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

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

Contributors and Content Editors

PoojaMoolya, Ranjana, Sandhya.np14

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