Avogadro/C2/Edit-molecules/English
{{| 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
/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
/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. |- |}
