Difference between revisions of "JChemPaint/C2/Introduction-to-JChemPaint/English"
(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…') |
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|| 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''' | ||
− | |||
|- | |- | ||
|| | || | ||
− | || 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 | + | ||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 | + | ||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 | + | || 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. | + | 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 | + | ||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 | + | 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 | + | ||Point to the dialog box. |
Click on Save File button. | Click on Save File button. | ||
− | || Save file | + | || '''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 | + | Click on '''Close'''. |
− | Jre-7 will be | + | '''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 | + | ||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/ | + | 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 | + | ||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 | + | ||Right click on the executable file. |
− | Select Open to open JChemPaint. | + | Select '''Open''' to open '''JChemPaint'''. |
|- | |- | ||
|| | || | ||
− | || | + | ||Alternately, you can open '''JChemPaint''' using '''Command prompt.''' |
|- | |- | ||
− | ||Press Windows and | + | ||Press Windows and R keys simultaneously on the key board. |
− | ||To open Command prompt, press Windows and | + | ||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 | + | ||Type “cd Downloads” >> press enter |
− | ||Type at the prompt “cd space Downloads” and press | + | ||Type at the '''prompt “cd space Downloads”''' and press '''Enter'''. |
|- | |- | ||
− | ||Type Java | + | ||Type Java -jar jchempaint3.3.jar>>press enter. |
− | ||Type java space -jar space jchempaint-3.3-1210.jar and press | + | ||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 | + | *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 | + | *'''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 | + | *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 | + | ||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 | + | ||Save as dialog box opens. |
− | ||Save as | + | ||'''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
We will also learn,
|
Slide Number 4
System Requirement |
To record this tutorial I am using,
|
Slide Number 5
Pre-requisites |
To follow this tutorial you must have,
|
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 |
|
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.
|
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.
|
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,
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Slide Number 9
Set up the path |
To set the path follow the steps.
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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,
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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
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Slide Number 9
Assignment |
As an assignment
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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. |