Difference between revisions of "JChemPaint/C2/Introduction-to-JChemPaint/English"

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(Created page with '{| border=1 || Visual Cue || Narration |- ||'''Slide Number 1 Title Slide''' || Hello everyone. Welcome to this tutorial on '''Introduction to JChemPaint'''. |- ||'''Slide Nu…')
 
Line 15: Line 15:
 
|| In this tutorial, we will learn  
 
|| In this tutorial, we will learn  
  
−
* About JChemPaint
+
* About '''JChemPaint'''
  
−
* Install JChemPaint on Windows OS
+
* Install '''JChemPaint''' on '''Windows OS'''
  
−
* Install JChemPaint on Ubuntu OS 12.04.  
+
* Install '''JChemPaint''' on '''Ubuntu OS''' 12.04.  
  
 
We will also learn,
 
We will also learn,
  
−
* Menu bar, Tool bars and Panel of JChemPaint interface  
+
* '''Menu bar, Tool bars''' and '''Panel''' of '''JChemPaint interface''',
−
Preferences window
+
 
 +
*'''Preferences''' window
  
 
* Draw structures using tools and
 
* Draw structures using tools and
  
−
* Save the drawing with .mol extension
+
* Save the drawing with '''.mol''' extension
 
|-
 
|-
 
||'''Slide Number 4
 
||'''Slide Number 4
Line 35: Line 36:
 
||To record this tutorial I am using,  
 
||To record this tutorial I am using,  
  
−
* Ubuntu Linux OS version 12.04  
+
* '''Ubuntu Linux OS''' version 12.04  
  
−
*Windows  version 7
+
*'''Windows''' version 7
  
−
*JChemPaint version 3.3-1210  
+
*'''JChemPaint''' version 3.3-1210  
  
−
*FireFox Browser 31.0
+
*'''FireFox Browser''' 31.0
−
*Java version 7
+
*'''Java''' version 7
 
|-
 
|-
 
||'''Slide Number 5
 
||'''Slide Number 5
Line 62: Line 63:
 
|| Please note,
 
|| Please note,
  
−
To run JChemPaint, you should have Java installed on your system.  
+
To run '''JChemPaint''', you should have '''Java''' installed on your system.  
  
−
Java can be installed on Ubuntu using Synaptic Package Manager
+
'''Java''' can be installed on '''Ubuntu''' using '''Synaptic Package Manager'''
 +
 
 +
For example: '''openjdk-7-jre'''
  
−
For example: openjdk-7-jre
 
 
|-
 
|-
 
||
 
||
−
|| Let's learn about JChemPaint.
+
|| Let's learn about '''JChemPaint'''.
 +
 
 
|-
 
|-
 
||Slide Number 7
 
||Slide Number 7
Line 75: Line 78:
 
About JChemPaint
 
About JChemPaint
 
||
 
||
−
* JChemPaint is a 2D chemical structures editor and viewer.
+
* '''JChemPaint''' is a 2D chemical structures editor and viewer.
  
−
*It is free and open-source cross platform application developed in Java.  
+
*It is free and open-source cross platform application developed in '''Java'''.  
  
−
*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'''.  
 
|-
 
|-
 
||
 
||
−
||Let's  start with JChemPaint installation on Ubuntu 12.04 OS.  రీప్లేస్  చేస్తుంది.
+
||Let's  start with '''JChemPaint''' installation on '''Ubuntu''' 12.04 OS.
 
|-
 
|-
 
||On the browser>> in the address bar, type the URL
 
||On the browser>> in the address bar, type the URL
−
||Open Firefox web browser.  
+
||Open '''Firefox''' web browser.  
  
−
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'''.  
 
|-
 
|-
 
||Point to the new web page
 
||Point to the new web page
−
||You will be directed to the download page of  JChemPaint.
+
||You will be directed to the download page of  '''JChemPaint'''.
 
|-
 
|-
 
||Move the cursor on the webpage.
 
||Move the cursor on the webpage.
Line 97: Line 100:
 
||On the webpage, locate
 
||On the webpage, locate
  
−
“download a recent jar file from github (current is 3.3-1210):”
+
'''“download a recent jar file from github (current is 3.3-1210):”'''
  
−
Click on " the desktop application (6.8 MB) ".
+
Click on '''" the desktop application (6.8 MB) ".'''
 
|-
 
|-
−
||Point to the dialogue box
+
||Point to the dialog box
−
|| Save file dialog box opens, click on Save File button.
+
|| Save file dialog box opens, click on '''Save File''' button.
 
|-
 
|-
 
||Point to the saved file in the Downloads folder
 
||Point to the saved file in the Downloads folder
−
||Let's move the saved file from Downloads folder to Desktop.
+
||Let's move the saved file from '''Downloads''' folder to '''Desktop'''.
 
|-
 
|-
 
||Right click on saved file >>select Move to Desktop.
 
||Right click on saved file >>select Move to Desktop.
−
||Right click on the saved file and select Move to Desktop.
+
||Right click on the saved file and select '''Move to Desktop'''.
 
|-
 
|-
 
||
 
||
−
||To open a new JChemPaint window we need Terminal.  
+
||To open a new '''JChemPaint''' window, we need '''Terminal.'''
 
|-
 
|-
  
 
||Press CTRl+ALt and T keys simultaneously  to open the Terminal.
 
||Press CTRl+ALt and T keys simultaneously  to open the Terminal.
−
||Press CTRl+ALt and T keys simultaneously  to open the Terminal.
+
||Press '''CTRl+ALt''' and '''T''' keys simultaneously  to open the '''Terminal'''.
 
|-
 
|-
 
||Type “cd space Desktop” and press enter.
 
||Type “cd space Desktop” and press enter.
  
 
Type java  -jar ./jchempaint-3.3-1210.jar and press enter.
 
Type java  -jar ./jchempaint-3.3-1210.jar and press enter.
−
|| Type “cd space Desktop” and press enter.
+
|| Type '''“cd space Desktop”''' and press '''Enter'''.
 +
 
 +
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.
+
'''JChemPaint''' window opens.
  
−
JChemPaint window opens.
 
  
−
Please note JChemPaint can be opened  through the Terminal only.   
+
Please note '''JChemPaint''' can be opened  through the '''Terminal''' only.   
 
|-
 
|-
 
||  
 
||  
−
|| Let's move on to Windows installation process.
+
|| Let's move on to '''Windows''' installation process.
 
|-
 
|-
 
||
 
||
−
||Let's  install java on Windows OS.
+
||Let's  install '''Java''' on '''Windows OS'''.
 
|-
 
|-
 
||On the browser>> in the address bar, type the URL
 
||On the browser>> in the address bar, type the URL
−
||Open Firefox web browser on your Windows machine.
+
||Open '''Firefox''' web browser on your '''Windows''' machine.
  
 
In the address bar,  
 
In the address bar,  
  
−
type  jre-7-downloads and press enter.
+
type  '''jre-7-downloads''' and press '''Enter'''.
 
|-
 
|-
 
||Point to the page.
 
||Point to the page.
Line 146: Line 150:
 
||A new webpage opens.
 
||A new webpage opens.
  
−
Click on the link Java SE Runtime Environment 7 Downloads-Oracle.  
+
Click on the link '''Java SE Runtime Environment 7 Downloads-Oracle.'''
  
 
Download page opens.
 
Download page opens.
Line 153: Line 157:
  
 
Select jre-7-windows-i586.exe.
 
Select jre-7-windows-i586.exe.
−
||On the web page, accept the License agreement.
+
||On the web page, accept the '''License agreement'''.
  
−
Select jre-7-windows-i586.exe  link.
+
Select '''jre-7-windows-i586.exe''' link.
 
|-
 
|-
−
||Point to the dialogue box.
+
||Point to the dialog box.
  
 
Click on Save File button.
 
Click on Save File button.
−
|| Save file dialogue box opens.  
+
|| '''Save file''' dialog box opens.  
  
−
Click on Save File button.
+
Click on '''Save File''' button.
  
−
The file will be downloaded in the Downloads folder.
+
 
 +
The file will be downloaded in the '''Downloads''' folder.
 
|-
 
|-
 
||Click on the downloaded file.  
 
||Click on the downloaded file.  
Line 170: Line 175:
 
|-
 
|-
 
||Point to install window.
 
||Point to install window.
−
||Follow the installation process to install Java.
+
||Follow the installation process to install '''Java'''.
  
−
Click on close.
+
Click on '''Close'''.
  
−
Jre-7 will be intalled on your machine.
+
'''Jre-7''' will be installed on your machine.
 
|-
 
|-
 
||  
 
||  
−
||Let's install JChemPaint.
+
||Let's install '''JChemPaint'''.
 
|-
 
|-
−
||On the browser>> in the address bar, type the UR
+
||On the browser>> in the address bar, type the URL
−
||Open Firefox web browser on your Windows machine.
+
||Open '''Firefox''' web browser on your '''Windows''' machine.
  
−
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'''.
 
|-
 
|-
 
||Point to the new webpage.
 
||Point to the new webpage.
−
||You will be directed to the download page of  JChemPaint.
+
||You will be directed to the download page of  '''JChemPaint'''.
 
|-
 
|-
 
||Move the cursor on the webpage.
 
||Move the cursor on the webpage.
Line 192: Line 197:
 
||On the webpage, locate
 
||On the webpage, locate
  
−
“download a recent jar file from github (current is 3.3-1210):”
+
'''“download a recent jar file from github (current is 3.3-1210):”'''
  
−
Click on  "the desktop application (6.8 MB) ".
+
Click on  '''"the desktop application (6.8 MB) "'''.
 
|-
 
|-
−
||Point to the dialogue box.
+
||Point to the dialog box.
  
 
Click on Save File button.
 
Click on Save File button.
−
||Save file dialog box opens.  
+
||'''Save file''' dialog box opens.  
  
−
Click on Save File button.
+
Click on '''Save File''' button.
 
|-
 
|-
 
||Open Downloads folder select the file.  
 
||Open Downloads folder select the file.  
−
||The .jar file will be downloaded to Downloads folder.
+
||The '''.jar''' file will be downloaded to '''Downloads''' folder.
  
−
Open Downloads folder and select the file jchempaint-3.3-1210.jar.  
+
Open '''Downloads''' folder and select the file '''jchempaint-3.3-1210.jar.'''
  
 
You can download available latest version.
 
You can download available latest version.
 
|-
 
|-
 
||Right click on the Executable file>>Select Open to open JchemPaint.
 
||Right click on the Executable file>>Select Open to open JchemPaint.
−
||Right click on the Executable file.  
+
||Right click on the executable file.  
  
−
Select Open to open JChemPaint.
+
Select '''Open''' to open '''JChemPaint'''.
 
|-
 
|-
 
||
 
||
−
||Alternatively you can open JChemPaint using Command prompt.
+
||Alternately, you can open '''JChemPaint''' using '''Command prompt.'''
 
|-
 
|-
−
||Press Windows and r keys simultanoeously on the key board.
+
||Press Windows and R keys simultaneously on the key board.
−
||To open Command prompt, press Windows and r keys simultanoeously on the keyboard.  
+
||To open '''Command prompt''', press '''Windows''' and '''R''' keys simultaneously on the keyboard.  
 
|-
 
|-
 
||Point to the box.
 
||Point to the box.
Line 226: Line 231:
  
 
Command prompt opens.
 
Command prompt opens.
−
||Run prompt box opens.
+
||'''Run prompt''' box opens.
  
−
In the Open box type “cmd” and click on OK.
+
In the '''Open box''' type '''“cmd”''' and click on '''OK'''.
  
−
Command prompt opens.
+
'''Command prompt''' opens.
 
|-
 
|-
 
||
 
||
−
||Let's go to Downloads folder where we have downloaded our .jar file.  
+
||Let's go to '''Downloads''' folder where we have downloaded our '''.jar''' file.  
 
|-
 
|-
−
||Type at the prompt “cd Downloads” >> press enter  
+
||Type “cd Downloads” >> press enter  
−
||Type at the prompt “cd space Downloads” and press enter.   
+
||Type at the '''prompt “cd space Downloads”''' and press '''Enter'''.   
 
|-
 
|-
−
||Type Java space -jar space jchempaint3.3.jar>>press enter.  
+
||Type Java -jar jchempaint3.3.jar>>press enter.  
−
||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'''.
  
−
JChemPaint window opens.
+
'''JChemPaint''' window opens.
 
|-
 
|-
 
||Slide Number 8
 
||Slide Number 8
  
 
"Error on Command Prompt".
 
"Error on Command Prompt".
−
|| If an error appears on command prompt,  
+
|| If an error appears on '''command prompt''',  
  
−
Go to Program files locate the java folder and click on it.
+
*Go to '''Program files''' locate the '''java''' folder and click on it.
  
−
Locate bin folder and right-click on it.
+
*Locate '''bin''' folder and right-click on it.
  
−
Navigate to Properties.
+
*Navigate to '''Properties'''.
  
−
Copy the address C:\Program Files within bracketts(x86)\Java\jre7.
+
*Copy the address '''C:\Program Files within bracketts(x86)\Java\jre7.'''
 
|-
 
|-
 
||Slide Number 9
 
||Slide Number 9
Line 261: Line 266:
 
||To set the path follow the steps.
 
||To set the path follow the steps.
  
−
Right click on My Computer, select Properties option.  
+
*Right-click on '''My Computer''', select '''Properties''' option.  
  
−
Click on Advanced System settings, then click on Environmemt Variables.  
+
*Click on '''Advanced System settings''', then click on '''Environment Variables.'''
  
−
In System Variables search for Path.
+
*In '''System Variables''' search for '''Path'''.
  
−
Click on Edit.
+
*Click on '''Edit'''.
  
−
Edit system  Variable dialogue box opens
+
*'''Edit system  Variable''' dialog box opens
  
−
Paste the address  C:\Program Files within bracketts (x86)\Java\jre7.
+
*Paste the address  '''C:\Program Files within bracketts (x86)\Java\jre7.'''
  
−
Click on OK and close the windows.
+
*Click on '''OK ''' and close the windows.
 
|-
 
|-
 
||Move the cursor on the window.
 
||Move the cursor on the window.
−
||JChemPaint window looks like this.
+
||'''JChemPaint''' window looks like this.
 
|-
 
|-
 
||Point to the Menu bar.
 
||Point to the Menu bar.
  
 
Move the cursor over all the menu items.
 
Move the cursor over all the menu items.
−
|| This the Menu bar.
+
|| This the '''Menu bar'''.
  
−
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'''.
 
|-
 
|-
 
||Point to the tool bars.
 
||Point to the tool bars.
−
||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'''.  
 
|-
 
|-
 
||Move the cursor on all the tools.
 
||Move the cursor on all the tools.
−
||JChempaint window has,
+
||'''JChempaint''' window has,
  
−
Formatting tools on top
+
*Formatting tools on top
−
 
+
*Bond tools on the left
−
Bond tools on the left
+
*Ring tools on the right and
−
 
+
*Element tools at the bottom
−
Ring tools on the right and
+
−
 
+
−
Element tools at the bottom
+
 
|-
 
|-
 
||Move the cursor on the Panel
 
||Move the cursor on the Panel
−
||Panel displays the drawn structures.
+
||'''Panel''' displays the drawn structures.
 
|-
 
|-
 
||
 
||
−
||Now to JChemPaint  Preferences window.
+
||Now to '''JChemPaint  Preferences''' window.
 
|-
 
|-
 
||Click on Draw a chain tool.
 
||Click on Draw a chain tool.
−
||Click on Draw a chain tool.
+
||Click on '''Draw a chain''' tool.
  
−
Click and drag the chain to 6 Carbon atoms on the Panel.
+
Click and drag the '''chain''' to '''6 Carbon atoms''' on the '''Panel'''.
  
−
Notice that Carbon chain does not contain any atoms.
+
Notice that '''Carbon chain''' does not contain any '''atoms'''.
 
|-
 
|-
 
||Go to Edit menu, navigate to Preferences >> click on it.
 
||Go to Edit menu, navigate to Preferences >> click on it.
 
Point to the window.
 
Point to the window.
−
|| Go to Edit menu, navigate to Preferences and click on it.
+
|| Go to '''Edit menu''', navigate to '''Preferences''' and click on it.
  
−
Preferences window opens.
+
'''Preferences''' window opens.
 
|-   
 
|-   
 
||Move the cursor on the tabs.
 
||Move the cursor on the tabs.
−
||Preferences window has two tabs Display Preferences and Other Preferences.
+
||'''Preferences''' window has two tabs '''Display Preferences''' and '''Other Preferences'''.
 
|-
 
|-
 
||Point to the tab.
 
||Point to the tab.
−
||By default Display Preferences tab is selected.
+
||By default '''Display Preferences''' tab is selected.
 
|-
 
|-
 
||Move the cursor on all the check boxes.
 
||Move the cursor on all the check boxes.
Line 335: Line 337:
  
 
click on Show explicit methyl groups.
 
click on Show explicit methyl groups.
−
||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.'''
 
|-
 
|-
 
||Point to the check box click on Show implicit hydrogens
 
||Point to the check box click on Show implicit hydrogens
−
||To show hydrogens click on Show implicit hydrogens.
+
||To show '''hydrogens''' click on '''Show implicit hydrogens.'''
 
|-
 
|-
 
||Click on Apply and OK buttons to apply the changes.
 
||Click on Apply and OK buttons to apply the changes.
−
||Click on Apply and OK buttons to apply the changes.
+
||Click on '''Apply''' and '''OK''' buttons to apply the changes.
 
|-
 
|-
 
||
 
||
−
||As an example let's draw Phosphoric acid(H3PO4).
+
||As an example let's draw '''Phosphoric acid(H3PO4)'''.
 
|-
 
|-
 
||Click on Phosphrous(P) tool  >> click on the Panel.
 
||Click on Phosphrous(P) tool  >> click on the Panel.
 
Point to  PH3
 
Point to  PH3
−
||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'''.
  
−
Phosphine(PH3) will be displayed
+
'''Phosphine(PH3)''' will be displayed
 
|-
 
|-
 
||Click on Oxygen(O) tool>> click on Single bond tool .
 
||Click on Oxygen(O) tool>> click on Single bond tool .
−
||Click on Oxygen(O) tool and click on Single bond tool.
+
||Click on '''Oxygen(O) tool''' and click on '''Single bond tool.'''
 
|-
 
|-
 
||Point to small blue circle.Click on Oxygen(O) tool and click on Single bond tool.
 
||Point to small blue circle.Click on Oxygen(O) tool and click on Single bond tool.
−
||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.
  
−
Click on P and drag to draw four Hydroxy bonds .
+
Click on '''P''' and drag to draw four '''Hydroxy bonds'''.
 
|-
 
|-
 
||Point to the red line below Phosphrous atom.
 
||Point to the red line below Phosphrous atom.
−
||You will notice a red line below Phosphrous atom.
+
||You will notice a red line below '''Phosphrous atom'''.
  
−
This indicates that valency is not complete.
+
This indicates that '''valency''' is not complete.
 
|-
 
|-
 
||Point to the top bond
 
||Point to the top bond
−
||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'''.  
 
|-   
 
|-   
 
||Click on double bond tool >>click on top the Phosphrous-hydroxy bond.
 
||Click on double bond tool >>click on top the Phosphrous-hydroxy bond.
−
||Click on double bond tool.
+
||Click on '''double bond tool'''.
  
−
Click on top Phosphrous-hydroxy bond.
+
Click on top '''Phosphrous-hydroxy bond'''.
  
−
The obtained structure is Phosphoric acid.   
+
The obtained structure is '''Phosphoric acid'''.   
 
|-
 
|-
 
||Point to the structure.
 
||Point to the structure.
Line 379: Line 381:
 
|-
 
|-
 
||Go to Edit menu and navigate to Preferences.
 
||Go to Edit menu and navigate to Preferences.
−
|| To show Rasmol color of the element,  
+
|| To show '''Rasmol''' color of the element,  
−
Go to Edit menu and navigate to Preferences.
+
Go to '''Edit menu''' and navigate to '''Preferences'''.
 
|-
 
|-
 
||In the window click on Color atoms by element check box>>It shows Rasmol color of the element.
 
||In the window click on Color atoms by element check box>>It shows Rasmol color of the element.
−
|| In the window click on Color atoms by element check box.
+
|| In the window click on '''Color atoms by element''' check box.
  
−
It shows Rasmol color of the element.
+
It shows '''Rasmol''' color of the element.
 
|-
 
|-
 
||Click on Apply and OK buttons .
 
||Click on Apply and OK buttons .
−
|| Click on Apply and OK buttons to apply the changes.
+
|| Click on '''Apply''' and '''OK''' buttons to apply the changes.
  
−
Note that elements appear with their  Rasmol colors.
+
Note that elements appear with their  '''Rasmol''' colors.
 
|-
 
|-
 
||
 
||
Line 396: Line 398:
 
|-
 
|-
 
||Click on File menu >> select Save as...
 
||Click on File menu >> select Save as...
−
||Click on File menu and select Save as....  
+
||Click on '''File menu''' and select '''Save as....'''
 
|-
 
|-
−
||Save as dialogue box opens.
+
||Save as dialog box opens.
−
||Save as dialogue box opens.
+
||'''Save as''' dialog box opens.
 
|-
 
|-
 
||Select Desktop folder to save the file on Desktop.
 
||Select Desktop folder to save the file on Desktop.
−
||Select Desktop folder to save the file on Desktop.
+
||Select '''Desktop''' folder to save the file on '''Desktop'''.
 
|-
 
|-
 
||Type the file name as Oxyacids of Phosphorus >> Click on Save button.
 
||Type the file name as Oxyacids of Phosphorus >> Click on Save button.
−
|| Type the file name as Phosphoric acid and  click on Save button.
+
|| Type the file name as '''Phosphoric acid''' and  click on '''Save''' button.
  
−
The file will be saved with .mol extension.
+
The file will be saved with '''.mol''' extension.
 
|-
 
|-
 
||
 
||
Line 417: Line 419:
 
|| In this tutorial, we have learnt  
 
|| In this tutorial, we have learnt  
  
−
* About JChemPaint
+
* About '''JChemPaint'''
  
−
* Install  JChemPaint on Windows OS
+
* Install  '''JChemPaint''' on''' Windows OS'''
  
−
* Install  JChemPaint on Ubuntu OS 12.04  
+
* Install  '''JChemPaint''' on '''Ubuntu OS''' 12.04  
  
−
* Menu bar, Tool bars and Panel of  JChemPaint interface  
+
* '''Menu bar, Tool bars''' and '''Panel''' of  '''JChemPaint''' interface  
  
−
* Preferences window
+
* '''Preferences''' window
  
 
* Draw structures using tools and
 
* Draw structures using tools and
  
−
* Save the drawing with .mol extension
+
* Save the drawing with '''.mol''' extension
 
|-
 
|-
 
||Slide Number 9
 
||Slide Number 9
Line 436: Line 438:
 
|| As an assignment
 
|| As an assignment
  
−
* Install JChemPaint.
+
* Install '''JChemPaint'''.
  
−
* Explore various menu items.
+
* Explore various '''menu''' items.
 
|-
 
|-
 
||Slide Number10
 
||Slide Number10

Revision as of 19:37, 29 August 2014

Visual Cue Narration
Slide Number 1

Title Slide

Hello everyone.

Welcome to this tutorial on Introduction to JChemPaint.

Slide Number 2+3

Learning Objectives

In this tutorial, we will learn
  • About JChemPaint
  • Install JChemPaint on Windows OS
  • Install JChemPaint on Ubuntu OS 12.04.

We will also learn,

  • Menu bar, Tool bars and Panel of JChemPaint interface,
  • Preferences window
  • Draw structures using tools and
  • Save the drawing with .mol extension
Slide Number 4

System Requirement

To record this tutorial I am using,
  • Ubuntu Linux OS version 12.04
  • Windows version 7
  • JChemPaint version 3.3-1210
  • FireFox Browser 31.0
  • Java version 7
Slide Number 5

Pre-requisites

To follow this tutorial you must have,
  • Internet connection
  • Synaptic Package Manager installed on your system.
  • Knowledge of Terminal on Ubuntu.
  • Knowledge of Command Prompt on Windows.
Slide Number 6

Java Installation

Please note,

To run JChemPaint, you should have Java installed on your system.

Java can be installed on Ubuntu using Synaptic Package Manager

For example: openjdk-7-jre

Let's learn about JChemPaint.
Slide Number 7

About JChemPaint

  • JChemPaint is a 2D chemical structures editor and viewer.
  • It is free and open-source cross platform application developed in Java.
  • It allows to import and export structure data in plain-text formats like SMILES, Molfile, CML and InChi keys.
Let's start with JChemPaint installation on Ubuntu 12.04 OS.
On the browser>> in the address bar, type the URL Open Firefox web browser.

In the address bar, type the URL http://jchempaint.github.io/ to install JChemPaint on Ubuntu.

Point to the new web page You will be directed to the download page of JChemPaint.
Move the cursor on the webpage.

Click on "the desktop application (6.8 MB) "

On the webpage, locate

“download a recent jar file from github (current is 3.3-1210):”

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

Point to the dialog box Save file dialog box opens, click on Save File button.
Point to the saved file in the Downloads folder Let's move the saved file from Downloads folder to Desktop.
Right click on saved file >>select Move to Desktop. Right click on the saved file and select Move to Desktop.
To open a new JChemPaint window, we need Terminal.
Press CTRl+ALt and T keys simultaneously to open the Terminal. Press CTRl+ALt and T keys simultaneously to open the Terminal.
Type “cd space Desktop” and press enter.

Type java -jar ./jchempaint-3.3-1210.jar and press enter.

Type “cd space Desktop” and press Enter.

Type java space -jar space ./jchempaint-3.3-1210.jar and press Enter.

JChemPaint window opens.


Please note JChemPaint can be opened through the Terminal only.

Let's move on to Windows installation process.
Let's install Java on Windows OS.
On the browser>> in the address bar, type the URL Open Firefox web browser on your Windows machine.

In the address bar,

type jre-7-downloads and press Enter.

Point to the page.

Click on Java SE Runtime Environment 7 Downloads-Oracle link.

A new webpage opens.

Click on the link Java SE Runtime Environment 7 Downloads-Oracle.

Download page opens.

Point to the License agreement.

Select jre-7-windows-i586.exe.

On the web page, accept the License agreement.

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

Point to the dialog box.

Click on Save File button.

Save file dialog box opens.

Click on Save File button.


The file will be downloaded in the Downloads folder.

Click on the downloaded file. “Click on the downloaded file.
Point to install window. Follow the installation process to install Java.

Click on Close.

Jre-7 will be installed on your machine.

Let's install JChemPaint.
On the browser>> in the address bar, type the URL Open Firefox web browser on your Windows machine.

In the address bar, type the URL http://jchempaint.github.io/ to install JChemPaint on Windows.

Point to the new webpage. You will be directed to the download page of JChemPaint.
Move the cursor on the webpage.

Click on "the desktop application (6.8 MB)"

On the webpage, locate

“download a recent jar file from github (current is 3.3-1210):”

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

Point to the dialog box.

Click on Save File button.

Save file dialog box opens.

Click on Save File button.

Open Downloads folder select the file. The .jar file will be downloaded to Downloads folder.

Open Downloads folder and select the file jchempaint-3.3-1210.jar.

You can download available latest version.

Right click on the Executable file>>Select Open to open JchemPaint. Right click on the executable file.

Select Open to open JChemPaint.

Alternately, you can open JChemPaint using Command prompt.
Press Windows and R keys simultaneously on the key board. To open Command prompt, press Windows and R keys simultaneously on the keyboard.
Point to the box.

Type “cmd” >> click on OK button.

Command prompt opens.

Run prompt box opens.

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

Command prompt opens.

Let's go to Downloads folder where we have downloaded our .jar file.
Type “cd Downloads” >> press enter Type at the prompt “cd space Downloads” and press Enter.
Type Java -jar jchempaint3.3.jar>>press enter. Type java space -jar space jchempaint-3.3-1210.jar and press Enter.

JChemPaint window opens.

Slide Number 8

"Error on Command Prompt".

If an error appears on command prompt,
  • Go to Program files locate the java folder and click on it.
  • Locate bin folder and right-click on it.
  • Navigate to Properties.
  • Copy the address C:\Program Files within bracketts(x86)\Java\jre7.
Slide Number 9

Set up the path

To set the path follow the steps.
  • Right-click on My Computer, select Properties option.
  • Click on Advanced System settings, then click on Environment Variables.
  • In System Variables search for Path.
  • Click on Edit.
  • Edit system Variable dialog box opens
  • Paste the address C:\Program Files within bracketts (x86)\Java\jre7.
  • Click on OK and close the windows.
Move the cursor on the window. JChemPaint window looks like this.
Point to the Menu bar.

Move the cursor over all the menu items.

This the Menu bar.

Menu bar contains menu items like:

File, Edit, View, Atom, Bond, Tools, R-groups, Templates and Help.

Point to the tool bars. Tool bars contain all the tools required for you to work with JChemPaint.
Move the cursor on all the tools. JChempaint window has,
  • Formatting tools on top
  • Bond tools on the left
  • Ring tools on the right and
  • Element tools at the bottom
Move the cursor on the Panel Panel displays the drawn structures.
Now to JChemPaint Preferences window.
Click on Draw a chain tool. Click on Draw a chain tool.

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

Notice that Carbon chain does not contain any atoms.

Go to Edit menu, navigate to Preferences >> click on it.

Point to the window.

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

Preferences window opens.

Move the cursor on the tabs. Preferences window has two tabs Display Preferences and Other Preferences.
Point to the tab. By default Display Preferences tab is selected.
Move the cursor on all the check boxes. Notice that none of the check boxes are selected here.
Let's click on a few check boxes and see how they are useful.
Point to the check box.

click on Show explicit methyl groups.

To show Methyl groups on the chain click on Show explicit methyl groups.
Point to the check box click on Show implicit hydrogens To show hydrogens click on Show implicit hydrogens.
Click on Apply and OK buttons to apply the changes. Click on Apply and OK buttons to apply the changes.
As an example let's draw Phosphoric acid(H3PO4).
Click on Phosphrous(P) tool >> click on the Panel.

Point to PH3

To draw, click on Phosphrous(P) tool and then click on the Panel.

Phosphine(PH3) will be displayed

Click on Oxygen(O) tool>> click on Single bond tool . Click on Oxygen(O) tool and click on Single bond tool.
Point to small blue circle.Click on Oxygen(O) tool and click on Single bond tool. Place the cursor on P; a small 'blue' colored circle appears on it.

Click on P and drag to draw four Hydroxy bonds.

Point to the red line below Phosphrous atom. You will notice a red line below Phosphrous atom.

This indicates that valency is not complete.

Point to the top bond To complete the valency let's make the top Phosphrous-hydroxy bond as a double bond.
Click on double bond tool >>click on top the Phosphrous-hydroxy bond. Click on double bond tool.

Click on top Phosphrous-hydroxy bond.

The obtained structure is Phosphoric acid.

Point to the structure. Notice that all the atoms in the structure are black colored.
Go to Edit menu and navigate to Preferences. To show Rasmol color of the element,

Go to Edit menu and navigate to Preferences.

In the window click on Color atoms by element check box>>It shows Rasmol color of the element. In the window click on Color atoms by element check box.

It shows Rasmol color of the element.

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

Note that elements appear with their Rasmol colors.

Now let's save the file.
Click on File menu >> select Save as... Click on File menu and select Save as....
Save as dialog box opens. Save as dialog box opens.
Select Desktop folder to save the file on Desktop. Select Desktop folder to save the file on Desktop.
Type the file name as Oxyacids of Phosphorus >> Click on Save button. Type the file name as Phosphoric acid and click on Save button.

The file will be saved with .mol extension.

Let's summarise,
Slide Number 7 +8

Summary

In this tutorial, we have learnt
  • About JChemPaint
  • Install JChemPaint on Windows OS
  • Install JChemPaint on Ubuntu OS 12.04
  • Menu bar, Tool bars and Panel of JChemPaint interface
  • Preferences window
  • Draw structures using tools and
  • Save the drawing with .mol extension
Slide Number 9

Assignment

As an assignment
  • Install JChemPaint.
  • Explore various menu items.
Slide Number10

Acknowledgement

This video summarises the Spoken Tutorial project

If you do not have good bandwidth, you can download and watch it.

Slide Number11 The Spoken Tutorial Team:

Conducts workshops using spoken tutorials

Gives certificates to those who pass an online test

For more details, please write to contact@spoken-tutorial.org

Slide number 12 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

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.

Contributors and Content Editors

Madhurig, Nancyvarkey

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