Difference between revisions of "JChemPaint/C2/Introduction-to-JChemPaint/English-timed"
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− | | We will also learn | + | | We will also learn: |
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| 00:20 | | 00:20 | ||
− | | * '''Menu bar, Tool bars''' and '''Panel''' of '''JChemPaint interface''' | + | | * '''Menu bar, Tool bars''' and '''Panel''' of '''JChemPaint interface''' |
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| 00:30 | | 00:30 | ||
− | | * Save the drawing with '''.mol''' extension | + | | * Save the drawing with ''''.mol'''' extension. |
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| 00:34 | | 00:34 | ||
− | | To record this tutorial I am using | + | | To record this tutorial, I am using: * '''Ubuntu Linux OS''' version 12.04 |
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| 00:41 | | 00:41 | ||
− | | *'''Windows''' version 7 | + | | * '''Windows''' version 7 |
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| 00:43 | | 00:43 | ||
− | | *'''JChemPaint''' version 3.3-1210 | + | | * '''JChemPaint''' version 3.3-1210 |
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| 00:48 | | 00:48 | ||
− | | *'''FireFox Browser''' 31.0 | + | | * '''FireFox Browser''' 31.0 |
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| 00:52 | | 00:52 | ||
− | | *'''Java''' version 7 | + | | * '''Java''' version 7. |
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| 00:55 | | 00:55 | ||
− | | To follow this tutorial you should have | + | | To follow this tutorial, you should have:* Internet connection |
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| 00:59 | | 00:59 | ||
− | | * '''Synaptic Package Manager''' installed on your system | + | | * '''Synaptic Package Manager''' installed on your system |
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| 01:03 | | 01:03 | ||
− | | * Knowledge of | + | | * Knowledge of '''Terminal''' on Ubuntu''' |
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| 01:06 | | 01:06 | ||
− | | * Knowledge of '''Command Prompt on Windows'''. | + | | * Knowledge of '''Command Prompt''' on '''Windows'''. |
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| 01:10 | | 01:10 | ||
− | | Please note to run '''JChemPaint''' you should have '''Java''' installed on your system. | + | | Please note: to run '''JChemPaint''', you should have '''Java''' installed on your system. |
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| 01:16 | | 01:16 | ||
− | | '''Java''' can be installed on '''Ubuntu''' using '''Synaptic Package Manager''' | + | | '''Java''' can be installed on '''Ubuntu''' using '''Synaptic Package Manager'''. |
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| 01:30 | | 01:30 | ||
− | | * '''JChemPaint''' is a 2D chemical structures editor and viewer. | + | | * '''JChemPaint''' is a '''2D chemical structures editor''' and '''viewer'''. |
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| 01:35 | | 01:35 | ||
− | | *It is free and open-source cross platform application developed in '''Java'''. | + | | * It is free and open-source cross platform application developed in '''Java'''. |
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| 01:43 | | 01:43 | ||
− | | *It allows to import and export structure data in plain-text formats like '''SMILES, Molfile, CML''' and '''InChi keys'''. | + | | * It allows to import and export '''structure data''' in plain-text formats like '''SMILES, Molfile, CML''' and '''InChi keys'''. |
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| 02:06 | | 02:06 | ||
− | | In the address bar, type the URL http://jchempaint.github.io/ to install '''JChemPaint''' on '''Ubuntu'''. | + | | In the address bar, type the URL "http://jchempaint.github.io/" to install '''JChemPaint''' on '''Ubuntu'''. |
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| 02:21 | | 02:21 | ||
− | | You will be directed to the download page of | + | | You will be directed to the download page of '''JChemPaint'''. |
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| 02:37 | | 02:37 | ||
− | | Click on ' | + | | Click on ''' the desktop application (6.8 MB).''' |
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| 02:42 | | 02:42 | ||
− | | Save file dialog box opens | + | | Save file dialog-box opens. click on '''Save File''' button and click on '''OK'''. |
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| 02:53 | | 02:53 | ||
− | | Right click on the saved file and select '''Move to Desktop'''. | + | | Right-click on the saved file and select '''Move to Desktop'''. |
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| 03:10 | | 03:10 | ||
− | | Type '''“cd space Desktop”''' and press '''Enter'''. | + | | Type: '''“cd space Desktop”''' and press '''Enter'''. |
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| 03:16 | | 03:16 | ||
− | | Type '''java space -jar space ./jchempaint-3.3-1210.jar''' and press '''Enter'''. | + | | Type: '''java space -jar space ./jchempaint-3.3-1210.jar''' and press '''Enter'''. |
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| 03:35 | | 03:35 | ||
− | | Please note '''JChemPaint''' can be opened through the '''Terminal''' only. | + | | Please note, '''JChemPaint''' can be opened through the '''Terminal''' only. |
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| 03:55 | | 03:55 | ||
− | | In the address bar, type '''jre-7-downloads''' and press '''Enter'''. | + | | In the address bar, type: '''jre-7-downloads''' and press '''Enter'''. |
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| 04:06 | | 04:06 | ||
− | | Click on the link '''Java SE Runtime Environment 7 Downloads-Oracle.''' | + | | Click on the link '''"Java SE Runtime Environment 7 Downloads-Oracle".''' |
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| 04:31 | | 04:31 | ||
− | | '''Save file''' dialog box opens. | + | | '''Save file''' dialog-box opens. |
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| 05:44 | | 05:44 | ||
− | | '''Save file''' dialog box opens. | + | | '''Save file''' dialog-box opens. |
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| 05:51 | | 05:51 | ||
− | | The '''.jar''' file will be downloaded to '''Downloads''' folder. | + | | The ''''.jar'''' file will be downloaded to '''Downloads''' folder. |
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| 05:57 | | 05:57 | ||
− | | Open '''Downloads''' folder and select the file '''jchempaint-3.3-1210.jar.''' | + | | Open '''Downloads''' folder and select the file ''''jchempaint-3.3-1210.jar'.''' |
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| 06:13 | | 06:13 | ||
− | | Right click on the executable file. | + | | Right-click on the executable file. |
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| 06:37 | | 06:37 | ||
− | | In the '''Open box''' type '''“cmd”''' and click on '''OK'''. | + | | In the '''Open box''', type: '''“cmd”''' and click on '''OK'''. |
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| 06:46 | | 06:46 | ||
− | | Let's go to '''Downloads''' folder where we have | + | | Let's go to '''Downloads''' folder where we have saved our downloaded ''''.jar'''' file. |
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| 06:54 | | 06:54 | ||
− | | Type at the '''prompt “cd space Downloads”''' and press '''Enter'''. | + | | Type at the '''prompt: “cd space Downloads”''' and press '''Enter'''. |
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| 07:00 | | 07:00 | ||
− | | Type '''java space -jar space jchempaint-3.3-1210.jar''' and press '''Enter'''. | + | | Type: '''java space -jar space jchempaint-3.3-1210.jar''' and press '''Enter'''. |
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| 07:20 | | 07:20 | ||
− | | *Go to '''Program files''' locate the '''java''' folder and click on it. | + | | * Go to '''Program files''', locate the '''java''' folder and click on it. |
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| 07:27 | | 07:27 | ||
− | | *Locate '''bin''' folder and right-click on it. | + | | * Locate '''bin''' folder and right-click on it. |
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| 07:32 | | 07:32 | ||
− | | *Navigate to '''Properties'''. | + | | * Navigate to '''Properties'''. |
|- | |- | ||
| 07:35 | | 07:35 | ||
− | | *Copy the address '''C:\Program Files''' within brackets '''(x86)\Java\jre7.''' | + | | * Copy the address '''C:\Program Files''' within brackets '''(x86)\Java\jre7.''' |
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| 07:48 | | 07:48 | ||
− | | To set the path follow the steps. | + | | To set the path, follow the steps. |
|- | |- | ||
| 07:51 | | 07:51 | ||
− | | *Right-click on '''My Computer''', select '''Properties''' option. | + | | * Right-click on '''My Computer''', select '''Properties''' option. |
|- | |- | ||
| 07:57 | | 07:57 | ||
− | | *Click on '''Advanced System settings''' | + | | * Click on '''Advanced System settings''' and then click on '''Environment Variables.''' |
|- | |- | ||
| 08:04 | | 08:04 | ||
− | | *In '''System Variables''' search for '''Path'''. | + | | * In '''System Variables''', search for '''Path'''. |
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| 08:09 | | 08:09 | ||
− | | *Click on '''Edit'''. | + | | * Click on '''Edit'''. |
|- | |- | ||
| 08:11 | | 08:11 | ||
− | | *'''Edit system Variable''' dialog box opens | + | | * '''Edit system Variable''' dialog-box opens. |
|- | |- | ||
| 08:16 | | 08:16 | ||
− | | *Paste the address '''C:\Program Files''' within brackets '''(x86)\Java\jre7.''' | + | | * '''Paste''' the address '''C:\Program Files''' within brackets '''(x86)\Java\jre7.''' |
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| 08:28 | | 08:28 | ||
− | | *Click on '''OK ''' and close the windows. | + | | * Click on '''OK ''' and close the windows. |
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| 08:36 | | 08:36 | ||
− | | This the '''Menu bar'''. | + | | This is the '''Menu bar'''. |
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| 09:02 | | 09:02 | ||
− | | '''JChempaint''' window has | + | | '''JChempaint''' window has- |
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| 09:04 | | 09:04 | ||
− | | *Formatting tools on top | + | | * Formatting tools on top |
|- | |- | ||
| 09:07 | | 09:07 | ||
− | | | + | | * '''Bond''' tools on the left |
|- | |- | ||
| 09:09 | | 09:09 | ||
− | | *Ring tools on the right and | + | | * '''Ring''' tools on the right and |
|- | |- | ||
| 09:12 | | 09:12 | ||
− | | *Element tools at the bottom | + | | * Element tools at the bottom |
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| 09:24 | | 09:24 | ||
− | | Click and drag the '''chain''' to | + | | Click and drag the '''chain''' to 6 Carbon atoms on the '''Panel'''. |
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| 09:30 | | 09:30 | ||
− | | Notice that '''Carbon chain''' does not contain any | + | | Notice that '''Carbon chain''' does not contain any atoms. |
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| 09:54 | | 09:54 | ||
− | | By default '''Display Preferences''' tab is selected. | + | | By default, '''Display Preferences''' tab is selected. |
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| 10:00 | | 10:00 | ||
− | | Notice that none of the check boxes are selected. | + | | Notice that none of the check-boxes are selected. |
|- | |- | ||
| 10:05 | | 10:05 | ||
− | | Let's click on a few check boxes and see how they are useful. | + | | Let's click on a few check-boxes and see how they are useful. |
|- | |- | ||
|10:12 | |10:12 | ||
− | | To show '''Methyl groups''' on the '''chain''' click on '''Show explicit methyl groups.''' | + | | To show '''Methyl groups''' on the '''chain''', click on '''Show explicit methyl groups.''' |
|- | |- | ||
| 10:18 | | 10:18 | ||
− | | To show '''hydrogens''' click on '''Show implicit hydrogens.''' | + | | To show '''hydrogens''', click on '''Show implicit hydrogens.''' |
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| 10:29 | | 10:29 | ||
− | | As an example let's draw '''Phosphoric acid(H3PO4)'''. | + | | As an example, let's draw '''Phosphoric acid(H3PO4)'''. |
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| 10:42 | | 10:42 | ||
− | | '''Phosphine(PH3)''' will be displayed | + | | '''Phosphine(PH3)''' will be displayed. |
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| 11:02 | | 11:02 | ||
− | | You will notice a red line below '''Phosphrous atom'''. | + | | You will notice a red line, below '''Phosphrous atom'''. |
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| 11:11 | | 11:11 | ||
− | | To complete the '''valency''' let's make the top '''Phosphrous-hydroxy bond''' as a '''double bond'''. | + | | To complete the '''valency''', let's make the top '''Phosphrous-hydroxy bond''' as a '''double bond'''. |
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| 11:44 | | 11:44 | ||
− | | In the window click on '''Color atoms by element''' check box. | + | | In the window, click on '''Color atoms by element''' check-box. |
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| 12:12 | | 12:12 | ||
− | | '''Save as''' dialog box opens. | + | | '''Save as''' dialog-box opens. |
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| 12:27 | | 12:27 | ||
− | | The file will be saved with '''.mol''' extension. | + | | The file will be saved with ''''.mol'''' extension. |
|- | |- | ||
| 12:31 | | 12:31 | ||
− | | Let's | + | | Let's summarize. |
|- | |- | ||
| 12:33 | | 12:33 | ||
− | | In this tutorial, we have learnt | + | | In this tutorial, we have learnt: |
|- | |- | ||
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| 12:58 | | 12:58 | ||
− | | * Save the drawing with '''.mol''' extension | + | | * Save the drawing with ''''.mol'''' extension. |
|- | |- | ||
| 13:02 | | 13:02 | ||
− | | As an assignment | + | | As an assignment- |
|- | |- | ||
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| 13:09 | | 13:09 | ||
− | | This video | + | | This video summarizes the '''Spoken Tutorial''' project. |
|- | |- | ||
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| 13:18 | | 13:18 | ||
− | | The Spoken Tutorial Team: Conducts workshops using spoken tutorials | + | | The Spoken Tutorial Team: * Conducts workshops using spoken tutorials. |
|- | |- | ||
| 13:22 | | 13:22 | ||
− | | Gives certificates to those who pass an online test | + | |* Gives certificates to those who pass an online test. |
|- | |- | ||
| 13:27 | | 13:27 | ||
− | | For more details, please write to contact@spoken-tutorial.org | + | | For more details, please write to: |
+ | contact@spoken-tutorial.org | ||
|- | |- | ||
| 13:34 | | 13:34 | ||
− | | Spoken Tutorial | + | | '''Spoken Tutorial''' project is a part of the '''Talk to a Teacher''' project. |
|- | |- | ||
| 13:39 | | 13:39 | ||
− | | It is supported by the National Mission on Education through ICT, MHRD, Government of India | + | | It is supported by the National Mission on Education through ICT, MHRD, Government of India. |
|- | |- | ||
| 13:46 | | 13:46 | ||
− | | More information on this | + | | More information on this mission is available at: |
+ | http://spoken-tutorial.org/NMEICT-Intro | ||
|- | |- | ||
| 13:52 | | 13:52 | ||
− | | This is Madhuri Ganpathi from IIT Bombay signing off. Thank you for joining. | + | | This is Madhuri Ganpathi from '''IIT Bombay''', signing off. Thank you for joining. |
|- | |- | ||
|} | |} |
Revision as of 10:48, 5 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. |