Difference between revisions of "GChemPaint/C2/Edit-Preferences-Templates-and-Residues/English"

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Title of the tutorial: Edit-Preferences-Templates-and-Residues
 +
 +
Author: Madhuri Ganapathi
 +
 +
Key words: Edit Preferences, Manage Templates, Add New Templates, Residues, edit Residues,Video tutorial.
 +
 +
GChemPaint tools-  Add an arrow for an irreversible reaction, Add a pair of Arrows for a reversible reaction, Add an arrow for a retrosynthesis step, Add a double headed arrow to represent mesomery.
 +
 
{|border =1
 
{|border =1
 
!Visual Cue
 
!Visual Cue
Line 8: Line 16:
 
||Hello everyone.
 
||Hello everyone.
  
−
Welcome the tutorial on '''Edit Preferences, Templates''' and '''Residues''' in '''GChemPaint'''.
+
Welcome to the tutorial on '''Edit Preferences, Templates''' and '''Residues''' in '''GChemPaint'''.
 
|-
 
|-
 
||
 
||
Line 27: Line 35:
 
We will also learn  
 
We will also learn  
  
−
* The uses of Residues  
+
* The uses of Residues and
  
 
* To edit Residues.
 
* To edit Residues.
Line 50: Line 58:
 
|-
 
|-
 
||Switch to '''GChemPaint''' application.
 
||Switch to '''GChemPaint''' application.
−
||I have opened a new '''GChemPaint''' application.
+
||I have already opened a new '''GChemPaint''' application.
 
|-
 
|-
 
||
 
||
Line 61: Line 69:
 
|-
 
|-
 
||Point to  the field
 
||Point to  the field
−
||The first field, '''Default Compression Level For GChemPaint Files''', is used when saving files.
+
||The first field, '''Default Compression Level For GChemPaint Files''', is used when saving files.
  
 
By default, it is zero.
 
By default, it is zero.
Line 72: Line 80:
 
|-
 
|-
 
||Point to '''Default Theme''' >> then click on the drop-down to show the options
 
||Point to '''Default Theme''' >> then click on the drop-down to show the options
−
||In''' GchemPaint,''' each document has an associated theme.  
+
||In ''' GchemPaint,''' each document has an associated theme.  
  
−
Let's retain the '''Default Theme''' as''' GChemPaint.'''
+
Let's retain the '''Default Theme''' as ''' GChemPaint.'''
 
|-
 
|-
 
||Point to ''' Arrows'''
 
||Point to ''' Arrows'''
−
||Now, I will explain about''' Arrows'''  in detail, under '''Themes''' section.
+
||Now, I will explain about ''' Arrows'''  in detail, under '''Themes''' section.
 
|-
 
|-
 
||Point to the arrows
 
||Point to the arrows
Line 86: Line 94:
 
* Add a pair of Arrows for a reversible reaction.
 
* Add a pair of Arrows for a reversible reaction.
  
−
* Add an arrow for a retrosynthetic step.
+
* Add an arrow for a retrosynthesis step.
  
 
* Add a double headed arrow to represent mesomery.
 
* Add a double headed arrow to represent mesomery.
Line 112: Line 120:
 
||Click on up or down arrow triangles with the mouse.
 
||Click on up or down arrow triangles with the mouse.
  
−
Observe the changes on the arrows in the '''Display area.'''
+
And Observe the changes in the arrows in the '''Display area.'''
 
|-
 
|-
 
||
 
||
−
||Next let's learn about Arrow heads.
+
||Now let's learn about Arrow heads.
 
|-
 
|-
 
||Point  A, B and C
 
||Point  A, B and C
−
||The default values of A, B and C are displaced here.
+
||The default values of A, B and C are displayed here.
 
|-
 
|-
  
Line 166: Line 174:
 
|-
 
|-
 
||Select and click '''Naphtalene''' structure
 
||Select and click '''Naphtalene''' structure
−
||Likewise let's select '''Naphtalene''' structure and click on '''Display area.'''
+
||Likewise let's select '''Naphtalene''' structure and click on the '''Display area.'''
 
|-
 
|-
 
||'''Slide Number 5
 
||'''Slide Number 5
Line 173: Line 181:
 
||Select and place other structures on the '''Display area''', on your own.
 
||Select and place other structures on the '''Display area''', on your own.
 
|-
 
|-
−
||Click on Save a current file icon on the toolbar
+
||Click on '''Save a current file''' icon on the toolbar
 
||Let's save the file now.
 
||Let's save the file now.
  
−
Click on Save the current file icon on the toolbar.
+
Click on '''Save the current file''' icon on the toolbar.
 
|-
 
|-
 
||'''Save as''' dialog box opens.  
 
||'''Save as''' dialog box opens.  
  
−
Enter the file name as '''Benzene''' and click on '''Save''' button.
+
Enter the file name as '''Benzene''' click on '''Save''' button.
 
||'''Save as''' dialog box opens
 
||'''Save as''' dialog box opens
  
−
Enter the file name as '''Benzene''' and click on '''Save''' button.
+
Enter the file name as '''Benzene''' click on '''Save''' button.
 
|-
 
|-
 
||
 
||
−
||Let's now learn to add a '''New template''' to the existing Template list.
+
||Now let's learn to add a '''New template''' to the existing Template list.
 
|-
 
|-
 
||Click on '''Open a file''' icon from the toolbar
 
||Click on '''Open a file''' icon from the toolbar
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A window with files and folders opens.
 
A window with files and folders opens.
 
|-
 
|-
−
||select “Hexane” >> click on '''Ope'''n button.
+
||select “Hexane” >> click on '''Open''' button.
 
||Select the file named “Hexane”  from the list.
 
||Select the file named “Hexane”  from the list.
  
−
Then, click on '''Open''' button.
+
Click on '''Open''' button.
 
|-
 
|-
 
||Click on '''Add''' button>>'''New template''' property page opens.
 
||Click on '''Add''' button>>'''New template''' property page opens.
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'''New template''' property page opens.
 
'''New template''' property page opens.
 
|-
 
|-
−
||
+
||Point to the fields.
 
||Property page has two fields – '''Name''' and '''Category.'''
 
||Property page has two fields – '''Name''' and '''Category.'''
 
|-
 
|-
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|-
 
|-
 
||Click on '''Ok''' button.
 
||Click on '''Ok''' button.
−
||It will be displayed on the '''New template''' property page.
+
||It will be displayed on the '''New template''' property page.
  
 
Click on '''Ok''' button.
 
Click on '''Ok''' button.
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Select '''Hydrocarbons''' category.
 
Select '''Hydrocarbons''' category.
  
−
Observe that '''Hexane''' structure is added to the '''Templates''' list.
+
Observe that '''Hexane''' structure is added to the '''Template''' list.
−
|-
+
−
||Go to '''File''' menu>> select '''Close''' to close the file.
+
−
||Let's  close the “hexane” file.
+
−
 
+
−
Go to '''File''' menu, select '''Close''' to close the file.
+
 
|-
 
|-
 
||'''Slide Number 6
 
||'''Slide Number 6
Line 241: Line 244:
 
Assignment'''
 
Assignment'''
 
||Add '''Octane''' structure to '''Hydrocarbons''' category, on your own.
 
||Add '''Octane''' structure to '''Hydrocarbons''' category, on your own.
 +
|-
 +
||Go to '''File''' menu>> select '''Close''' to close the file.
 +
||Let's  close the “hexane” file.
 +
 +
Go to '''File''' menu, select '''Close''' to close the file.
 
|-
 
|-
 
||Click on '''Select one or more objects''' tool >> Close '''Templates''' property page.
 
||Click on '''Select one or more objects''' tool >> Close '''Templates''' property page.
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|-
 
|-
 
||
 
||
−
||Next, let's learn about '''Residues.'''
+
||Now, let's learn about '''Residues.'''
 
|-
 
|-
 
||'''Slide Number 7
 
||'''Slide Number 7
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|-
 
|-
 
||Go to '''Tools''' menu>>Click on '''Edit residues.'''
 
||Go to '''Tools''' menu>>Click on '''Edit residues.'''
−
||Go to '''Tools''' menu and click on '''Edit residues.'''
+
||Go to '''Tools''' menu click on '''Edit residues.'''
  
 
'''Residues''' window opens.
 
'''Residues''' window opens.
 
|-
 
|-
 
||Point to the  buttons
 
||Point to the  buttons
−
||It has three buttons - '''New, Save, Delete.'''
+
||It has three buttons - '''New, Save''' and '''Delete.'''
 
|-
 
|-
 
||Point to the list
 
||Point to the list
 
||'''New''' button  has a drop down list.
 
||'''New''' button  has a drop down list.
−
Click on it.
 
 
|-
 
|-
−
||Select '''n-Pr''' for propyl
+
||Select '''n-Pr''' from the list.
−
||Select n-Pr for propyl.
+
||Select '''n-Pr''' for from the list.
 
|-
 
|-
 
||Point to the '''Identity''' tab
 
||Point to the '''Identity''' tab
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|-
 
|-
 
||Point to the '''Formula''' tab  
 
||Point to the '''Formula''' tab  
−
||'''Formula''' tab shows the skeletal structure of the selected residue.
+
||'''Formula''' tab shows the Skeletal structure of the selected residue.
 
|-
 
|-
 
||Point to Symbol, Name and skeletal structure  
 
||Point to Symbol, Name and skeletal structure  
 
||Likewise, let's select  '''s-Bu''' for Secondary Butyl.
 
||Likewise, let's select  '''s-Bu''' for Secondary Butyl.
  
−
Observe the '''Symbol, Name''' and '''Skeletal''' structure of the residue.
+
Observe the '''Symbol, Name''' and '''Skeletal''' structure of the selected residue.
 
|-
 
|-
 
||
 
||
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Name it as '''Hydroxy.'''  
 
Name it as '''Hydroxy.'''  
−
||In the '''Symbo'''l field type ''' O-H.'''
+
||In the '''Symbol''' field type ''' O-H.'''
 
Name it as '''Hydroxy'''.  
 
Name it as '''Hydroxy'''.  
 
|-
 
|-
−
||Click on '''Formula''' tab.
+
||Click on the '''Formula''' tab.
−
||Click on '''Formula''' tab.
+
||Click on the '''Formula''' tab.
 +
 
 
You will see a bulleted bond.
 
You will see a bulleted bond.
 
|-
 
|-
 
||Place the cursor near the bond >> press capital '''O'''.
 
||Place the cursor near the bond >> press capital '''O'''.
 +
 
Point to '''Submenu.'''
 
Point to '''Submenu.'''
 
||Place the cursor near the bond and press capital '''O'''.
 
||Place the cursor near the bond and press capital '''O'''.
  
−
A '''Submenu''' with '''O''' and '''Os''' opens.
+
A '''Submenu''' opens with '''O''' and '''Os'''.
 
|-
 
|-
 
||Select '''O'''
 
||Select '''O'''
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||Click on the list .
 
||Click on the list .
 
||
 
||
−
Now, click on the New button to view the list.
+
Now, click on '''New''' button to view the list.
  
−
Observe that  '''O-H''' residue is now added to the list.
+
Observe that  '''O-H''' residue is added to the list.
 
|-
 
|-
 
||Click on '''Close''' button to close the window
 
||Click on '''Close''' button to close the window
Line 338: Line 347:
 
* Manage Templates
 
* Manage Templates
  
−
* Select and use ready Templates and
+
* Select and use ready Templates  
  
 
* Add a New Template  
 
* Add a New Template  
−
 
−
We will also learn
 
  
 
* Uses of Residues and
 
* Uses of Residues and
Line 362: Line 369:
 
||Watch the video available at this URL.
 
||Watch the video available at this URL.
  
−
'''http://spoken-tutorial.org/What is a Spoken Tutorial'''
+
'''http://spoken-tutorial.org/What_is_a_Spoken_Tutorial'''
  
 
It summarises the Spoken Tutorial project
 
It summarises the Spoken Tutorial project

Latest revision as of 17:34, 18 December 2013

Title of the tutorial: Edit-Preferences-Templates-and-Residues

Author: Madhuri Ganapathi

Key words: Edit Preferences, Manage Templates, Add New Templates, Residues, edit Residues,Video tutorial.

GChemPaint tools- Add an arrow for an irreversible reaction, Add a pair of Arrows for a reversible reaction, Add an arrow for a retrosynthesis step, Add a double headed arrow to represent mesomery.

Visual Cue Narration
Slide Number 1

Title Slide

Hello everyone.

Welcome to the tutorial on Edit Preferences, Templates and Residues in GChemPaint.

Slide Number 2

Learning Objectives

In this tutorial, we will learn to

  • Edit Preferences
  • Manage Templates
  • Select and use ready Templates
  • Add a New Template

We will also learn

  • The uses of Residues and
  • To edit Residues.
Slide Number 3

System Requirement

Here I am using

Ubuntu Linux OS version. 12.04

GChemPaint version 0.12.10

Slide Number 4

Pre-requisites

To follow this tutorial, you should be familiar with,

GChemPaint chemical structure editor.

If not, for relevant tutorials, please visit our website.

Switch to GChemPaint application. I have already opened a new GChemPaint application.
Let's begin the tutorial by editing Preferences.
Go to Edit menu>> navigate to Preferences>> click on it. Go to Edit menu, navigate to Preferences and click on it.

GChemPaint Preferences window opens.

Point to the field The first field, Default Compression Level For GChemPaint Files, is used when saving files.

By default, it is zero.

If not zero, the file will be compressed using gzip.
Point to Invert wedge hashes. I will cover Invert wedge hashes in an another tutorial.
Point to Default Theme >> then click on the drop-down to show the options In GchemPaint, each document has an associated theme.

Let's retain the Default Theme as GChemPaint.

Point to Arrows Now, I will explain about Arrows in detail, under Themes section.
Point to the arrows Observe the different types of arrows on the tool box
  • Add an arrow for an irreversible reaction.
  • Add a pair of Arrows for a reversible reaction.
  • Add an arrow for a retrosynthesis step.
  • Add a double headed arrow to represent mesomery.
Let's add these 4 arrows to the Display area.
Click on>> Add an arrow for an irreversible reaction tool >> click on Display area. Click on Add an arrow for an irreversible reaction tool,

Then click on Display area.

Add arrows to Display area Likewise I will add other types of arrows to the Display area.
Select Arrows from Themes >>A contextual menu opens Select Arrows from the Themes field in the Preferences dialog box.

A Contextual menu opens.

Point the fields Here we can increase or decrease Length, Width and Distance of the arrows.
Click on up or down arrow triangles Click on up or down arrow triangles with the mouse.

And Observe the changes in the arrows in the Display area.

Now let's learn about Arrow heads.
Point A, B and C The default values of A, B and C are displayed here.
Point to the Arrows heads parameters A, B and C. The A, B and C parameters help to vary the shape of the arrow heads.
Increase or decrease A, B and C. Increase or decrease each one and observe the changes in the arrow heads.

let's Click on Close button to close the window

Press CTRL +A to select all objects>> Go to Edit menu, click on Clear. Let's clear the Display area.

Press CTRL +A to select all objects.

Go to Edit menu, click on Clear.

Next, let's learn how to manage Templates.
Click on Use or manage templates tool. Click on Use or manage templates tool.

The property dialog box opens below.

Point to Templates.

Property dialog box contains Templates with a drop down list.

Point to the list. List contains Amino acids, Aromatic hydrocarbons, Nucleic bases, Nucleosides and Saccharides.
Point to the Submenu Each item has a Submenu.
Select Aromatic Hydrocarbons >>click on Benzene from the Submenu. Let's select Aromatic Hydrocarbons and click on Benzene from the Submenu.
Point to Benzene structure Benzene structure is displayed on the property page.
click on the Display area to display Benzene structure to the Display area. Now click on the Display area to display Benzene structure.
Select and click Naphtalene structure Likewise let's select Naphtalene structure and click on the Display area.
Slide Number 5

Assignment

Select and place other structures on the Display area, on your own.
Click on Save a current file icon on the toolbar Let's save the file now.

Click on Save the current file icon on the toolbar.

Save as dialog box opens.

Enter the file name as Benzene click on Save button.

Save as dialog box opens

Enter the file name as Benzene click on Save button.

Now let's learn to add a New template to the existing Template list.
Click on Open a file icon from the toolbar Click on Open a file icon from the toolbar.

A window with files and folders opens.

select “Hexane” >> click on Open button. Select the file named “Hexane” from the list.

Click on Open button.

Click on Add button>>New template property page opens. Click on Add button on the template's property page.

New template property page opens.

Point to the fields. Property page has two fields – Name and Category.
Point to the drop down list. Category field has a drop down list.

We can select from the list or add our own category.

Add a new Category, Hydrocarbons. Let's add a new Category, by typing Hydrocarbons in the text field.
In the Name field type the name of the compound as “Hexane”. In the Name field, enter the name of the compound as “Hexane”.
Click on Hexane structure. Click on the Hexane structure on the Display area.
Click on Ok button. It will be displayed on the New template property page.

Click on Ok button.

Click on Templates drop-down. Now, click on Templates drop-down.

Select Hydrocarbons category.

Observe that Hexane structure is added to the Template list.

Slide Number 6

Assignment

Add Octane structure to Hydrocarbons category, on your own.
Go to File menu>> select Close to close the file. Let's close the “hexane” file.

Go to File menu, select Close to close the file.

Click on Select one or more objects tool >> Close Templates property page. Click on Select one or more objects tool to close the Templates property page.
Now, let's learn about Residues.
Slide Number 7

Uses of Residues

Residues are used to,
  • Find the nature of functional group attached to carbon chain.
  • Know the structure of functional group.
  • Add a new functional group to the database.
Go to Tools menu>>Click on Edit residues. Go to Tools menu click on Edit residues.

Residues window opens.

Point to the buttons It has three buttons - New, Save and Delete.
Point to the list New button has a drop down list.
Select n-Pr from the list. Select n-Pr for from the list.
Point to the Identity tab The Identity tab shows Symbol and Name of the selected residue.
Point to the Formula tab Formula tab shows the Skeletal structure of the selected residue.
Point to Symbol, Name and skeletal structure Likewise, let's select s-Bu for Secondary Butyl.

Observe the Symbol, Name and Skeletal structure of the selected residue.

Let's now add a new residue - Hydroxy group.
To add a new residue , click on New button. To add a new residue, click on New button.
In the Symbol field type O-H.

Name it as Hydroxy.

In the Symbol field type O-H.

Name it as Hydroxy.

Click on the Formula tab. Click on the Formula tab.

You will see a bulleted bond.

Place the cursor near the bond >> press capital O.

Point to Submenu.

Place the cursor near the bond and press capital O.

A Submenu opens with O and Os.

Select O

Click on Save button.

Select O

O-H group attaches to the bond.

Click on Save button.

Click on the list .

Now, click on New button to view the list.

Observe that O-H residue is added to the list.

Click on Close button to close the window Let's click on Close button to close the window
With this we come to the end of this tutorial.

Let's summarise

Side Number 8

Summary

In this tutorial, we have learnt to
  • Edit Preferences
  • Manage Templates
  • Select and use ready Templates
  • Add a New Template
  • Uses of Residues and
  • To edit Residues.
Slide Number 9

Assignment

As an assignment
  • Select and use Saccharides from Templates list.
  • Explore other residues.
Slide Number 10

Acknowledgement

Watch the video available at this URL.

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

Slide Number 11 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

Slide number 12 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 this link

http://spoken-tutorial.org/NMEICT-Intro ]

This is Madhuri Ganpathi from IIT Bombay signing off. Thank you for joining.

Contributors and Content Editors

Madhurig

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