JChemPaint/C2/Introduction-to-JChemPaint/English-timed

Time	Narration
00:00	Hello everyone. Welcome to this tutorial on Introduction to JChemPaint.
00:06	In this tutorial, we will learn:
00:08	* About JChemPaint
00:10	* Install JChemPaint on Windows Operating system
00:13	* Install JChemPaint on Ubuntu OS 12.04.
00:18	We will also learn,
00:20	* Menu bar, Tool bars and Panel of JChemPaint interface,
00:25	*Preferences window
00:27	* Draw structures using tools and
00:30	* Save the drawing with .mol extension
00:34	To record this tutorial I am using, Ubuntu Linux OS version 12.04
00:41	*Windows version 7
00:43	*JChemPaint version 3.3-1210
00:48	*FireFox Browser 31.0
00:52	*Java version 7
00:55	To follow this tutorial you should have, Internet connection
00:59	* Synaptic Package Manager installed on your system.
01:03	* Knowledge of Terminal on Ubuntu.
01:06	* Knowledge of Command Prompt on Windows.
01:10	Please note to run JChemPaint you should have Java installed on your system.
01:16	Java can be installed on Ubuntu using Synaptic Package Manager
01:21	For example: openjdk-7-jre
01:27	Let's learn about JChemPaint.
01:30	* JChemPaint is a 2D chemical structures editor and viewer.
01:35	*It is free and open-source cross platform application developed in Java.
01:43	*It allows to import and export structure data in plain-text formats like SMILES, Molfile, CML and InChi keys.
01:56	Let's start with JChemPaint installation on Ubuntu 12.04 OS.
02:02	Open Firefox web browser.
02:06	In the address bar, type the URL http://jchempaint.github.io/ to install JChemPaint on Ubuntu.
02:21	You will be directed to the download page of JChemPaint.
02:26	On the webpage, locate “download a recent jar file from github (current is 3.3-1210):”
02:37	Click on '" the desktop application (6.8 MB).
02:42	Save file dialog box opens, click on Save File button and Click on OK
02:48	Let's move the saved file from Downloads folder to Desktop.
02:53	Right click on the saved file and select Move to Desktop.
03:00	To open a new JChemPaint window, we need Terminal.
03:04	Press CTRl+Alt and T keys simultaneously to open the Terminal.
03:10	Type “cd space Desktop” and press Enter.
03:16	Type java space -jar space ./jchempaint-3.3-1210.jar and press Enter.
03:32	JChemPaint window opens.
03:35	Please note JChemPaint can be opened through the Terminal only.
03:41	Let's move on to Windows installation process.
03:45	Let's install Java on Windows OS.
03:50	Open Firefox web browser on your Windows machine.
03:55	In the address bar, type jre-7-downloads and press Enter.
04:02	A new webpage opens.
04:06	Click on the link Java SE Runtime Environment 7 Downloads-Oracle.
04:14	Download page opens.
04:17	On the web page, accept the License agreement.
04:22	Select jre-7-windows-i586.exe link.
04:31	Save file dialog box opens.
04:35	Click on Save File button.
04:38	The file will be downloaded into the Downloads folder.
04:42	Click on the downloaded file.
04:46	Follow the installation process to install Java.
04:51	Click on Close.
04:54	Jre-7 will be installed on your machine.
04:59	Let's install JChemPaint.
05:02	Open Firefox web browser on your Windows machine.
05:06	In the address bar, type the URL http://jchempaint.github.io/ to install JChemPaint on Windows.
05:21	You will be directed to the download page of JChemPaint.
05:26	On the webpage, locate “download a recent jar file from github (current is 3.3-1210):”
05:39	Click on "the desktop application (6.8 MB) ".
05:44	Save file dialog box opens.
05:47	Click on Save File button.
05:51	The .jar file will be downloaded to Downloads folder.
05:57	Open Downloads folder and select the file jchempaint-3.3-1210.jar.
06:08	You can download available latest version.
06:13	Right click on the executable file.
06:16	Select Open to open JChemPaint.
06:20	Alternately, you can open JChemPaint using Command prompt.
06:26	To open Command prompt, press Windows and R keys simultaneously on the keyboard.
06:34	Run prompt box opens.
06:37	In the Open box type “cmd” and click on OK.
06:43	Command prompt opens.
06:46	Let's go to Downloads folder where we have save our downloaded .jar file.
06:54	Type at the prompt “cd space Downloads” and press Enter.
07:00	Type java space -jar space jchempaint-3.3-1210.jar and press Enter.
07:13	JChemPaint window opens.
07:17	If an error appears on command prompt,
07:20	*Go to Program files locate the java folder and click on it.
07:27	*Locate bin folder and right-click on it.
07:32	*Navigate to Properties.
07:35	*Copy the address C:\Program Files within brackets (x86)\Java\jre7.
07:48	To set the path follow the steps.
07:51	*Right-click on My Computer, select Properties option.
07:57	*Click on Advanced System settings, and then click on Environment Variables.
08:04	*In System Variables search for Path.
08:09	*Click on Edit.
08:11	*Edit system Variable dialog box opens
08:16	*Paste the address C:\Program Files within brackets (x86)\Java\jre7.
08:28	*Click on OK and close the windows.
08:32	JChemPaint window looks like this.
08:36	This the Menu bar.
08:38	Menu bar contains menu items like: File, Edit, View, Atom, Bond, Tools, R-groups, Templates and Help.
08:54	Tool bars contain all the tools required for you to work with JChemPaint.
09:02	JChempaint window has,
09:04	*Formatting tools on top
09:07	*Bond tools on the left
09:09	*Ring tools on the right and
09:12	*Element tools at the bottom
09:15	Panel displays the drawn structures.
09:18	Now to JChemPaint Preferences window.
09:22	Click on Draw a chain tool.
09:24	Click and drag the chain to 6 Carbon atoms on the Panel.
09:30	Notice that Carbon chain does not contain any atoms.
09:35	Go to Edit menu, navigate to Preferences and click on it.
09:42	Preferences window opens.
09:45	Preferences window has two tabs Display Preferences and Other Preferences.
09:54	By default Display Preferences tab is selected.
10:00	Notice that none of the check boxes are selected.
10:05	Let's click on a few check boxes and see how they are useful.
10:12	To show Methyl groups on the chain click on Show explicit methyl groups.
10:18	To show hydrogens click on Show implicit hydrogens.
10:23	Click on Apply and OK buttons to apply the changes.
10:29	As an example let's draw Phosphoric acid(H3PO4).
10:35	To draw, click on Phosphrous(P) tool and then click on the Panel.
10:42	Phosphine(PH3) will be displayed
10:46	Click on Oxygen(O) tool and then click on Single bond tool.
10:51	Place the cursor on P; a small 'blue' colored circle appears on it.
10:57	Click on P and drag to draw four Hydroxy bonds.
11:02	You will notice a red line below Phosphrous atom.
11:07	This indicates that valency is not complete.
11:11	To complete the valency let's make the top Phosphrous-hydroxy bond as a double bond.
11:19	Click on double bond tool.
11:21	Click on top Phosphrous-hydroxy bond.
11:26	The obtained structure is Phosphoric acid.
11:30	Notice that all the atoms in the structure are black colored.
11:36	To show Rasmol color of the element,
11:39	Go to Edit menu and navigate to Preferences.
11:44	In the window click on Color atoms by element check box.
11:50	It shows Rasmol color of the element.
11:55	Click on Apply and OK buttons to apply the changes.
12:00	Note that elements appear with their Rasmol colors.
12:05	Let's save the file.
12:07	Click on File menu and select Save as.
12:12	Save as dialog box opens.
12:15	Select Desktop folder to save the file on Desktop.
12:21	Type the file name as Phosphoric acid and click on Save button.
12:27	The file will be saved with .mol extension.
12:31	Let's summarise,
12:33	In this tutorial, we have learnt
12:36	* About JChemPaint
12:38	* Install JChemPaint on Windows Operating System
12:42	* Install JChemPaint on Ubuntu Operating system 12.04
12:47	* Menu bar, Tool bars and Panel of JChemPaint interface
12:52	* Preferences window
12:55	* Draw structures using tools and
12:58	* Save the drawing with .mol extension
13:02	As an assignment
13:04	* Install JChemPaint.
13:06	* Explore various menu items.
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Contributors and Content Editors

PoojaMoolya, Ranjana, Sandhya.np14