Difference between revisions of "Avogadro/C2/Edit-molecules/English"

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−
{| style="border-spacing:1;"
+
{| border=1
−
! <center>Visual Cue</center>
+
||'''Visual Cue'''
−
! <center>Narration</center>
+
||'''Narration'''
−
 
+
 
|-
 
|-
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 1'''
+
||'''Title Slide'''
−
 
+
|| Warm greetings everyone.
−
'''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;"| Warm greetings everyone.
+
  
 
Welcome to this tutorial on '''Edit molecules.'''
 
Welcome to this tutorial on '''Edit molecules.'''
  
 
|-
 
|-
−
| 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-
 +
 
 +
Add and delete atoms
 +
 
 +
Add and delete bonds
 +
 
 +
Rotate bonds
 +
 
 +
Change length of the bond
 +
 
 +
Change hydrogen to methyl group
  
−
* Add and delete atoms
+
Copy, paste and join structures.
−
* Add and delete bonds
+
−
* Rotate bonds
+
−
* Change length of the bond
+
−
* Change hydrogen to methyl group
+
−
* Copy, paste and join structures.
+
 
|-
 
|-
−
| 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'''
  
 
'''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;"| Here I am using
+
|| Here I am using
  
−
'''Ubuntu Linux '''OS version. 14.04
+
'''Ubuntu Linux''' OS version. 14.04
  
 
'''Avogadro''' version 1.1.1.
 
'''Avogadro''' version 1.1.1.
  
 
|-
 
|-
−
| 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'''
  
 
'''Pre-requisties'''
 
'''Pre-requisties'''
  
−
You should be familiar with:
+
You should be familiar with,
  
  
Line 46: Line 48:
 
For relevant tutorials, visit our website.  
 
For relevant tutorials, visit our website.  
  
−
'''www.spoken-tutorial.org.'''
+
'''www.spoken-tutorial.org'''.
−
| 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:
  
 
'''Avogadro ''' interface.
 
'''Avogadro ''' interface.
Line 55: Line 57:
  
 
|-
 
|-
−
| 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;"| Here I will show how to open '''Avogadro '''using the '''Terminal. '''
+
|| Here I will show how to open '''Avogadro ''' using the '''Terminal'''.
  
 
|-
 
|-
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Press CTRL+ALT+T keys simultaneously.
+
|| Press '''CTRL+ALT+T''' keys simultaneously.
−
| 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 terminal press '''CTRL, ALT''' and '''T '''keys simultaneously.
+
|| To open the terminal press '''CTRL, ALT''' and '''T '''keys simultaneously.
  
 
|-
 
|-
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Type '''avogadro''' at the prompt, press enter.
+
|| Type '''avogadro''' at the prompt, press enter.
−
| 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 '''avogadro '''at the prompt and press enter.
+
|| Type '''avogadro '''at the prompt and press enter.
  
  
Line 70: Line 72:
  
 
|-
 
|-
−
| 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;"| For demonstration, I will display a molecule of '''n-butane''' from the '''Fragment''' library.
+
|| For demonstration, I will display a molecule of '''n-butane''' from the '''Fragment''' library.
  
 
|-
 
|-
−
|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 '''Build''' menu.  
+
|| Click on '''Build''' menu.  
  
 
Navigate to '''Insert->Fragment'''
 
Navigate to '''Insert->Fragment'''
Line 80: Line 82:
 
'''Insert fragment''' dialog box appears.  
 
'''Insert fragment''' dialog box appears.  
  
−
| 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 '''Build''' menu.  
+
|| Click on '''Build''' menu.  
  
 
Navigate to '''Insert->Fragment'''
 
Navigate to '''Insert->Fragment'''
Line 87: Line 89:
  
 
|-
 
|-
−
| 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 '''Insert Fragment''' dialog box
+
|| Point to '''Insert Fragment''' 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;"| From the list of fragments, double click on '''alkanes''' folder to open.
+
|| From the list of fragments, double click on '''alkanes''' folder to open.
  
  
Line 96: Line 98:
  
 
|-
 
|-
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Close '''Insert Fragment''' dialog box
+
|| Close '''Insert Fragment''' 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''' Insert''' button.
+
|| Click on''' Insert''' button.
  
 
Click on X to close '''Insert Fragment''' dialog box.
 
Click on X to close '''Insert Fragment''' dialog box.
  
 
|-
 
|-
−
| 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 Butane molecule
+
|| Point to Butane 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;"| Butane molecule highlighted in blue color appears on the '''Panel'''.
+
|| Butane molecule highlighted in blue color appears on the '''Panel'''.
  
 
To remove the highlighting, Press '''Ctrl, Shift '''and '''A '''keys simultaneously.
 
To remove the highlighting, Press '''Ctrl, Shift '''and '''A '''keys simultaneously.
−
 
−
 
 
|-
 
|-
−
| 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 navigation tool.
+
|| Point to the navigation tool.
−
| 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;"| Rotate the structure using '''Navigation '''tool to get proper alignment.
+
|| Rotate the structure using '''Navigation '''tool to get proper alignment.
  
 
|-
 
|-
−
| 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;"| We will now learn how to add atoms to the molecule.
+
|| We will now learn how to add atoms to the 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''' Draw tool''' icon  
+
|| Click on''' Draw tool''' 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 '''Draw tool''' icon on the tool bar.
+
|| Click on '''Draw tool''' 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;"| Click on end carbon atom, drag on the '''Panel.'''
+
|| Click on end carbon atom, drag on the '''Panel.'''
  
 
Point to molecule.
 
Point to 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;"| Click on end '''Carbon''' atom and drag on the '''Panel.'''
+
|| Click on end '''Carbon''' atom and drag on the '''Panel.'''
  
  
Line 130: Line 130:
  
 
|-
 
|-
−
| 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 molecule.
+
|| Point to 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 now have a molecule of '''pentane''' on '''Panel'''.
+
|| We now have a molecule of '''pentane''' on '''Panel'''.
  
  
 
Similarly, you can add atoms using '''Draw tool''' to make a series of alkanes.
 
Similarly, you can add atoms using '''Draw tool''' to make a series of alkanes.
−
 
−
 
 
|-
 
|-
−
| 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 '''Draw tool.'''
+
|| Point to '''Draw tool.'''
−
| 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 a new window.  
+
|| Open a new window.  
  
 
Draw propane using '''Draw tool.'''
 
Draw propane using '''Draw tool.'''
  
 
|-
 
|-
−
| 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;"| Let us delete the end Carbon atom with hydrogens to get a molecule of '''Ethane'''.
+
|| Let us delete the end Carbon atom with hydrogens to get a molecule of '''Ethane'''.
  
 
|-
 
|-
−
| 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 Selection tool icon
+
|| Click on the Selection tool 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 delete atoms, click on the '''Selection tool''' icon on the tool bar.
+
|| To delete atoms, click on the '''Selection tool''' 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 end carbon atom
+
|| Cursor on the end carbon 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 and drag over the end Carbon atom to make the selection.
+
|| Click and drag over the end Carbon atom to make the selection.
  
 
Selected atoms appears blue in color.
 
Selected atoms appears blue in color.
  
 
|-
 
|-
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Press Backspace to delete.
+
|| Press Backspace to delete.
  
  
 
Point to '''Edit '''menu
 
Point to '''Edit '''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;"| Press '''Backspace''' to delete.
+
|| Press '''Backspace''' to delete.
  
  
Line 170: Line 168:
  
 
|-
 
|-
−
| 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;"| We will demonstrate on how to add and delete bonds in a molecule.
+
|| We will demonstrate on how to add and delete bonds in a molecule.
  
 
|-
 
|-
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Select the '''Draw tool''' icon
+
|| Select the '''Draw tool''' icon
  
  
 
'''Draw settings''' appears
 
'''Draw settings''' appears
−
| 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 add bonds select the '''Draw tool''' icon on the tool bar.  
+
|| To add bonds select the '''Draw tool''' icon on the tool bar.  
  
 
'''Draw Settings''' menu open on the left.
 
'''Draw Settings''' menu open on the left.
  
 
|-
 
|-
−
| 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 '''Element '''drop down list.
+
|| Point to '''Element ''' drop down list.
  
−
Point to '''Bond Order '''drop down.
+
Point to '''Bond Order ''' drop down.
−
| 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;"| By default '''Carbon''' is selected in '''Element '''drop down list.
+
|| By default '''Carbon''' is selected in '''Element '''drop down list.
  
 
To introduce a double bond select '''Double''' from '''Bond Order '''drop down.
 
To introduce a double bond select '''Double''' from '''Bond Order '''drop down.
  
 
|-
 
|-
−
| 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 C-1 and C-2
+
|| Cursor on the Bond between C-1 and C-2
−
| 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 bond between C-1 and C-2 to convert it to a double bond.
+
|| Click on the bond between C-1 and C-2 to convert it to a double bond.
  
  
 
|-
 
|-
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Select Triple from bond order.
+
|| Select Triple from bond order.
  
 
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;"| To convert double bond into a triple bond, select '''Triple''' from '''Bond Order.'''
+
|| To convert double bond into a triple bond, select '''Triple''' from '''Bond Order.'''
  
 
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:none;padding:0.097cm;"| Hold the right mouse button and click on the bonds.
+
|| Hold the right mouse button and click on the bonds.
  
  
 
Point to the molecules.
 
Point to the molecules.
−
| 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 delete bonds, hold the right mouse button and click on the bonds.
+
|| To delete bonds, hold the right mouse button and click on the bonds.
  
  
Line 214: Line 212:
  
 
|-
 
|-
−
| 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;"| Let's rejoin the molecules.
+
|| Let's rejoin the molecules.
  
 
|-
 
|-
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Select Carbon from draw tool settings
+
|| Select Carbon from draw tool settings
−
| 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 Carbon of one molecule, drag and click on carbon of other molecule.
+
|| Click on Carbon of one molecule, drag and click on carbon of other 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 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 can rotate bonds and change bond lengths using '''Bond Centric Manipulation''' tool.
+
|| We can rotate bonds and change bond lengths using '''Bond Centric Manipulation''' tool.
  
 
|-
 
|-
−
| 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 '''Bond Centric Manipulation tool'''
+
|| Cursor on '''Bond Centric Manipulation tool'''
−
| 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 '''Bond Centric Manipulation tool''' on the tool bar.
+
|| Click on '''Bond Centric Manipulation tool''' 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;"| '''Bond Centric Manipulate''' settings appears
+
|| '''Bond Centric Manipulate''' settings appears
−
| 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;"| '''Bond Centric Manipulate '''settings menu opens on the left.
+
|| '''Bond Centric Manipulate '''settings menu opens on the left.
  
 
|-
 
|-
−
| 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 '''Bond Centric Manipulate''' settings  
+
|| Cursor on '''Bond Centric Manipulate''' settings  
−
| 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;"| By default, '''Show Angles''' and '''Snap-to Bonds''' are checked.
+
|| By default, '''Show Angles''' and '''Snap-to Bonds''' are checked.
  
 
'''Snap-to Threshold''' set to '''10<sup>0'''</sup>(10 degree).
 
'''Snap-to Threshold''' set to '''10<sup>0'''</sup>(10 degree).
Line 243: Line 241:
  
 
|-
 
|-
−
| 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
+
|| Cursor 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;"| To show angles, click on the bond between two atoms.
+
|| To show angles, click on the bond between two atoms.
  
 
|-
 
|-
−
| 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;"| We need to fix the plane of rotation of the bonds.
+
|| We need to fix the plane of rotation of the bonds.
  
 
|-
 
|-
−
| 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.
+
|| Cursor on the Bond.
  
  
 
Point to the plane.
 
Point to the plane.
−
| 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 fix the plane you want, click on the bond and move upwards or downwards.
+
|| To fix the plane you want, click on the bond and move upwards or downwards.
  
  
Line 261: Line 259:
  
 
|-
 
|-
−
| 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 atom, move.
+
|| Click on atom, move.
−
| 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 Rotate, click on one of the atoms and move.
+
|| To Rotate, click on one of the atoms and move.
  
  
Line 268: Line 266:
  
 
|-
 
|-
−
| 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 atom with right mouse button
+
|| Click on atom with right 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;"| To change length of the bond hold the right mouse button and drag.
+
|| To change length of the bond hold the right mouse button and drag.
  
 
|-
 
|-
−
| 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 molecule
+
|| Cursor on 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 we will show how to change Hydrogens to methyl groups.
+
|| Now we will show how to change Hydrogens to methyl groups.
  
 
|-
 
|-
−
| 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 '''Build menu'''
+
|| Click on '''Build 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 '''Build '''menu''' and click on '''Change H To Methyl.'''
+
|| Click on '''Build ''' menu and click on '''Change H To Methyl.'''
  
 
|-
 
|-
−
| 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 molecule
+
|| Point to 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;"| All Hydrogens are now replaced by Methyl groups.
+
|| All Hydrogens are now replaced by Methyl groups.
  
−
Press''' CTRL '''and''' Z keys '''simultaneously to undo the changes.
+
Press '''CTRL''' and ''' Z keys''' simultaneously to undo the changes.
  
 
|-
 
|-
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"|
+
||Cursor on the Panel.  
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| We can also select a particular hydrogen atom and change it to a methyl group.
+
|| We can also select a particular hydrogen atom and change it to a methyl group.
  
 
|-
 
|-
−
| 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 selection tool
+
| | Click on selection tool
−
| 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 '''Selection tool '''icon on the tool bar
+
|| Click on '''Selection tool ''' 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;"| Click on the hydrogen
+
|| Click on the hydrogen.
−
| 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 attached to end carbon atom to select.
+
|| Click on the hydrogen attached to end carbon atom to select.
  
 
|-
 
|-
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Go to '''Build''' menu, click on '''Change H to Methyl'''.
+
|| Go to '''Build''' menu, click on '''Change H to Methyl'''.
  
  
 
Cursor on molecule
 
Cursor on 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;"| Go to '''Build''' menu and click on  '''Change H to Methyl.'''
+
|| Go to '''Build''' menu and click on  '''Change H to Methyl'''.
  
  
 
The selected Hydrogen gets replaced by methyl group.
 
The selected Hydrogen gets replaced by methyl group.
−
 
−
 
 
|-
 
|-
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Press Ctrl+Shift+A.
+
|| Press Ctrl+Shift+A.
−
| 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 deselect, Press '''Ctrl, Shift''' and '''A''' keys simultaneously.
+
|| To deselect, Press '''Ctrl, Shift''' and '''A''' keys simultaneously.
  
 
|-
 
|-
−
| 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;"| Let us take a look as how to copy, paste and join structures.
+
|| Let us take a look as how to copy, paste and join structures.
  
 
|-
 
|-
−
| 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 '''File'''->New
+
|| Click on '''File'''-> New
−
| 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 '''File'''->'''New''' to open a new window.
+
|| Click on '''File'''-> '''New''' to open a new 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 panel
+
|| Cursor on 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 will learn to build a '''Maltose''' molecule.
+
|| We will learn to build a '''Maltose''' molecule.
  
  
Line 328: Line 324:
  
 
|-
 
|-
−
| 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 '''Build '''menu
+
|| Click on '''Build '''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 insert a glucose molecule, click on '''Build''' menu.
+
|| To insert a glucose molecule, click on '''Build''' menu.
  
 
|-
 
|-
−
| 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 and click on  
+
|| Scroll down and click on  
  
 
'''Insert->Fragment '''
 
'''Insert->Fragment '''
−
| 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;"| Scroll down and click on '''Insert->Fragment '''
+
|| Scroll down and click on '''Insert''' -> '''Fragment'''
  
 
|-
 
|-
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Insert->Fragment''' dialog box appears
+
|| '''Insert''' -> '''Fragment''' dialog box appears
−
| 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;"| '''Insert->Fragment''' dialog box appears.
+
|| '''Insert''' -> '''Fragment''' dialog box appears.
  
 
|-
 
|-
−
| 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 '''Insert Fragment '''dialog box
+
|| Cursor on '''Insert Fragment '''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;"| Scroll down the list and click on '''Cyclic sugar''' folders.
+
|| Scroll down the list and click on '''Cyclic sugar''' folders.
  
 
|-
 
|-
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| A sub menu appears
+
|| A sub menu appears
−
| 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 sub menu appears.
+
|| A sub menu appears.
  
 
|-
 
|-
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Navigate down and select beta-d-glucopyranose.cml  
+
|| Navigate down and select '''beta-d-glucopyranose.cml'''.
  
 
Close the dialog box
 
Close 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;"| Navigate down and select
+
|| Navigate down and select
  
 
'''beta-d-glucopyranose.cml.'''
 
'''beta-d-glucopyranose.cml.'''
Line 362: Line 358:
  
 
|-
 
|-
−
| 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 molecule
+
|| Point to 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;"| '''beta-D-glucopyranose.cml '''appears on panel highlighted in blue color.
+
|| '''beta-D-glucopyranose.cml''' appears on panel highlighted in blue color.
  
 
Translate it to the center using hand tool.
 
Translate it to the center using hand tool.
  
 
|-
 
|-
−
| 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 Panel
+
|| Cursor on 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 us copy and paste another glucose molecule.
+
|| Let us copy and paste another glucose 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 '''Edit''' menu
+
|| Click on '''Edit''' 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 '''Edit''' menu on the menu bar.
+
|| Click on '''Edit''' menu on 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;"| Scroll down and click on Copy
+
|| Scroll down and click on Copy
−
| 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;"| And click on '''Copy'''.
+
|| And click on '''Copy'''.
−
 
+
  
 
Again Scroll down the edit menu and then click '''Paste'''.
 
Again Scroll down the edit menu and then click '''Paste'''.
  
 
|-
 
|-
−
| 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 panel
+
|| Cursor on 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;"| Please note during copy, paste operation, window dims for a moment and then recovers.
+
|| Please note during copy, paste operation, window dims for a moment and then recovers.
  
 
|-
 
|-
−
| 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 new molecule.
+
|| Point to the new 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;"| A new molecule gets copied and pasted on the existing molecule on the Panel.
+
|| A new molecule gets copied and pasted on the existing molecule on the Panel.
  
 
|-
 
|-
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Move with the left mouse button
+
|| Move with the left 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;"| The cursor changes to a hand tool.
+
|| The cursor changes to a hand tool.
  
 
Move the copied molecule from the original molecule.
 
Move the copied molecule from the original molecule.
Line 399: Line 394:
  
 
|-
 
|-
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Press Ctrl+Shift+A.
+
|| Press Ctrl+Shift+A.
−
| 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 de-select Press '''Ctrl, Shift '''and''' A''' keys simultaneously.
+
|| To de-select Press '''Ctrl, Shift ''' and '''A''' keys simultaneously.
  
 
|-
 
|-
−
| 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;"| Let us label the molecules.
+
|| Let us label the molecules.
  
 
Labeling helps to identify the positions of all the atoms.
 
Labeling helps to identify the positions of all the 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 '''Label''' check box from the''' Display Types''' drop down.
+
|| Click on '''Label''' check box from the''' Display Types''' drop down.
−
| 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 label, Click on '''Label''' check box from the''' Display Types''' drop down.
+
|| To label, Click on '''Label''' check box from the''' Display Types''' drop down.
−
 
+
 
|-
 
|-
−
| 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 molecule
+
|| Cursor on 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;"| To get Maltose we need to remove a water molecule.  
+
|| To get Maltose we need to remove a water molecule.  
−
 
+
 
|-
 
|-
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Delete atoms.
+
|| Delete 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;"| Delete the OH group on C-1 of first molecule and hydrogen on C-9 of second molecule.
+
|| Delete the OH group on C-1 of first molecule and hydrogen on C-9 of second molecule.
  
 
|-
 
|-
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Select Carbon in draw tool settings
+
|| Select Carbon in draw tool settings
−
| 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 '''Carbon''' in '''Draw tool settings.'''
+
|| Select '''Carbon''' in '''Draw tool settings.'''
  
 
|-
 
|-
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Select Single as bond order
+
|| Select '''Single'''' as '''Bond Order'''
−
| 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''' Single''' as '''Bond Order'''.
+
|| Select ''' Single''' as '''Bond Order'''.
  
 
|-
 
|-
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Uncheck the adjust hydrogens check box
+
|| Uncheck the '''Adjust Hydrogens''' check 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;"| Uncheck '''Adjust Hydrogens''' check box.
+
|| Uncheck '''Adjust Hydrogens''' check 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 molecule
+
|| Cursor on 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;"| Click and drag to join C-1 of first molecule and C-9 of second molecule through oxygen atom.
+
|| Click and drag to join C-1 of first molecule and C-9 of second molecule through oxygen atom.
  
 
|-
 
|-
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"|  
+
||  
−
| 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 need to optimize the geometry.
+
|| We need to optimize the geometry.
  
 
|-
 
|-
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Select auto optimization tool
+
|| Select '''Auto Optimization tool'''.
−
| 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 '''Auto Optimization tool.'''
+
|| Select '''Auto Optimization tool'''.
  
 
|-
 
|-
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Auto optimization settings appears
+
|| '''Auto optimization settings''' appears.
−
| 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;"| '''Auto Optimization settings''' menu appears on the left.
+
|| '''Auto Optimization settings''' menu appears on the left.
  
 
|-
 
|-
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Select MMFF94 force field
+
|| Select '''MMFF94''' force field, click on '''Start'''.
−
| 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 '''MMFF94''' force field and click on '''Start'''.
+
|| Select '''MMFF94''' force field and click on '''Start'''.
  
 
|-
 
|-
−
| 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;"| The optimization may take a few seconds to complete.
+
|| The optimization may take a few seconds to complete.
  
 
You may remove the labels now
 
You may remove the labels now
  
 
|-
 
|-
−
| 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 an optimized structure of Maltose on Panel.
+
|| We now have an optimized structure of Maltose on Panel.
  
 
|-
 
|-
−
| 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'''
  
 
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. In this tutorial we have learnt to:  
+
|| Let's summarize. In this tutorial we have learnt to:  
  
−
* Add and delete atoms
+
Add and delete atoms
−
* Add and delete bonds
+
 
−
* Rotate bonds  
+
Add and delete bonds
−
* Change Bond length
+
 
−
* Change Hydrogen to Methyl group
+
Rotate bonds  
−
* Copy, paste and join structures.
+
 
 +
Change Bond length
 +
 
 +
Change Hydrogen to Methyl group
 +
 
 +
Copy, paste and join structures.
  
 
|-
 
|-
−
| 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'''
+
|| '''Slide Number 6'''
  
 
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;"| As an assignment,
+
|| As an assignment,
  
−
* Create a Butane molecule using draw tool
+
Create a Butane molecule using draw tool
−
* Convert it into 2,3 dimethyl Butane
+
−
* Rotate the bonds and change bond lengths.
+
  
 +
Convert it into 2,3 dimethyl Butane
 +
 +
Rotate the bonds and change bond lengths.
 
|-
 
|-
−
| 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'''
+
|| '''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;"| * Create a molecule of cellulose<br/> (Hint: D- glucose monomer is available in the Insert fragment library)
+
||Create a molecule of cellulose<br/> (Hint: D- glucose monomer is available in the Insert fragment library)
−
* Optimize the geometry using UFF force field.
+
 
 +
Optimize the geometry using UFF force field.
  
 
|-
 
|-
−
| 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 '''
Line 510: Line 510:
  
 
you can download and watch it.
 
you can download and watch it.
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| This video summarises the Spoken Tutorial project
+
|| This video summarises the Spoken Tutorial project
−
* 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.
 
|-
 
|-
−
| 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'''
  
 
The Spoken Tutorial Project Team  
 
The Spoken Tutorial Project Team  
Line 528: Line 527:
  
 
'''contact@spoken-tutorial.org'''
 
'''contact@spoken-tutorial.org'''
−
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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'''
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'''Acknowledgement'''
 
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| 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 tutorial is contributed by Viswa Janani Vasudhevan and Madhuri Ganapathi.
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Latest revision as of 12:55, 6 June 2017

Visual Cue Narration
Title Slide Warm greetings everyone.

Welcome to this tutorial on Edit molecules.

Slide Number 2

Learning Objectives

In this tutorial, we will learn to-

Add and delete atoms

Add and delete bonds

Rotate bonds

Change length of the bond

Change hydrogen to methyl group

Copy, paste and join structures.

Slide Number 3

System Requirement

Here I am using

Ubuntu Linux OS version. 14.04

Avogadro version 1.1.1.

Slide Number 4

Pre-requisties

You should be familiar with,


Avogadro interface.

For relevant tutorials, visit our website.

www.spoken-tutorial.org.

To follow this tutorial, you should be familiar with:

Avogadro interface.


If not, for relevant tutorials, please visit our website.

Here I will show how to open Avogadro using the Terminal.
Press CTRL+ALT+T keys simultaneously. To open the terminal press CTRL, ALT and T keys simultaneously.
Type avogadro at the prompt, press enter. Type avogadro at the prompt and press enter.


Avogadro application window opens.

Cursor on the Panel For demonstration, I will display a molecule of n-butane from the Fragment library.
Click on Build menu.

Navigate to Insert->Fragment

Insert fragment dialog box appears.

Click on Build menu.

Navigate to Insert->Fragment

Insert fragment dialog box appears.

Point to Insert Fragment dialog box


From the list of fragments, double click on alkanes folder to open.


Select butane.cml from the drop down that appears.

Close Insert Fragment dialog box Click on Insert button.

Click on X to close Insert Fragment dialog box.

Point to Butane molecule Butane molecule highlighted in blue color appears on the Panel.

To remove the highlighting, Press Ctrl, Shift and A keys simultaneously.

Point to the navigation tool. Rotate the structure using Navigation tool to get proper alignment.
Cursor on the molecule We will now learn how to add atoms to the molecule.
Click on Draw tool icon. Click on Draw tool icon on the tool bar.
Click on end carbon atom, drag on the Panel.

Point to molecule.

Click on end Carbon atom and drag on the Panel.


A carbon atom with required hydrogens get added.

Point to molecule. We now have a molecule of pentane on Panel.


Similarly, you can add atoms using Draw tool to make a series of alkanes.

Point to Draw tool. Open a new window.

Draw propane using Draw tool.

Cursor on the molecule. Let us delete the end Carbon atom with hydrogens to get a molecule of Ethane.
Click on the Selection tool icon To delete atoms, click on the Selection tool icon on the tool bar.
Cursor on the end carbon atom Click and drag over the end Carbon atom to make the selection.

Selected atoms appears blue in color.

Press Backspace to delete.


Point to Edit menu

Press Backspace to delete.


Alternatively you can use clear option in Edit menu.

To redo, press Ctrl and Z keys simultaneously.

Cursor on the molecule We will demonstrate on how to add and delete bonds in a molecule.
Select the Draw tool icon


Draw settings appears

To add bonds select the Draw tool icon on the tool bar.

Draw Settings menu open on the left.

Point to Element drop down list.

Point to Bond Order drop down.

By default Carbon is selected in Element drop down list.

To introduce a double bond select Double from Bond Order drop down.

Cursor on the Bond between C-1 and C-2 Click on the bond between C-1 and C-2 to convert it to a double bond.


Select Triple from bond order.

Click on the bond.

To convert double bond into a triple bond, select Triple from Bond Order.

Click on the bond.

Hold the right mouse button and click on the bonds.


Point to the molecules.

To delete bonds, hold the right mouse button and click on the bonds.


This results in two different molecules.

Let's rejoin the molecules.
Select Carbon from draw tool settings Click on Carbon of one molecule, drag and click on carbon of other molecule.
Cursor on the Panel We can rotate bonds and change bond lengths using Bond Centric Manipulation tool.
Cursor on Bond Centric Manipulation tool Click on Bond Centric Manipulation tool on the tool bar.
Bond Centric Manipulate settings appears Bond Centric Manipulate settings menu opens on the left.
Cursor on Bond Centric Manipulate settings By default, Show Angles and Snap-to Bonds are checked.

Snap-to Threshold set to 100(10 degree).


Users can make their own choice of settings as per the requirements.

Cursor on the Bond To show angles, click on the bond between two atoms.
We need to fix the plane of rotation of the bonds.
Cursor on the Bond.


Point to the plane.

To fix the plane you want, click on the bond and move upwards or downwards.


The plane between the atoms appears in blue or yellow color.

Click on atom, move. To Rotate, click on one of the atoms and move.


Attached bond along with the atoms rotates in the fixed plane.

Click on atom with right mouse button To change length of the bond hold the right mouse button and drag.
Cursor on molecule Now we will show how to change Hydrogens to methyl groups.
Click on Build menu. Click on Build menu and click on Change H To Methyl.
Point to molecule All Hydrogens are now replaced by Methyl groups.

Press CTRL and Z keys simultaneously to undo the changes.

Cursor on the Panel. We can also select a particular hydrogen atom and change it to a methyl group.
Click on selection tool Click on Selection tool icon on the tool bar
Click on the hydrogen. Click on the hydrogen attached to end carbon atom to select.
Go to Build menu, click on Change H to Methyl.


Cursor on molecule

Go to Build menu and click on Change H to Methyl.


The selected Hydrogen gets replaced by methyl group.

Press Ctrl+Shift+A. To deselect, Press Ctrl, Shift and A keys simultaneously.
Let us take a look as how to copy, paste and join structures.
Click on File-> New Click on File-> New to open a new window.
Cursor on panel We will learn to build a Maltose molecule.


Maltose is made up of two glucose molecules.

Click on Build menu To insert a glucose molecule, click on Build menu.
Scroll down and click on

Insert->Fragment

Scroll down and click on Insert -> Fragment
Insert -> Fragment dialog box appears Insert -> Fragment dialog box appears.
Cursor on Insert Fragment dialog box Scroll down the list and click on Cyclic sugar folders.
A sub menu appears A sub menu appears.
Navigate down and select beta-d-glucopyranose.cml.

Close the dialog box

Navigate down and select

beta-d-glucopyranose.cml.

Click on Insert button.

Close the dialog box.

Point to molecule beta-D-glucopyranose.cml appears on panel highlighted in blue color.

Translate it to the center using hand tool.

Cursor on Panel Let us copy and paste another glucose molecule.
Click on Edit menu Click on Edit menu on the menu bar.
Scroll down and click on Copy And click on Copy.

Again Scroll down the edit menu and then click Paste.

Cursor on panel Please note during copy, paste operation, window dims for a moment and then recovers.
Point to the new molecule. A new molecule gets copied and pasted on the existing molecule on the Panel.
Move with the left mouse button The cursor changes to a hand tool.

Move the copied molecule from the original molecule.

Now we have two separate molecules on the Panel

Press Ctrl+Shift+A. To de-select Press Ctrl, Shift and A keys simultaneously.
Let us label the molecules.

Labeling helps to identify the positions of all the atoms.

Click on Label check box from the Display Types drop down. To label, Click on Label check box from the Display Types drop down.
Cursor on molecule To get Maltose we need to remove a water molecule.
Delete atoms. Delete the OH group on C-1 of first molecule and hydrogen on C-9 of second molecule.
Select Carbon in draw tool settings Select Carbon in Draw tool settings.
Select Single' as Bond Order Select Single as Bond Order.
Uncheck the Adjust Hydrogens check box Uncheck Adjust Hydrogens check box.
Cursor on molecule Click and drag to join C-1 of first molecule and C-9 of second molecule through oxygen atom.
We need to optimize the geometry.
Select Auto Optimization tool. Select Auto Optimization tool.
Auto optimization settings appears. Auto Optimization settings menu appears on the left.
Select MMFF94 force field, click on Start. Select MMFF94 force field and click on Start.
The optimization may take a few seconds to complete.

You may remove the labels now

Cursor on the Panel We now have an optimized structure of Maltose on Panel.
Slide Number 5

Summary

Let's summarize. In this tutorial we have learnt to:

Add and delete atoms

Add and delete bonds

Rotate bonds

Change Bond length

Change Hydrogen to Methyl group

Copy, paste and join structures.

Slide Number 6

Assignment

As an assignment,

Create a Butane molecule using draw tool

Convert it into 2,3 dimethyl Butane

Rotate the bonds and change bond lengths.

Slide Number 7

Assignment

Create a molecule of cellulose
(Hint: D- glucose monomer is available in the Insert fragment library)

Optimize the geometry using UFF force field.

Slide Number 8

Acknowledgement

Watch the video available at

http://spoken-tutorial.org

/What is a Spoken Tutorial

It summarises the Spoken Tutorial

project.

If you do not have good bandwidth,

you can download and watch it.

This video summarises the Spoken Tutorial project

If you do not have good bandwidth, you can download and watch it.

Slide Number 9

The Spoken Tutorial Project Team

Conducts workshops using spoken

tutorials

Gives certificates to those who pass an online test

For more details, please write to

contact@spoken-tutorial.org

We conduct workshops using Spoken Tutorials and give certificates.

Please contact us.

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

http://spoken-tutorial.org

/NMEICT-Intro

The Spoken Tutorial Project is funded by NMEICT, MHRD Government of India
This tutorial is contributed by Viswa Janani Vasudhevan and Madhuri Ganapathi.

Thank you for joining.

Contributors and Content Editors

Madhurig, Visjan

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