Difference between revisions of "JChemPaint/C3/Features-of-JChemPaint/English-timed"
From Script | Spoken-Tutorial
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− | |Hello everyone. Welcome to this tutorial on '''Features of JChemPaint | + | |Hello everyone. Welcome to this tutorial on '''Features of JChemPaint'''. |
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| 00:18 | | 00:18 | ||
− | | We will also learn to | + | | We will also learn to: |
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| 00:22 | | 00:22 | ||
− | | * Generate '''SMILES''' and '''InChi''' keys for a given structure | + | | * Generate '''SMILES''' and '''InChi''' keys for a given structure |
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| 00:31 | | 00:31 | ||
− | | To record this tutorial I am using | + | | To record this tutorial, I am using: |
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| 00:33 | | 00:33 | ||
− | | *'''Ubuntu Linux''' OS version 12.04 | + | | * '''Ubuntu Linux''' OS version 12.04 |
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| 00:38 | | 00:38 | ||
− | | *'''JChemPaint''' version 3.3-1210 | + | | * '''JChemPaint''' version 3.3-1210 |
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| 00:43 | | 00:43 | ||
− | | *'''Java''' version 7 | + | | * '''Java''' version 7 |
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| 00:46 | | 00:46 | ||
− | | To follow this tutorial you should be familiar with '''JChemPaint''' chemical structures editor. | + | | To follow this tutorial, you should be familiar with '''JChemPaint''' chemical structures editor. |
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| 01:04 | | 01:04 | ||
− | | Recall that we had saved our '''.jar''' file on the '''Desktop'''. | + | | Recall that we had saved our ''''.jar'''' file on the '''Desktop'''. |
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| 01:10 | | 01:10 | ||
− | | Press ''' | + | | Press '''Ctrl+ALt''' and '''T''' keys simultaneously to open the '''Terminal'''. |
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| 01:17 | | 01:17 | ||
− | | Type | + | | Type: '''“cd space Desktop”''' and press '''Enter'''. |
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| 01:24 | | 01:24 | ||
− | | Type ''' “java space -jar space ./jchempaint-3.3-1210.jar”''' and press '''Enter'''. | + | | Type: ''' “java space -jar space ./jchempaint-3.3-1210.jar”''' and press '''Enter'''. |
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| 02:07 | | 02:07 | ||
− | | This window has three tabs namely '''Swatches, HSB''' and '''RGB'''. | + | | This window has three tabs namely- '''Swatches, HSB''' and '''RGB'''. |
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| 02:15 | | 02:15 | ||
− | | Depending on your '''Operating System''' this window | + | | Depending on your '''Operating System''', this window may vary a little. |
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| 03:01 | | 03:01 | ||
− | | Next about '''Other Preferences''' tab. | + | | Next, about '''Other Preferences''' tab. |
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| 03:05 | | 03:05 | ||
− | | Go to '''Edit''' menu and click on '''Preferences''' | + | | Go to '''Edit''' menu and click on '''Preferences'''. |
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| 03:19 | | 03:19 | ||
− | | This field has a drop down list. | + | | This field has a drop-down list. |
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| 03:40 | | 03:40 | ||
− | | Click on Edit menu then click on '''Preferences'''. | + | | Click on '''Edit''' menu, then click on '''Preferences'''. |
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| 03:53 | | 03:53 | ||
− | | This field has a drop down list. | + | | This field has a drop-down list. |
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| 04:02 | | 04:02 | ||
− | | By default '''American English''' is selected. | + | | By default, '''American English''' is selected. |
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| 04:19 | | 04:19 | ||
− | | I will undo the changes. | + | | I will '''undo''' the changes. |
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| 04:23 | | 04:23 | ||
− | | Now let's insert '''Templates''' onto the '''Panel'''. | + | | Now, let's insert '''Templates''' onto the '''Panel'''. |
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| 04:30 | | 04:30 | ||
− | | '''Templates''' drop down opens. | + | | '''Templates''' drop-down opens. |
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| 04:33 | | 04:33 | ||
− | | Alternately you can open '''Templates''' menu from side tool bar. | + | | Alternately you can open '''Templates''' menu from side tool-bar. |
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| 04:39 | | 04:39 | ||
− | | Here you can see various '''Templates''' tabs. | + | | Here, you can see various '''Templates''' tabs. |
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| 04:56 | | 04:56 | ||
− | | I will scroll down the window to view various structures. | + | | I will scroll-down the window to view various structures. |
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| 05:10 | | 05:10 | ||
− | | Click on '''Penicillin''' structure | + | | Click on '''Penicillin''' structure to display it on the '''Panel'''. |
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| 05:16 | | 05:16 | ||
− | | Press '''Ctrl+ Z''' to undo the changes. | + | | Press '''Ctrl+ Z''' to '''undo''' the changes. |
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| 05:25 | | 05:25 | ||
− | | Then click on '''C60 Fullerene''' | + | | Then click on '''C60 Fullerene''' to display it on the '''Panel'''. |
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| 05:36 | | 05:36 | ||
− | | Next we will learn about '''SMILES''' and '''InChi keys'''. | + | | Next, we will learn about '''SMILES''' and '''InChi keys'''. |
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| 05:57 | | 05:57 | ||
− | | * Molecular Editors import '''SMILES''' strings | + | | * Molecular Editors import '''SMILES''' strings to convert structures into 2D drawings. |
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| 06:06 | | 06:06 | ||
− | | | + | | For example, '''CCCCCC''' is a '''Canonical SMILES''' of '''Hexane''' |
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| 06:34 | | 06:34 | ||
− | | | + | | For example, this is the '''InChi''' key of '''Propane'''. |
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| 06:47 | | 06:47 | ||
− | | To generate '''SMILES''' I will load an '''Alkaloid, Morhphine''' from the '''Templates''' menu. | + | | To generate '''SMILES''', I will load an '''Alkaloid, Morhphine''' from the '''Templates''' menu. |
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− | | '''SMILES''' dialog box opens with '''Generated SMILES'''. | + | | '''SMILES''' dialog-box opens with '''Generated SMILES'''. |
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| 07:07 | | 07:07 | ||
− | | Dialog box contains '''SMILES''' and '''Chiral SMILES'''. | + | | Dialog-box contains '''SMILES''' and '''Chiral SMILES'''. |
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| 07:13 | | 07:13 | ||
− | | Click '''OK''' to close the dialog box. | + | | Click '''OK''' to close the dialog-box. |
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− | | '''InChi''' dialog box opens with '''InChi generation''' of ''''Morphine''''. | + | | '''InChi''' dialog-box opens with '''InChi generation''' of ''''Morphine''''. |
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| 07:36 | | 07:36 | ||
− | | Click '''OK''' to close the dialog box. | + | | Click '''OK''' to close the dialog-box. |
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| 07:59 | | 07:59 | ||
− | | Click in the '''Insert bar''' and type | + | | Click in the '''Insert bar''' and type "c1ccc1" and click on '''Insert''' button. |
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| 08:14 | | 08:14 | ||
− | | Press '''Ctrl+Z''' to undo the changes. | + | | Press '''Ctrl+Z''' to '''undo''' the changes. |
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| 08:27 | | 08:27 | ||
− | | I will copy a '''SMILES''' from “Text Editor” and paste it into the '''Insert bar''' | + | | I will copy a '''SMILES''' from “Text Editor” and paste it into the '''Insert bar''' |
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| 08:34 | | 08:34 | ||
− | | | + | | and click on '''Insert''' button. |
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| 08:44 | | 08:44 | ||
− | | Press '''Ctrl+Z''' to undo the changes. | + | | Press '''Ctrl+Z''' to '''undo''' the changes. |
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| 09:00 | | 09:00 | ||
− | | Inserted '''Inchi Key''' displays | + | | Inserted '''Inchi Key''' displays '''Benzene''' structure onto the '''Panel'''. |
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| 09:18 | | 09:18 | ||
− | | In this tutorial, we have learnt to change | + | | In this tutorial, we have learnt to change: |
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| 09:37 | | 09:37 | ||
− | | * Insert '''SMILES''' and '''InChi Keys''' to generate structures | + | | * Insert '''SMILES''' and '''InChi Keys''' to generate structures. |
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| 09:43 | | 09:43 | ||
− | | This video summarizes the Spoken Tutorial project. | + | | This video summarizes the '''Spoken Tutorial''' project. |
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| 09:53 | | 09:53 | ||
− | | *Conducts workshops using spoken tutorials | + | | * Conducts workshops using spoken tutorials. |
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| 09:56 | | 09:56 | ||
− | | *Gives certificates to those who pass an on-line test | + | | * Gives certificates to those who pass an on-line test. |
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| 09:59 | | 09:59 | ||
− | | For more details, please write to '''contact@spoken-tutorial.org''' | + | | For more details, please write to: |
+ | '''contact@spoken-tutorial.org''' | ||
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| 10:06 | | 10:06 | ||
− | | Spoken Tutorial | + | | '''Spoken Tutorial''' project is a part of the '''Talk to a Teacher''' project. |
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| 10:09 | | 10:09 | ||
− | | It is supported by the National Mission on Education through ICT, MHRD, Government of India | + | | It is supported by the National Mission on Education through ICT, MHRD, Government of India. |
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| 10:17 | | 10:17 | ||
− | | More information on this | + | | More information on this mission is available at this link. |
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| 10:23 | | 10:23 | ||
− | | This is '''Madhuri Ganapathi''' from '''IIT Bombay''' signing off. Thank you for joining. | + | | This is '''Madhuri Ganapathi''' from '''IIT Bombay''', signing off. Thank you for joining. |
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|} | |} |
Revision as of 16:37, 6 December 2015
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 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 OK button. |
04:12 | Observe the change in 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: |
09:53 | * 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. |