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

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|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
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| In this tutorial, we will learn to,
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| In this tutorial, we will learn to:
  
 
|-
 
|-
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|-
 
|-
 
| 00:29
 
| 00:29
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| To follow this tutorial you should be familiar with,
+
| To follow this tutorial, you should be familiar with-
  
 
|-
 
|-
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|-
 
|-
 
| 00:36
 
| 00:36
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| * '''Modelkit''' function that is used to create molecular models
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| * '''Modelkit''' function that is used to create molecular models.
  
 
|-
 
|-
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|-
 
|-
 
| 00:46
 
| 00:46
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| To record this tutorial, I am using
+
| To record this tutorial, I am using:
  
 
|-
 
|-
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|-
 
|-
 
| 01:08
 
| 01:08
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| '''Jmol''' icon appears on the screen
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| '''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
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| 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.
  
 
|-
 
|-
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|-
 
|-
 
| 01:27
 
| 01:27
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|A dialog box appears on the screen.
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|A '''dialog box''' appears on the screen.
  
 
|-
 
|-
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|-
 
|-
 
| 01:51
 
| 01:51
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| The Model of '''Propane''' appears on screen.
+
| The Model of '''Propane''' appears on the screen.
  
 
|-
 
|-
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|-
 
|-
 
| 02:07
 
| 02:07
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| I want to add a '''hydroxy''' group to the '''Propane''' molecule, to convert it to '''Propanol'''.
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| I want to add a '''hydroxy''' group to the '''Propane''' molecule to convert it to '''Propanol'''.
  
 
|-
 
|-
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|-
 
|-
 
| 02:28
 
| 02:28
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| 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.
  
 
|-
 
|-
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|-
 
|-
 
|03:04  
 
|03:04  
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| 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-
  
 
|-
 
|-
 
| 03:11
 
| 03:11
−
| * Create models of the following molecules.'''3-bromo-1-butanol '''and '''2-amino-4-chloro-pentane'''
+
| * Create models of the following molecules.'''3-bromo-1-butanol '''and '''2-amino-4-chloro-pentane'''.
  
 
|-
 
|-
 
| 03:20
 
| 03:20
−
| * Do energy minimization and save the image in JPEG format.
+
| * Do energy minimization and save the image in '''JPEG''' format.
  
 
|-
 
|-
 
| 03:25
 
| 03:25
−
| To save the image in different file formats:
+
| To save the image in different file formats,
  
 
|-
 
|-
 
| 03:28
 
| 03:28
−
| Use “Save current view as an image” icon in the Tool bar.
+
| use “Save current view as an image” icon in the Tool bar.
  
 
|-
 
|-
 
| 03:33
 
| 03:33
−
| Your completed assignment should look as follows
+
| Your completed assignment should look as follows.
  
 
|-
 
|-
 
| 03:40
 
| 03:40
−
| Now lets go back to the Jmol Application window.
+
| Now, let's go back to the '''Jmol Application''' window.
  
 
|-
 
|-
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|-
 
|-
 
| 03:59
 
| 03:59
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| Scroll down the '''model kit''' menu and click '''“exit model kit mode”.'''
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| Scroll down the '''model kit''' menu and click '''“Exit model kit mode”.'''
  
 
|-
 
|-
 
| 04:04
 
| 04:04
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| To open the '''Pop-up '''menu, right-click the mouse button on the panel.  
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| To open the '''Pop-up '''menu, right-click the '''mouse''' button on the panel.  
  
 
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|-
 
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| 04:49
 
| 04:49
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| Now let's see how to edit this molecule and convert it to '''Ethane '''molecule.
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| Now, let's see how to '''edit''' this molecule and convert it to '''Ethane '''molecule.
  
 
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|-
 
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|05:26
 
|05:26
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| Click on '''“add hydrogens”''' option from the '''model kit''' menu.
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| Click on '''“Add hydrogens”''' option from the '''model kit''' menu.
  
 
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|-
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|-
 
|-
 
| 05:36
 
| 05:36
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| We now have the model of '''Ethane '''on the screen.
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| We now have the model of '''Ethane '''on the '''screen'''.
  
 
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|-
 
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| 05:45
 
| 05:45
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| To introduce a double bond in the molecule, open the '''model kit''' menu.
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| To introduce a double-bond in the molecule, open the '''model kit''' menu.
  
 
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| 06:01
 
| 06:01
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| Click on the bond.
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| Click on the '''bond'''.
  
 
|-
 
|-
 
| 06:05
 
| 06:05
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| Observe that the single bond is converted to a double bond.
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| Observe that the single-bond is converted to a double-bond.
  
 
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|-
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| 06:13
 
| 06:13
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| Now lets convert Ethene to Ethyne,
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| Now, let's convert Ethene to Ethyne.
  
 
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| 06:21
 
| 06:21
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| Place the cursor on the double bond in the '''Ethene''' molecule and click on it.
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| Place the cursor on the double-bond in the '''Ethene''' molecule and click on it.
  
 
|-
 
|-
 
| 06:28
 
| 06:28
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| The double bond is converted to a triple bond.
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| The double-bond is converted to a triple-bond.
  
 
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|-
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|  06:34
 
|  06:34
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| Do the energy minimization to get the most stable conformation and save.  
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| Do the energy minimization to get the most stable conformation and '''save'''.  
  
 
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| 06:41
 
| 06:41
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| In this tutorial we have learnt to
+
| In this tutorial, we have learnt to:
  
 
|-
 
|-
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|-
 
|-
 
| 06:48
 
| 06:48
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| * Add bonds to convert '''alkanes''' to '''alkenes''' and '''alkynes'''
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| * Add '''bond'''s to convert '''alkanes''' to '''alkenes''' and '''alkynes'''
  
 
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| 06:58
 
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| For the Assignment
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| For the Assignment-
  
 
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|-
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| 07:06
 
| 07:06
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| # '''Use the Pop-up '''menu to change the display of the model to wireframe.
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| # '''Use the Pop-up '''menu to change the display of the model to '''wireframe'''.
  
 
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| 07:16
 
| 07:16
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| Your completed assignment should look as follows
+
| Your completed assignment should look as follows.
  
 
|-
 
|-
 
| 07:24
 
| 07:24
−
| Watch the video available at this URL.
+
| Watch the video available at this URL:
−
[http://spoken-tutorial.org/What http://spoken-tutorial.org/What]_is_a_Spoken_ Tutorial
+
http://spoken-tutorial.org/What_is_a_Spoken_ Tutorial
  
 
|-
 
|-
 
| 07:27
 
| 07:27
−
| It summarizes the Spoken Tutorial project
+
| It summarizes the Spoken Tutorial project.
  
 
|-
 
|-
 
| 07:31
 
| 07:31
−
| If you do not have good bandwidth, you can download and watch it  
+
| If you do not have good bandwidth, you can download and watch it.
  
 
|-
 
|-
 
| 07:36
 
| 07:36
−
| The Spoken Tutorial Project Team:  
+
| The Spoken Tutorial Project team:  
  
 
|-
 
|-
 
| 07:38
 
| 07:38
−
| Conducts workshops using spoken tutorials
+
|* Conducts workshops using spoken tutorials.
  
 
|-
 
|-
 
| 07:41
 
| 07:41
−
| Gives certificates to those who pass an on-line test  
+
|* Gives certificates to those who pass an on-line test.
  
 
|-
 
|-
 
| 07:45
 
| 07:45
−
| For more details, please write to contact@spoken-tutorial.org  
+
| For more details, please write to: contact@spoken-tutorial.org  
  
 
|-
 
|-
 
| 07:52
 
| 07:52
−
| Spoken Tutorial Project is a part of the Talk to a Teacher project  
+
| '''Spoken Tutorial''' project is a part of the '''Talk to a Teacher''' project.
  
 
|-
 
|-
 
| 07:57
 
| 07:57
−
| It is supported by the National Mission on Education through ICT, MHRD, Government of India
+
| It is supported by the National Mission on Education through ICT, MHRD, Government of India.
  
 
|-
 
|-
 
| 08:04
 
| 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] ]
+
| More information on this mission is available at the following link: http://spoken-tutorial.org/NMEICT-Intro  
  
 
|-
 
|-
 
| 08:08
 
| 08:08
−
| This is Snehalatha from IIT Bombay signing off. Thank you for joining.  
+
| This is Snehalatha from IIT Bombay, signing off. Thank you for joining.  
  
 
|}
 
|}

Revision as of 21:31, 13 September 2015

Title of script: Create and Edit Molecular models

Author: Snehalatha Kaliappan

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

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.
00:23 * and 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-
03:11 * 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.
06:41 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-
06:59 # 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

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