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

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|-
 
|-
−
|| Cursor on the '''Menu bar'''
+
|style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the Panel
 +
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Cursor on the '''Menu bar'''
  
 
Insert fragment dialog box appears.
 
Insert fragment dialog box appears.
−
| | Click on '''Build''' menu.  
+
|-
 +
|style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Click on '''Build''' menu.
 +
 
 +
Navigate to '''Insert->Fragment'''
 +
 
 +
'''Insert fragment''' dialog box appears.
 +
 
 +
|  style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Click on '''Build''' menu.  
  
 
Navigate to '''Insert->Fragment'''
 
Navigate to '''Insert->Fragment'''
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| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Click on''' Insert''' button.
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Click on''' Insert''' button.
  
−
Click on X to close '''Insert Fragment''' dialogue box.
+
Click on X to close '''Insert Fragment''' dialog box.
  
 
|-
 
|-
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Alternatively you can use clear option in '''Edit''' menu.
 
Alternatively you can use clear option in '''Edit''' menu.
  
−
To redo, press '''Ctrl and Z keys '''simutaneously.
+
To redo, press '''Ctrl and Z keys '''simultaneously.
  
 
|-
 
|-
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|-
 
|-
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"|  
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Point to '''Element '''drop down list.
 +
 
 +
Point to '''Bond Order '''drop down.
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| By default '''Carbon''' is selected in '''Element '''drop down list.
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| By default '''Carbon''' is selected in '''Element '''drop down list.
  
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|-
 
|-
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Bond Centric Manipulation''' settings appears
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Bond Centric Manipulate''' settings appears
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| '''Bond Centric Manipulation '''settings menu opens on the left.
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| '''Bond Centric Manipulation '''settings menu opens on the left.
  
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|-
 
|-
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on '''Build menu'''
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on '''Build menu'''
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Click on '''Build '''menu''', '''navigate down and click on '''Change H To Methyl.'''
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Click on '''Build '''menu''' and click on '''Change H To Methyl.'''
  
 
|-
 
|-
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|-
 
|-
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on selection tool
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on selection tool
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Click on '''Selection tool '''on the tool bar
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Click on '''Selection tool '''icon on the tool bar
  
 
|-
 
|-
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|-
 
|-
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Go to Build menu
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Go to '''Build''' menu, click on '''Change H to Methyl'''.
−
 
+
−
 
+
−
Navigate down and click on Change H to Methyl group
+
  
  
 
Cursor on molecule
 
Cursor on molecule
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Go to '''Build''' menu, navigate down and click on change '''H to Methyl.'''
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Go to '''Build''' menu and click on '''Change H to Methyl.'''
  
  
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| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Navigate down and select beta-d-glucopyranose.cml  
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Navigate down and select beta-d-glucopyranose.cml  
  
−
Click on X to close the dialog box
+
Close the dialog box
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Navigate down and select
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Navigate down and select
  
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Click on '''Insert''' button.
 
Click on '''Insert''' button.
  
−
Click on X to close the dialog box.
+
Close the dialog box.
  
 
|-
 
|-
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|-
 
|-
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Scroll down and click on Copy
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Scroll down and click on Copy
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Scroll down and click on '''Copy'''.
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| And click on '''Copy'''.
  
  
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|-
 
|-
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Press Ctrl+Shift+A.
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Press Ctrl+Shift+A.
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To de-select Press '''Ctrl, Shift '''and''' A''' keys simutaneously.
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To de-select Press '''Ctrl, Shift '''and''' A''' keys simultaneously.
  
 
|-
 
|-
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|-
 
|-
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"|  
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on '''Label''' check box from the''' Display Types''' drop down.
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To label, Click on '''Label''' check box from the''' Display Types''' drop down.
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To label, Click on '''Label''' check box from the''' Display Types''' drop down.
  

Revision as of 11:58, 20 January 2016

Visual Cue
Narration
Slide Number 1

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.
Cursor on the Panel Cursor on the Menu bar

Insert fragment dialog box appears.

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 Manipulation settings menu opens on the left.
Cursor on Bond Centric Manipulation 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.

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 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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