Ethane '''on the '''screen'''.
+
|We now have the model of '''Ethane '''on the '''screen'''.
  
 
|-
 
|-
−
| 05:40
+
|05:40
−
| Let's learn how to create '''alkenes '''and '''alkynes'''.  
+
|Let's learn how to create '''alkenes '''and '''alkynes'''.  
  
 
|-
 
|-
−
| 05:45
+
|05:45
−
| To introduce a double-bond in the molecule, open the '''model kit''' menu.
+
|To introduce a double-bond in the molecule, open the '''model kit''' menu.
  
 
|-
 
|-
−
| 05:50
+
|05:50
−
| Check against “'''double'''” option.
+
|Check against “'''double'''” option.
  
 
|-
 
|-
−
| 05:53
+
|05:53
−
| Place the cursor on the bond between two carbon atoms in the '''Ethane''' molecule.
+
|Place the cursor on the bond between two carbon atoms in the '''Ethane''' molecule.
  
 
|-
 
|-
−
| 05:58
+
|05:58
−
| Red colored rings appear around the '''carbon''' atoms.  
+
|Red colored rings appear around the '''carbon''' atoms.  
  
 
|-
 
|-
−
| 06:01
+
|06:01
−
| Click on the '''bond'''.
+
|Click on the '''bond'''.
  
 
|-
 
|-
−
| 06:05
+
|06:05
−
| Observe that the single-bond is converted to a double-bond.
+
|Observe that the single-bond is converted to a double-bond.
  
 
|-
 
|-
−
| 06:09
+
|06:09
−
| We have a model of '''Ethene''' on the panel.
+
|We have a model of '''Ethene''' on the panel.
  
 
|-
 
|-
−
| 06:13
+
|06:13
−
| Now, let's convert Ethene to Ethyne.  
+
|Now, let's convert Ethene to Ethyne.  
  
 
|-
 
|-
−
| 06:16
+
|06:16
−
| Click on the '''modelkit '''menu and check against “'''triple'''” option.  
+
|Click on the '''modelkit '''menu and check against “'''triple'''” option.  
  
 
|-
 
|-
−
| 06:21
+
|06:21
−
| Place the cursor on the double-bond in the '''Ethene''' molecule and click on it.
+
|Place the cursor on the double-bond in the '''Ethene''' molecule and click on it.
  
 
|-
 
|-
−
| 06:28
+
|06:28
−
| The '''double-bond''' is converted to a '''triple-bond'''.
+
|The '''double-bond''' is converted to a '''triple-bond'''.
  
 
|-
 
|-
−
| 06:31
+
|06:31
−
| This is the model of '''Ethyne.'''
+
|This is the model of '''Ethyne.'''
  
 
|-
 
|-
−
| 06:34
+
|06:34
−
| Do the energy minimization to get the most stable conformation and '''save'''.  
+
|Do the energy minimization to get the most stable conformation and '''save'''.  
  
 
|-
 
|-
−
| 06:40
+
|06:40
−
| Let's summarize.
+
|Let's summarize.In this tutorial, we have learnt to:
  
 
|-
 
|-
−
| 06:41
+
|06:43
−
| In this tutorial, we have learnt to:
+
|Substitute the '''hydrogen''' atom in '''alkanes''' with a functional group.
  
 
|-
 
|-
−
| 06:43
+
|06:48
−
| * Substitute the '''hydrogen''' atom in '''alkanes''' with a functional group.
+
|Add '''bond'''s to convert '''alkanes''' to '''alkenes''' and '''alkynes'''
  
 
|-
 
|-
−
| 06:48
+
|06:52
−
| * Add '''bond'''s to convert '''alkanes''' to '''alkenes''' and '''alkynes'''
+
|Add and delete atoms and
  
 
|-
 
|-
−
| 06:52
+
|06:54
−
| * Add and delete atoms and
+
|Use the Pop-up-menu.
  
 
|-
 
|-
−
| 06:54
+
|06:58
−
| * Use the Pop-up-menu.
+
|For the Assignment-Create the models of  '''2-fluoro-1,3-butadiene '''and''' 2-pentyne.'''
  
 
|-
 
|-
−
| 06:58
+
|07:06
−
| For the Assignment-
+
|Use the Pop-up menu to change the display of the model to '''wireframe'''.
  
 
|-
 
|-
−
| 06:59
+
|07:10
−
| # Create the models of  '''2-fluoro-1,3-butadiene '''and''' 2-pentyne.'''
+
|Do energy minimization and '''save''' the image in '''PDF '''format.
  
 
|-
 
|-
−
| 07:06
+
|07:16
−
| # Use the Pop-up menu to change the display of the model to '''wireframe'''.
+
|Your completed assignment should look as follows.
  
 
|-
 
|-
−
| 07:10
+
|07:24
−
| # Do energy minimization and '''save''' the image in '''PDF '''format.
+
|Watch the video available at this URL:http://spoken-tutorial.org/What_is_a_Spoken_Tutorial
  
 
|-
 
|-
−
| 07:16
+
|07:27
−
| Your completed assignment should look as follows.
+
|It summarizes the '''Spoken Tutorial''' project.
  
 
|-
 
|-
−
| 07:24
+
|07:31
−
| Watch the video available at this URL:
+
|If you do not have good bandwidth, you can download and watch it.  
−
http://spoken-tutorial.org/What_is_a_Spoken_Tutorial
+
  
 
|-
 
|-
−
| 07:27
+
|07:36
−
| It summarizes the '''Spoken Tutorial''' project.
+
|The Spoken Tutorial Project team:
  
 
|-
 
|-
−
| 07:31
+
|07:38
−
| If you do not have good bandwidth, you can download and watch it.  
+
|Conducts workshops using spoken tutorials.
  
 
|-
 
|-
−
| 07:36
+
|07:41
−
| The Spoken Tutorial Project team:
+
|Gives certificates to those who pass an on-line test.
  
 
|-
 
|-
−
| 07:38
+
|07:45
−
|* Conducts workshops using spoken tutorials.
+
|For more details, please write to: '''contact@spoken-tutorial.org'''
  
 
|-
 
|-
−
| 07:41
+
|07:52
−
|* Gives certificates to those who pass an on-line test.  
+
|'''Spoken Tutorial''' project is a part of the '''Talk to a Teacher''' project.  
  
 
|-
 
|-
−
| 07:45
+
|07:57
−
| For more details, please write to: '''contact@spoken-tutorial.org'''
+
|It is supported by the National Mission on Education through ICT, MHRD, Government of India.
  
 
|-
 
|-
−
| 07:52
+
|08:04
−
| '''Spoken Tutorial''' project is a part of the '''Talk to a Teacher''' project.  
+
|More information on this mission is available at the following link: http://spoken-tutorial.org/NMEICT-Intro
  
 
|-
 
|-
−
| 07:57
+
|08:08
−
| It is supported by the National Mission on Education through ICT, MHRD, Government of India.
+
|This is Snehalatha from IIT Bombay, signing off. Thank you for joining.  
−
 
+
−
|-
+
−
| 08:04
+
−
| More information on this mission is available at the following link: http://spoken-tutorial.org/NMEICT-Intro
+
−
 
+
−
|-
+
−
| 08:08
+
−
| This is Snehalatha from IIT Bombay, signing off. Thank you for joining.  
+
−
 
+
 
|}
 
|}

Latest revision as of 15:56, 28 March 2017

Time Narration
00:01 Hello everyone.Welcome to this tutorial on Create and Edit molecular models in Jmol Application.
00:09 In this tutorial, we will learn to:
00:12 Substitute hydrogen atom in a molecular model with a functional group.
00:17 Add and delete bonds
00:20 Add and delete atoms and
00:23 learn how to use the Pop-up menu, also known as contextual menu.
00:29 To follow this tutorial, you should be familiar with-
00:32 Jmol Application window and
00:36 Modelkit function that is used to create molecular models.
00:41 For relevant tutorials, please visit our website.
00:46 To record this tutorial, I am using:
00:49 Ubuntu OS version 12.04
00:53 Jmol version 12.2.2
00:57 And Java version 7.
01:00 To open the Jmol Application, click on Dash home.
01:05 Type Jmol in the search box.
01:08 Jmol icon appears on the screen.
01:11 Click on the Jmol icon to open the Jmol application window.
01:17 Let's begin with the model of Propane which we had created earlier.
01:22 To open the file, click on “Open file” icon on the tool bar.
01:27 A dialog-box appears on the screen.
01:30 Click on the folder where the required file is located.
01:34 My file is located on the Desktop.
01:37 So, I will select Desktop and click on the Open button.
01:43 Type the file name in the “File or URL” text box.
01:48 Then, click on the Open button.
01:51 The Model of Propane appears on the screen.
01:55 We can substitute hydrogens in the Propane with functional groups like:
01:59 hydroxy, amino, halogens like fluro, chloro, bromo and others.
02:07 I want to add a hydroxy group to the Propane molecule to convert it to Propanol.
02:13 Open the model kit menu. A list of functional groups is available here.
02:20 Check the box against oxygen atom.
02:23 Click on the hydrogen atom attached to the first carbon atom.
02:28 Observe that the hydrogen atom is replaced by hydroxy group. Oxygen atom is seen in red color here.
02:37 Propane is now converted to 1-Propanol.
02:41 Let's now try to convert 1-Propanol to 2-chloro-1-propanol.
02:47 Select Chloro group from the model kit menu.
02:51 Click on the hydrogen atom attached to the second carbon atom.
02:57 We now have the model of 2-chloro-1-propanol. Chlorine is seen in green color here.
03:04 You can do energy minimization and save the image as dot mol file.
03:10 Here is an assignment-Create models of the following molecules:3-bromo-1-butanol and 2-amino-4-chloro-pentane.
03:20 Do energy minimization and save the image in JPEG format.
03:25 To save the image in different file formats,
03:28 use “Save current view as an image” icon in the Tool bar.
03:33 Your completed assignment should look as follows.
03:40 Now, let's go back to the Jmol Application window.
03:45 Jmol Application also offers a Pop-up menu.
03:50 You can access the pop-up menu by two different methods.
03:55 Exit the model kit menu, if it is open.
03:59 Scroll down the model kit menu and click “Exit model kit mode”.
04:04 To open the Pop-up menu, right-click the mouse button on the panel.
04:09 Pop-up menu appears on the panel.
04:12 Pop-up menu offers many functions to modify the display of atoms.
04:18 It has a variety of selection and rendering options.
04:22 Most of the functions in this menu are duplicated in the menu bar.
04:28 The items in the Pop-up menu are self-explanatory.
04:32 They don't need a detailed description.
04:35 Click on the Jmol panel to exit the Pop-up menu.
04:39 The second way to access the Pop-up menu is to click on the Jmol logo.
04:44 It is located at the bottom right corner of the Jmol panel.
04:49 Now, let's see how to edit this molecule and convert it to Ethane molecule.
04:55 For this, we will delete the hydroxy group, the chlorine group, the carbon and two hydrogen atoms.
05:05 Open the model kit menu.
05:08 Check the box against “delete atom”.
05:12 Click on the atoms you want to delete-
05:15 Oxygen, chlorine and the carbon atom.
05:21 We have to add hydrogens to this molecule, to create an ethane molecule.
05:26 Click on “add hydrogens” option from the model kit menu.
05:32 Two hydrogen atoms are added to the molecule.
05:36 We now have the model of Ethane on the screen.
05:40 Let's learn how to create alkenes and alkynes.
05:45 To introduce a double-bond in the molecule, open the model kit menu.
05:50 Check against “double” option.
05:53 Place the cursor on the bond between two carbon atoms in the Ethane molecule.
05:58 Red colored rings appear around the carbon atoms.
06:01 Click on the bond.
06:05 Observe that the single-bond is converted to a double-bond.
06:09 We have a model of Ethene on the panel.
06:13 Now, let's convert Ethene to Ethyne.
06:16 Click on the modelkit menu and check against “triple” option.
06:21 Place the cursor on the double-bond in the Ethene molecule and click on it.
06:28 The double-bond is converted to a triple-bond.
06:31 This is the model of Ethyne.
06:34 Do the energy minimization to get the most stable conformation and save.
06:40 Let's summarize.In this tutorial, we have learnt to:
06:43 Substitute the hydrogen atom in alkanes with a functional group.
06:48 Add bonds to convert alkanes to alkenes and alkynes
06:52 Add and delete atoms and
06:54 Use the Pop-up-menu.
06:58 For the Assignment-Create the models of 2-fluoro-1,3-butadiene and 2-pentyne.
07:06 Use the Pop-up menu to change the display of the model to wireframe.
07:10 Do energy minimization and save the image in PDF format.
07:16 Your completed assignment should look as follows.
07:24 Watch the video available at this URL:http://spoken-tutorial.org/What_is_a_Spoken_Tutorial
07:27 It summarizes the Spoken Tutorial project.
07:31 If you do not have good bandwidth, you can download and watch it.
07:36 The Spoken Tutorial Project team:
07:38 Conducts workshops using spoken tutorials.
07:41 Gives certificates to those who pass an on-line test.
07:45 For more details, please write to: contact@spoken-tutorial.org
07:52 Spoken Tutorial project is a part of the Talk to a Teacher project.
07:57 It is supported by the National Mission on Education through ICT, MHRD, Government of India.
08:04 More information on this mission is available at the following link: http://spoken-tutorial.org/NMEICT-Intro
08:08 This is Snehalatha from IIT Bombay, signing off. Thank you for joining.

Contributors and Content Editors

PoojaMoolya, Pratik kamble, Sandhya.np14

Retrieved from "https://script.spoken-tutorial.org/index.php?title=Jmol-Application/C2/Create-and-edit-molecular-models/English-timed&oldid=34526"