Madhurig at 11:32, 14 August 2025

2025-08-14T11:32:02Z

Ketkinaina: Created page with "'''Title of script''': '''2D Editor Tool''' '''Author: Dr. Snehalatha Kaliappan''' '''Keywords: Jmol, 2D editor, model kit menu, 3D model, SMILES string, video tutorial'''..."

2025-08-08T10:41:12Z

Created page with "'''Title of script''': '''2D Editor Tool''' '''Author: Dr. Snehalatha Kaliappan''' '''Keywords: Jmol, 2D editor, model kit menu, 3D model, SMILES string, video tutorial'''..."

New page

'''Title of script''': '''2D Editor Tool'''

'''Author: Dr. Snehalatha Kaliappan'''

'''Keywords: Jmol, 2D editor, model kit menu, 3D model, SMILES string, video tutorial'''

{|border=1
|-
|| '''Visual cue'''
|| '''Narration'''
|-
|| '''Slide Number 1'''

'''Title Slide'''
|| Welcome to this Spoken tutorial on '''2D Editor Tool''' in '''Jmol'''.
|-
|| '''Slide Number 2'''

'''Learning Objectives'''
|| In this tutorial, we will learn to,
* Convert a 3D model to 2D drawing using the '''2D-Editor''' tool
* Edit the 2D drawing
* Save the 2D drawing
|-
|| '''Slide Number 3'''

'''Learning Objectives'''
||
* Create 2D drawing using tools in the 2D Editor window.
* Generate SMILES string for the structure
* Convert 2D drawing to 3D model
|-
|| '''Slide Number 4'''

'''System Requirements'''
|| Here I am using,
* '''Ubuntu Linux OS version 22.04'''
* '''Jmol version 16.2.35'''
* '''Java version 11.0.25'''
* A working internet connection
|-
|| '''Slide Number 5'''

'''Pre-requisites'''
|| To follow this tutorial,
* learner must be familiar with basic operations on Jmol interface.
|-
|| Click on the '''File '''menu, select GetMOL option.

In the Input box that appears type Phenylalanine and click OK
|| Here I have opened the Jmol interface.

Click on the '''File''' menu and select '''Get MOL''' option.

In the Input box that appears, type '''Phenylalanine''' and click '''OK'''.
|-
|| Point to the model of Phenylalanine on the panel.

Click the Open the model kit icon.

Click on minimize option.

Select the exit the model kit mode.
|| This will load a model of '''phenylalanine''' on the panel.

Open the '''model kit '''menu.

Click on''' minimize''' option to do energy minimization.

Exit the '''model kit '''menu.
|-
|| Point to the 3D model of phenylalanine.
|| The 3D model of '''phenylalanine''' can be visualized as 2D drawing using the '''2D Editor''' tool.
|-
|| Click on Tools menu, select 2-D Editor from the drop-down
|| Click on''' Tools''' menu.

Select '''2-D Editor '''from the drop-down.
|-
|| Point to the drawing in the window.
|| '''Jmol 2D Molecular Editor''' window opens with a 2D drawing of '''phenylalanine'''.
|-
|| Point to the various size rings , bonds and elements.
|| The '''2D editor '''window has tools in the top menu to draw various sized rings, bonds etc.

You will find various buttons at the left side and bottom of the window.
|-
|| Cursor on the 2D editor.
|| You can save this drawing in various formats using the buttons at the bottom.
|-
|| Click on '''to PNG''' button at the bottom of the 2d Editor window.
|| I would like to save this drawing in the '''png''' format.

Click on '''to PNG''' button at the bottom of the''' 2D Editor '''window.
|-
|| Point to the Save dialog box.

phenylalanine.png
|| '''Save '''dialog box opens.

Choose the location to save this file.

I will type the '''File Name '''as '''phenylAlanine.png'''.

Choose the '''Files of Type '''as '''PNG'''.

Click on the '''Save''' button at the bottom right corner.
|-
|| Cursor near phenylalanine
|| Let us edit the 2d drawing of '''phenylAlanine''' by adding a functional group.

Select the '''chloride''' group from the left menu.
|-
|| Click on the OH group on Phenylalanine.
|| Click on the hydroxy('''OH) '''group on the '''phenylalanine''' to replace it with the '''chloride''' group.
|-
|| Click on the X button and then click on the NH2 group.
|| We can also delete atoms or groups using the red '''X''' button in the tools menu on the top.

Click on the '''X''' button and then click on the amino(NH2) group to delete it.
|-
|| Cursor on the panel.
|| Now let us convert this 2D structure to a 3D model.
|-
|| Click on the “'''replace 3D'''” button at the bottom of the window.
|| In the '''2D Editor '''window, click on the '''replace 3D''' button at the bottom of the window.
|-
|| Cursor on the Jmol panel
|| The updated 3D model is seen on the Jmol panel.

Notice that groups modified in the 2D structure are updated in the 3D model.
|-
|| Cursor on the top left yellow smiley button.
|| On the 2D editor window, '''SMILES''' string can be generated using the yellow smiley button at the top left corner.
|-
|| Click on the yellow smiley button
|| Click on the yellow smiley button.
|-
|| Cursor on the pop-up window.
|| A small pop-up window opens with the '''SMILES''' string for the molecule.
|-
|| Click on the '''Close''' button on the '''SMILES''' window
|| Click on the '''Close''' button on the '''SMILES''' window.
|-
|| Click on the white rectangle button in the toolbar at the top.
|| To clear the panel, click on the white rectangle button in the toolbar at the top.
|-
|| Cursor on the top and left side toolbars.
|| We can also create a 2D drawing of the chemical structures atom by atom.

The required tools are available in the top and side toolbars.
|-
|| Click on the zig-zag line tool available in the toolbar at the top.

Bring the cursor to the drawing area, click and drag.
|| For example, let us draw 2-bromo hexane.

Click on the zig-zag line tool available on the toolbar at the top.

Bring the cursor to the drawing area, click and drag.
|-
|| Cursor on the panel.

Click on the single bond tool from the top toolbar.

Click on the 2nd carbon atom.
|| Stop when you have 6 carbon atom line drawing.

Click on the single bond tool from the top toolbar.

Click on the second carbon atom.
|-
|| Click on the '''Br''' button in the left tool panel.

Click on the single bond on the 2nd carbon atom.
|| Click on the '''Br''' button in the left toolbar.

Then click on the single bond on the second carbon atom.

This is the 2D drawing of 2-bromo hexane.
|-
|| Click on the '''replace 3D''' button at the bottom.

Cursor on the Jmol panel.
|| We can convert this 2D drawing to a 3D model as shown before.

Click on the '''replace 3D''' button at the bottom.

Notice the 3D model of 2-bromo hexane on the Jmol panel.
|-
|| Click on X at the top left corner.
|| Close the 2D Editor window.
|-
|| Cursor on the panel.
|| With this we have come to the end of this tutorial.
|-
|| '''Slide Number 6'''

'''Summary'''

We have learned to,
* Convert a 3D model to 2D drawing using the '''2D-Editor''' tool
* Edit the 2D drawing
* Save the 2D drawing
|| Let's summarize,
|-
|| '''Slide Number 7'''

'''Summary'''
* Create 2D drawing using tools in the 2D Editor window.
* Generate SMILES string for the structure.
* Convert 2D drawing to 3D model.

|| what we have learned.
|-
|| '''Slide Number 8'''

'''Assignment 1'''
|| As an assignment,

* Create a 3D model of your choice on the Jmol panel.
* Convert it to the 2D drawing and save in mol format.
|-
|| '''Slide Number 9'''

'''Assignment 2'''
||
* Create a 2D structure of your choice in the 2D Editor.
* Convert it to the 3D model.
|-
|| '''Slide Number 10'''

'''Thank you'''
|| Thank you for joining.
|-
|}

@@ Line 1: / Line 1: @@
 '''Title of script''': '''2D Editor Tool'''
-'''Author: Dr. Snehalatha Kaliappan'''
+'''Author''': Dr. Snehalatha Kaliappan
 {|border=1
@@ Line 49: / Line 50: @@
 In the Input box that appears type Phenylalanine and click OK
-|| Here I have opened the Jmol interface.
+|| Here I have opened the '''Jmol''' interface.
 Click on the '''File''' menu and select '''Get MOL''' option.
@@ Line 74: / Line 75: @@
 |-
 || Click on Tools menu, select 2-D Editor from the drop-down
-|| Click on''' Tools''' menu.
+|| Click on ''' Tools''' menu.
 Select '''2-D Editor '''from the drop-down.
@@ Line 82: / Line 83: @@
 |-
 || Point to the various size rings , bonds and elements.
-|| The '''2D editor '''window has tools in the top menu to draw various sized rings, bonds etc.
+|| The '''2D editor ''' window has tools in the top menu to draw various sized rings, bonds etc.
 You will find various buttons at the left side and bottom of the window.
@@ Line 183: / Line 184: @@
 Cursor on the Jmol panel.
-|| We can convert this 2D drawing to a 3D model as shown before.
+|| We can convert this 2D drawing as a 3D model as shown before.
 Click on the '''replace 3D''' button at the bottom.

Jmol-Application/C2/2D-Editor-Tool/English - Revision history

Madhurig at 11:32, 14 August 2025

Ketkinaina: Created page with "'''Title of script''': '''2D Editor Tool''' '''Author: Dr. Snehalatha Kaliappan''' '''Keywords: Jmol, 2D editor, model kit menu, 3D model, SMILES string, video tutorial'''..."