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

From Script | Spoken-Tutorial
Jump to: navigation, search
Line 57: Line 57:
 
|-
 
|-
 
| 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'''.
  
 
|-
 
|-
Line 73: Line 73:
 
|-
 
|-
 
| 01:10
 
| 01:10
−
| Press '''Ctrl+ALt''' and '''T''' keys simultaneously  to open the '''Terminal'''.  
+
| Press '''Ctrl+ALt''' and 'T' keys simultaneously  to open the '''Terminal'''.  
  
 
|-
 
|-
 
| 01:17
 
| 01:17
−
| Type: '''“cd space Desktop”''' and press '''Enter'''.
+
| Type: '''cd space Desktop''' and press '''Enter'''.
  
 
|-
 
|-
 
| 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'''.
  
 
|-
 
|-
Line 101: Line 101:
 
|-
 
|-
 
| 02:00
 
| 02:00
−
|  Click on '''Choose background color''' button.
+
|  Click on '''Choose Background Color''' button.
  
 
|-
 
|-
 
| 02:04
 
| 02:04
−
| '''Choose background color''' window opens.
+
| '''Choose Background Color''' window opens.
  
 
|-
 
|-
Line 145: Line 145:
 
|-
 
|-
 
| 02:55
 
| 02:55
−
| Try various color combinations using '''Choose background color''' window.
+
| 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 '''other Preferences'''.  
+
| Click on '''Other Preferences'''.  
  
 
|-
 
|-
 
| 03:49
 
| 03:49
−
| Go to '''User Interface Language''' field.
+
| 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.
+
| * '''SMILES''' is '''simplified molecular input line entry system'''.
  
 
|-
 
|-
Line 309: Line 309:
 
|-
 
|-
 
| 05:57
 
| 05:57
−
| * Molecular Editors import '''SMILES''' strings to convert structures into 2D drawings.
+
| * 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'''.
+
| '''InChi''' is '''International Chemical Identifier'''.
  
 
|-
 
|-
Line 325: Line 325:
 
|-
 
|-
 
| 06:25
 
| 06:25
−
| * Atoms and their bond connectivity,
+
| * Atoms and their bond connectivity  
  
 
|-
 
|-
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'''.  
  
 
|-
 
|-

Revision as of 18:29, 14 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 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:
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

Retrieved from "https://script.spoken-tutorial.org/index.php?title=JChemPaint/C3/Features-of-JChemPaint/English-timed&oldid=25014"