JChemPaint/C3/Features-of-JChemPaint/English-timed
From Script | Spoken-Tutorial
| 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. |
