Difference between revisions of "JChemPaint/C3/Features-of-JChemPaint/English-timed"
From Script | Spoken-Tutorial
Sandhya.np14 (Talk | contribs) |
PoojaMoolya (Talk | contribs) |
||
(2 intermediate revisions by 2 users not shown) | |||
Line 13: | Line 13: | ||
|- | |- | ||
| 00:10 | | 00:10 | ||
− | | | + | | Background color of the '''Panel''' |
|- | |- | ||
| 00:12 | | 00:12 | ||
− | | | + | | Look and feel of the window |
|- | |- | ||
| 00:14 | | 00:14 | ||
− | | | + | | User interface language. |
|- | |- | ||
Line 29: | Line 29: | ||
|- | |- | ||
| 00:20 | | 00:20 | ||
− | | | + | | Insert '''Templates''' |
|- | |- | ||
| 00:22 | | 00:22 | ||
− | | | + | | Generate '''SMILES''' and '''InChi''' keys for a given structure |
|- | |- | ||
| 00:26 | | 00:26 | ||
− | | | + | | Insert '''SMILES''' and '''InChi''' keys to generate structures. |
|- | |- | ||
Line 45: | Line 45: | ||
|- | |- | ||
| 00:33 | | 00:33 | ||
− | | | + | | '''Ubuntu Linux''' OS version 12.04 |
|- | |- | ||
| 00:38 | | 00:38 | ||
− | | | + | | '''JChemPaint''' version 3.3-1210 |
|- | |- | ||
| 00:43 | | 00:43 | ||
− | | | + | | '''Java''' version 7 |
|- | |- | ||
| 00:46 | | 00:46 | ||
− | | To follow this tutorial, you should be familiar with '''JChemPaint | + | | To follow this tutorial, you should be familiar with ''''JChemPaint' chemical structures editor'''. |
|- | |- | ||
Line 73: | Line 73: | ||
|- | |- | ||
| 01:10 | | 01:10 | ||
− | | Press '''Ctrl+ALt''' and | + | | Press '''Ctrl+ALt''' and 'T' keys simultaneously to open the '''Terminal'''. |
|- | |- | ||
| 01:17 | | 01:17 | ||
− | | Type: ''' | + | | Type: '''cd space Desktop''' and press '''Enter'''. |
|- | |- | ||
| 01:24 | | 01:24 | ||
− | | Type: ''' | + | | Type: ''' java space -jar space ./jchempaint-3.3-1210.jar''' and press '''Enter'''. |
|- | |- | ||
Line 101: | Line 101: | ||
|- | |- | ||
| 02:00 | | 02:00 | ||
− | | Click on '''Choose | + | | Click on '''Choose Background Color''' button. |
|- | |- | ||
| 02:04 | | 02:04 | ||
− | | '''Choose | + | | '''Choose Background Color''' window opens. |
|- | |- | ||
Line 145: | Line 145: | ||
|- | |- | ||
| 02:55 | | 02:55 | ||
− | | Try various color combinations using '''Choose | + | | Try various color combinations using '''Choose Background Color''' window. |
|- | |- | ||
Line 185: | Line 185: | ||
|- | |- | ||
| 03:35 | | 03:35 | ||
− | | Observe the change in look and feel of the window. | + | | Observe the change in the look and feel of the window. |
|- | |- | ||
Line 193: | Line 193: | ||
|- | |- | ||
| 03:45 | | 03:45 | ||
− | | Click on ''' | + | | Click on '''Other Preferences'''. |
|- | |- | ||
| 03:49 | | 03:49 | ||
− | | Go to '''User Interface Language''' | + | | Go to ''''User Interface Language' field'''. |
|- | |- | ||
Line 217: | Line 217: | ||
|- | |- | ||
| 04:09 | | 04:09 | ||
− | | Click '''OK''' button. | + | | Click on '''OK''' button. |
|- | |- | ||
| 04:12 | | 04:12 | ||
− | | Observe the change in language on the '''Menu bar''' and on the '''Status bar'''. | + | | Observe the change in the language on the '''Menu bar''' and on the '''Status bar'''. |
|- | |- | ||
Line 301: | Line 301: | ||
|- | |- | ||
| 05:45 | | 05:45 | ||
− | | | + | | '''SMILES''' is '''simplified molecular input line entry system'''. |
|- | |- | ||
| 05:51 | | 05:51 | ||
− | | | + | | It describes chemical structures using short '''ASCII''' strings. |
|- | |- | ||
| 05:57 | | 05:57 | ||
− | | | + | | Molecular Editors import ''''SMILES' strings''' to convert structures into 2D drawings. |
|- | |- | ||
| 06:06 | | 06:06 | ||
− | | For example, '''CCCCCC''' is a '''Canonical SMILES''' of '''Hexane''' | + | | For example, '''CCCCCC''' is a '''Canonical SMILES''' of '''Hexane'''. |
|- | |- | ||
| 06:15 | | 06:15 | ||
− | | | + | | '''InChi''' is '''International Chemical Identifier'''. |
|- | |- | ||
| 06:19 | | 06:19 | ||
− | | | + | | It describes a chemical in terms of layers of information. |
|- | |- | ||
| 06:25 | | 06:25 | ||
− | | | + | | Atoms and their bond connectivity |
|- | |- | ||
| 06:28 | | 06:28 | ||
− | | | + | | '''Isotopic, stereochemical''' and '''electronic charge''' information. |
|- | |- | ||
Line 389: | Line 389: | ||
|- | |- | ||
| 07:45 | | 07:45 | ||
− | | Now we will learn to obtain a structure from inserted '''SMILES'''. | + | | Now, we will learn to obtain a structure from inserted '''SMILES'''. |
|- | |- | ||
Line 441: | Line 441: | ||
|- | |- | ||
| 09:07 | | 09:07 | ||
− | | As an assignment, insert the given '''SMILES''' and '''InChi Keys''' | + | | As an assignment, insert the given '''SMILES''' and '''InChi Keys''' to obtain various structures. |
− | to obtain various structures. | + | |
|- | |- | ||
Line 454: | Line 453: | ||
|- | |- | ||
| 09:21 | | 09:21 | ||
− | | | + | |Background color of the '''Panel''' |
|- | |- | ||
| 09:24 | | 09:24 | ||
− | | | + | | Look and feel of the window |
|- | |- | ||
| 09:27 | | 09:27 | ||
− | | | + | | User interface language |
|- | |- | ||
| 09:30 | | 09:30 | ||
− | | | + | | Insert '''Templates''' |
|- | |- | ||
| 09:32 | | 09:32 | ||
− | | | + | | Generate '''SMILES''' and '''InChi keys''' for a given structure |
|- | |- | ||
| 09:37 | | 09:37 | ||
− | | | + | | Insert '''SMILES''' and '''InChi Keys''' to generate structures. |
|- | |- | ||
Line 486: | Line 485: | ||
|- | |- | ||
| 09:52 | | 09:52 | ||
− | | Spoken Tutorial Team: | + | | Spoken Tutorial Team: Conducts workshops using spoken tutorials. |
− | + | ||
− | + | ||
− | + | ||
− | + | ||
|- | |- | ||
| 09:56 | | 09:56 | ||
− | | | + | | Gives certificates to those who pass an on-line test. |
|- | |- | ||
| 09:59 | | 09:59 | ||
− | | For more details, please write to: | + | | For more details, please write to: '''contact@spoken-tutorial.org''' |
− | '''contact@spoken-tutorial.org''' | + | |
|- | |- |
Latest revision as of 16:28, 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. |