JChemPaint/C3/Features-of-JChemPaint/English

Visual Cue	Narration
Slide Number 1 Title Slide	Hello everyone. Welcome to this tutorial on Features of JChemPaint..
Slide Number 2+3 Learning Objectives	In this tutorial, we will learn to change Background color of the Panel Look and feel of the window User interface language. We will also learn to, Insert Templates Generate SMILES and InChi keys for a given structure. Insert SMILES and InChi keys to generate structures.
Slide Number 4 System Requirement	To record this tutorial I am using, Ubuntu Linux OS version 12.04 JChemPaint version 3.3-1210 Java version 7
Slide Number 5 Pre-requisites	To follow this tutorial you should be familiar with JChemPaint chemical structures editor. If not, for relevant tutorial, please visit our website.
	Let's switch to JChemPaint window.
Point to .jar file	Recall that we had saved our .jar file on the Desktop.
Press CTRl+ALt+T keys.	Press CTRl+ALt and T keys simultaneously to open the Terminal.
Type “cd space Desktop”>>press Enter. Type java -jar ./jchempaint-3.3-1210.jar >> 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.
Move the cursor on the Panel.	Let's see how to change the background color of the Panel.
Go to Edit menu >> click on Preferences Move the cursor on the window.	Go to Edit menu, navigate to Preferences and click on it. JChemPaint Preferences window opens.
Click on Choose background color button. Point to Choose background color window.	Click on Choose background color button. Choose background color window opens.
Point to the tabs.	This window has three tabs namely Swatches, HSB and RGB.
	Depending on your Operating System this window, may vary a little.
Show the screen shots of the other Choose background windows.	HSB may be HSV. You may not see Swatches tab.
Show the screen shot of Windows OS.	Windows Operating System has two additional tabs namely HSL and CMYK.
Point to light green Swatch.	You can select the background color of your choice. I will click on light green color Swatch to change background color to light green.
Click on OK to close window.	Click on OK to close the window.
Click on OK button.	Click on OK to close the Preferences window.
Slide Number 5 Assignment	Try various color combinations using Choose background color window.
	Next about Other Preferences tab.
Go to Edit menu navigate to Preferences >> click on it. Move the cursor on the window.	Go to Edit menu and click on Preferences Preferences window opens.
Click on Other Preferences tab.	Click on Other Preferences tab.
Move the cursor to Look and feel field. Point to the drop down list.	Go to Look and feel field. This field has a drop down list. List contains Sytem, Metal, Nimbus, Motif, GTK and Windows.
Click on Nimbus>>click on OK button.	I will click on Nimbus. Then click on OK button. Observe the change in look and feel of the window.
Click on Edit menu >> click Preferences.	Click on Edit menu then click Preferences. Click on other Preferences.
Move the cursor on the window.	Go to User Interface Language field. This field has a drop down list. List contains American English and other languages. By default American English is selected.
Click on Spanish>> Click OK buttons. Point to the menu bar and status bar.	I will click on Spanish. Click OK button. Observe the change in language on the Menu bar and on the Status bar.
	I will undo the changes.
Point to Templates menu	Now let's insert Templates onto the Panel.
Click on Templates menu.	Click on Templates menu. Templates drop down opens.
Point to right side tool bar.	Alternately you can open Templates menu from side tool bar.
Move the cursor on the list.	Here you can see various Templates tabs. Click on All Templates tab. Structure Templates window opens.
Scroll down the window.	Window shows list of Templates along with their structures. I will scroll down the window to view different structures.
Point to the Templates.	I will click on a few Template tabs to display structures.
Click on Beta Lactums tab >> Click on Penicillin structure.	Click on Beta Lactums tab. Click on Penicillin structure, to display it on the Panel.
Press Ctrl+ Z	Press Ctrl+ Z to undo the changes.
Click on Miscellaneous tab. Click on C60 Fullerene.	Click on Templates tab, click on Miscellaneous. Then click on C60 Fullerene, to display it on the Panel.
Slide Number 6 Assignment.	You can load other Templates of your choice onto the Panel.
	Next we will learn about SMILES and InChi keys.
Slide Number 7 SMILES	What are SMILES and InChi Keys? SMILES is simplified molecular input line entry system. It describes chemical structures using short ASCII strings. Molecular Editors import SMILES strings, to convert structures into 2D drawings. For example, CCCCCC is a Canonical SMILES of Hexane
Slide Number 8 InChi	InChi is International Chemical Identifier. It describes a chemical in terms of layers of information. Atoms and their bond connectivity, Isotopic, stereochemical and electronic charge information. For example, this (InChI=1S/C3H8/c1-3-2/h3H2,1-2H3) is the InChi key of Propane.
Press Delete on the Keyboard.	I will clear the window. Press Delete on the Keyboard.
Point to the Templates and Morhphine.	To generate SMILES I will load an Alkaloid, Morhphine from the Templates menu.
Click on Tools Menu>> click on Create SMILES.	Click on Tools Menu, then click on Create SMILES.
Point to the dialog box. Move the cursor onto SMILES and Chiral SMILES	SMILES dialog box opens with Generated SMILES. Dialog box contains SMILES and Chiral SMILES.
Click OK to close the dialog box.	Click OK to close the dialog box.
Go to Tools menu. Click on Create InChi.	Press CTRL+A to select the structure, if it is not selected. To generate InChi key of Morphine, go to Tools menu. Click on Create InChi.
Point to InChi details.	InChi dialog box opens with InChi generation of 'Morphine'.
Click OK to close the dialog box.	Click OK to close the dialog box.
Press Delete on the keyboard.	Press Delete on the keyboard to delete the Morphine structure.
	Now we will learn to obtain a structure from inserted SMILES.
Point to the Insert bar and Insert button.	Below the Formatting toolbar, we have an Insert bar with an Insert button next to it.
Click in the Insert bar >> type c1ccc1.	Click in the Insert bar and type c1ccc1 and click on Insert button.
Point to the structure.	Cyclobutene structure is generated on the Panel.
Press Ctrl+Z.	Press Ctrl+Z to undo the changes.
Open and show the Text editor.	I had already saved a few SMILES and InChi keys from PubChem Page into a "Text Editor".
Copy and Paste the SMILES. Point to the structure.	I will copy a SMILES from “Text Editor” and paste it into the Insert bar. And click on Insert button. Inserted SMILES displays Aspartic acid (C(C(C(=O)O)N)C(=O)O) structure on the Panel.
Press Ctrl+Z.	Press Ctrl+Z to undo the changes.
Copy and paste the InChi Key.	I will copy an Inchi Key from the Text Editor and paste it into the Insert bar. Then click on Insert button. Inserted Inchi Key displays, Benzene (InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H) structure onto the Panel.
Slide Number 9 Assignment	As an assignment, insert the given SMILES and InChi Keys to obtain various structures. 1)CC1=CC=CC=C1 2)CC(C(=O)O)N 3)InChI=1S/C5H10/c1-2-4-5-3-1/h1-5H2 4)InChI=1S/H2O4S/c1-5(2,3)4/h(H2,1,2,3,4)
	Let's Summarize.
Slide Number 10 Summary	In this tutorial, we have learnt to change, Background color of the Panel Look and feel of the window User interface language Insert Templates Generate SMILES and InChi keys for a given structure Insert SMILES and InChi Keys to generate structures
Slide Number 11 Acknowledgement	This video summarizes the Spoken Tutorial project. If you do not have good bandwidth, you can download and watch it.
Slide Number 12	Spoken Tutorial Team: Conducts workshops using spoken tutorials Gives certificates to those who pass an on-line test For more details, please write to contact@spoken-tutorial.org
Slide number 13	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 this link. http://spoken-tutorial.org/NMEICT-Intro ]
	This is Madhuri Ganapathi from IIT Bombay signing off. Thank you for joining.

Contributors and Content Editors

Madhurig, Nancyvarkey