Difference between revisions of "JChemPaint/C2/Introduction-to-JChemPaint/English-timed"
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− | | * Install '''JChemPaint''' on '''Windows | + | | * Install '''JChemPaint''' on '''Windows Operating system''' |
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− | | 00: | + | | 00:18 |
| We will also learn, | | We will also learn, | ||
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− | | 00: | + | | 00:20 |
| * '''Menu bar, Tool bars''' and '''Panel''' of '''JChemPaint interface''', | | * '''Menu bar, Tool bars''' and '''Panel''' of '''JChemPaint interface''', | ||
|- | |- | ||
− | | 00: | + | | 00:25 |
| *'''Preferences''' window | | *'''Preferences''' window | ||
|- | |- | ||
− | | 00: | + | | 00:27 |
| * Draw structures using tools and | | * Draw structures using tools and | ||
|- | |- | ||
− | | 00: | + | | 00:30 |
| * Save the drawing with '''.mol''' extension | | * Save the drawing with '''.mol''' extension | ||
|- | |- | ||
− | | 00: | + | | 00:34 |
| To record this tutorial I am using, '''Ubuntu Linux OS''' version 12.04 | | To record this tutorial I am using, '''Ubuntu Linux OS''' version 12.04 | ||
|- | |- | ||
− | | 00: | + | | 00:41 |
| *'''Windows''' version 7 | | *'''Windows''' version 7 | ||
|- | |- | ||
− | | 00: | + | | 00:43 |
| *'''JChemPaint''' version 3.3-1210 | | *'''JChemPaint''' version 3.3-1210 | ||
|- | |- | ||
− | | 00: | + | | 00:48 |
| *'''FireFox Browser''' 31.0 | | *'''FireFox Browser''' 31.0 | ||
|- | |- | ||
− | | 00: | + | | 00:52 |
| *'''Java''' version 7 | | *'''Java''' version 7 | ||
|- | |- | ||
− | | 00: | + | | 00:55 |
− | | To follow this tutorial you | + | | To follow this tutorial you should have, Internet connection |
|- | |- | ||
− | | 00: | + | | 00:59 |
− | + | ||
− | + | ||
− | + | ||
− | + | ||
| * '''Synaptic Package Manager''' installed on your system. | | * '''Synaptic Package Manager''' installed on your system. | ||
|- | |- | ||
− | | | + | | 01:03 |
| * Knowledge of '''Terminal on Ubuntu'''. | | * Knowledge of '''Terminal on Ubuntu'''. | ||
|- | |- | ||
− | | 01: | + | | 01:06 |
| * Knowledge of '''Command Prompt on Windows'''. | | * Knowledge of '''Command Prompt on Windows'''. | ||
|- | |- | ||
− | | 01: | + | | 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. | ||
|- | |- | ||
− | | 01: | + | | 01:16 |
| '''Java''' can be installed on '''Ubuntu''' using '''Synaptic Package Manager''' | | '''Java''' can be installed on '''Ubuntu''' using '''Synaptic Package Manager''' | ||
|- | |- | ||
− | | 01: | + | | 01:21 |
| For example: '''openjdk-7-jre''' | | For example: '''openjdk-7-jre''' | ||
|- | |- | ||
− | | 01: | + | | 01:27 |
| Let's learn about '''JChemPaint'''. | | Let's learn about '''JChemPaint'''. | ||
|- | |- | ||
− | | 01: | + | | 01:30 |
| * '''JChemPaint''' is a 2D chemical structures editor and viewer. | | * '''JChemPaint''' is a 2D chemical structures editor and viewer. | ||
|- | |- | ||
− | | 01: | + | | 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'''. | ||
|- | |- | ||
− | | 01: | + | | 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'''. | ||
|- | |- | ||
− | | 01: | + | | 01:56 |
| Let's start with '''JChemPaint''' installation on '''Ubuntu''' 12.04 OS. | | Let's start with '''JChemPaint''' installation on '''Ubuntu''' 12.04 OS. | ||
|- | |- | ||
− | | | + | | 02:02 |
| Open '''Firefox''' web browser. | | Open '''Firefox''' web browser. | ||
|- | |- | ||
− | | | + | | 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'''. | ||
|- | |- | ||
− | | 02: | + | | 02:21 |
| You will be directed to the download page of '''JChemPaint'''. | | You will be directed to the download page of '''JChemPaint'''. | ||
|- | |- | ||
− | | 02: | + | | 02:26 |
| On the webpage, locate '''“download a recent jar file from github (current is 3.3-1210):”''' | | On the webpage, locate '''“download a recent jar file from github (current is 3.3-1210):”''' | ||
|- | |- | ||
− | | 02: | + | | 02:37 |
| Click on '" the desktop application (6.8 MB).''' | | Click on '" the desktop application (6.8 MB).''' | ||
|- | |- | ||
− | | 02: | + | | 02:42 |
− | | Save file dialog box opens, click on '''Save File''' button | + | | Save file dialog box opens, click on '''Save File''' button and Click on '''OK''' |
|- | |- | ||
− | | 02: | + | | 02:48 |
| Let's move the saved file from '''Downloads''' folder to '''Desktop'''. | | Let's move the saved file from '''Downloads''' folder to '''Desktop'''. | ||
|- | |- | ||
− | | 02: | + | | 02:53 |
| Right click on the saved file and select '''Move to Desktop'''. | | Right click on the saved file and select '''Move to Desktop'''. | ||
|- | |- | ||
− | | | + | | 03:00 |
| To open a new '''JChemPaint''' window, we need '''Terminal.''' | | To open a new '''JChemPaint''' window, we need '''Terminal.''' | ||
|- | |- | ||
− | | | + | | 03:04 |
− | | Press '''CTRl+ | + | | Press '''CTRl+Alt''' and '''T''' keys simultaneously to open the '''Terminal'''. |
|- | |- | ||
− | | | + | | 03:10 |
| Type '''“cd space Desktop”''' and press '''Enter'''. | | Type '''“cd space Desktop”''' and press '''Enter'''. | ||
|- | |- | ||
− | | | + | | 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'''. | ||
|- | |- | ||
− | | 03: | + | | 03:32 |
| '''JChemPaint''' window opens. | | '''JChemPaint''' window opens. | ||
|- | |- | ||
− | | 03: | + | | 03:35 |
| Please note '''JChemPaint''' can be opened through the '''Terminal''' only. | | Please note '''JChemPaint''' can be opened through the '''Terminal''' only. | ||
|- | |- | ||
− | | 03: | + | | 03:41 |
| Let's move on to '''Windows''' installation process. | | Let's move on to '''Windows''' installation process. | ||
|- | |- | ||
− | | 03: | + | | 03:45 |
| Let's install '''Java''' on '''Windows OS'''. | | Let's install '''Java''' on '''Windows OS'''. | ||
|- | |- | ||
− | | 03: | + | | 03:50 |
| Open '''Firefox''' web browser on your '''Windows''' machine. | | Open '''Firefox''' web browser on your '''Windows''' machine. | ||
|- | |- | ||
− | | 03: | + | | 03:55 |
| In the address bar, type '''jre-7-downloads''' and press '''Enter'''. | | In the address bar, type '''jre-7-downloads''' and press '''Enter'''. | ||
|- | |- | ||
− | | | + | | 04:02 |
| A new webpage opens. | | A new webpage opens. | ||
|- | |- | ||
− | | | + | | 04:06 |
| Click on the link '''Java SE Runtime Environment 7 Downloads-Oracle.''' | | Click on the link '''Java SE Runtime Environment 7 Downloads-Oracle.''' | ||
|- | |- | ||
− | | | + | | 04:14 |
| Download page opens. | | Download page opens. | ||
|- | |- | ||
− | | | + | | 04:17 |
| On the web page, accept the '''License agreement'''. | | On the web page, accept the '''License agreement'''. | ||
|- | |- | ||
− | | | + | | 04:22 |
| Select '''jre-7-windows-i586.exe''' link. | | Select '''jre-7-windows-i586.exe''' link. | ||
|- | |- | ||
− | | 04: | + | | 04:31 |
| '''Save file''' dialog box opens. | | '''Save file''' dialog box opens. | ||
|- | |- | ||
− | | 04: | + | | 04:35 |
| Click on '''Save File''' button. | | Click on '''Save File''' button. | ||
|- | |- | ||
− | | 04: | + | | 04:38 |
− | | The file will be downloaded | + | | The file will be downloaded into the '''Downloads''' folder. |
|- | |- | ||
− | | 04: | + | | 04:42 |
− | | | + | | Click on the downloaded file. |
|- | |- | ||
− | | 04: | + | | 04:46 |
| Follow the installation process to install '''Java'''. | | Follow the installation process to install '''Java'''. | ||
|- | |- | ||
− | | 04: | + | | 04:51 |
| Click on '''Close'''. | | Click on '''Close'''. | ||
|- | |- | ||
− | | 04: | + | | 04:54 |
| '''Jre-7''' will be installed on your machine. | | '''Jre-7''' will be installed on your machine. | ||
|- | |- | ||
− | | 04: | + | | 04:59 |
| Let's install '''JChemPaint'''. | | Let's install '''JChemPaint'''. | ||
|- | |- | ||
− | | | + | | 05:02 |
| Open '''Firefox''' web browser on your '''Windows''' machine. | | 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'''. | | 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'''. | | You will be directed to the download page of '''JChemPaint'''. | ||
|- | |- | ||
− | | | + | | 05:26 |
− | | On the webpage, locate | + | | On the webpage, locate '''“download a recent jar file from github (current is 3.3-1210):”''' |
− | + | ||
− | + | ||
− | + | ||
− | + | ||
|- | |- | ||
− | | 05: | + | | 05:39 |
| Click on '''"the desktop application (6.8 MB) "'''. | | Click on '''"the desktop application (6.8 MB) "'''. | ||
|- | |- | ||
− | | 05: | + | | 05:44 |
| '''Save file''' dialog box opens. | | '''Save file''' dialog box opens. | ||
|- | |- | ||
− | | 05: | + | | 05:47 |
| Click on '''Save File''' button. | | Click on '''Save File''' button. | ||
|- | |- | ||
− | | 05: | + | | 05:51 |
| The '''.jar''' file will be downloaded to '''Downloads''' folder. | | The '''.jar''' file will be downloaded to '''Downloads''' folder. | ||
|- | |- | ||
− | | 05: | + | | 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.''' | ||
|- | |- | ||
− | | | + | | 06:08 |
| You can download available latest version. | | You can download available latest version. | ||
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− | | | + | | 06:13 |
| Right click on the executable file. | | Right click on the executable file. | ||
|- | |- | ||
− | | | + | | 06:16 |
| Select '''Open''' to open '''JChemPaint'''. | | Select '''Open''' to open '''JChemPaint'''. | ||
|- | |- | ||
− | | | + | | 06:20 |
| Alternately, you can open '''JChemPaint''' using '''Command prompt.''' | | Alternately, you can open '''JChemPaint''' using '''Command prompt.''' | ||
|- | |- | ||
− | | | + | | 06:26 |
| To open '''Command prompt''', press '''Windows''' and '''R''' keys simultaneously on the keyboard. | | To open '''Command prompt''', press '''Windows''' and '''R''' keys simultaneously on the keyboard. | ||
|- | |- | ||
− | | | + | | 06:34 |
| '''Run prompt''' box opens. | | '''Run prompt''' box opens. | ||
|- | |- | ||
− | | | + | | 06:37 |
| In the '''Open box''' type '''“cmd”''' and click on '''OK'''. | | In the '''Open box''' type '''“cmd”''' and click on '''OK'''. | ||
|- | |- | ||
− | | | + | | 06:43 |
| '''Command prompt''' opens. | | '''Command prompt''' opens. | ||
|- | |- | ||
− | | 06: | + | | 06:46 |
− | | Let's go to '''Downloads''' folder where we have | + | | Let's go to '''Downloads''' folder where we have save our downloaded '''.jar''' file. |
|- | |- | ||
− | | 06: | + | | 06:54 |
| Type at the '''prompt “cd space Downloads”''' and press '''Enter'''. | | 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'''. | | Type '''java space -jar space jchempaint-3.3-1210.jar''' and press '''Enter'''. | ||
|- | |- | ||
− | | | + | | 07:13 |
| '''JChemPaint''' window opens. | | '''JChemPaint''' window opens. | ||
|- | |- | ||
− | | | + | | 07:17 |
| If an error appears on '''command prompt''', | | If an error appears on '''command prompt''', | ||
|- | |- | ||
− | | | + | | 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. | ||
|- | |- | ||
− | | | + | | 07:27 |
| *Locate '''bin''' folder and right-click on it. | | *Locate '''bin''' folder and right-click on it. | ||
|- | |- | ||
− | | | + | | 07:32 |
| *Navigate to '''Properties'''. | | *Navigate to '''Properties'''. | ||
|- | |- | ||
− | | | + | | 07:35 |
| *Copy the address '''C:\Program Files''' within brackets '''(x86)\Java\jre7.''' | | *Copy the address '''C:\Program Files''' within brackets '''(x86)\Java\jre7.''' | ||
|- | |- | ||
− | | | + | | 07:48 |
| To set the path follow the steps. | | To set the path follow the steps. | ||
|- | |- | ||
− | | | + | | 07:51 |
| *Right-click on '''My Computer''', select '''Properties''' option. | | *Right-click on '''My Computer''', select '''Properties''' option. | ||
|- | |- | ||
− | | 07: | + | | 07:57 |
| *Click on '''Advanced System settings''', and then click on '''Environment Variables.''' | | *Click on '''Advanced System settings''', and then click on '''Environment Variables.''' | ||
|- | |- | ||
− | | | + | | 08:04 |
| *In '''System Variables''' search for '''Path'''. | | *In '''System Variables''' search for '''Path'''. | ||
|- | |- | ||
− | | | + | | 08:09 |
| *Click on '''Edit'''. | | *Click on '''Edit'''. | ||
|- | |- | ||
− | | | + | | 08:11 |
| *'''Edit system Variable''' dialog box opens | | *'''Edit system Variable''' dialog box opens | ||
|- | |- | ||
− | | | + | | 08:16 |
| *Paste the address '''C:\Program Files''' within brackets '''(x86)\Java\jre7.''' | | *Paste the address '''C:\Program Files''' within brackets '''(x86)\Java\jre7.''' | ||
|- | |- | ||
− | | | + | | 08:28 |
| *Click on '''OK ''' and close the windows. | | *Click on '''OK ''' and close the windows. | ||
|- | |- | ||
− | | | + | | 08:32 |
| '''JChemPaint''' window looks like this. | | '''JChemPaint''' window looks like this. | ||
|- | |- | ||
− | | | + | | 08:36 |
| This the '''Menu bar'''. | | This the '''Menu bar'''. | ||
|- | |- | ||
− | | | + | | 08:38 |
− | | '''Menu bar''' contains menu items like: | + | | '''Menu bar''' contains menu items like: '''File, Edit, View, Atom, Bond, Tools, R-groups, Templates''' and '''Help'''. |
− | + | ||
− | '''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'''. | | '''Tool bars''' contain all the tools required for you to work with '''JChemPaint'''. | ||
|- | |- | ||
− | | | + | | 09:02 |
| '''JChempaint''' window has, | | '''JChempaint''' window has, | ||
|- | |- | ||
− | | | + | | 09:04 |
| *Formatting tools on top | | *Formatting tools on top | ||
|- | |- | ||
− | | | + | | 09:07 |
| *Bond tools on the left | | *Bond tools on the left | ||
|- | |- | ||
− | | | + | | 09:09 |
| *Ring tools on the right and | | *Ring tools on the right and | ||
|- | |- | ||
− | | | + | | 09:12 |
| *Element tools at the bottom | | *Element tools at the bottom | ||
|- | |- | ||
− | | | + | | 09:15 |
| '''Panel''' displays the drawn structures. | | '''Panel''' displays the drawn structures. | ||
|- | |- | ||
− | | | + | | 09:18 |
| Now to '''JChemPaint Preferences''' window. | | Now to '''JChemPaint Preferences''' window. | ||
|- | |- | ||
− | | | + | | 09:22 |
| Click on '''Draw a chain''' tool. | | Click on '''Draw a chain''' tool. | ||
|- | |- | ||
− | | | + | | 09:24 |
| Click and drag the '''chain''' to '''6 Carbon atoms''' on the '''Panel'''. | | Click and drag the '''chain''' to '''6 Carbon atoms''' on the '''Panel'''. | ||
|- | |- | ||
− | | | + | | 09:30 |
| Notice that '''Carbon chain''' does not contain any '''atoms'''. | | Notice that '''Carbon chain''' does not contain any '''atoms'''. | ||
|- | |- | ||
− | | | + | | 09:35 |
| Go to '''Edit''' menu, navigate to '''Preferences''' and click on it. | | Go to '''Edit''' menu, navigate to '''Preferences''' and click on it. | ||
|- | |- | ||
− | | | + | | 09:42 |
| '''Preferences''' window opens. | | '''Preferences''' window opens. | ||
|- | |- | ||
− | | | + | | 09:45 |
| '''Preferences''' window has two tabs '''Display Preferences''' and '''Other Preferences'''. | | '''Preferences''' window has two tabs '''Display Preferences''' and '''Other Preferences'''. | ||
|- | |- | ||
− | | | + | | 09:54 |
| By default '''Display Preferences''' tab is selected. | | By default '''Display Preferences''' tab is selected. | ||
|- | |- | ||
− | | | + | | 10:00 |
− | | Notice that none of the check boxes are selected | + | | 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. | | 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.''' | | To show '''Methyl groups''' on the '''chain''' click on '''Show explicit methyl groups.''' | ||
|- | |- | ||
− | | | + | | 10:18 |
| To show '''hydrogens''' click on '''Show implicit hydrogens.''' | | To show '''hydrogens''' click on '''Show implicit hydrogens.''' | ||
|- | |- | ||
− | | | + | | 10:23 |
| Click on '''Apply''' and '''OK''' buttons to apply the changes. | | Click on '''Apply''' and '''OK''' buttons to apply the changes. | ||
|- | |- | ||
− | | | + | | 10:29 |
| As an example let's draw '''Phosphoric acid(H3PO4)'''. | | As an example let's draw '''Phosphoric acid(H3PO4)'''. | ||
|- | |- | ||
− | | | + | | 10:35 |
| To draw, click on '''Phosphrous(P) tool''' and then click on the '''Panel'''. | | To draw, click on '''Phosphrous(P) tool''' and then click on the '''Panel'''. | ||
|- | |- | ||
− | | | + | | 10:42 |
| '''Phosphine(PH3)''' will be displayed | | '''Phosphine(PH3)''' will be displayed | ||
|- | |- | ||
− | | | + | | 10:46 |
− | | Click on '''Oxygen(O) tool''' and click on '''Single bond tool.''' | + | | 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. | | 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'''. | | Click on '''P''' and drag to draw four '''Hydroxy bonds'''. | ||
|- | |- | ||
− | | | + | | 11:02 |
| You will notice a red line below '''Phosphrous atom'''. | | You will notice a red line below '''Phosphrous atom'''. | ||
|- | |- | ||
− | | | + | | 11:07 |
| This indicates that '''valency''' is not complete. | | 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'''. | | To complete the '''valency''' let's make the top '''Phosphrous-hydroxy bond''' as a '''double bond'''. | ||
|- | |- | ||
− | | | + | | 11:19 |
| Click on '''double bond tool'''. | | Click on '''double bond tool'''. | ||
|- | |- | ||
− | | | + | | 11:21 |
| Click on top '''Phosphrous-hydroxy bond'''. | | Click on top '''Phosphrous-hydroxy bond'''. | ||
|- | |- | ||
− | | | + | | 11:26 |
| The obtained structure is '''Phosphoric acid'''. | | The obtained structure is '''Phosphoric acid'''. | ||
|- | |- | ||
− | | | + | | 11:30 |
| Notice that all the atoms in the structure are black colored. | | Notice that all the atoms in the structure are black colored. | ||
|- | |- | ||
− | | | + | | 11:36 |
| To show '''Rasmol''' color of the element, | | To show '''Rasmol''' color of the element, | ||
|- | |- | ||
− | | | + | | 11:39 |
| Go to '''Edit''' menu and navigate to '''Preferences'''. | | Go to '''Edit''' menu and navigate to '''Preferences'''. | ||
|- | |- | ||
− | | | + | | 11:44 |
| In the window click on '''Color atoms by element''' check box. | | In the window click on '''Color atoms by element''' check box. | ||
|- | |- | ||
− | | | + | | 11:50 |
| It shows '''Rasmol''' color of the element. | | It shows '''Rasmol''' color of the element. | ||
|- | |- | ||
− | | | + | | 11:55 |
| Click on '''Apply''' and '''OK''' buttons to apply the changes. | | Click on '''Apply''' and '''OK''' buttons to apply the changes. | ||
|- | |- | ||
− | | | + | | 12:00 |
| Note that elements appear with their '''Rasmol''' colors. | | Note that elements appear with their '''Rasmol''' colors. | ||
|- | |- | ||
− | | | + | | 12:05 |
| Let's save the file. | | Let's save the file. | ||
|- | |- | ||
− | | | + | | 12:07 |
− | | Click on '''File menu''' and select '''Save as | + | | Click on '''File menu''' and select '''Save as.''' |
|- | |- | ||
− | | | + | | 12:12 |
| '''Save as''' dialog box opens. | | '''Save as''' dialog box opens. | ||
|- | |- | ||
− | | | + | | 12:15 |
| Select '''Desktop''' folder to save the file on '''Desktop'''. | | Select '''Desktop''' folder to save the file on '''Desktop'''. | ||
|- | |- | ||
− | | | + | | 12:21 |
| Type the file name as '''Phosphoric acid''' and click on '''Save''' button. | | Type the file name as '''Phosphoric acid''' and click on '''Save''' button. | ||
|- | |- | ||
− | | | + | | 12:27 |
| The file will be saved with '''.mol''' extension. | | The file will be saved with '''.mol''' extension. | ||
|- | |- | ||
− | | | + | | 12:31 |
| Let's summarise, | | Let's summarise, | ||
|- | |- | ||
− | | | + | | 12:33 |
| In this tutorial, we have learnt | | In this tutorial, we have learnt | ||
|- | |- | ||
− | | | + | | 12:36 |
| * About '''JChemPaint''' | | * About '''JChemPaint''' | ||
|- | |- | ||
− | | | + | | 12:38 |
− | | * Install '''JChemPaint''' on''' Windows | + | | * Install '''JChemPaint''' on''' Windows Operating System''' |
|- | |- | ||
− | | | + | | 12:42 |
− | | * Install '''JChemPaint''' on '''Ubuntu | + | | * Install '''JChemPaint''' on '''Ubuntu Operating system''' 12.04 |
|- | |- | ||
− | | | + | | 12:47 |
| * '''Menu bar, Tool bars''' and '''Panel''' of '''JChemPaint''' interface | | * '''Menu bar, Tool bars''' and '''Panel''' of '''JChemPaint''' interface | ||
|- | |- | ||
− | | | + | | 12:52 |
| * '''Preferences''' window | | * '''Preferences''' window | ||
|- | |- | ||
− | | | + | | 12:55 |
| * Draw structures using tools and | | * Draw structures using tools and | ||
|- | |- | ||
− | | | + | | 12:58 |
| * Save the drawing with '''.mol''' extension | | * Save the drawing with '''.mol''' extension | ||
|- | |- | ||
− | | | + | | 13:02 |
| As an assignment | | As an assignment | ||
|- | |- | ||
− | | | + | | 13:04 |
| * Install '''JChemPaint'''. | | * Install '''JChemPaint'''. | ||
|- | |- | ||
− | | | + | | 13:06 |
| * Explore various '''menu''' items. | | * Explore various '''menu''' items. | ||
|- | |- | ||
− | | | + | | 13:09 |
| This video summarises the Spoken Tutorial project | | This video summarises the Spoken Tutorial project | ||
|- | |- | ||
− | | | + | | 13:12 |
| If you do not have good bandwidth, you can download and watch it. | | If you do not have good bandwidth, you can download and watch it. | ||
|- | |- | ||
− | | | + | | 13:18 |
| The Spoken Tutorial Team: Conducts workshops using spoken tutorials | | The Spoken Tutorial Team: Conducts workshops using spoken tutorials | ||
|- | |- | ||
− | | | + | | 13:22 |
| Gives certificates to those who pass an online test | | Gives certificates to those who pass an online test | ||
|- | |- | ||
− | | | + | | 13:27 |
− | | For more details, please write to | + | | For more details, please write to contact@spoken-tutorial.org |
− | contact@spoken-tutorial.org | + | |
|- | |- | ||
− | | | + | | 13:34 |
| Spoken Tutorial Project is a part of the Talk to a Teacher project | | 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 | | 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 http://spoken-tutorial.org/NMEICT-Intro ] | | More information on this Mission is available at http://spoken-tutorial.org/NMEICT-Intro ] | ||
|- | |- | ||
− | | | + | | 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 14:40, 1 April 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 save 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 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 summarise, |
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 summarises 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 http://spoken-tutorial.org/NMEICT-Intro ] |
13:52 | This is Madhuri Ganpathi from IIT Bombay signing off. Thank you for joining. |