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 OS
00:13	* Install JChemPaint on Ubuntu OS 12.04.
00:17	We will also learn,
00:18	* Menu bar, Tool bars and Panel of JChemPaint interface,
00:23	*Preferences window
00:25	* Draw structures using tools and
00:27	* Save the drawing with .mol extension
00:31	To record this tutorial I am using, Ubuntu Linux OS version 12.04
00:37	*Windows version 7
00:39	*JChemPaint version 3.3-1210
00:44	*FireFox Browser 31.0
00:47	*Java version 7
00:49	To follow this tutorial you must have,
00:51	* Internet connection
00:53	* Synaptic Package Manager installed on your system.
00:57	* Knowledge of Terminal on Ubuntu.
01:00	* Knowledge of Command Prompt on Windows.
01:03	Please note to run JChemPaint you should have Java installed on your system.
01:08	Java can be installed on Ubuntu using Synaptic Package Manager
01:14	For example: openjdk-7-jre
01:19	Let's learn about JChemPaint.
01:21	* JChemPaint is a 2D chemical structures editor and viewer.
01:26	*It is free and open-source cross platform application developed in Java.
01:32	*It allows to import and export structure data in plain-text formats like SMILES, Molfile, CML and InChi keys.
01:44	Let's start with JChemPaint installation on Ubuntu 12.04 OS.
01:51	Open Firefox web browser.
01:53	In the address bar, type the URL http://jchempaint.github.io/ to install JChemPaint on Ubuntu.
02:05	You will be directed to the download page of JChemPaint.
02:09	On the webpage, locate “download a recent jar file from github (current is 3.3-1210):”
02:19	Click on '" the desktop application (6.8 MB).
02:25	Save file dialog box opens, click on Save File button.
02:31	Let's move the saved file from Downloads folder to Desktop.
02:35	Right click on the saved file and select Move to Desktop.
02:42	To open a new JChemPaint window, we need Terminal.
02:46	Press CTRl+ALt and T keys simultaneously to open the Terminal.
02:52	Type “cd space Desktop” and press Enter.
02:58	Type java space -jar space ./jchempaint-3.3-1210.jar and press Enter.
03:14	JChemPaint window opens.
03:17	Please note JChemPaint can be opened through the Terminal only.
03:22	Let's move on to Windows installation process.
03:26	Let's install Java on Windows OS.
03:29	Open Firefox web browser on your Windows machine.
03:33	In the address bar, type jre-7-downloads and press Enter.
03:41	A new webpage opens.
03:44	Click on the link Java SE Runtime Environment 7 Downloads-Oracle.
03:52	Download page opens.
03:56	On the web page, accept the License agreement.
03:59	Select jre-7-windows-i586.exe link.
04:07	Save file dialog box opens.
04:10	Click on Save File button.
04:12	The file will be downloaded in the Downloads folder.
04:16	“Click on the downloaded file.
04:19	Follow the installation process to install Java.
04:27	Click on Close.
04:29	Jre-7 will be installed on your machine.
04:33	Let's install JChemPaint.
04:35	Open Firefox web browser on your Windows machine.
04:39	In the address bar, type the URL http://jchempaint.github.io/ to install JChemPaint on Windows.
04:50	You will be directed to the download page of JChemPaint.
04:55	On the webpage, locate
04:57	“download a recent jar file from github (current is 3.3-1210):”
05:04	Click on "the desktop application (6.8 MB) ".
05:09	Save file dialog box opens.
05:12	Click on Save File button.
05:15	The .jar file will be downloaded to Downloads folder.
05:19	Open Downloads folder and select the file jchempaint-3.3-1210.jar.
05:28	You can download available latest version.
05:32	Right click on the executable file.
05:35	Select Open to open JChemPaint.
05:38	Alternately, you can open JChemPaint using Command prompt.
05:43	To open Command prompt, press Windows and R keys simultaneously on the keyboard.
05:50	Run prompt box opens.
05:53	In the Open box type “cmd” and click on OK.
05:58	Command prompt opens.
06:00	Let's go to Downloads folder where we have downloaded our .jar file.
06:07	Type at the prompt “cd space Downloads” and press Enter.
06:14	Type java space -jar space jchempaint-3.3-1210.jar and press Enter.
06:27	JChemPaint window opens.
06:30	If an error appears on command prompt,
06:34	*Go to Program files locate the java folder and click on it.
06:39	*Locate bin folder and right-click on it.
06:43	*Navigate to Properties.
06:44	*Copy the address C:\Program Files within brackets (x86)\Java\jre7.
06:55	To set the path follow the steps.
06:58	*Right-click on My Computer, select Properties option.
07:02	*Click on Advanced System settings, and then click on Environment Variables.
07:08	*In System Variables search for Path.
07:12	*Click on Edit.
07:13	*Edit system Variable dialog box opens
07:17	*Paste the address C:\Program Files within brackets (x86)\Java\jre7.
07:27	*Click on OK and close the windows.
07:30	JChemPaint window looks like this.
07:33	This the Menu bar.
07:34	Menu bar contains menu items like: File, Edit, View, Atom, Bond, Tools, R-groups, Templates and Help.
07:49	Tool bars contain all the tools required for you to work with JChemPaint.
07:55	JChempaint window has,
07:56	*Formatting tools on top
08:00	*Bond tools on the left
08:03	*Ring tools on the right and
08:06	*Element tools at the bottom
08:10	Panel displays the drawn structures.
08:13	Now to JChemPaint Preferences window.
08:16	Click on Draw a chain tool.
08:18	Click and drag the chain to 6 Carbon atoms on the Panel.
08:24	Notice that Carbon chain does not contain any atoms.
08:29	Go to Edit menu, navigate to Preferences and click on it.
08:35	Preferences window opens.
08:38	Preferences window has two tabs Display Preferences and Other Preferences.
08:44	By default Display Preferences tab is selected.
08:48	Notice that none of the check boxes are selected here.
08:52	Let's click on a few check boxes and see how they are useful.
08:57	To show Methyl groups on the chain click on Show explicit methyl groups.
09:03	To show hydrogens click on Show implicit hydrogens.
09:08	Click on Apply and OK buttons to apply the changes.
09:12	As an example let's draw Phosphoric acid(H3PO4).
09:18	To draw, click on Phosphrous(P) tool and then click on the Panel.
09:23	Phosphine(PH3) will be displayed
09:26	Click on Oxygen(O) tool and click on Single bond tool.
09:31	Place the cursor on P; a small 'blue' colored circle appears on it.
09:37	Click on P and drag to draw four Hydroxy bonds.
09:43	You will notice a red line below Phosphrous atom.
09:47	This indicates that valency is not complete.
09:51	To complete the valency let's make the top Phosphrous-hydroxy bond as a double bond.
09:57	Click on double bond tool.
10:00	Click on top Phosphrous-hydroxy bond.
10:05	The obtained structure is Phosphoric acid.
10:09	Notice that all the atoms in the structure are black colored.
10:14	To show Rasmol color of the element,
10:17	Go to Edit menu and navigate to Preferences.
10:21	In the window click on Color atoms by element check box.
10:26	It shows Rasmol color of the element.
10:29	Click on Apply and OK buttons to apply the changes.
10:34	Note that elements appear with their Rasmol colors.
10:39	Let's save the file.
10:41	Click on File menu and select Save as....
10:45	Save as dialog box opens.
10:48	Select Desktop folder to save the file on Desktop.
10:52	Type the file name as Phosphoric acid and click on Save button.
10:56	The file will be saved with .mol extension.
11:01	Let's summarise,
11:03	In this tutorial, we have learnt
11:05	* About JChemPaint
11:07	* Install JChemPaint on Windows OS
11:10	* Install JChemPaint on Ubuntu OS 12.04
11:14	* Menu bar, Tool bars and Panel of JChemPaint interface
11:19	* Preferences window
11:20	* Draw structures using tools and
11:23	* Save the drawing with .mol extension
11:27	As an assignment
11:28	* Install JChemPaint.
11:30	* Explore various menu items.
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Contributors and Content Editors

PoojaMoolya, Ranjana, Sandhya.np14