JChemPaint/C3/Features-of-JChemPaint/English - Revision history

Nancyvarkey at 09:53, 1 October 2014

2014-10-01T09:53:08Z

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Madhurig at 06:41, 1 October 2014

2014-10-01T06:41:43Z

Madhurig at 06:20, 1 October 2014

2014-10-01T06:20:48Z

Madhurig at 06:18, 1 October 2014

2014-10-01T06:18:46Z

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Madhurig: Created page with " {| border=1 || '''Visual Cue''' || '''Narration''' |- ||'''Slide Number 1 Title Slide''' ||Hello everyone. Welcome to this tutorial on '''Features of JChemPaint.'''. |- ||''..."

2014-10-01T06:06:05Z

Created page with " {| border=1 || '''Visual Cue''' || '''Narration''' |- ||'''Slide Number 1 Title Slide''' ||Hello everyone. Welcome to this tutorial on '''Features of JChemPaint.'''. |- ||''..."

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{| border=1
|| '''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 simultaneously to open the terminal.
||Press '''CTRl+ALt''' and '''T''' keys simultaneously to open the '''Terminal'''.
|-
||Type '''“cd space Desktop”''' and press enter.
Type '''java -jar ./jchempaint-3.3-1210.jar''' and 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''' to open '''Preferences''' window.
|| 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>>'''Templates''' drop down opens.
|| 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''', to display on the Panel.
|| 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'''
|-
||Slider Number 8
||'''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.
|-
|}

@@ Line 91: / Line 91: @@
 |-
 ||Show the screen shots of the other Choose background windows.
-||'''HSB''' may be '''HSV''.
+||'''HSB''' may be '''HSV'''.
 You may not see '''Swatches''' tab.
@@ Line 107: / Line 107: @@
 |-
 ||Click on '''OK'''  button.
-||Click on '''OK''  to close the '''Preferences''' window.
+||Click on '''OK'''  to close the '''Preferences''' window.
 |-
 ||'''Slide Number 5'''
@@ Line 160: / Line 160: @@
 Point to the menu bar and status bar.
-||I will click on ''Spanish'''.
+||I will click on '''Spanish'''.
 Click '''OK'''  button.
@@ Line 212: / Line 212: @@
 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.
 |-
@@ Line 220: / Line 220: @@
 ||Next we will learn about '''SMILES''' and '''InChi keys'''.
 |-
-||'''Slide Number 7
+||'''Slide Number 7'''
-SMILES'''
+'''SMILES'''
 || What are '''SMILES''' and '''InChi Keys'''?
@@ Line 242: / Line 242: @@
 * Atoms and their bond connectivity,
-* Isotopic, stereochemical and electronic charge information.
+* '''Isotopic, stereochemical''' and '''electronic charge''' information.
-*For example, this (InChI=1S/C3H8/c1-3-2/h3H2,1-2H3) is the '''InChi'''  key of '''Propane'''.
+* For example, this (InChI=1S/C3H8/c1-3-2/h3H2,1-2H3) is the '''InChi'''  key of '''Propane'''.
 |-
 ||Press '''Delete''' on the Keyboard.
@@ Line 251: / Line 251: @@
 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'''.
@@ Line 262: / Line 262: @@
 || '''SMILES''' dialogue box opens with '''Generated SMILES'''.
-Dialogue box contains SMILES and Chiral SMILES.
+Dialogue box contains '''SMILES''' and '''Chiral SMILES'''.
 |-
 ||Click '''OK''' to close the dialogue box.
@@ Line 269: / Line 269: @@
 ||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.
@@ Line 280: / Line 280: @@
 |-
 ||Click '''OK''' to close the dialogue box.
-||Click '''OK'''  to close the dialogue box.
+||Click '''OK''' to close the dialogue box.
 |-
 ||Press '''Delete''' on the keyboard.
@@ Line 292: / Line 292: @@
 |-
 ||Click in the '''Insert''' bar >> type '''c1ccc1'''.
-||Click in the Insert bar and type '''c1ccc1''' and click on '''Insert''' button.
+||Click in the '''Insert bar''' and type '''c1ccc1''' and click on '''Insert''' button.
 |-
 ||Point to the structure.
@@ Line 301: / Line 301: @@
 |-
 ||Open and show the Text editor.
-||I had already saved a few '''SMILES'''  and '''InChi''' keys from '''PubChem Page''' into a 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
+|| I will copy a '''SMILES''' from “Text Editor” and
 Paste it into '''Insert bar''' and click on  '''Insert''' button.
@@ Line 322: / Line 322: @@
 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'''
 to obtain various structures .
@@ Line 339: / Line 339: @@
 ||Let's Summarize.
 |-
-||'''Slide Number 10
+||'''Slide Number 10'''
-Summary'''
+'''Summary'''
 ||In this tutorial, we have learnt to change,
-* Background color of the Panel
+* Background color of the '''Panel'''
 * Look and feel of the window
@@ Line 350: / Line 350: @@
 * User interface language.
-* Insert Templates
+* Insert '''Templates'''
-* Generate Smiles and InChi keys for a given structure.
+* Generate '''SMILES''' and '''InChi keys''' for a given structure.
-* Insert Smiles and InChi keys to generate structures.
+* Insert '''SMILES''' and '''InChi Keys''' to generate structures.
 |-
-||'''Slide Number11
+||'''Slide Number 11'''
-Acknowledgement'''
+'''Acknowledgement'''
 ||This video summarizes the Spoken Tutorial project