Difference between revisions of "Jmol-Application/C2/2D-Editor-Tool/English"
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Revision as of 16:11, 8 August 2025
Title of script: 2D Editor Tool
Author: Dr. Snehalatha Kaliappan
Keywords: Jmol, 2D editor, model kit menu, 3D model, SMILES string, video tutorial
| 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,
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| Slide Number 3
Learning Objectives |
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| Slide Number 4
System Requirements |
Here I am using,
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| Slide Number 5
Pre-requisites |
To follow this tutorial,
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| 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,
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Let's summarize, |
| Slide Number 7
Summary
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what we have learned. |
| Slide Number 8
Assignment 1 |
As an assignment,
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| Slide Number 9
Assignment 2 |
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| Slide Number 10
Thank you |
Thank you for joining. |
