Difference between revisions of "Jmol-Application/C2/Structures-from-Database/English"

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(Created page with ''''Title of script''': Structures from Database '''Author: Snehalatha Kaliappan''' '''Keywords: Video tutorial, Chemical structures from Database, Jmol video tutorial''' {| st…')
 
 
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| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Here is another assignment for you.
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Here is another assignment for you.
  
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# Draw structures of the following '''Amino acids''' in '''GChemPaint.'''
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1. Draw 2D structures of the following '''Amino acids''' in '''GChemPaint.'''
  
 
* '''Cysteine '''
 
* '''Cysteine '''
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* '''Phenylalanine'''
 
* '''Phenylalanine'''
  
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# Save the 2D structures as '''.mol '''files.
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2. Save as '''.mol '''files.
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# Open these files in '''Jmol''' and modify the display.  
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3. Open the files in '''Jmol''' and modify the display.  
  
 
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Latest revision as of 18:00, 26 August 2019

Title of script: Structures from Database

Author: Snehalatha Kaliappan

Keywords: Video tutorial, Chemical structures from Database, Jmol video tutorial

Visual Cue
Narration
Slide Number 1

Title Slide

Welcome to this tutorial on Structures from Databases in Jmol
Slide Number 2

Learning Objectives

In this tutorial, we will learn to
  • Load chemical structures from PubChem database.
    And
  • Convert 2D structures drawn in GChemPaint to 3D models in Jmol.
Slide Number 3

Pre-requisites

To follow this tutorial you should be familiar with Jmol Application.

If not, watch the relevant tutorials available at our website.

Slide Number 4

System Requirement

To record this tutorial I am using


  • Ubuntu Linux OS version. 12.04
  • Jmol version 12.2.2
  • Java version 7
  • GChemPaint version 0.12.10
  • Mozilla Firefox browser 22.0
Cursor on the panel I have opened a new Jmol Application window.


Jmol has a feature to load structures of compounds listed in the database.

Click on the 'File' menu.

Scroll down the menu.

The 'File' menu on the menu bar, has an option 'Get MOL'.

This loads molecules from chemical structure data base 'PubChem'.

Cursor on 'Get PDB'. It also has another option 'Get PDB' to load protein structures from Protein Data Bank.

This feature will be explained in detail in another tutorial.

Click on 'Get Mol'. To load a chemical structure on the panel, click on 'Get Mol'.
Cursor on the 'Input' dialog box. An 'Input' dialog box opens on the screen.
Slide Number 5

Identification of Molecules

Any molecule listed in the database can be loaded by typing the following in the text box:
  • Common name or IUPAC name
  • CAS number (Chemical Abstracts Service) registry number
  • CID number (Compound Identification Number).
Slide Number 6

Identification of Molecules

* InChi identifier (IUPAC International Chemical Identifier or
  • SMILES identifier that is (Simplified Molecular Input Line Entry System)
Switch to the browser with the Pubchem database website. Please visit Pubchem database website for information on identification numbers for a particular chemical
Type Phenol in the text box. let us display phenol on screen.


So type 'phenol' in the Input text box.

Press OK button. Press OK button.
Cursor on Phenol. Model of phenol is displayed on panel.
Cursor on the panel. We can modify the display of phenol using various rendering options.

These options are listed in Menu bar and Pop-up menu.

Click on display menu, and select label. Click on number from the options. We can add substituents to the benzene ring of phenol.

First let us label the atoms in the model.

Click on display menu, and select label. Click on number option.

Cursor on the panel. Now, let's replace a hydrogen number 10 attached to carbon atom number 4 with an amino group.
Open modelkit menu, select nitrogen. Open the modelkit menu select nitrogen from options.
Click on hydrogen attached to Atom number 3. Click on hydrogen number 10.

This is a molecule of Para-Amino Phenol on the panel.

Open pop-up menu, scroll to style and select sticks from the options. We will change the display to Sticks display.

Exit the modelkit menu.

Open the Pop-up menu, scroll down to Style and select Scheme. Select Sticks from the options.

Cursor on the panel. On the panel we have a model of Para-Amino-phenol in sticks display.
Type cholesterol in the text box. Complex structures, which are difficult to create, can easily be loaded on the panel.

For example cholesterol.

Click on file menu

Click on Get Mol option once again and type Cholesterol in the text box.

Press OK button. Press OK button.
Cursor on the panel. A molecule of Cholesterol is displayed on the panel.
Cursor on the double-bond and side-chain. We can highlight the features like double-bond and side-chain in the molecule.
Cursor on the panel. To highlight double-bond, first let us change the color of carbon atoms of the double-bond.
Click on 'Select a set of atoms' icon in the tool bar.

Click on Carbons involved in double-bond

Click on 'Select atoms' icon in the tool bar.

Then click on the carbon atoms involved in the double-bond.

Cursor on the yellow halo. A yellow halo appears around the atoms.
Right click on the panel, scroll down to 'Colors', select 'Atoms' then click on Orange. Open the Pop-up-menu.

Scroll down to Color, select Atoms and click on Orange option.

Click anywhere on the panel. Click on “Rotate molecule” option in the tool bar.
Cursor on the double-bond. The double-bond in the cholesterol model is now in orange color.
Click on 'Select a set of atoms' icon in the tool bar.

Click on all the atoms of the side-chain.

Similarly, we can highlight the carbons in the side-chain.
Right click on the panel, scroll down to 'Colors', select 'Atoms' then click on Violet. Using Pop-up-menu change the color to violet.
Cursor on the panel. On the panel, we have a model of Cholesterol with important features highlighted.
Slide Number 7

Assignment

As an assignment,
  • Load structure of caffeine from Pubchem database .
  • Highlight the important features in the molecule.
  • Modify the display to wireframe.
Cursor on panel with Alanine. Now I will discuss another important feature of Jmol.

We can convert 2D structures of molecules drawn in another software into 3D models.

Cursor on panel with Alanine. Here I have a model of aminoacid Alanine on the panel.

2D structure of this molecule was drawn in software called GChemPaint.

Cursor on panel with Alanine. The structure was saved as a .mol file.
Slide Number 8

About GChemPaint

GchemPaint is an Open source software for drawing 2D chemical structures.

Tutorials on GChemPaint are available at the following link.

To draw structures and save in .mol format, refer to Analysis of Compounds tutorial.

Open GchemPaint window load 2D -structures of Alanine, Shown on this Gchempaint display area are 2D drawings of
  • Amino acid -Alanine
  • Nuclioside -Adenosine
  • Saccharide -Alpha-D glucopyranose

I have saved them in .mol format on my Desktop.

Cursor on the panel. First, let's view the 2D structure of Alanine as 3D model in Jmol Application.
Exit the GchemPaint program.

Open a new Jmol window.

So, I will open a new Jmol window.
Click on 'Open a file 'option in the tool bar. Click on 'Open a file' icon in the tool bar.
Click on Desktop and click open button. I will choose Desktop folder and click on open. Choose the file Alanine.mol and click on Open button.
Cursor on the screen. A 3D model of 'Alanine' opens on screen.
Click on modelkit icon and scroll down the menu and click on 'fix hydrogens and minimize' option. Open the modelkit menu and click on 'fix hydrogens and minimize' option.
Cursor on the panel. Hydrogens are added to the structure and the energy minimized.
Cursor on menu bar.

Right click on the panel to open the Pop-up menu.

As with any .mol file, we can change the display using menu bar and also Pop-up menu.
Open the model of Adenosine on screen. Here is the 3D model of Adenosine.mol in Jmol.
Open the model of Alpha D glucopyranose on jmol panel. And this is a 3D model of Alpha-D-glucopyranose.mol in Jmol.
Slide Number 9

Summary

Let's summarize

In this tutorial we have learnt to


  • Load chemical structures from Pubchem data base.
  • Modify the display of Phenol and Cholesterol.
Slide Number 10

Summary

* Convert 2D structures drawn in GChemPaint to 3D models in Jmol.
  • Convert 2D structures of Alanine, Adenosine and Alpha-D-glucopyranose to 3D models.
Slide Number 11

Assignment

Here is another assignment for you.

1. Draw 2D structures of the following Amino acids in GChemPaint.

  • Cysteine
  • Histidine
  • Phenylalanine

2. Save as .mol files.

3. Open the files in Jmol and modify the display.

Slide Number 12

Acknowledgement

Watch the video available at this URL.

http://spoken-tutorial.org/What_is_a_Spoken_ Tutorial

It summarizes the Spoken Tutorial project

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

Slide Number 13 The Spoken Tutorial Project 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 14 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 Snehalatha from IIT Bombay signing off. Thank you for joining.

Contributors and Content Editors

Snehalathak

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