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

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'''Author: Snehalatha Kaliappan'''
 
'''Author: Snehalatha Kaliappan'''
  
−
'''Keyword: 3D models of chemical structures, molecular visualization, video tutorial.'''
+
'''Keyword''': 3D models of chemical structures, molecular visualization, video tutorial.
  
 
* '''Outline:- '''
 
* '''Outline:- '''
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−
{| style="border-spacing:0;"
+
{| border=1
 
! <center>Visual Cue</center>
 
! <center>Visual Cue</center>
 
! <center>Narration</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'''
+
|| '''Slide Number 1'''
  
 
'''Title Slide'''
 
'''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.
+
|| 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.'''
  
 
|-
 
|-
−
| 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'''
+
|| '''Slide Number 2'''
  
 
'''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;"| In this tutorial, we will learn to,
+
|| In this tutorial, we will learn to,
  
  
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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;"| '''Slide Number 3'''
+
|| '''Slide Number 3'''
  
 
'''Pr-requisites'''
 
'''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,
+
|| To follow this tutorial you should be familiar with,
  
  
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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;"| '''Slide Number 4'''
+
|| '''Slide Number 4'''
  
 
'''System Requirement'''
 
'''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
+
|| To record this tutorial, I am using
  
 
* '''Ubuntu '''OS version. 12.04
 
* '''Ubuntu '''OS version. 12.04
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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 '''“Dash Home”'''
+
|| 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'''.  
+
|| 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.
+
|| 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.
+
|| 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.
+
|| 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
+
|| 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.
+
|| 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.
+
|| 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.
+
|| 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'''.'''
+
|| 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
+
|| Cursor on Jmol panel
  
 
Click on “open a file” icon.
 
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.
+
|| 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
+
|| 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.
+
|| 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
+
|| 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.
+
|| 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 “desktop”.
  
 
Click on the “open” button
 
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'''.
+
|| My file is located on the '''Desktop'''.
  
  
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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 “propane” file
+
|| 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.'''
+
|| Type the file name in the '''“File or URL” text box.'''
  
  
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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 propane molecule.
+
|| 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.
+
|| 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.
+
|| 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:
+
|| We can substitute '''hydrogens''' in the '''Propane''' with functional groups like:
  
 
'''hydroxy, amino, halogens '''like''' fluro, chloro, bromo''' and others.
 
'''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 Modelkit menu
  
  
 
Click on the check box against oxygen atom.  
 
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'''.
+
|| I want to add a '''hydroxy''' group to the '''Propane''' molecule, to convert it to '''Propanol'''.
  
  
Line 139: Line 139:
  
 
|-
 
|-
−
| 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.  
+
|| 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.
+
|| 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 Hydroxyl group
  
  
 
Cursor on the propanol molecule
 
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.
+
|| Observe that the '''hydrogen '''atom is replaced by '''hydroxy '''group. '''Oxygen atom''' is seen in red color here.
  
  
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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 propanol molecule
+
|| 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.'''
+
|| 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.
+
|| 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.
+
|| Select '''Chloro''' group from the '''model kit '''menu.
  
  
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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 hydrogen atom
+
|| 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.  
+
|| 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
+
|| 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.
+
|| We now have the model of''' 2-chloro-1-propanol'''. '''Chlorine '''is seen in green color.
  
  
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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;"| '''Slide number 5'''
+
|| '''Slide number 5'''
  
 
'''Assignment'''
 
'''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.
+
|| Here is an assignment.
  
 
* Create models of the following molecules.<br/> '''3-bromo-1-butanol '''and '''2-amino-4-chloro-pentane'''<br/>  
 
* Create models of the following molecules.<br/> '''3-bromo-1-butanol '''and '''2-amino-4-chloro-pentane'''<br/>  
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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 Jmol panel with 2-chloro-1-propanol molecule.
+
|| 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.
+
|| Now lets go back to the Jmol Application window.
  
  
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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;"| Right click the mouse button.
+
|| 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.  
+
|| Exit the '''model kit '''menu, if it is open.  
  
  
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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;"| Scroll down the Pop-up menu
+
|| 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.
+
|| '''Pop-up '''menu offers many functions to modify the display of atoms.
  
  
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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;"| Scroll down the Pop-up menu
+
|| 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.
+
|| 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.
+
|| 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.
+
|| The items in the '''Pop-up '''menu are self-explanatory.
  
  
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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 Jmol panel
+
|| 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.
+
|| 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.
+
|| 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.
+
|| The second way to access the '''Pop-up '''menu is to click on the '''Jmol '''logo.
  
  
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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 2-chloro-1-propanol molecule
+
|| 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.
+
|| 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.
+
|| 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.  
+
|| 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.
+
|| 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.
+
|| 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 the box against “delete atom”.
  
  
 
Click on oxygen, chlorine and carbon.
 
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”. '''
+
|| Check the box against '''“delete 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 panel
+
|| 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.
+
|| 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.
+
|| 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.
+
|| 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.
+
|| 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.
+
|| Two '''hydrogen '''atoms are added to the molecule.
  
  
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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 ethane molecule
+
|| 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'''.  
+
|| 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 modelkit menu.
  
  
 
Click on the “double” option in 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.
+
|| To introduce a double bond in the molecule, open the '''model kit''' menu.
  
  
Line 309: Line 309:
  
 
|-
 
|-
−
| 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.
+
|| 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.
+
|| 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.
+
|| 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.  
+
|| Red colored rings appear around the '''carbon''' atoms.  
  
 
Click on the bond.
 
Click on the bond.
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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 jmol panel
+
|| 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,  
+
|| 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 the modelkit menu.
  
 
Click on “triple”
 
Click on “triple”
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Click on the 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.  
+
|| Click on the '''modelkit '''menu and select “'''triple'''” option.  
  
  
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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 molecule
+
|| 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.
+
|| 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.
+
|| 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.'''
+
|| 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
+
|| 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.  
+
|| 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'''
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|| '''Slide Number 6'''
  
 
Summary
 
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.
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|| Let's summarize.
  
  
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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;"| '''Slide Number 7'''
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|| '''Slide Number 7'''
  
 
Assignment
 
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
+
|| For the Assignment
  
  
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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;"| '''Slide Number 8'''
+
|| '''Slide Number 8'''
  
 
'''Acknowledgement '''
 
'''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.
+
|| 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 http://spoken-tutorial.org/What]_is_a_Spoken_ Tutorial
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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;"| '''Slide Number 9'''
+
|| '''Slide Number 9'''
  
 
'''Acknowledgement '''
 
'''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:  
+
|| The Spoken Tutorial Project Team:  
  
 
Conducts workshops using spoken tutorials
 
Conducts workshops using spoken tutorials
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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;"| '''Slide number 10'''
+
|| '''Slide number 10'''
  
 
'''Acknowledgement '''
 
'''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  
+
|| 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
 
It is supported by the National Mission on Education through ICT, MHRD, Government of India
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|-
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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;"|  
+
||  
−
| 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.  
+
|| This is Snehalatha from IIT Bombay signing off. Thank you for joining.  
  
 
|}
 
|}

Latest revision as of 18:34, 19 March 2025

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)


Visual Cue
Narration
Slide Number 1

Title Slide

Hello everyone.

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

Slide Number 2

Learning Objectives

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.


Slide Number 3

Pr-requisites

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.

Slide Number 4

System Requirement

To record this tutorial, I am using
  • Ubuntu OS version. 12.04
  • Jmol version 12.2.2
  • And Java version 7.


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.
Cursor on Jmol icon. Jmol icon appears on the screen
Click on the Jmol icon. Click on the Jmol icon to open the Jmol application window.
Cursor on Jmol panel.


Let's begin with the model of Propane, which we had created earlier.
Cursor on Jmol panel

Click on “open a file” icon.

To open the file, click on “Open a file” icon on the tool bar.
Cursor on the dialog box A dialog box appears on the screen.
Cursor on the dialog box Click on the folder where the required file is located.
Click on the “desktop”.

Click on the “open” button

My file is located on the Desktop.


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

Click on the “propane” file Type the file name in the “File or URL” text box.


Then, click on the Open button.

Cursor on the propane molecule. The Model of Propane appears on screen.
Cursor on the propane molecule. We can substitute hydrogens in the Propane with functional groups like:

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

Click on the Modelkit menu


Click on the check box against oxygen atom.

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.

Cursor on hydrogen atom >> Click on the hydrogen atom. Click on the hydrogen atom attached to the first carbon atom.
Cursor on the Hydroxyl group


Cursor on the propanol molecule

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.

Cursor on the propanol molecule Let's now try to convert 1-Propanol to 2-chloro-1-propanol.
Click on the check box against chloro group. Select Chloro group from the model kit menu.



Click on hydrogen atom Click on the hydrogen atom attached to the second carbon atom.
Cursor on the panel 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.

Slide number 5

Assignment

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



Cursor on Jmol panel with 2-chloro-1-propanol molecule.


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.

Right click the mouse button. 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.



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


It has a variety of selection and rendering options.

Scroll down the Pop-up menu Most of the functions in this menu are duplicated in the menu bar.
Cursor on the Pop-up menu. The items in the Pop-up menu are self-explanatory.


They don't need a detailed description.

Click on the Jmol panel Click on the Jmol panel to exit the Pop-up menu.
Cursor on the “Jmol” logo.


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.

Cursor on the 2-chloro-1-propanol molecule Now let's see how to edit this molecule and convert it to Ethane molecule.
Cursor on hydroxyl group, chlorine group, carbon and hydrogen atoms. For this, we will delete the hydroxy group, the chlorine group, the carbon and two hydrogen atoms.
Click on the modelkit menu. Open the model kit menu.
Click on the box against “delete atom”.


Click on oxygen, chlorine and carbon.

Check the box against “delete atom”.


Click on the atoms you want to delete.

Oxygen, chlorine and the carbon atom.

Cursor on the panel We have to add hydrogens to this molecule to create an ethane molecule.
Click on “add hydrogens” option from the modelkit menu. Click on “add hydrogens” option from the model kit menu.
Cursor on the Jmol panel. Two hydrogen atoms are added to the molecule.


We now have the model of Ethane on the screen.

Cursor on ethane molecule Let's learn how to create alkenes and alkynes.
Click on the modelkit menu.


Click on the “double” option in the modelkit menu.

To introduce a double bond in the molecule, open the model kit menu.


Check against “double” option.

Cursor on the bond between two carbon atoms. Place the cursor on the bond between two carbon atoms in the Ethane molecule.
Click on the bond. 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.

Cursor on jmol panel Now lets convert Ethene to Ethyne,
Click on the modelkit menu.

Click on “triple”


Place the cursor on the double bond.

Click on the bond.

Click on the modelkit menu and select “triple” option.


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

Cursor on the molecule The double bond is converted to a triple bond.
Point to the model. This is the model of Ethyne.
Cursor on jmol panel Do the energy minimization to get the most stable conformation and save.
Slide Number 6

Summary

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.


Slide Number 7

Assignment

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

Slide Number 8

Acknowledgement

Watch the video available at this URL.

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 9

Acknowledgement

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 10

Acknowledgement

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, Snehalathak

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