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 | ||
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||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'''. |
|- | |- | ||
|| | || | ||
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* Edit Preferences | * Edit Preferences | ||
+ | |||
* Manage Templates | * Manage Templates | ||
+ | |||
* Select and use ready Templates | * Select and use ready Templates | ||
+ | |||
* Add a New Template | * Add a New Template | ||
We will also learn | We will also learn | ||
− | * The uses of Residues | + | * The uses of Residues and |
+ | |||
* To edit Residues. | * To edit Residues. | ||
|- | |- | ||
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|- | |- | ||
||Switch to '''GChemPaint''' application. | ||Switch to '''GChemPaint''' application. | ||
− | ||I have opened a new '''GChemPaint''' application. | + | ||I have already opened a new '''GChemPaint''' application. |
|- | |- | ||
|| | || | ||
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|- | |- | ||
||Point to the field | ||Point to the field | ||
− | ||The first field, '''Default Compression Level For | + | ||The first field, '''Default Compression Level For GChemPaint Files''', is used when saving files. |
By default, it is zero. | By default, it is zero. | ||
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|- | |- | ||
||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 | + | ||Now, I will explain about ''' Arrows''' in detail, under '''Themes''' section. |
|- | |- | ||
||Point to the arrows | ||Point to the arrows | ||
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* Add a pair of Arrows for a reversible reaction. | * Add a pair of Arrows for a reversible reaction. | ||
− | * Add an arrow for a | + | * Add an arrow for a retrosynthesis step. |
* Add a double headed arrow to represent mesomery. | * Add a double headed arrow to represent mesomery. | ||
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||Click on up or down arrow triangles with the mouse. | ||Click on up or down arrow triangles with the mouse. | ||
− | Observe the changes | + | And Observe the changes in the arrows in the '''Display area.''' |
|- | |- | ||
|| | || | ||
− | || | + | ||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 | + | ||The default values of A, B and C are displayed here. |
|- | |- | ||
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||'''Benzene''' structure is displayed on the property page. | ||'''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. | ||Now click on the '''Display area''' to display '''Benzene''' structure. | ||
|- | |- | ||
||Select and click '''Naphtalene''' structure | ||Select and click '''Naphtalene''' structure | ||
− | ||Likewise let's select '''Naphtalene''' structure and click on | + | ||Likewise let's select '''Naphtalene''' structure and click on the '''Display area.''' |
|- | |- | ||
||'''Slide Number 5 | ||'''Slide Number 5 | ||
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||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. Enter the file name as '''Benzene''' | + | ||'''Save as''' dialog box opens. |
+ | |||
+ | 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''' | + | |
+ | 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 | ||
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A window with files and folders opens. | A window with files and folders opens. | ||
|- | |- | ||
− | ||select “Hexane” >> click on ''' | + | ||select “Hexane” >> click on '''Open''' button. |
||Select the file named “Hexane” from the list. | ||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>>'''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 | + | ||It will be displayed on the '''New template''' property page. |
Click on '''Ok''' button. | Click on '''Ok''' button. | ||
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||Now, click on '''Templates''' drop-down. | ||Now, click on '''Templates''' drop-down. | ||
− | Select Hydrocarbons category. | + | Select '''Hydrocarbons''' category. |
− | Observe that '''Hexane''' structure is added to the ''' | + | Observe that '''Hexane''' structure is added to the '''Template''' list. |
− | + | ||
− | + | ||
− | + | ||
− | + | ||
|- | |- | ||
||'''Slide Number 6 | ||'''Slide Number 6 | ||
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||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. | ||
||Click on '''Select one or more objects''' tool to close the '''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 | ||'''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 | + | ||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 | + | ||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. | ||
− | |||
|- | |- | ||
− | ||Select '''n-Pr''' | + | ||Select '''n-Pr''' from the list. |
− | ||Select n-Pr for | + | ||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 | + | ||'''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 | + | Observe the '''Symbol, Name''' and '''Skeletal''' structure of the selected residue. |
|- | |- | ||
|| | || | ||
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||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 | + | ||In the '''Symbol''' field type '''O-H'''. |
+ | |||
Name it as '''Hydroxy.''' | Name it as '''Hydroxy.''' | ||
− | ||In the ''' | + | ||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''' | + | 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 | + | Now, click on '''New''' button to view the list. |
− | Observe that '''O-H''' residue is | + | 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 | ||
|- | |- | ||
|| | || | ||
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* Manage Templates | * Manage Templates | ||
− | * Select and use ready Templates | + | * Select and use ready Templates |
* Add a New Template | * Add a New Template | ||
− | + | * Uses of Residues and | |
− | + | ||
− | * | + | |
* To edit Residues. | * To edit Residues. | ||
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Assignment''' | Assignment''' | ||
− | ||As | + | ||As an assignment |
* Select and use Saccharides from Templates list. | * Select and use Saccharides from Templates list. | ||
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||Watch the video available at this URL. | ||Watch the video available at this URL. | ||
− | '''http://spoken-tutorial.org/ | + | '''http://spoken-tutorial.org/What_is_a_Spoken_Tutorial''' |
It summarises the Spoken Tutorial project | It summarises the Spoken Tutorial project | ||
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It is supported by the National Mission on Education through ICT, MHRD, Government of India | 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 | + | 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. | This is '''Madhuri Ganpathi''' from '''IIT Bombay''' signing off. Thank you for joining. | ||
|- | |- |
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
We will also learn
|
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
|
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,
|
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
|
Slide Number 9
Assignment |
As an assignment
|
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. |