Difference between revisions of "JChemPaint/C2/Introduction-to-JChemPaint/English-timed"

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| * About '''JChemPaint'''
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| * Install '''JChemPaint''' on '''Windows Operating system'''
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| * '''JChemPaint''' is a '''2D chemical structures editor''' and '''viewer'''.
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| * It is free and open-source cross platform application developed in '''Java'''.  
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| * It allows to '''import''' and '''export''' '''structure data''' in plain-text formats like- '''SMILES, Molfile, CML''' and '''InChi keys'''.  
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| * Explore various '''menu''' items.
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http://spoken-tutorial.org/NMEICT-Intro   
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Latest revision as of 16:21, 28 March 2017

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 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 system.
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 saved 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 is 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 bar contains all the tools required for you to work with JChemPaint.
09:02 JChempaint window has-
09:04 Formatting tools on the 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 summarize.
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 bar 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.
13:09 This video summarizes the Spoken Tutorial project.
13:12 If you do not have good bandwidth, you can download and watch it.
13:18 The Spoken Tutorial Team: * Conducts workshops using spoken tutorials.
13:22 Gives certificates to those who pass an online test.
13:27 For more details, please write to: contact@spoken-tutorial.org
13:34 Spoken Tutorial project is a part of the Talk to a Teacher project.
13:39 It is supported by the National Mission on Education through ICT, MHRD, Government of India.
13:46 More information on this mission is available at this link: http://spoken-tutorial.org/NMEICT-Intro
13:52 This is Madhuri Ganpathi from IIT Bombay, signing off. Thank you for joining.

Contributors and Content Editors

PoojaMoolya, Ranjana, Sandhya.np14

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