Difference between revisions of "JChemPaint/C2/Introduction-to-JChemPaint/English"
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− | *Copy the address '''C:\Program Files within | + | *Copy the address '''C:\Program Files''' within brackets '''(x86)\Java\jre7.''' |
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*'''Edit system Variable''' dialog box opens | *'''Edit system Variable''' dialog box opens | ||
− | *Paste the address '''C:\Program Files within | + | *Paste the address '''C:\Program Files''' within brackets '''(x86)\Java\jre7.''' |
*Click on '''OK ''' and close the windows. | *Click on '''OK ''' and close the windows. |
Latest revision as of 08:08, 30 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,
|
Slide Number 9
Set up the path |
To set the path follow the steps.
|
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,
|
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
|
Slide Number 9
Assignment |
As an assignment
|
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. |