Difference between revisions of "JChemPaint/C3/Features-of-JChemPaint/English-timed"

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|  As an assignment, insert the given '''SMILES''' and '''InChi Keys'''  
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| Spoken Tutorial Team:  
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| Spoken Tutorial Team: Conducts workshops using spoken tutorials.
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| * Conducts workshops using spoken tutorials.
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| * Gives certificates to those who pass an on-line test.  
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| For more details, please write to:
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| For more details, please write to: '''contact@spoken-tutorial.org'''  
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'''contact@spoken-tutorial.org'''  
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Revision as of 16:27, 28 March 2017

Time Narration
00:01 Hello everyone. Welcome to this tutorial on Features of JChemPaint.
00:07 In this tutorial, we will learn to change:
00:10 Background color of the Panel
00:12 Look and feel of the window
00:14 User interface language.
00:18 We will also learn to:
00:20 Insert Templates
00:22 Generate SMILES and InChi keys for a given structure
00:26 Insert SMILES and InChi keys to generate structures.
00:31 To record this tutorial, I am using:
00:33 Ubuntu Linux OS version 12.04
00:38 JChemPaint version 3.3-1210
00:43 Java version 7
00:46 To follow this tutorial, you should be familiar with 'JChemPaint' chemical structures editor.
00:54 If not, for relevant tutorial, please visit our website.
01:01 Let's switch to JChemPaint window.
01:04 Recall that we had saved our '.jar' file on the Desktop.
01:10 Press Ctrl+ALt and 'T' keys simultaneously to open the Terminal.
01:17 Type: cd space Desktop and press Enter.
01:24 Type: java space -jar space ./jchempaint-3.3-1210.jar and press Enter.
01:43 JChemPaint window opens.
01:45 Let's see how to change the background color of the Panel.
01:50 Go to Edit menu, navigate to Preferences and click on it.
01:56 JChemPaint Preferences window opens.
02:00 Click on Choose Background Color button.
02:04 Choose Background Color window opens.
02:07 This window has three tabs namely- Swatches, HSB and RGB.
02:15 Depending on your Operating System, this window may vary a little.
02:21 HSB may be HSV.
02:25 You may not see Swatches tab.
02:28 Windows Operating System has two additional tabs namely HSL and CMYK.
02:37 You can select the background color of your choice.
02:40 I will click on light green color Swatch to change background color to light green.
02:47 Click on OK to close the window.
02:50 Click on OK to close the Preferences window.
02:55 Try various color combinations using Choose Background Color window.
03:01 Next, about Other Preferences tab.
03:05 Go to Edit menu and click on Preferences.
03:09 Preferences window opens.
03:12 Click on Other Preferences tab.
03:15 Go to Look and feel field.
03:19 This field has a drop-down list.
03:21 List contains Sytem, Metal, Nimbus, Motif, GTK and Windows.
03:29 I will click on Nimbus.
03:32 Then click on OK button.
03:35 Observe the change in the look and feel of the window.
03:40 Click on Edit menu, then click on Preferences.
03:45 Click on Other Preferences.
03:49 Go to 'User Interface Language' field.
03:53 This field has a drop-down list.
03:56 List contains American English and other languages.
04:02 By default, American English is selected.
04:06 I will click on Spanish.
04:09 Click on OK button.
04:12 Observe the change in the language on the Menu bar and on the Status bar.
04:19 I will undo the changes.
04:23 Now, let's insert Templates onto the Panel.
04:27 Click on Templates menu.
04:30 Templates drop-down opens.
04:33 Alternately you can open Templates menu from side tool-bar.
04:39 Here, you can see various Templates tabs.
04:43 Click on All Templates tab.
04:47 Structure Templates window opens.
04:51 Window shows list of Templates along with their structures.
04:56 I will scroll-down the window to view various structures.
05:01 I will click on a few Template tabs to display structures.
05:06 Click on Beta Lactums tab.
05:10 Click on Penicillin structure to display it on the Panel.
05:16 Press Ctrl+ Z to undo the changes.
05:20 Click on Templates tab, click on Miscellaneous.
05:25 Then click on C60 Fullerene to display it on the Panel.
05:31 You can load other Templates of your choice onto the Panel.
05:36 Next, we will learn about SMILES and InChi keys.
05:41 What are SMILES and InChi Keys?
05:45 SMILES is simplified molecular input line entry system.
05:51 It describes chemical structures using short ASCII strings.
05:57 Molecular Editors import 'SMILES' strings to convert structures into 2D drawings.
06:06 For example, CCCCCC is a Canonical SMILES of Hexane.
06:15 InChi is International Chemical Identifier.
06:19 It describes a chemical in terms of layers of information.
06:25 Atoms and their bond connectivity
06:28 * Isotopic, stereochemical and electronic charge information.
06:34 For example, this is the InChi key of Propane.
06:41 I will clear the window.
06:43 Press Delete on the Keyboard.
06:47 To generate SMILES, I will load an Alkaloid, Morhphine from the Templates menu.
06:55 Click on Tools Menu, then click on Create SMILES.
07:02 SMILES dialog-box opens with Generated SMILES.
07:07 Dialog-box contains SMILES and Chiral SMILES.
07:13 Click OK to close the dialog-box.
07:17 Press CTRL+A to select the structure, if it is not selected.
07:22 To generate InChi key of Morphine, go to Tools menu.
07:27 Click on Create InChi.
07:30 InChi dialog-box opens with InChi generation of 'Morphine'.
07:36 Click OK to close the dialog-box.
07:40 Press Delete on the keyboard to delete the Morphine structure.
07:45 Now, we will learn to obtain a structure from inserted SMILES.
07:50 Below the Formatting toolbar, we have an Insert bar with an Insert button next to it.
07:59 Click in the Insert bar and type "c1ccc1" and click on Insert button.
08:09 Cyclobutene structure is generated on the Panel.
08:14 Press Ctrl+Z to undo the changes.
08:19 I had already saved a few SMILES and InChi keys from PubChem Page into a "Text Editor".
08:27 I will copy a SMILES from “Text Editor” and paste it into the Insert bar
08:34 and click on Insert button.
08:38 Inserted SMILES displays Aspartic acid structure on the Panel.
08:44 Press Ctrl+Z to undo the changes.
08:48 I will copy an Inchi Key from the Text Editor and paste it into the Insert bar.
08:57 Then click on Insert button.
09:00 Inserted Inchi Key displays Benzene structure onto the Panel.
09:07 As an assignment, insert the given SMILES and InChi Keys to obtain various structures.
09:16 Let's Summarize.
09:18 In this tutorial, we have learnt to change:
09:21 Background color of the Panel
09:24 Look and feel of the window
09:27 User interface language
09:30 Insert Templates
09:32 Generate SMILES and InChi keys for a given structure
09:37 Insert SMILES and InChi Keys to generate structures.
09:43 This video summarizes the Spoken Tutorial project.
09:47 If you do not have good bandwidth, you can download and watch it.
09:52 Spoken Tutorial Team: Conducts workshops using spoken tutorials.
09:56 Gives certificates to those who pass an on-line test.
09:59 For more details, please write to: contact@spoken-tutorial.org
10:06 Spoken Tutorial project is a part of the Talk to a Teacher project.
10:09 It is supported by the National Mission on Education through ICT, MHRD, Government of India.
10:17 More information on this mission is available at this link.
10:23 This is Madhuri Ganapathi from IIT Bombay, signing off. Thank you for joining.

Contributors and Content Editors

PoojaMoolya, Ranjana, Sandhya.np14

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