JChemPaint/C2/Introduction-to-JChemPaint/English

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.
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 dialog 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 dialog box. Click on Save File button.	Save file dialog 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 installed on your machine.
	Let's install JChemPaint.
On the browser>> in the address bar, type the URL	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 dialog 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.
	Alternately, you can open JChemPaint using Command prompt.
Press Windows and R keys simultaneously on the key board.	To open Command prompt, press Windows and R keys simultaneously 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 “cd Downloads” >> press enter	Type at the prompt “cd space Downloads” and press Enter.
Type Java -jar 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 brackets (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 Environment Variables. In System Variables search for Path. Click on Edit. Edit system Variable dialog box opens Paste the address C:\Program Files within brackets (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 dialog box opens.	Save as dialog 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.

Contributors and Content Editors

Madhurig, Nancyvarkey