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

Latest revision as of 12:55, 6 June 2017

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

Contributors and Content Editors

Madhurig, Visjan

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 ||  Warm greetings everyone.

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

Latest revision as of 12:55, 6 June 2017

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