Avogadro/C2/Edit-molecules/English-timed

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.
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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