Avogadro/C2/Build-molecules/English-timed

Time	Narration
00:01	Warm greetings everyone!! Welcome to this tutorial on Build Molecules.
00:07	In this tutorial, we will learn to: Import molecules from database,
00:11	Rotate, zoom in and zoom out,
00:15	build molecules on the panel,
00:17	set up force field and optimize geometry,
00:21	measure bond lengths, bond angles, dihedral angles,
00:25	show fragment library,
00:27	build DNA molecules and Peptides.
00:31	Here I am using: Ubuntu Linux OS version 14.04 , Avogadro version 1.1.1, working internet connection.
00:44	To follow this tutorial, you should have knowledge of basic Chemistry. To download Avogadro, please use the link shown sourceforge.net/projects/avogadro.
00:53	I have already downloaded Avogadro.
00:56	To open Avogadro , click on Dash home .
01:00	In the search bar, type avogadro .
01:02	Click on Avogadro icon to open the application.
01:08	Let's begin by importing a xylene molecule from chemical structure database .
01:15	To import a molecule, we need a working internet connection.
01:19	Click on File menu, navigate to Import .
01:23	A sub-menu opens.
01:25	Select Fetch by chemical name .
01:28	Chemical name dialog box appears.
01:30	For demonstration, I will type xylene in the search box.
01:36	Click on OK button.
01:38	We now have a xylene molecule on the Panel .
01:42	Let's rotate the molecule on the Panel .
01:45	Click on Navigation tool on the tool bar.
01:49	Place the cursor on the molecule.
01:52	Hold the left mouse button and drag.
01:56	Notice the direction arrows indicating the drag.
02:00	To translate the molecule, use right mouse button and drag.
02:06	Scroll the mouse wheel to zoom in and zoom out the structure.
02:10	Let's learn how to create a molecule.
02:14	To create a molecule, click on Draw Tool icon on the tool bar.
02:19	Under Draw Settings menu, we can see Element drop down button, Bond Order drop down button, Adjust Hydrogens check box.
02:30	If you don't want hydrogens on the structure, un-check Adjust Hydrogens check box.
02:37	Element drop-down list shows list of elements.
02:42	Click on Other to view the entire Periodic table in a separate window.
02:48	Click on Close (X) to close the window.
02:51	Let's draw structure of Aniline on the Panel .
02:55	Select Carbon from Element drop down list.
02:59	Select Single from Bond Order drop down.
03:03	Click on the Panel .
03:05	Drag and drop to make a closed chain of six carbon atoms.
03:10	To show double-bonds, select Double from Bond Order drop-down.
03:16	Click on alternate bonds to obtain Benzene structure.
03:21	Let's complete Aniline structure.
03:24	Select Nitrogen from Element drop down list.
03:29	Select Single from Bond Order drop down.
03:33	Click on any one of the carbon atoms on the structure and drag.
03:39	Go to Build menu and select Add Hydrogens .
03:45	We have the structure of Aniline on the Panel.
03:49	To get a stable conformation, Aniline structure on the Panel needs to be optimized.
03:56	To optimize, click on Auto Optimization Tool on the tool bar.
04:02	AutoOptimization Settings menu appears on the left.
04:06	Click on Force Field drop-down list, select MMFF94 .
04:13	MMFF94 is generally used to optimize small organic molecules.
04:20	Click on Start button.
04:23	It will take a few seconds to complete the optimization.
04:28	Click on Stop to close the Optimization Settings.
04:33	Let's measure bond lengths, bond angles and dihedral angles of Aniline .
04:40	Select Click to Measure icon on the tool bar.
04:44	To measure distance, click on any two consecutive carbon atoms.
04:49	To measure angles, click on any 3 consecutive atoms.
04:55	To measure dihedral angles, click on any 4 consecutive atoms.
05:02	Measured values appear at the bottom of the Panel .
05:07	To save the file, click on File and Save As .
05:13	Save Molecule As dialog-box appears.
05:17	Type the File Name as Aniline.cml .
05:21	Choose the location as Desktop and click on Save button.
05:28	Click on New icon to open a new window.
05:32	Avogadro software has a feature to build complex molecules using fragment library.
05:38	Go to Build menu.
05:40	Navigate to Insert and select Fragment option.
05:45	Insert Fragment dialog box opens.
05:49	We can see list of folders having cml files of different chemical structures.
05:55	For example, let's open alkenes folder.
06:00	Double click on the folder to view the contents of the folder.
06:04	Select 2-methyl-buta-1,3-diene.cml .
06:10	Click on Insert button.
06:13	Click on Close to close the dialog box.
06:17	2-methyl-1,3-butadiene structure is displayed on the Panel .
06:22	It is commonly called as Isoprene.
06:26	We can build many natural products using Isoprene .
06:30	The molecule is in select mode.
06:33	To de-select, press CTRL, SHIFT and A keys simultaneously.
06:39	As an example: I will show Vitamin A and natural rubber which were built using Isoprene .
06:47	Vitamin A, natural rubber .
06:51	I will translate Isoprene to a corner.
06:56	Click on Build menu, navigate to Insert and select Fragment .
07:02	Scroll down to macrocycles folder; double click to open.
07:08	Select porphin fragment and click on Insert .
07:14	Close the dialog box.
07:16	Using porphyrin fragment, we can build complex chemical structures such as: Chlorophyll and Vitamin B12 .
07:25	Chlorophyll
07:27	Vitamin B12.
07:30	Complex molecules like DNA and peptides can be easily built using Avogadro .
07:37	Open a new window using New icon.
07:41	To insert a DNA molecule, go to Build menu, navigate to Insert and click on DNA/RNA from the sub-menu.
07:51	Insert Nucleic Acids dialog box appears.
07:55	Select DNA from DNA/RNA Builder drop down.
08:00	Four nucleic acid bases are shown as buttons.
08:05	Click on the buttons to choose the nucleic acid sequence.
08:10	You can choose your own sequence of acids .
08:14	For demonstration, I will select A T G C A T G C.
08:26	The order of selection of nucleic acids appear in the Sequence text box.
08:32	In the Bases Per Turn drop down, select A, select "5" which is the number of base pairs per Helix .
08:41	Select Strands as Single and click on Insert button.
08:47	Click on Close to close the dialog box.
08:51	We now have a single stranded DNA molecule on the Panel .
08:56	Zoom out the structure and drag to the center of the Panel .
09:01	To deselect the DNA molecule on the Panel , press CTRL, Shift and A keys simultaneously.
09:09	We can also create a Peptide sequence using Peptide option in the Insert menu.
09:16	Again click on New icon to open a new window.
09:21	Go to Build menu, scroll down to Insert and Peptide .
09:26	Insert Peptide dialog box appears.
09:29	Select amino acids for the Peptide sequence by clicking on the amino acids button.
09:36	For demonstration, I will choose the sequence as Glycine(Gly) -Valine(Val) -Proline(Pro) and Cystine(Cys) .
09:45	The order of selection appears in the Sequence text box.
09:50	Click on Insert Peptide button.
09:53	Close the Insert Peptide dialog box.
09:57	Peptide chain appears on the Panel .
10:00	To de-select the Peptide on Panel , press CTRL, Shift and A keys simultaneously.
10:07	You can choose the amino acids of your choice and build the Peptide sequence.
10:13	Let's summarize.
10:15	In this tutorial, we learnt to :
10:18	import molecules from the database,
10:21	rotate, zoom in and zoom out,
10:24	build molecules on the panel,
10:26	set up force field and optimize geometry,
10:30	measure bond lengths, bond angles, dihedral angles,
10:35	show fragment library,
10:37	Build DNA molecules and Peptides .
10:41	As an assignment - Create a protein sequence using the following amino acid residues:
10:49	Optimize the geometry using UFF force field.
10:53	Save the image as .cml file.
10:58	Build RNA sequence using the Nucleic acids: AUGC .
11:04	Optimize geometry using MMFF94 force field.
11:10	Save the image as .cml file.
11:14	This video summarizes the Spoken Tutorial project.
11:18	If you do not have good bandwidth, you can download and watch it.
11:23	We conduct workshops using Spoken Tutorials and give certificates. Please contact us.
11:30	Spoken Tutorial Project is funded by NMEICT, MHRD Government of India.
11:36	This tutorial is contributed by Viswa Janani Vasudhevan and Madhuri Ganapathi. Thank you for joining.

Contributors and Content Editors

PoojaMoolya, Sandhya.np14