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

Revision as of 12:52, 6 June 2017

{{| border=1 ||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. |- |}