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

From Script | Spoken-Tutorial
Jump to: navigation, search
(Created page with " {| border=1 || '''Visual Cue''' || '''Narration''' |- ||'''Slide Number 1 Title Slide''' ||Hello everyone. Welcome to this tutorial on '''Features of JChemPaint.'''. |- ||''...")
 
Line 5: Line 5:
 
|-
 
|-
 
||'''Slide Number 1
 
||'''Slide Number 1
 +
 
Title Slide'''
 
Title Slide'''
 
||Hello everyone.
 
||Hello everyone.
 +
 
Welcome to this tutorial on '''Features of JChemPaint.'''.  
 
Welcome to this tutorial on '''Features of JChemPaint.'''.  
 
|-
 
|-
 
||'''Slide Number 2+3
 
||'''Slide Number 2+3
 +
 
Learning Objectives'''
 
Learning Objectives'''
 
|| In this tutorial, we will learn  to change
 
|| In this tutorial, we will learn  to change
−
Background color of the Panel
+
 
−
Look and feel of the window
+
* Background color of the Panel
−
User interface language.
+
 
 +
* Look and feel of the window
 +
 
 +
* User interface language.
 +
 
 
We will also learn to,
 
We will also learn to,
−
Insert '''Templates'''  
+
 
−
Generate '''SMILES''' and '''InChi''' keys for a given structure.
+
* Insert '''Templates'''  
−
Insert '''SMILES''' and '''InChi''' keys to generate structures.  
+
 
 +
* Generate '''SMILES''' and '''InChi''' keys for a given structure.
 +
 
 +
* Insert '''SMILES''' and '''InChi''' keys to generate structures.  
 
|-
 
|-
 
||'''Slide Number 4
 
||'''Slide Number 4
 +
 
System Requirement'''
 
System Requirement'''
 
||To record this tutorial I am using,  
 
||To record this tutorial I am using,  
 +
 
'''Ubuntu Linux''' OS version 12.04  
 
'''Ubuntu Linux''' OS version 12.04  
 +
 
'''JChemPaint''' version 3.3-1210  
 
'''JChemPaint''' version 3.3-1210  
 +
 
'''Java''' version 7
 
'''Java''' version 7
 
|-
 
|-
 
||'''Slide Number 5
 
||'''Slide Number 5
 +
 
Pre-requisites'''
 
Pre-requisites'''
 
|| To follow this tutorial you should be familiar with,
 
|| To follow this tutorial you should be familiar with,
 +
 
'''JChemPaint''' chemical structures editor .
 
'''JChemPaint''' chemical structures editor .
 +
 
If not, for relevant tutorial,  please visit our website.
 
If not, for relevant tutorial,  please visit our website.
 
|-
 
|-
Line 39: Line 56:
 
||Recall that we had saved our '''.jar''' file on the '''Desktop'''.
 
||Recall that we had saved our '''.jar''' file on the '''Desktop'''.
 
|-
 
|-
−
||Press '''CTRl+ALt+T''' keys simultaneously  to open the terminal.  
+
||Press '''CTRl+ALt+T''' keys.
 
||Press '''CTRl+ALt''' and '''T''' keys simultaneously  to open the '''Terminal'''.  
 
||Press '''CTRl+ALt''' and '''T''' keys simultaneously  to open the '''Terminal'''.  
 
|-
 
|-
−
||Type '''“cd space Desktop”''' and press enter.
+
||Type '''“cd space Desktop”'''>>press enter.
−
Type '''java  -jar ./jchempaint-3.3-1210.jar''' and press enter.
+
 
 +
Type '''java  -jar ./jchempaint-3.3-1210.jar''' >> press enter.
 
||Type ''''“cd space Desktop”''' and press enter.
 
||Type ''''“cd space Desktop”''' and press enter.
 +
 
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.
 +
 
'''JChemPaint''' window opens.
 
'''JChemPaint''' window opens.
 
|-
 
|-
Line 52: Line 72:
 
|-
 
|-
 
||Go to '''Edit''' menu navigate to '''Preferences''' >> click on it.
 
||Go to '''Edit''' menu navigate to '''Preferences''' >> click on it.
 +
 
Move the cursor on the window.
 
Move the cursor on the window.
 
|| Go to '''Edit''' menu navigate to '''Preferences''' and click on it.
 
|| Go to '''Edit''' menu navigate to '''Preferences''' and click on it.
 +
 
'''JChemPaint Preferences''' window opens.
 
'''JChemPaint Preferences''' window opens.
 
|-
 
|-
 
||Click on '''Choose background color''' button.
 
||Click on '''Choose background color''' button.
 +
 
Point to '''Choose background color''' window.
 
Point to '''Choose background color''' window.
 
|| Click on '''Choose background color''' button.
 
|| Click on '''Choose background color''' button.
 +
 
'''Choose background color''' window opens.
 
'''Choose background color''' window opens.
 
|-
 
|-
Line 67: Line 91:
 
|| Depending on your '''Operating System''' this  window, may vary a little.
 
|| Depending on your '''Operating System''' this  window, may vary a little.
 
|-
 
|-
−
||Show the screen shots of the other Choose background windows
+
||Show the screen shots of the other Choose background windows.
 
||'''HSB''' may be '''HSV''.
 
||'''HSB''' may be '''HSV''.
 +
 
You may not see '''Swatches''' tab.
 
You may not see '''Swatches''' tab.
 
|-
 
|-
Line 76: Line 101:
 
||Point to light green Swatch.  
 
||Point to light green Swatch.  
 
||You can select the background color of your choice.
 
||You can select the background color of your choice.
 +
 
I will click on light green color '''Swatch''' to change background color to light green.
 
I will click on light green color '''Swatch''' to change background color to light green.
 
|-
 
|-
Line 85: Line 111:
 
|-
 
|-
 
||'''Slide Number 5
 
||'''Slide Number 5
 +
 
Assignment'''
 
Assignment'''
 
||Try various color combinations using '''Choose background color''' window.
 
||Try various color combinations using '''Choose background color''' window.
Line 92: Line 119:
 
|-
 
|-
 
||Go to Edit menu navigate to Preferences >> click on it.
 
||Go to Edit menu navigate to Preferences >> click on it.
 +
 
Move the cursor on the window.
 
Move the cursor on the window.
 
||Go to '''Edit''' menu and click on '''Preferences'''  
 
||Go to '''Edit''' menu and click on '''Preferences'''  
 +
 
'''Preferences''' window opens.
 
'''Preferences''' window opens.
 
|-
 
|-
Line 100: Line 129:
 
|-
 
|-
 
|| Move the cursor to Look and feel field.
 
|| Move the cursor to Look and feel field.
 +
 
Point to the drop down list.
 
Point to the drop down list.
 
||Go to '''Look and feel''' field.  
 
||Go to '''Look and feel''' field.  
 +
 
This field has a drop down list.
 
This field has a drop down list.
 +
 
List contains '''Sytem, Metal, Nimbus, Motif, GTK''' and '''Windows'''.
 
List contains '''Sytem, Metal, Nimbus, Motif, GTK''' and '''Windows'''.
 
|-
 
|-
 
||Click on Nimbus>>click on OK  button.
 
||Click on Nimbus>>click on OK  button.
 
||I will  click on '''Nimbus'''.
 
||I will  click on '''Nimbus'''.
 +
 
Then click on '''OK''' button.
 
Then click on '''OK''' button.
 +
 
Observe the change in look and feel of the window.
 
Observe the change in look and feel of the window.
 
|-
 
|-
−
||Click on Edit menu >> click '''Preferences''' to open '''Preferences''' window.
+
||Click on Edit menu >> click '''Preferences'''.  
 
|| Click on Edit menu then click '''Preferences'''.  
 
|| Click on Edit menu then click '''Preferences'''.  
 +
 
Click on '''other Preferences'''.  
 
Click on '''other Preferences'''.  
 
|-
 
|-
 
||Move the cursor on the window.
 
||Move the cursor on the window.
 
||Go to '''User Interface Language''' field.
 
||Go to '''User Interface Language''' field.
 +
 
This field has a drop down list.
 
This field has a drop down list.
 +
 
List contains '''American English''' and other languages.
 
List contains '''American English''' and other languages.
 +
 
By default  '''American English''' is selected.
 
By default  '''American English''' is selected.
 
|-
 
|-
 
||Click on '''Spanish'''>> Click '''OK'''  buttons.
 
||Click on '''Spanish'''>> Click '''OK'''  buttons.
 +
 
Point to the menu bar and status bar.
 
Point to the menu bar and status bar.
 
||I will click on ''Spanish'''.
 
||I will click on ''Spanish'''.
 +
 
Click '''OK'''  button.
 
Click '''OK'''  button.
 +
 
Observe the change in language on the Menu bar and on the Status bar.
 
Observe the change in language on the Menu bar and on the Status bar.
 
|-
 
|-
Line 132: Line 173:
 
|| Now let's insert '''Templates''' onto the '''Panel'''.
 
|| Now let's insert '''Templates''' onto the '''Panel'''.
 
|-
 
|-
−
||Click on '''Templates''' menu>>'''Templates''' drop down opens.
+
||Click on '''Templates''' menu.
 
|| Click on '''Templates''' menu.
 
|| Click on '''Templates''' menu.
 +
 
'''Templates''' drop down opens.
 
'''Templates''' drop down opens.
 
|-
 
|-
Line 141: Line 183:
 
||Move the cursor on the list.
 
||Move the cursor on the list.
 
||Here you can see various '''Templates''' tabs.
 
||Here you can see various '''Templates''' tabs.
 +
 
Click on '''All Templates''' tab.
 
Click on '''All Templates''' tab.
 +
 
'''Structure Templates''' window opens.
 
'''Structure Templates''' window opens.
 
|-
 
|-
 
||Scroll down the window.
 
||Scroll down the window.
 
||Window shows list of '''Templates''' along with their structures.
 
||Window shows list of '''Templates''' along with their structures.
 +
 
I will scroll down the window to view different  structures.
 
I will scroll down the window to view different  structures.
 
|-
 
|-
Line 152: Line 197:
 
|-
 
|-
 
||Click on '''Beta Lactums''' tab.
 
||Click on '''Beta Lactums''' tab.
 +
 
Click on '''Penicillin''' structure.
 
Click on '''Penicillin''' structure.
 
||Click on Beta Lactums tab.
 
||Click on Beta Lactums tab.
 +
 
Click on Penicillin structure, to display it on the Panel.
 
Click on Penicillin structure, to display it on the Panel.
 
|-
 
|-
Line 160: Line 207:
 
|-
 
|-
 
||Click on '''Miscellaneous''' tab.  
 
||Click on '''Miscellaneous''' tab.  
−
Click on '''C60 Fullerene''', to display on the Panel.
+
 
 +
Click on '''C60 Fullerene'''.
 
|| Click on '''Templates''' tab,  click on '''Miscellaneous'''.
 
|| Click on '''Templates''' tab,  click on '''Miscellaneous'''.
 +
 
Then click on '''C60 Fullerene''', to display it on the Panel.
 
Then click on '''C60 Fullerene''', to display it on the Panel.
 
|-
 
|-
 
||'''Slide Number 6
 
||'''Slide Number 6
 +
 
Assignment'''.
 
Assignment'''.
 
||You can load other '''Templates''' of your choice onto the Panel.
 
||You can load other '''Templates''' of your choice onto the Panel.
Line 172: Line 222:
 
|-
 
|-
 
||'''Slide Number 7  
 
||'''Slide Number 7  
 +
 
SMILES'''
 
SMILES'''
 
|| What are '''SMILES''' and '''InChi Keys'''?
 
|| What are '''SMILES''' and '''InChi Keys'''?
−
'''SMILES''' is simplified molecular input line entry system.
+
 
−
It describes chemical structures using short '''ASCII''' strings.  
+
* '''SMILES''' is simplified molecular input line entry system.
−
Molecular Editors import '''SMILES''' strings, to convert structures into 2D drawings.
+
 
−
For example, '''CCCCCC'''  is a '''Canonical SMILES''' of '''Hexane'''
+
* It describes chemical structures using short '''ASCII''' strings.  
 +
 
 +
* Molecular Editors import '''SMILES''' strings, to convert structures into 2D drawings.
 +
 
 +
* For example, '''CCCCCC'''  is a '''Canonical SMILES''' of '''Hexane'''
 
|-
 
|-
−
||Slider Number 8
+
||'''Slide Number 8'''
−
||'''InChi''' is International Chemical Identifier.
+
 
−
It describes a chemical in terms of layers of information.
+
'''InChi'''
−
Atoms and their bond connectivity,  
+
||* '''InChi''' is '''International Chemical Identifier'''.
−
Isotopic, stereochemical and electronic charge information.  
+
 
−
For example, this (InChI=1S/C3H8/c1-3-2/h3H2,1-2H3) is the '''InChi'''  key of '''Propane'''.
+
* It describes a chemical in terms of layers of information.
 +
 
 +
* Atoms and their bond connectivity,  
 +
 
 +
* Isotopic, stereochemical and electronic charge information.  
 +
 
 +
*For example, this (InChI=1S/C3H8/c1-3-2/h3H2,1-2H3) is the '''InChi'''  key of '''Propane'''.
 
|-
 
|-
 
||Press '''Delete''' on the Keyboard.
 
||Press '''Delete''' on the Keyboard.
 
||I will clear the window.
 
||I will clear the window.
 +
 
Press '''Delete''' on the Keyboard.
 
Press '''Delete''' on the Keyboard.
 
|-
 
|-
 
||Point to the Templates and Morhphine.
 
||Point to the Templates and Morhphine.
−
||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.
 
|-
 
|-
 
||Click on '''Tools''' Menu>> click on '''Create SMILES'''.
 
||Click on '''Tools''' Menu>> click on '''Create SMILES'''.
Line 197: Line 259:
 
|-
 
|-
 
||Point to the dialogue box.
 
||Point to the dialogue box.
 +
 
Move the cursor onto '''SMILES''' and '''Chiral SMILES'''
 
Move the cursor onto '''SMILES''' and '''Chiral SMILES'''
 
|| '''SMILES''' dialogue box opens with '''Generated SMILES'''.
 
|| '''SMILES''' dialogue box opens with '''Generated SMILES'''.
 +
 
Dialogue box contains SMILES and Chiral SMILES.  
 
Dialogue box contains SMILES and Chiral SMILES.  
 
|-
 
|-
Line 205: Line 269:
 
|-   
 
|-   
 
||Go to '''Tools''' menu.
 
||Go to '''Tools''' menu.
 +
 
Click on Create InChi.
 
Click on Create InChi.
 
||Press CTRL+A to select the structure, if it is not selected.
 
||Press CTRL+A to select the structure, if it is not selected.
 +
 
To generate  '''InChi''' key of '''Morphine''', go to '''Tools''' menu.
 
To generate  '''InChi''' key of '''Morphine''', go to '''Tools''' menu.
 +
 
Click on '''Create InChi'''.
 
Click on '''Create InChi'''.
 
|-
 
|-
Line 223: Line 290:
 
|-
 
|-
 
||Point to the '''Insert bar''' and '''Insert''' button.
 
||Point to the '''Insert bar''' and '''Insert''' button.
−
||Below the '''Formatting''' toolbar, we have an '''Insert bar''' with an '''Insert''' button next to it.
+
||Below the '''Formatting''' toolbar, we have an '''Insert bar''' with an '''Insert''' button next to it.
 
|-
 
|-
 
||Click in the '''Insert''' bar >> type '''c1ccc1'''.
 
||Click in the '''Insert''' bar >> type '''c1ccc1'''.
Line 238: Line 305:
 
|-
 
|-
 
||Copy and Paste the '''SMILES'''.
 
||Copy and Paste the '''SMILES'''.
 +
 
Point to the structure.
 
Point to the structure.
 
|| I will copy a '''SMILES''' from “'Text Editor” and
 
|| I will copy a '''SMILES''' from “'Text Editor” and
 +
 
Paste it into '''Insert bar''' and click on  '''Insert''' button.  
 
Paste it into '''Insert bar''' and click on  '''Insert''' button.  
 +
 
Inserted '''SMILES''' displays  '''Aspartic acid (C(C(C(=O)O)N)C(=O)O)''' structure on the '''Panel'''.
 
Inserted '''SMILES''' displays  '''Aspartic acid (C(C(C(=O)O)N)C(=O)O)''' structure on the '''Panel'''.
 
|-
 
|-
Line 248: Line 318:
 
||Copy and paste the '''InChi Key'''.
 
||Copy and paste the '''InChi Key'''.
 
|| I will copy an '''Inchi Key'''  from the '''Text Editor''', and
 
|| I will copy an '''Inchi Key'''  from the '''Text Editor''', and
 +
 
Paste it into the '''Insert bar''' then click on  '''Insert''' button.  
 
Paste it into the '''Insert bar''' then click on  '''Insert''' button.  
 +
 
Inserted '''Inchi Key''' displays, '''Benzene''' (InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H) structure onto the '''Panel'''.
 
Inserted '''Inchi Key''' displays, '''Benzene''' (InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H) structure onto the '''Panel'''.
 
|-
 
|-
 
||'''Slide Number 9
 
||'''Slide Number 9
 +
 
Assignment'''
 
Assignment'''
 
|| As an assignment insert the given '''SMILES''' and '''InChi Keys'''  
 
|| As an assignment insert the given '''SMILES''' and '''InChi Keys'''  
Line 257: Line 330:
  
 
1)CC1=CC=CC=C1  
 
1)CC1=CC=CC=C1  
 +
 
2)CC(C(=O)O)N       
 
2)CC(C(=O)O)N       
 +
 
3)InChI=1S/C5H10/c1-2-4-5-3-1/h1-5H2   
 
3)InChI=1S/C5H10/c1-2-4-5-3-1/h1-5H2   
  
Line 265: Line 340:
 
||Let's Summarize.
 
||Let's Summarize.
 
|-
 
|-
−
||'''Slide Number 10
+
||'''Slide Number 10
 +
 
 
Summary'''
 
Summary'''
−
||In this tutorial, we have learnt to change
+
||In this tutorial, we have learnt to change,
−
Background color of the Panel  
+
 
−
Look and feel of the window
+
* Background color of the Panel  
−
User interface language.  
+
 
−
Insert Templates  
+
* Look and feel of the window
−
Generate Smiles and InChi keys for a given structure.
+
 
−
Insert Smiles and InChi keys to generate structures.  
+
* User interface language.  
 +
 
 +
* Insert Templates  
 +
 
 +
* Generate Smiles and InChi keys for a given structure.
 +
 
 +
* Insert Smiles and InChi keys to generate structures.  
 
|-   
 
|-   
 
||'''Slide Number11
 
||'''Slide Number11
 +
 
Acknowledgement'''
 
Acknowledgement'''
 
||This video summarizes the Spoken Tutorial project
 
||This video summarizes the Spoken Tutorial project
 +
 
If you do not have good bandwidth, you can download and watch it.   
 
If you do not have good bandwidth, you can download and watch it.   
 
|-
 
|-
 
||'''Slide Number 12'''
 
||'''Slide Number 12'''
 
||  Spoken Tutorial Team:  
 
||  Spoken Tutorial Team:  
 +
 
Conducts workshops using spoken tutorials
 
Conducts workshops using spoken tutorials
 +
 
Gives certificates to those who pass an on-line test  
 
Gives certificates to those who pass an on-line test  
 +
 
For more details, please write to
 
For more details, please write to
 +
 
'''contact@spoken-tutorial.org'''  
 
'''contact@spoken-tutorial.org'''  
 
|-
 
|-
 
||'''Slide number 13'''
 
||'''Slide number 13'''
 
|| 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  
 +
 
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
−
More information on this Mission is available at this link.
+
 
 +
More information on this Mission is available at this link.
 +
 
 
'''http://spoken-tutorial.org/NMEICT-Intro ]'''  
 
'''http://spoken-tutorial.org/NMEICT-Intro ]'''  
 +
 
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.  
 
|-
 
|-
 
|}
 
|}

Revision as of 11:48, 1 October 2014

Visual Cue Narration
Slide Number 1

Title Slide

Hello everyone.

Welcome to this tutorial on Features of JChemPaint..

Slide Number 2+3

Learning Objectives

In this tutorial, we will learn to change
  • Background color of the Panel
  • Look and feel of the window
  • User interface language.

We will also learn to,

  • Insert Templates
  • Generate SMILES and InChi keys for a given structure.
  • Insert SMILES and InChi keys to generate structures.
Slide Number 4

System Requirement

To record this tutorial I am using,

Ubuntu Linux OS version 12.04

JChemPaint version 3.3-1210

Java version 7

Slide Number 5

Pre-requisites

To follow this tutorial you should be familiar with,

JChemPaint chemical structures editor .

If not, for relevant tutorial, please visit our website.

Let's switch to JChemPaint window.
Point to .jar file Recall that we had saved our .jar file on the Desktop.
Press CTRl+ALt+T keys. Press CTRl+ALt and T keys simultaneously to open the Terminal.
Type “cd space Desktop”>>press enter.

Type java -jar ./jchempaint-3.3-1210.jar >> press enter.

Type '“cd space Desktop” and press enter.

Type “java space -jar space ./jchempaint-3.3-1210.jar” and press enter.

JChemPaint window opens.

Move the cursor on the Panel. Let's see, how to change the background color of the Panel.
Go to Edit menu navigate to Preferences >> click on it.

Move the cursor on the window.

Go to Edit menu navigate to Preferences and click on it.

JChemPaint Preferences window opens.

Click on Choose background color button.

Point to Choose background color window.

Click on Choose background color button.

Choose background color window opens.

Point to the tabs. This window has three tabs namely Swatches, HSB and RGB.
Depending on your Operating System this window, may vary a little.
Show the screen shots of the other Choose background windows. 'HSB may be HSV.

You may not see Swatches tab.

Show the screen shot of Windows OS. Windows Operating System has two additional tabs namely HSL and CMYK.
Point to light green Swatch. You can select the background color of your choice.

I will click on light green color Swatch to change background color to light green.

Click on OK to close window. Click on OK to close the window.
Click on OK button. Click on OK to close the Preferences' window.
Slide Number 5

Assignment

Try various color combinations using Choose background color window.
Next about Other Preferences tab.
Go to Edit menu navigate to Preferences >> click on it.

Move the cursor on the window.

Go to Edit menu and click on Preferences

Preferences window opens.

Click on Other Preferences tab. Click on Other Preferences tab.
Move the cursor to Look and feel field.

Point to the drop down list.

Go to Look and feel field.

This field has a drop down list.

List contains Sytem, Metal, Nimbus, Motif, GTK and Windows.

Click on Nimbus>>click on OK button. I will click on Nimbus.

Then click on OK button.

Observe the change in look and feel of the window.

Click on Edit menu >> click Preferences. Click on Edit menu then click Preferences.

Click on other Preferences.

Move the cursor on the window. Go to User Interface Language field.

This field has a drop down list.

List contains American English and other languages.

By default American English is selected.

Click on Spanish>> Click OK buttons.

Point to the menu bar and status bar.

I will click on Spanish'.

Click OK button.

Observe the change in language on the Menu bar and on the Status bar.

I will undo the changes.
Point to Templates menu Now let's insert Templates onto the Panel.
Click on Templates menu. Click on Templates menu.

Templates drop down opens.

Point to right side tool bar. Alternately you can open Templates menu from side tool bar.
Move the cursor on the list. Here you can see various Templates tabs.

Click on All Templates tab.

Structure Templates window opens.

Scroll down the window. Window shows list of Templates along with their structures.

I will scroll down the window to view different structures.

Point to the Templates. I will click on a few Template tabs to display structures.
Click on Beta Lactums tab.

Click on Penicillin structure.

Click on Beta Lactums tab.

Click on Penicillin structure, to display it on the Panel.

Press Ctrl+ Z Press Ctrl+ Z to undo the changes.
Click on Miscellaneous tab.

Click on C60 Fullerene.

Click on Templates tab, click on Miscellaneous.

Then click on C60 Fullerene, to display it on the Panel.

Slide Number 6

Assignment.

You can load other Templates of your choice onto the Panel.
Next we will learn about SMILES and InChi keys.
Slide Number 7

SMILES

What are SMILES and InChi Keys?
  • SMILES is simplified molecular input line entry system.
  • It describes chemical structures using short ASCII strings.
  • Molecular Editors import SMILES strings, to convert structures into 2D drawings.
  • For example, CCCCCC is a Canonical SMILES of Hexane
Slide Number 8

InChi

* InChi is International Chemical Identifier.
  • It describes a chemical in terms of layers of information.
  • Atoms and their bond connectivity,
  • Isotopic, stereochemical and electronic charge information.
  • For example, this (InChI=1S/C3H8/c1-3-2/h3H2,1-2H3) is the InChi key of Propane.
Press Delete on the Keyboard. I will clear the window.

Press Delete on the Keyboard.

Point to the Templates and Morhphine. To generate SMILES I will load an Alkaloid, Morhphine from the Templates menu.
Click on Tools Menu>> click on Create SMILES. Click on Tools Menu, then click on Create SMILES.
Point to the dialogue box.

Move the cursor onto SMILES and Chiral SMILES

SMILES dialogue box opens with Generated SMILES.

Dialogue box contains SMILES and Chiral SMILES.

Click OK to close the dialogue box. Click OK to close the dialogue box.
Go to Tools menu.

Click on Create InChi.

Press CTRL+A to select the structure, if it is not selected.

To generate InChi key of Morphine, go to Tools menu.

Click on Create InChi.

Point to InChi details. InChi dialogue box opens with InChi generation of 'Morphine'.
Click OK to close the dialogue box. Click OK to close the dialogue box.
Press Delete on the keyboard. Press Delete on the keyboard to delete the Morphine structure.
Now we will learn to obtain a structure from inserted SMILES.
Point to the Insert bar and Insert button. Below the Formatting toolbar, we have an Insert bar with an Insert button next to it.
Click in the Insert bar >> type c1ccc1. Click in the Insert bar and type c1ccc1 and click on Insert button.
Point to the structure. Cyclobutene structure is generated on the Panel.
Press Ctrl+Z. Press Ctrl+Z to undo the changes.
Open and show the Text editor. I had already saved a few SMILES and InChi keys from PubChem Page into a Text Editor.
Copy and Paste the SMILES.

Point to the structure.

I will copy a SMILES from “'Text Editor” and

Paste it into Insert bar and click on Insert button.

Inserted SMILES displays Aspartic acid (C(C(C(=O)O)N)C(=O)O) structure on the Panel.

Press Ctrl+Z. Press Ctrl+Z to undo the changes.
Copy and paste the InChi Key. I will copy an Inchi Key from the Text Editor, and

Paste it into the Insert bar then click on Insert button.

Inserted Inchi Key displays, Benzene (InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H) structure onto the Panel.

Slide Number 9

Assignment

As an assignment insert the given SMILES and InChi Keys

to obtain various structures .

1)CC1=CC=CC=C1

2)CC(C(=O)O)N

3)InChI=1S/C5H10/c1-2-4-5-3-1/h1-5H2

4)InChI=1S/H2O4S/c1-5(2,3)4/h(H2,1,2,3,4)

Let's Summarize.
Slide Number 10

Summary

In this tutorial, we have learnt to change,
  • Background color of the Panel
  • Look and feel of the window
  • User interface language.
  • Insert Templates
  • Generate Smiles and InChi keys for a given structure.
  • Insert Smiles and InChi keys to generate structures.
Slide Number11

Acknowledgement

This video summarizes the Spoken Tutorial project

If you do not have good bandwidth, you can download and watch it.

Slide Number 12 Spoken Tutorial Team:

Conducts workshops using spoken tutorials

Gives certificates to those who pass an on-line test

For more details, please write to

contact@spoken-tutorial.org

Slide number 13 Spoken Tutorial Project is a part of the Talk to a Teacher project

It is supported by the National Mission on Education through ICT, MHRD, Government of India

More information on this Mission is available at this link.

http://spoken-tutorial.org/NMEICT-Intro ]

This is Madhuri Ganapathi from IIT Bombay signing off. Thank you for joining.

Contributors and Content Editors

Madhurig, Nancyvarkey

Retrieved from "https://script.spoken-tutorial.org/index.php?title=JChemPaint/C3/Features-of-JChemPaint/English&oldid=17191"