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− | {| Border = 1 | + | {| border=1 |
− | |'''Time''' | + | ||'''Visual Cue''' |
− | | '''NARRATION''' | + | ||'''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. | + | |
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| Welcome to this tutorial on '''Edit molecules.''' | | Welcome to this tutorial on '''Edit molecules.''' |
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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 2''' | + | || '''Slide Number 2''' |
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| '''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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| + | Add and delete atoms |
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| + | Add and delete bonds |
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| + | Rotate bonds |
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| + | Change length of the bond |
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| + | Change hydrogen to methyl group |
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− | * Add and delete atoms
| + | Copy, paste and join structures. |
− | * Add and delete bonds
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− | * Rotate bonds
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− | * Change length of the bond
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− | * Change hydrogen to methyl group
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− | * Copy, paste and join structures.
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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''' |
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| '''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 |
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− | '''Ubuntu Linux '''OS version. 14.04 | + | '''Ubuntu Linux''' OS version. 14.04 |
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| '''Avogadro''' version 1.1.1. | | '''Avogadro''' version 1.1.1. |
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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''' |
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| '''Pre-requisties''' | | '''Pre-requisties''' |
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− | You should be familiar with: | + | You should be familiar with, |
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| For relevant tutorials, visit our website. | | For relevant tutorials, visit our website. |
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− | '''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: |
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| '''Avogadro ''' interface. | | '''Avogadro ''' interface. |
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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;"| Here I will show how to open '''Avogadro '''using the '''Terminal. ''' | + | || Here I will show how to open '''Avogadro ''' using the '''Terminal'''. |
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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;"| 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. |
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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;"| 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. |
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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;"| 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. |
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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;"| Click on '''Build''' menu. | + | || Click on '''Build''' menu. |
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| Navigate to '''Insert->Fragment''' | | Navigate to '''Insert->Fragment''' |
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| '''Insert fragment''' dialog box appears. | | '''Insert fragment''' dialog box appears. |
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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;"| Click on '''Build''' menu. | + | || Click on '''Build''' menu. |
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| Navigate to '''Insert->Fragment''' | | Navigate to '''Insert->Fragment''' |
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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;"| Point to '''Insert Fragment''' dialog box | + | || Point to '''Insert Fragment''' dialog box |
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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;"| From the list of fragments, double click on '''alkanes''' folder to open. | + | || From the list of fragments, double click on '''alkanes''' folder to 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;"| 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. |
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| Click on X to close '''Insert Fragment''' dialog box. | | Click on X to close '''Insert Fragment''' dialog 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;"| 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'''. |
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| To remove the highlighting, Press '''Ctrl, Shift '''and '''A '''keys simultaneously. | | To remove the highlighting, Press '''Ctrl, Shift '''and '''A '''keys simultaneously. |
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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;"| 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. |
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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;"| We will now learn how to add atoms to the molecule. | + | || We will now learn how to add atoms 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;"| 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. |
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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 end carbon atom, drag on the '''Panel.''' | + | || Click on end carbon atom, drag on the '''Panel.''' |
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| 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.''' |
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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;"| 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'''. |
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| 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. |
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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;"| 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. |
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| Draw propane using '''Draw tool.''' | | Draw propane using '''Draw tool.''' |
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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;"| 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'''. |
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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 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. |
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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 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. |
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| Selected atoms appears blue in color. | | Selected atoms appears blue in 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;"| Press Backspace to delete. | + | || Press Backspace to delete. |
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| 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. |
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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;"| 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. |
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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;"| Select the '''Draw tool''' icon | + | || Select the '''Draw tool''' icon |
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| '''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. |
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| '''Draw Settings''' menu open on the left. | | '''Draw Settings''' menu open on the left. |
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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;"| Point to '''Element '''drop down list. | + | || Point to '''Element ''' drop down list. |
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− | 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. |
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| To introduce a double bond select '''Double''' from '''Bond Order '''drop down. | | To introduce a double bond select '''Double''' from '''Bond Order '''drop down. |
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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 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. |
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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;"| Select Triple from bond order. | + | || Select Triple from bond order. |
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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;"| 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.''' |
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| 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;"| Hold the right mouse button and click on the bonds. | + | || Hold the right mouse button and click on the bonds. |
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| 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. |
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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;"| Let's rejoin the molecules. | + | || Let's rejoin the molecules. |
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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;"| 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. |
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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 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. |
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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 '''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. |
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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;"| '''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. |
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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 '''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. |
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| '''Snap-to Threshold''' set to '''10<sup>0'''</sup>(10 degree). | | '''Snap-to Threshold''' set to '''10<sup>0'''</sup>(10 degree). |
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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 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. |
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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;"| We need to fix the plane of rotation of the bonds. | + | || We need to fix the plane of rotation of the bonds. |
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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 Bond. | + | || Cursor on the Bond. |
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| 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. |
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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 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 267: |
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 327: |
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 361: |
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 398: |
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 ''' |
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| | | |
| 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 |
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Line 527: |
| | | |
| '''contact@spoken-tutorial.org''' | | '''contact@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;"| * We conduct workshops using Spoken Tutorials and give certificates. | + | || We conduct workshops using Spoken Tutorials and give certificates. |
− | * Please contact us.
| + | |
− | | + | |
| | | |
| + | Please contact us. |
| |- | | |- |
− | | 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''' |
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| '''/NMEICT-Intro ''' | | '''/NMEICT-Intro ''' |
− | | + | || The Spoken Tutorial Project is funded by '''NMEICT, MHRD''' '''Government of '''India |
− | | + | |
− | | + | |
− | | 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 is funded by '''NMEICT, MHRD''' '''Government of '''India | + | |
− | | + | |
− | | + | |
| |- | | |- |
− | | 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 tutorial is contributed by Viswa Janani Vasudhevan and Madhuri Ganapathi. | + | || This tutorial is contributed by Viswa Janani Vasudhevan and Madhuri Ganapathi. |
| | | |
| Thank you for joining. | | Thank you for joining. |
− | | + | |- |
− | | + | |
| |} | | |} |
Visual Cue
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Narration
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Title Slide
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Warm greetings everyone.
Welcome to this tutorial on Edit molecules.
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Slide Number 2
Learning Objectives
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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.
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Slide Number 3
System Requirement
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Here I am using
Ubuntu Linux OS version. 14.04
Avogadro version 1.1.1.
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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.
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Press CTRL+ALT+T keys simultaneously.
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To open the terminal press CTRL, ALT and T keys simultaneously.
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Type avogadro at the prompt, press enter.
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Type avogadro at the prompt and press enter.
Avogadro application window opens.
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Cursor on the Panel
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For demonstration, I will display a molecule of n-butane from the Fragment library.
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Click on Build menu.
Navigate to Insert->Fragment
Insert fragment dialog box appears.
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Click on Build menu.
Navigate to Insert->Fragment
Insert fragment dialog box appears.
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Point to Insert Fragment dialog box
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From the list of fragments, double click on alkanes folder to open.
Select butane.cml from the drop down that appears.
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Close Insert Fragment dialog box
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Click on Insert button.
Click on X to close Insert Fragment dialog box.
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Point to Butane molecule
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Butane molecule highlighted in blue color appears on the Panel.
To remove the highlighting, Press Ctrl, Shift and A keys simultaneously.
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Point to the navigation tool.
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Rotate the structure using Navigation tool to get proper alignment.
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Cursor on the molecule
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We will now learn how to add atoms to the molecule.
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Click on Draw tool icon.
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Click on Draw tool icon on the tool bar.
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Click on end carbon atom, drag on the Panel.
Point to molecule.
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Click on end Carbon atom and drag on the Panel.
A carbon atom with required hydrogens get added.
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Point to molecule.
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We now have a molecule of pentane on Panel.
Similarly, you can add atoms using Draw tool to make a series of alkanes.
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Point to Draw tool.
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Open a new window.
Draw propane using Draw tool.
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Cursor on the molecule.
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Let us delete the end Carbon atom with hydrogens to get a molecule of Ethane.
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Click on the Selection tool icon
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To delete atoms, click on the Selection tool icon on the tool bar.
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Cursor on the end carbon atom
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Click and drag over the end Carbon atom to make the selection.
Selected atoms appears blue in color.
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Press Backspace to delete.
Point to Edit menu
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Press Backspace to delete.
Alternatively you can use clear option in Edit menu.
To redo, press Ctrl and Z keys simultaneously.
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Cursor on the molecule
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We will demonstrate on how to add and delete bonds in a molecule.
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Select the Draw tool icon
Draw settings appears
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To add bonds select the Draw tool icon on the tool bar.
Draw Settings menu open on the left.
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Point to Element drop down list.
Point to Bond Order drop down.
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By default Carbon is selected in Element drop down list.
To introduce a double bond select Double from Bond Order drop down.
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Cursor on the Bond between C-1 and C-2
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Click on the bond between C-1 and C-2 to convert it to a double bond.
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Select Triple from bond order.
Click on the bond.
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To convert double bond into a triple bond, select Triple from Bond Order.
Click on the bond.
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Hold the right mouse button and click on the bonds.
Point to the molecules.
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To delete bonds, hold the right mouse button and click on the bonds.
This results in two different molecules.
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Let's rejoin the molecules.
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Select Carbon from draw tool settings
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Click on Carbon of one molecule, drag and click on carbon of other molecule.
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Cursor on the Panel
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We can rotate bonds and change bond lengths using Bond Centric Manipulation tool.
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Cursor on Bond Centric Manipulation tool
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Click on Bond Centric Manipulation tool on the tool bar.
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Bond Centric Manipulate settings appears
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Bond Centric Manipulate settings menu opens on the left.
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Cursor on Bond Centric Manipulate settings
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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.
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Cursor on the Bond
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To show angles, click on the bond between two atoms.
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We need to fix the plane of rotation of the bonds.
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Cursor on the Bond.
Point to the plane.
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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.
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Click on atom, move.
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To Rotate, click on one of the atoms and move.
Attached bond along with the atoms rotates in the fixed plane.
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Click on atom with right mouse button
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To change length of the bond hold the right mouse button and drag.
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Cursor on molecule
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Now we will show how to change Hydrogens to methyl groups.
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Click on Build menu.
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Click on Build menu and click on Change H To Methyl.
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Point to molecule
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All Hydrogens are now replaced by Methyl groups.
Press CTRL and Z keys simultaneously to undo the changes.
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Cursor on the Panel.
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We can also select a particular hydrogen atom and change it to a methyl group.
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Click on selection tool
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Click on Selection tool icon on the tool bar
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Click on the hydrogen.
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Click on the hydrogen attached to end carbon atom to select.
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Go to Build menu, click on Change H to Methyl.
Cursor on molecule
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Go to Build menu and click on Change H to Methyl.
The selected Hydrogen gets replaced by methyl group.
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Press Ctrl+Shift+A.
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To deselect, Press Ctrl, Shift and A keys simultaneously.
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Let us take a look as how to copy, paste and join structures.
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Click on File-> New
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Click on File-> New to open a new window.
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Cursor on panel
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We will learn to build a Maltose molecule.
Maltose is made up of two glucose molecules.
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Click on Build menu
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To insert a glucose molecule, click on Build menu.
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Scroll down and click on
Insert->Fragment
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Scroll down and click on Insert -> Fragment
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Insert -> Fragment dialog box appears
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Insert -> Fragment dialog box appears.
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Cursor on Insert Fragment dialog box
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Scroll down the list and click on Cyclic sugar folders.
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A sub menu appears
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A sub menu appears.
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Navigate down and select beta-d-glucopyranose.cml.
Close the dialog box
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Navigate down and select
beta-d-glucopyranose.cml.
Click on Insert button.
Close the dialog box.
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Point to molecule
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beta-D-glucopyranose.cml appears on panel highlighted in blue color.
Translate it to the center using hand tool.
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Cursor on Panel
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Let us copy and paste another glucose molecule.
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Click on Edit menu
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Click on Edit menu on the menu bar.
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Scroll down and click on Copy
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And click on Copy.
Again Scroll down the edit menu and then click Paste.
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Cursor on panel
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Please note during copy, paste operation, window dims for a moment and then recovers.
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Point to the new molecule.
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A new molecule gets copied and pasted on the existing molecule on the Panel.
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Move with the left mouse button
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The cursor changes to a hand tool.
Move the copied molecule from the original molecule.
Now we have two separate molecules on the Panel
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Press Ctrl+Shift+A.
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To de-select Press Ctrl, Shift and A keys simultaneously.
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Let us label the molecules.
Labeling helps to identify the positions of all the atoms.
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Click on Label check box from the Display Types drop down.
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To label, Click on Label check box from the Display Types drop down.
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Cursor on molecule
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To get Maltose we need to remove a water molecule.
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Delete atoms.
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Delete the OH group on C-1 of first molecule and hydrogen on C-9 of second molecule.
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Select Carbon in draw tool settings
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Select Carbon in Draw tool settings.
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Select Single' as Bond Order
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Select Single as Bond Order.
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Uncheck the Adjust Hydrogens check box
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Uncheck Adjust Hydrogens check box.
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Cursor on molecule
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Click and drag to join C-1 of first molecule and C-9 of second molecule through oxygen atom.
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We need to optimize the geometry.
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Select Auto Optimization tool.
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Select Auto Optimization tool.
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Auto optimization settings appears.
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Auto Optimization settings menu appears on the left.
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Select MMFF94 force field, click on Start.
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Select MMFF94 force field and click on Start.
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The optimization may take a few seconds to complete.
You may remove the labels now
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Cursor on the Panel
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We now have an optimized structure of Maltose on Panel.
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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.
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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.
|