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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| * '''Menu bar, Tool bars''' and '''Panel''' of '''JChemPaint interface''',  

| * '''Menu bar, Tool bars''' and '''Panel''' of '''JChemPaint interface''',  

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| *'''Preferences''' window

| *'''Preferences''' window

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| * Draw structures using tools and

| * Draw structures using tools and

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|  * Save the drawing with '''.mol''' extension

|  * Save the drawing with '''.mol''' extension

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| 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  

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| *'''Windows'''  version 7

| *'''Windows'''  version 7

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| *'''JChemPaint''' version 3.3-1210  

| *'''JChemPaint''' version 3.3-1210  

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| *'''FireFox Browser''' 31.0

| *'''FireFox Browser''' 31.0

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| *'''Java''' version 7

| *'''Java''' version 7

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| * '''Synaptic Package Manager''' installed on your system.

| * '''Synaptic Package Manager''' installed on your system.

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| * Knowledge of  '''Terminal on Ubuntu'''.  

| * Knowledge of  '''Terminal on Ubuntu'''.  

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| * Knowledge of '''Command Prompt on Windows'''.

| * Knowledge of '''Command Prompt on Windows'''.

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| 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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| '''Java''' can be installed on '''Ubuntu''' using '''Synaptic Package Manager'''

| '''Java''' can be installed on '''Ubuntu''' using '''Synaptic Package Manager'''

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| For example: '''openjdk-7-jre'''

| For example: '''openjdk-7-jre'''

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| Let's learn about '''JChemPaint'''.

| Let's learn about '''JChemPaint'''.

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| * '''JChemPaint''' is a 2D chemical structures editor and viewer.

| * '''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'''.  

| *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'''.  

| *It allows to import and export structure data in plain-text formats like '''SMILES, Molfile, CML''' and '''InChi keys'''.  

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| Let's  start with '''JChemPaint''' installation on '''Ubuntu''' 12.04 OS.

| Let's  start with '''JChemPaint''' installation on '''Ubuntu''' 12.04 OS.

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| Open '''Firefox''' web browser.  

| Open '''Firefox''' web browser.  

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| 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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| You will be directed to the download page of  '''JChemPaint'''.

| You will be directed to the download page of  '''JChemPaint'''.

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| 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):”'''

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| Click on '" the desktop application (6.8 MB).'''

| Click on '" the desktop application (6.8 MB).'''

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| Let's move the saved file from '''Downloads''' folder to '''Desktop'''.

| Let's move the saved file from '''Downloads''' folder to '''Desktop'''.

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| 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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| To open a new '''JChemPaint''' window, we need '''Terminal.'''  

| To open a new '''JChemPaint''' window, we need '''Terminal.'''  

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| Type '''“cd space Desktop”''' and press '''Enter'''.

| Type '''“cd space Desktop”''' and press '''Enter'''.

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| 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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| '''JChemPaint''' window opens.

| '''JChemPaint''' window opens.

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| Please note '''JChemPaint''' can be opened  through the '''Terminal''' only.   

| Please note '''JChemPaint''' can be opened  through the '''Terminal''' only.   

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| Let's move on to '''Windows''' installation process.

| Let's move on to '''Windows''' installation process.

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| Let's  install '''Java''' on '''Windows OS'''.

| Let's  install '''Java''' on '''Windows OS'''.

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| Open '''Firefox''' web browser on your '''Windows''' machine.

| Open '''Firefox''' web browser on your '''Windows''' machine.

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| 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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| A new webpage opens.

| A new webpage opens.

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| 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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| Download page opens.

| Download page opens.

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| On the web page, accept the '''License agreement'''.

| On the web page, accept the '''License agreement'''.

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| Select '''jre-7-windows-i586.exe'''  link.

| Select '''jre-7-windows-i586.exe'''  link.

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|  '''Save file''' dialog box opens.  

|  '''Save file''' dialog box opens.  

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| Click on '''Save File''' button.

| Click on '''Save File''' button.

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| Follow the installation process to install '''Java'''.

| Follow the installation process to install '''Java'''.

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| Click on '''Close'''.

| Click on '''Close'''.

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| '''Jre-7''' will be installed on your machine.

| '''Jre-7''' will be installed on your machine.

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| Let's install '''JChemPaint'''.

| Let's install '''JChemPaint'''.

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| Open '''Firefox''' web browser on your '''Windows''' machine.

| Open '''Firefox''' web browser on your '''Windows''' machine.

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| 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'''.

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| You will be directed to the download page of  '''JChemPaint'''.

| You will be directed to the download page of  '''JChemPaint'''.

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| Click on  '''"the desktop application (6.8 MB) "'''.

| Click on  '''"the desktop application (6.8 MB) "'''.

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| '''Save file''' dialog box opens.  

| '''Save file''' dialog box opens.  

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| Click on '''Save File''' button.

| Click on '''Save File''' button.

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| The '''.jar''' file will be downloaded to '''Downloads''' folder.

| The '''.jar''' file will be downloaded to '''Downloads''' folder.

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| 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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| You can download available latest version.

| You can download available latest version.

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| Right click on the executable file.  

| Right click on the executable file.  

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| Select '''Open''' to open '''JChemPaint'''.

| Select '''Open''' to open '''JChemPaint'''.

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| Alternately, you can open '''JChemPaint''' using '''Command prompt.'''

| Alternately, you can open '''JChemPaint''' using '''Command prompt.'''

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| 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.  

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| '''Run prompt''' box opens.

| '''Run prompt''' box opens.

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| In the '''Open box''' type '''“cmd”''' and click on '''OK'''.

| In the '''Open box''' type '''“cmd”''' and click on '''OK'''.

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| '''Command prompt''' opens.

| '''Command prompt''' opens.

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| Type at the '''prompt “cd space Downloads”''' and press '''Enter'''.   

| Type at the '''prompt “cd space Downloads”''' and press '''Enter'''.   

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| 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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| '''JChemPaint''' window opens.

| '''JChemPaint''' window opens.

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|  If an error appears on '''command prompt''',  

|  If an error appears on '''command prompt''',  

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| *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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| *Locate '''bin''' folder and right-click on it.

| *Locate '''bin''' folder and right-click on it.

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| *Navigate to '''Properties'''.

| *Navigate to '''Properties'''.

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| *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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| To set the path follow the steps.

| To set the path follow the steps.

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| *Right-click on '''My Computer''', select '''Properties''' option.  

| *Right-click on '''My Computer''', select '''Properties''' option.  

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| *Click on '''Advanced System settings''', and then click on '''Environment  Variables.'''  

| *Click on '''Advanced System settings''', and then click on '''Environment  Variables.'''  

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| *In '''System Variables''' search for '''Path'''.

| *In '''System Variables''' search for '''Path'''.

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| *Click on '''Edit'''.

| *Click on '''Edit'''.

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| *'''Edit system  Variable''' dialog box opens

| *'''Edit system  Variable''' dialog box opens

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| *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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| *Click on '''OK ''' and close the windows.

| *Click on '''OK ''' and close the windows.

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| '''JChemPaint''' window looks like this.

| '''JChemPaint''' window looks like this.

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| This the '''Menu bar'''.

| This the '''Menu bar'''.

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| '''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'''.  

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| '''JChempaint''' window has,

| '''JChempaint''' window has,

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| *Formatting tools on top

| *Formatting tools on top

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|  *Bond tools on the left

|  *Bond tools on the left

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| *Ring tools on the right and

| *Ring tools on the right and

   

   

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| *Element tools at the bottom

| *Element tools at the bottom

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| '''Panel''' displays the drawn structures.

| '''Panel''' displays the drawn structures.

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| Now to '''JChemPaint  Preferences''' window.

| Now to '''JChemPaint  Preferences''' window.

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| Click on '''Draw a chain''' tool.

| Click on '''Draw a chain''' tool.

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| Click and drag the '''chain'''  to '''6 Carbon atoms''' on the '''Panel'''.

| Click and drag the '''chain'''  to '''6 Carbon atoms''' on the '''Panel'''.

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| Notice that '''Carbon chain''' does not contain any '''atoms'''.

| Notice that '''Carbon chain''' does not contain any '''atoms'''.

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| Go to '''Edit''' menu, navigate to '''Preferences''' and click on it.

| Go to '''Edit''' menu, navigate to '''Preferences''' and click on it.

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| '''Preferences''' window opens.

| '''Preferences''' window opens.

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| '''Preferences''' window has two tabs '''Display Preferences''' and '''Other Preferences'''.

| '''Preferences''' window has two tabs '''Display Preferences''' and '''Other Preferences'''.

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| By default '''Display Preferences''' tab is selected.

| By default '''Display Preferences''' tab is selected.

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| 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.

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| 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.'''

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| To show '''hydrogens''' click on '''Show implicit hydrogens.'''

| To show '''hydrogens''' click on '''Show implicit hydrogens.'''

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| Click on '''Apply''' and '''OK''' buttons to apply the changes.

| Click on '''Apply''' and '''OK''' buttons to apply the changes.

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| As an example let's draw '''Phosphoric acid(H3PO4)'''.

| As an example let's draw '''Phosphoric acid(H3PO4)'''.

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| 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'''.

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| '''Phosphine(PH3)''' will be displayed

| '''Phosphine(PH3)''' will be displayed

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| 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.

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| Click on '''P''' and drag to draw four '''Hydroxy bonds'''.

| Click on '''P''' and drag to draw four '''Hydroxy bonds'''.

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| You will notice a red line below '''Phosphrous atom'''.

| You will notice a red line below '''Phosphrous atom'''.

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| This indicates that '''valency''' is not complete.

| This indicates that '''valency''' is not complete.

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| 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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| Click on '''double bond tool'''.

| Click on '''double bond tool'''.

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| Click on top '''Phosphrous-hydroxy bond'''.

| Click on top '''Phosphrous-hydroxy bond'''.

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| The obtained structure is '''Phosphoric acid'''.   

| The obtained structure is '''Phosphoric acid'''.   

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|  Notice that all the atoms in the structure are black colored.

|  Notice that all the atoms in the structure are black colored.

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| To show '''Rasmol''' color of the element,  

| To show '''Rasmol''' color of the element,  

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| Go to '''Edit''' menu and navigate to '''Preferences'''.

| Go to '''Edit''' menu and navigate to '''Preferences'''.

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|  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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| It shows '''Rasmol''' color of the element.

| It shows '''Rasmol''' color of the element.

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|  Click on '''Apply''' and '''OK''' buttons to apply the changes.

|  Click on '''Apply''' and '''OK''' buttons to apply the changes.

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| Note that elements appear with their  '''Rasmol''' colors.

| Note that elements appear with their  '''Rasmol''' colors.

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| Let's save the file.

| Let's save the file.

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| '''Save as''' dialog box opens.

| '''Save as''' dialog box opens.

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| Select '''Desktop''' folder to save the file on '''Desktop'''.

| Select '''Desktop''' folder to save the file on '''Desktop'''.

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|  Type the file name as '''Phosphoric acid''' and  click on '''Save''' button.

|  Type the file name as '''Phosphoric acid''' and  click on '''Save''' button.

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| The file will be saved with '''.mol''' extension.

| The file will be saved with '''.mol''' extension.

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| Let's summarise,

| Let's summarise,

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| In this tutorial, we have learnt  

| In this tutorial, we have learnt  

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| * About '''JChemPaint'''

| * About '''JChemPaint'''

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| * '''Menu bar, Tool bars''' and '''Panel''' of  '''JChemPaint''' interface  

| * '''Menu bar, Tool bars''' and '''Panel''' of  '''JChemPaint''' interface  

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| * '''Preferences''' window

| * '''Preferences''' window

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| * Draw structures using tools and

| * Draw structures using tools and

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| * Save the drawing with '''.mol''' extension

| * Save the drawing with '''.mol''' extension

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|  As an assignment

|  As an assignment

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| * Install '''JChemPaint'''.

| * Install '''JChemPaint'''.

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| * Explore various '''menu''' items.

| * Explore various '''menu''' items.

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| This video summarises the Spoken Tutorial project

| This video summarises the Spoken Tutorial project

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|-

| 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.

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|-

| The Spoken Tutorial  Team: Conducts workshops using spoken tutorials

| The Spoken Tutorial  Team: Conducts workshops using spoken tutorials

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|-

| Gives certificates to those who pass an online test  

| Gives certificates to those who pass an online test  

|-

|-

|-

|-

| 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  

|-

|-

| 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

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|-

| 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 ]  

|-

|-

| 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.  

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|}

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