JChemPaint/C2/Introduction-to-JChemPaint/English-timed
From Script | Spoken-Tutorial
| Visual Cue | 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. |
| 11:33 | This video summarises the Spoken Tutorial project |
| 11:37 | If you do not have good bandwidth, you can download and watch it. |
| 11:41 | The Spoken Tutorial Team: Conducts workshops using spoken tutorials |
| 11:43 | Gives certificates to those who pass an online test |
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contact@spoken-tutorial.org |
| 11:53 | Spoken Tutorial Project is a part of the Talk to a Teacher project |
| 11:57 | It is supported by the National Mission on Education through ICT, MHRD, Government of India |
| 12:04 | More information on this Mission is available at http://spoken-tutorial.org/NMEICT-Intro ] |
| 12:09 | This is Madhuri Ganpathi from IIT Bombay signing off. Thank you for joining. |
