Avogadro/C2/Edit-molecules/English-timed
From Script | Spoken-Tutorial
| 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. |
