Nancyvarkey at 02:38, 30 August 2014

2014-08-30T02:38:47Z

Nancyvarkey at 14:07, 29 August 2014

2014-08-29T14:07:53Z

Madhurig: Created page with '{| border=1 || Visual Cue || Narration |- ||'''Slide Number 1 Title Slide''' || Hello everyone. Welcome to this tutorial on '''Introduction to JChemPaint'''. |- ||'''Slide Nu…'

2014-08-28T11:09:25Z

Created page with '{| border=1 || Visual Cue || Narration |- ||'''Slide Number 1 Title Slide''' || Hello everyone. Welcome to this tutorial on '''Introduction to JChemPaint'''. |- ||'''Slide Nu…'

New page

{| border=1
|| Visual Cue
|| Narration
|-
||'''Slide Number 1

Title Slide'''
|| Hello everyone.

Welcome to this tutorial on '''Introduction to JChemPaint'''.
|-
||'''Slide Number 2+3

Learning Objectives'''
|| In this tutorial, we will learn

* About JChemPaint

* Install JChemPaint on Windows OS

* Install JChemPaint on Ubuntu OS 12.04.

We will also learn,

* Menu bar, Tool bars and Panel of JChemPaint interface
Preferences window

* Draw structures using tools and

* Save the drawing with .mol extension
|-
||'''Slide Number 4

System Requirement'''
||To record this tutorial I am using,

* Ubuntu Linux OS version 12.04

*Windows version 7

*JChemPaint version 3.3-1210

*FireFox Browser 31.0
*Java version 7
|-
||'''Slide Number 5

Pre-requisites'''
|| To follow this tutorial you must have,

* Internet connection

* '''Synaptic Package Manager''' installed on your system.

* Knowledge of '''Terminal on Ubuntu'''.

* Knowledge of '''Command Prompt on Windows'''.
|-
||'''Slide Number 6

Java Installation'''
|| Please note,

To run JChemPaint, you should have Java installed on your system.

Java can be installed on Ubuntu using Synaptic Package Manager

For example: openjdk-7-jre
|-
||
|| Let's learn about JChemPaint.
|-
||Slide Number 7

About JChemPaint
||
* JChemPaint is a 2D chemical structures editor and viewer.

*It is free and open-source cross platform application developed in Java.

*It allows to import and export structure data in plain-text formats like SMILES, Molfile, CML and InChi keys.
|-
||
||Let's start with JChemPaint installation on Ubuntu 12.04 OS. రీప్లేస్ చేస్తుంది.
|-
||On the browser>> in the address bar, type the URL
||Open Firefox web browser.

In the address bar, type the URL http://jchempaint.github.io/ to install JChemPaint on Ubuntu.
|-
||Point to the new web page
||You will be directed to the download page of JChemPaint.
|-
||Move the cursor on the webpage.

Click on "the desktop application (6.8 MB) "
||On the webpage, locate

“download a recent jar file from github (current is 3.3-1210):”

Click on " the desktop application (6.8 MB) ".
|-
||Point to the dialogue box
|| Save file dialog box opens, click on Save File button.
|-
||Point to the saved file in the Downloads folder
||Let's move the saved file from Downloads folder to Desktop.
|-
||Right click on saved file >>select Move to Desktop.
||Right click on the saved file and select Move to Desktop.
|-
||
||To open a new JChemPaint window we need Terminal.
|-

||Press CTRl+ALt and T keys simultaneously to open the Terminal.
||Press CTRl+ALt and T keys simultaneously to open the Terminal.
|-
||Type “cd space Desktop” and press enter.

Type java -jar ./jchempaint-3.3-1210.jar and press enter.
|| Type “cd space Desktop” and press enter.

Type java space -jar space ./jchempaint-3.3-1210.jar and press enter.

JChemPaint window opens.

Please note JChemPaint can be opened through the Terminal only.
|-
||
|| Let's move on to Windows installation process.
|-
||
||Let's install java on Windows OS.
|-
||On the browser>> in the address bar, type the URL
||Open Firefox web browser on your Windows machine.

In the address bar,

type jre-7-downloads and press enter.
|-
||Point to the page.

Click on Java SE Runtime Environment 7 Downloads-Oracle link.
||A new webpage opens.

Click on the link Java SE Runtime Environment 7 Downloads-Oracle.

Download page opens.
|-
||Point to the License agreement.

Select jre-7-windows-i586.exe.
||On the web page, accept the License agreement.

Select jre-7-windows-i586.exe link.
|-
||Point to the dialogue box.

Click on Save File button.
|| Save file dialogue box opens.

Click on Save File button.

The file will be downloaded in the Downloads folder.
|-
||Click on the downloaded file.
||“Click on the downloaded file.
|-
||Point to install window.
||Follow the installation process to install Java.

Click on close.

Jre-7 will be intalled on your machine.
|-
||
||Let's install JChemPaint.
|-
||On the browser>> in the address bar, type the UR
||Open Firefox web browser on your Windows machine.

In the address bar, type the URL http://jchempaint.github.io/ to install JChemPaint on Windows.
|-
||Point to the new webpage.
||You will be directed to the download page of JChemPaint.
|-
||Move the cursor on the webpage.

Click on "the desktop application (6.8 MB)"
||On the webpage, locate

“download a recent jar file from github (current is 3.3-1210):”

Click on "the desktop application (6.8 MB) ".
|-
||Point to the dialogue box.

Click on Save File button.
||Save file dialog box opens.

Click on Save File button.
|-
||Open Downloads folder select the file.
||The .jar file will be downloaded to Downloads folder.

Open Downloads folder and select the file jchempaint-3.3-1210.jar.

You can download available latest version.
|-
||Right click on the Executable file>>Select Open to open JchemPaint.
||Right click on the Executable file.

Select Open to open JChemPaint.
|-
||
||Alternatively you can open JChemPaint using Command prompt.
|-
||Press Windows and r keys simultanoeously on the key board.
||To open Command prompt, press Windows and r keys simultanoeously on the keyboard.
|-
||Point to the box.

Type “cmd” >> click on OK button.

Command prompt opens.
||Run prompt box opens.

In the Open box type “cmd” and click on OK.

Command prompt opens.
|-
||
||Let's go to Downloads folder where we have downloaded our .jar file.
|-
||Type at the prompt “cd Downloads” >> press enter
||Type at the prompt “cd space Downloads” and press enter.
|-
||Type Java space -jar space jchempaint3.3.jar>>press enter.
||Type java space -jar space jchempaint-3.3-1210.jar and press enter.

JChemPaint window opens.
|-
||Slide Number 8

"Error on Command Prompt".
|| If an error appears on command prompt,

Go to Program files locate the java folder and click on it.

Locate bin folder and right-click on it.

Navigate to Properties.

Copy the address C:\Program Files within bracketts(x86)\Java\jre7.
|-
||Slide Number 9

Set up the path
||To set the path follow the steps.

Right click on My Computer, select Properties option.

Click on Advanced System settings, then click on Environmemt Variables.

In System Variables search for Path.

Click on Edit.

Edit system Variable dialogue box opens

Paste the address C:\Program Files within bracketts (x86)\Java\jre7.

Click on OK and close the windows.
|-
||Move the cursor on the window.
||JChemPaint window looks like this.
|-
||Point to the Menu bar.

Move the cursor over all the menu items.
|| This the Menu bar.

Menu bar contains menu items like:

File, Edit, View, Atom, Bond, Tools, R-groups, Templates and Help.
|-
||Point to the tool bars.
||Tool bars contain all the tools required for you to work with JChemPaint.
|-
||Move the cursor on all the tools.
||JChempaint window has,

Formatting tools on top

Bond tools on the left

Ring tools on the right and

Element tools at the bottom
|-
||Move the cursor on the Panel
||Panel displays the drawn structures.
|-
||
||Now to JChemPaint Preferences window.
|-
||Click on Draw a chain tool.
||Click on Draw a chain tool.

Click and drag the chain to 6 Carbon atoms on the Panel.

Notice that Carbon chain does not contain any atoms.
|-
||Go to Edit menu, navigate to Preferences >> click on it.
Point to the window.
|| Go to Edit menu, navigate to Preferences and click on it.

Preferences window opens.
|-
||Move the cursor on the tabs.
||Preferences window has two tabs Display Preferences and Other Preferences.
|-
||Point to the tab.
||By default Display Preferences tab is selected.
|-
||Move the cursor on all the check boxes.
||Notice that none of the check boxes are selected here.
|-
||
||Let's click on a few check boxes and see how they are useful.
|-
||Point to the check box.

click on Show explicit methyl groups.
||To show Methyl groups on the chain click on Show explicit methyl groups.
|-
||Point to the check box click on Show implicit hydrogens
||To show hydrogens click on Show implicit hydrogens.
|-
||Click on Apply and OK buttons to apply the changes.
||Click on Apply and OK buttons to apply the changes.
|-
||
||As an example let's draw Phosphoric acid(H3PO4).
|-
||Click on Phosphrous(P) tool >> click on the Panel.
Point to PH3
||To draw, click on Phosphrous(P) tool and then click on the Panel.

Phosphine(PH3) will be displayed
|-
||Click on Oxygen(O) tool>> click on Single bond tool .
||Click on Oxygen(O) tool and click on Single bond tool.
|-
||Point to small blue circle.Click on Oxygen(O) tool and click on Single bond tool.
||Place the cursor on P, a small 'blue' colored circle appears on it.

Click on P and drag to draw four Hydroxy bonds .
|-
||Point to the red line below Phosphrous atom.
||You will notice a red line below Phosphrous atom.

This indicates that valency is not complete.
|-
||Point to the top bond
||To complete the valency let's make the top Phosphrous-hydroxy bond as a double bond.
|-
||Click on double bond tool >>click on top the Phosphrous-hydroxy bond.
||Click on double bond tool.

Click on top Phosphrous-hydroxy bond.

The obtained structure is Phosphoric acid.
|-
||Point to the structure.
|| Notice that all the atoms in the structure are black colored.
|-
||Go to Edit menu and navigate to Preferences.
|| To show Rasmol color of the element,
Go to Edit menu and navigate to Preferences.
|-
||In the window click on Color atoms by element check box>>It shows Rasmol color of the element.
|| In the window click on Color atoms by element check box.

It shows Rasmol color of the element.
|-
||Click on Apply and OK buttons .
|| Click on Apply and OK buttons to apply the changes.

Note that elements appear with their Rasmol colors.
|-
||
||Now let's save the file.
|-
||Click on File menu >> select Save as...
||Click on File menu and select Save as....
|-
||Save as dialogue box opens.
||Save as dialogue box opens.
|-
||Select Desktop folder to save the file on Desktop.
||Select Desktop folder to save the file on Desktop.
|-
||Type the file name as Oxyacids of Phosphorus >> Click on Save button.
|| Type the file name as Phosphoric acid and click on Save button.

The file will be saved with .mol extension.
|-
||
|| Let's summarise,
|-
||Slide Number 7 +8

Summary
|| In this tutorial, we have learnt

* About JChemPaint

* Install JChemPaint on Windows OS

* Install JChemPaint on Ubuntu OS 12.04

* Menu bar, Tool bars and Panel of JChemPaint interface

* Preferences window

* Draw structures using tools and

* Save the drawing with .mol extension
|-
||Slide Number 9

Assignment
|| As an assignment

* Install JChemPaint.

* Explore various menu items.
|-
||Slide Number10

Acknowledgement
||This video summarises the Spoken Tutorial project

If you do not have good bandwidth, you can download and watch it.
|-
||Slide Number11
||The Spoken Tutorial 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 http://spoken-tutorial.org/NMEICT-Intro ]

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

@@ Line 259: / Line 259: @@
 *Navigate to '''Properties'''.
-*Copy the address '''C:\Program Files within bracketts(x86)\Java\jre7.'''
+*Copy the address '''C:\Program Files''' within brackets '''(x86)\Java\jre7.'''
 |-
 ||Slide Number 9
@@ Line 276: / Line 276: @@
 *'''Edit system  Variable''' dialog box opens
-*Paste the address  '''C:\Program Files within bracketts (x86)\Java\jre7.'''
+*Paste the address  '''C:\Program Files''' within brackets '''(x86)\Java\jre7.'''
 *Click on '''OK ''' and close the windows.

JChemPaint/C2/Introduction-to-JChemPaint/English - Revision history

Nancyvarkey at 02:38, 30 August 2014

Nancyvarkey at 14:07, 29 August 2014

Madhurig: Created page with '{| border=1 || Visual Cue || Narration |- ||'''Slide Number 1 Title Slide''' || Hello everyone. Welcome to this tutorial on '''Introduction to JChemPaint'''. |- ||'''Slide Nu…'