Difference between revisions of "JChemPaint/C2/Introduction-to-JChemPaint/English-timed"
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| − | | In the address bar, type the URL | + | | In the address bar, type the URL http://jchempaint.github.io/ to install '''JChemPaint''' on '''Ubuntu'''. |
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Revision as of 12:04, 6 December 2015
| 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 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 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 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 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. |
| 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: |
| 13:52 | This is Madhuri Ganpathi from IIT Bombay, signing off. Thank you for joining. |
