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

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|| And click on '''Copy'''. Again Scroll down the edit menu and then click '''Paste'''.
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|| And click on '''Copy'''. Again scroll down the '''Edit''' menu and then click '''Paste'''.
  
 
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|| Please note: during copy, paste operation, window dims for a moment and then recovers.
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|| Please note: during '''copy, paste''' operation, window dims for a moment and then recovers.
  
 
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|| A new molecule gets copied and pasted on the existing molecule on the '''Panel'''.
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||Now we have two separate molecules on the Panel.
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|| To de-select Press '''Ctrl, Shift ''' and '''A''' keys simultaneously.
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|| To de-select, press '''Ctrl, Shift ''' and '''A''' keys simultaneously.
  
 
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|| To label, 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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|| To get '''Maltose''', we need to remove a water molecule.  
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|| To get '''maltose''', we need to remove a water molecule.  
 
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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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|| Click and drag to join C-1 of first molecule and C-9 of second molecule through '''oxygen''' atom.
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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 now have an optimized structure of '''Maltose''' on Panel.
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||add and delete bonds,
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||change Hydrogen to Methyl group,
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|| As an assignment, create a '''Butane''' molecule using draw tool.
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|| As an assignment, create a '''Butane''' molecule using '''draw''' tool.
  
 
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||Create a molecule of '''cellulose'''  (Hint: D- glucose monomer is available in the Insert fragment library)
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||Create a molecule of '''cellulose'''  (Hint: D- glucose monomer is available in the '''Insert fragment''' library)
  
 
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Latest revision as of 21:46, 6 July 2018

Time Narration
00:01 Warm greetings everyone. Welcome to this tutorial on Edit molecules.
00:08 In this tutorial, we will learn to- add and delete atoms,
00:14 add and delete bonds,
00:16 rotate bonds,
00:18 change length of the bond,
00:20 change hydrogen to methyl group,
00:23 copy, paste and join structures.
00:27 Here I am using:

Ubuntu Linux OS version. 14.04,

Avogadro version 1.1.1.

00:37 To follow this tutorial, you should be familiar with: Avogadro interface.
00:43 If not, for relevant tutorials, please visit our website.
00:49 Here I will show how to open Avogadro using the Terminal.
00:55 To open the terminal, press CTRL, ALT and T keys simultaneously.
01:03 Type avogadro at the prompt and press Enter.
01:08 Avogadro application window opens.
01:12 For demonstration, I will display a molecule of n-butane from the Fragment library.
01:19 Click on Build menu. Navigate to Insert->Fragment
01:25 Insert fragment dialog box appears.
01:29 From the list of fragments, double click on alkanes folder to open.
01:35 Select butane.cml from the drop down that appears.
01:41 Click on Insert button. Click on X to close Insert Fragment dialog box.
01:49 Butane molecule, highlighted in blue color, appears on the Panel.
01:54 To remove the highlighting, Press Ctrl, Shift and A keys simultaneously.
02:02 Rotate the structure using Navigation tool to get proper alignment.
02:09 We will now learn how to add atoms to the molecule.
02:14 Click on Draw tool icon on the tool bar.
02:18 Click on end Carbon atom and drag on the Panel.
02:23 A carbon atom with required hydrogens get added.
02:27 We now have a molecule of pentane on Panel.
02:32 Similarly, you can add atoms using Draw tool to make a series of alkanes.
02:39 Open a new window. Draw propane using Draw tool.
02:45 Let us delete the end Carbon atom with hydrogens to get a molecule of Ethane.
02:52 To delete atoms, click on the Selection tool icon on the tool bar.
02:57 Click and drag over the end Carbon atom to make the selection.
03:02 Selected atoms appear blue in color.
03:06 Press Backspace to delete. Alternatively, you can use clear option in Edit menu.
03:14 To redo, press Ctrl and Z keys simultaneously.
03:20 We will demonstrate on how to add and delete bonds in a molecule.
03:26 To add bonds, select the Draw tool icon on the tool bar.
03:31 Draw Settings menu opens on the left.
03:35 By default, Carbon is selected in the Element drop down list.
03:40 To introduce a double bond, select Double from Bond Order drop down.
03:46 Click on the bond between C-1 and C-2 to convert it to a double bond.
03:52 To convert double bond into a triple bond, select Triple from Bond Order.

Click on the bond.

03:59 To delete bonds, hold the right mouse button and click on the bonds.
04:04 This results in two different molecules.
04:08 Let's rejoin the molecules.
04:11 Click on Carbon of one molecule, drag and click on carbon of other molecule.
04:18 We can rotate bonds and change bond lengths using Bond Centric Manipulation tool.
04:24 Click on Bond Centric Manipulation tool on the tool bar.
04:29 Bond Centric Manipulate settings menu opens on the left.
04:34 By default, Show Angles and Snap-to Bonds are checked.
04:39 Snap-to Threshold set to 100(10 degree).
04:43 Users can make their own choice of settings as per the requirements.
04:49 To show angles, click on the bond between two atoms.
04:55 We need to fix the plane of rotation of the bonds.
04:59 To fix the plane you want, click on the bond and move upwards or downwards.
05:05 The plane between the atoms appears in blue or yellow color.
05:11 To Rotate, click on one of the atoms and move.
05:16 Attached bond along with the atoms rotates in the fixed plane.
05:21 To change length of the bond, hold the right mouse button and drag.
05:27 Now we will show how to change Hydrogens to methyl groups.
05:32 Click on Build menu and click on Change H To Methyl.
05:38 All Hydrogens are now replaced by Methyl groups.
05:43 Press CTRL and Z keys simultaneously to undo the changes.
05:49 We can also select a particular hydrogen atom and change it to a methyl group.
05:55 Click on Selection tool icon on the tool bar
05:59 Click on the hydrogen attached to end carbon atom to select.
06:04 Go to Build menu and click on Change H to Methyl.
06:10 The selected Hydrogen gets replaced by methyl group.
06:15 To deselect, Press Ctrl, Shift and A keys simultaneously.
06:22 Let us take a look as how to copy, paste and join structures.
06:28 Click on File-> New to open a new window.
06:33 We will learn to build a Maltose molecule.
06:37 Maltose is made up of two glucose molecules.
06:41 To insert a glucose molecule, click on Build menu.
06:46 Scroll down and click on Insert -> Fragment
06:51 Insert Fragment dialog box appears.
06:55 Scroll down the list and click on Cyclic sugar folders.
07:01 A sub menu appears.
07:04 Navigate down and select beta-d-glucopyranose.cml.
07:10 Click on Insert button. Close the dialog box.
07:16 beta-D-glucopyranose.cml appears on panel highlighted in blue color.
07:24 Translate it to the center, using hand tool.
07:28 Let us copy and paste another glucose molecule.
07:33 Click on Edit menu on the menu bar.
07:36 And click on Copy. Again scroll down the Edit menu and then click Paste.
07:44 Please note: during copy, paste operation, window dims for a moment and then recovers.
07:51 A new molecule gets copied and pasted on the existing molecule on the panel.
07:58 The cursor changes to a hand tool.
08:01 Move the copied molecule from the original molecule.
08:06 Now we have two separate molecules on the panel.
08:10 To de-select, press Ctrl, Shift and A keys simultaneously.
08:17 Let us label the molecules. Labeling helps to identify the positions of all the atoms.
08:25 To label, click on Label check-box from the Display Types drop down.
08:32 To get maltose, we need to remove a water molecule.
08:37 Delete the OH group on C-1 of first molecule and hydrogen on C-9 of second molecule.
08:46 Select Carbon in Draw tool settings.
08:50 Select Single as Bond Order.
08:54 Uncheck Adjust Hydrogens check box.
08:58 Click and drag to join C-1 of first molecule and C-9 of second molecule through oxygen atom.
09:07 We need to optimize the geometry.
09:11 Select Auto Optimization tool.
09:15 Auto Optimization settings menu appears on the left.
09:20 Select MMFF94 force field and click on Start.
09:27 The optimization may take a few seconds to complete. You may remove the labels now.
09:35 We now have an optimized structure of maltose on panel.
09:40 Let's summarize. In this tutorial, we have learnt to: add and delete atoms,
09:47 add and delete bonds,
09:50 rotate bonds,
09:52 change bond length,
09:54 change hydrogen to methyl group,
09:56 copy, paste and join structures.
10:00 As an assignment, create a Butane molecule using draw tool.
10:06 Convert it into 2,3 dimethyl Butane.
10:10 Rotate the bonds and change bond lengths.
10:14 Create a molecule of cellulose (Hint: D- glucose monomer is available in the Insert fragment library)
10:22 Optimize the geometry using UFF force field.
10:27 This video summarises the Spoken Tutorial project. If you do not have good bandwidth, you can download and watch it.
10:36 We conduct workshops using Spoken Tutorials and give certificates. Please contact us.
10:44 The Spoken Tutorial Project is funded by NMEICT, MHRD Government of India.
10:52 This tutorial is contributed by Viswa Janani Vasudhevan and Madhuri Ganapathi.

Thank you for joining.

Contributors and Content Editors

PoojaMoolya, Sandhya.np14

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