Difference between revisions of "Jmol-Application/C2/Overview-of-Jmol-Application/English"

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'''System Requirement'''
 
'''System Requirement'''
 
|| To record this tutorial, I am using,
 
|| To record this tutorial, I am using,
−
 
−
 
 
* '''Ubuntu Linux''' OS version 14.04
 
* '''Ubuntu Linux''' OS version 14.04
 
* '''Java '''(JVM) version 1. 8
 
* '''Java '''(JVM) version 1. 8
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'''Jmol''' is an open source '''3D viewer''' for:
 
'''Jmol''' is an open source '''3D viewer''' for:
  
−
* Chemical structures.
+
* Chemical structures
 
* Biomolecules  
 
* Biomolecules  
 
* Crystal structures and  
 
* Crystal structures and  
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−
'''Jmol''' is used by students, educators, and researchers in the fields of '''chemistry''' and '''biochemistry'''.
+
'''Jmol''' is used by students, educators, and researchers in the fields of '''Chemistry''' and '''Biochemistry'''.
  
 
|-
 
|-
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Press Enter.
 
Press Enter.
−
 
  
 
Point to webpage.
 
Point to webpage.
 
|| Open this link in any '''web browser'''.  
 
|| Open this link in any '''web browser'''.  
 
A web-page opens.
 
A web-page opens.
−
 
  
 
|-
 
|-
Line 138: Line 134:
  
 
|-
 
|-
−
|| Scroll up, under heading '''Downloading Jmol, '''
+
|| Scroll up, under heading '''Downloading Jmol, ''' click on '''Download link.'''
−
 
+
−
 
+
−
Click on '''Download link.'''
+
 
|| Scroll up the page.  
 
|| Scroll up the page.  
 
Under the heading '''Downloading Jmol, '''click on '''download link.'''
 
Under the heading '''Downloading Jmol, '''click on '''download link.'''
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|-
 
|-
−
|| Right-click and click on Extract Here.
+
|| Right-click and click on '''Extract Here'''.
  
  
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|-
 
|-
 
|| Cursor on Jmol.jar file.
 
|| Cursor on Jmol.jar file.
−
|| For windows and Mac double-click on Jmol.jar file to open the Jmol interface.
+
|| For '''Windows''' and '''Mac''', double-click on '''Jmol.jar''' file to open the '''Jmol''' interface.
  
 
|-
 
|-
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|-
 
|-
−
|| At the prompt type, cd Downloads, press enter.
+
|| At the prompt type, cd Downloads, press Enter.
  
 
Then type, jmol-14.29.42
 
Then type, jmol-14.29.42
  
−
Press enter.
+
Press Enter.
  
 
|| Navigate to '''Jmol''' folder which we had downloaded and extracted earlier.
 
|| Navigate to '''Jmol''' folder which we had downloaded and extracted earlier.
Line 244: Line 237:
  
  
−
Then type '''cd''' space and the name of the '''Jmol''' folder. In my case, it is '''Jmol hyphen fourteen dot twenty-nine dot four two'''
+
Then type '''cd''' space and the name of the '''Jmol''' folder.  
 +
In my case, it is '''Jmol hyphen fourteen dot twenty-nine dot four two'''
  
  
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'''https://spoken-tutorial.org'''
 
'''https://spoken-tutorial.org'''
−
|| Linux users can also install '''Jmol''' using '''Ubuntu Software Center '''or''' Synaptic Package Manager.'''
+
|| '''Linux''' users can also install '''Jmol''' using '''Ubuntu Software Center '''or''' Synaptic Package Manager.'''
  
  
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* No special hardware is required for high quality 3D-rendering.
 
* No special hardware is required for high quality 3D-rendering.
  
−
* If you are connected to internet you can directly  
+
* If you are connected to internet you can directly load models on '''Jmol '''panel from  
−
 
+
**'''PubChem''' and  
−
load models on '''Jmol '''panel from '''PubChem''' and '''PDB databases'''.
+
**'''PDB databases'''.
  
 
|-
 
|-
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||
 
||
  
−
* High quality 3D images can be produced,
+
* High quality 3D images can be produced, they can be used in publications and presentations
−
 
+
−
they can be used in publications and presentations
+
  
 
* View simulated '''proton and carbon 13 NMR spectra '''for molecules.  
 
* View simulated '''proton and carbon 13 NMR spectra '''for molecules.  
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* Molecular modelling
 
* Molecular modelling
 
* Animation of molecules
 
* Animation of molecules
−
 
  
 
|-
 
|-
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Show the tutorial clipping of '''Introduction to Jmol Application''' tutorial.
 
Show the tutorial clipping of '''Introduction to Jmol Application''' tutorial.
−
|| The first tutorial is '''Introduction to Jmol Application''',
+
|| The first tutorial is '''Introduction to Jmol Application'''.
  
  
 
It explains various features available on '''Jmol '''window.  
 
It explains various features available on '''Jmol '''window.  
−
 
  
 
* Create models of simple organic molecules.
 
* Create models of simple organic molecules.
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Show the tutorial clipping of “Create and Edit” tutorial.
 
Show the tutorial clipping of “Create and Edit” tutorial.
 
|| Next tutorial '''Create and Edit Molecular Models''' explains how to
 
|| Next tutorial '''Create and Edit Molecular Models''' explains how to
−
 
  
 
* Add functional group
 
* Add functional group
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'''Modify Display and View'''
 
'''Modify Display and View'''
−
 
  
 
Show the tutorial clipping of '''Modify Display and View''' tutorial.
 
Show the tutorial clipping of '''Modify Display and View''' tutorial.
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Show the tutorial clipping of '''Measurements and labeling'''
 
Show the tutorial clipping of '''Measurements and labeling'''
 
|| '''Next tutorial Measurements and Labeling''' tutorial explains,  
 
|| '''Next tutorial Measurements and Labeling''' tutorial explains,  
−
 
  
 
* How to measure bond lengths, bond angles and dihedral angles for a model.
 
* How to measure bond lengths, bond angles and dihedral angles for a model.
Line 491: Line 478:
 
Show the tutorial clipping of '''Script console and Script commands'''
 
Show the tutorial clipping of '''Script console and Script commands'''
 
|| Next tutorial '''Script Console and Script Commands''' explains  
 
|| Next tutorial '''Script Console and Script Commands''' explains  
−
 
  
 
* How to use script console and write script commands.
 
* How to use script console and write script commands.
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Show the tutorial clipping of '''Surface and orbitals'''.
 
Show the tutorial clipping of '''Surface and orbitals'''.
 
|| Next tutorial '''Surfaces and Orbitals '''demonstrates how to-
 
|| Next tutorial '''Surfaces and Orbitals '''demonstrates how to-
−
 
  
 
* show surfaces, create models of aromatic molecules, atomic orbitals and molecular orbitals.
 
* show surfaces, create models of aromatic molecules, atomic orbitals and molecular orbitals.
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Show the tutorial clipping of “Structures from Database”
 
Show the tutorial clipping of “Structures from Database”
 
|| Next tutorial '''Structures from Database '''explains-
 
|| Next tutorial '''Structures from Database '''explains-
−
 
  
 
* How to load structures directly from chemical structure database such as '''PubChem'''.  
 
* How to load structures directly from chemical structure database such as '''PubChem'''.  
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'''Crystal structure and Unit Cell'''
 
'''Crystal structure and Unit Cell'''
 
|| Next tutorial '''Crystal structure and Unit Cell '''shows demonstration of-
 
|| Next tutorial '''Crystal structure and Unit Cell '''shows demonstration of-
−
 
  
 
* Download and open '''CIF''' files in Jmol.
 
* Download and open '''CIF''' files in Jmol.
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Show the tutorial clipping of '''Proteins and macromolecules''' and “3D models of Enzymes”
 
Show the tutorial clipping of '''Proteins and macromolecules''' and “3D models of Enzymes”
 
|| Next tutorial,''' Proteins and macromolecules '''tutorial demonstrates how to  
 
|| Next tutorial,''' Proteins and macromolecules '''tutorial demonstrates how to  
−
 
  
 
* Download '''pdb''' files from database.
 
* Download '''pdb''' files from database.
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Show the tutorial clipping of “Plane of symmetry and point-groups”  
 
Show the tutorial clipping of “Plane of symmetry and point-groups”  
 
|| Next tutorial '''3D Models of Enzymes''' explains how to-
 
|| Next tutorial '''3D Models of Enzymes''' explains how to-
−
 
  
 
* Modify the display of secondary structure.
 
* Modify the display of secondary structure.
 
* Highlight amino acid residues and substrate.
 
* Highlight amino acid residues and substrate.
−
* View Ramachandran plot for proteins.
+
* View '''Ramachandran''' plot for proteins.
  
 
Here is the video clipping of this tutorial.  
 
Here is the video clipping of this tutorial.  
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Show the tutorial clipping of '''Animation using Script Commands '''
 
Show the tutorial clipping of '''Animation using Script Commands '''
 
|| Next tutorial '''Animation using Script Commands''' demonstrates  
 
|| Next tutorial '''Animation using Script Commands''' demonstrates  
−
 
  
 
* Animation using '''script commands'''.
 
* Animation using '''script commands'''.
Line 619: Line 599:
 
|| As an assignment-
 
|| As an assignment-
  
−
1. Explore Jmol Application interface.
+
#Explore Jmol Application interface.
−
 
+
#On the '''Jmol Wiki''' main page, explore '''Jmol Documentation''' page.
−
2. On the '''Jmol Wiki''' main page, explore '''Jmol Documentation''' page.
+
  
 
|-
 
|-
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|| The '''Spoken Tutorial Project '''team:
 
|| The '''Spoken Tutorial Project '''team:
  
−
* conducts workshops using spoken tutorials and</nowiki>
+
* conducts workshops using spoken tutorials and
  
−
* gives certificates on passing online tests.</nowiki>
+
* gives certificates on passing online tests.
  
 
For more details, please write to us.
 
For more details, please write to us.

Latest revision as of 18:43, 21 May 2019


Visual Cue Narration
Slide Number 1

Title Slide

Welcome to this tutorial on Overview of Jmol Application.
Slide Number 2

Learning Objectives

In this tutorial we will learn,
  • About Jmol Application.
  • Download and run Jmol Application on Linux Operating System.
  • Uses and advantages.
  • Play video clippings of Jmol Application tutorials available on our website.
Slide Number 3

System Requirement

To record this tutorial, I am using,
  • Ubuntu Linux OS version 14.04
  • Java (JVM) version 1. 8
  • Firefox web browser 54.0, and
  • A working internet connection
Slide Number 4

Pre-requisites

To follow this tutorial you should have knowledge of high school chemistry.
Slide Number 5

About Jmol Application


About Jmol Application.

Jmol is an open source 3D viewer for:

  • Chemical structures
  • Biomolecules
  • Crystal structures and
  • Materials.

It runs on Windows, Mac, Linux operating systems and Android devices.

Slide Number 6

About Jmol Application


It can be used to create and edit models of chemical structures.


Jmol is used by students, educators, and researchers in the fields of Chemistry and Biochemistry.

Slide Number 7

Official Jmol Website


Here is the official website address for Jmol Application.


http://jmol.sourceforge.net

Open Firefox browser and type

http://jmol.sourceforge.net

Press Enter.

Point to webpage.

Open this link in any web browser.

A web-page opens.

Point to the links. At the top-right corner of the page we see links for
  • Demonstration pages,
  • Documentation,
  • Wiki,
  • Download and others
Click on “Download” link provided at the top right corner of the page. To download Jmol Application, click on the Download link.
Point towards headings.


Scroll down to show each heading.

The Download page opens with headings:

Scroll down to see the details.

  • Downloading Jmol,
  • Requirements
  • Installing and running Jmol
  • Subversion Access
Scroll down to requirements page.

Point to the line standalone Jmol Application requires Java 1.4 or higher.

Scroll up to the Requirements section.

Please note - standalone Jmol Application requires Java 1.4 or higher.

High-light the sentence on the page. If you do not have Java installed on your system, click on the link provided here.

Follow the instructions.

Scroll down, high-light the sentence. Also read instructions for Installing and Running Jmol.
Scroll up, under heading Downloading Jmol, click on Download link. Scroll up the page.

Under the heading Downloading Jmol, click on download link.

Point to the prompt. A new page opens.

A prompt appears that says download will start in a few seconds.

A dialog box appears, click on save file option.

Click on OK button.

After this, a dialog box appears which prompts you to save the file.

Click on Save file option.

Then click on OK button.

Depending on the Internet speed, It may take a few minutes to complete the download.
Open the downloads directory.


Jmol binary.zip file gets downloaded to the Downloads directory.


Point to the file in the directory. Go to the directory where you have downloaded the file.
Right-click and click on Extract Here.


Then extract the contents of the folder.


Right-click on the zip file, from the context menu select Extract Here.

Double-Click on open the folder.

Scroll down.

Double-click on the extracted folder to open it.

Scroll down and find Jmol.jar file.

Cursor on Jmol.jar file. For Windows and Mac, double-click on Jmol.jar file to open the Jmol interface.
Cursor on the window. I am using Ubuntu Linux operating system.


I will show how to run Jmol Application on my system.

Right-click on Jmol.jar file.


From the options in the context menu, I will select Open with Oracle Java 8 Runtime.


Cursor on Jmol window.

Right-click on Jmol.jar file. A context menu opens with options.


I have already installed Java 8 Runtime Environment on my system.


Fom the options in the context menu, I will select Open with Oracle Java 8 Runtime.


Jmol Application interface opens.

Another method to open Jmol interface is through terminal.
Press Ctrl, Alt and T keys simultaneously. Open the terminal by pressing Ctrl, Alt and T keys simultaneously.
At the prompt type, cd Downloads, press Enter.

Then type, jmol-14.29.42

Press Enter.

Navigate to Jmol folder which we had downloaded and extracted earlier.


To do so, at the prompt type cd space Downloads, press Enter.


Then type cd space and the name of the Jmol folder. In my case, it is Jmol hyphen fourteen dot twenty-nine dot four two


You may have a different name depending on the version you have downloaded.


Press Enter.

Then type, java -jar Jmol.jar. Press enter. Then type java space hyphen jar space Jmol.jar


Press Enter.


Jmol Application interface opens.

Slide number 8

Installation on Linux OS


https://spoken-tutorial.org

Linux users can also install Jmol using Ubuntu Software Center or Synaptic Package Manager.


For information on how to use these, please see the Linux series on this website.

Point to Jmol menu bar and toolbar.


Back to Jmol interface.


Many features of Jmol are available in the menus on the menu bar and the toolbar.

Click on Help Menu.


Click on Jmol Wiki.


Close the page.

Click on Help menu.


Here we have link for Jmol Wiki main page.


Click on Jmol Wiki.


If you are connected to the internet Jmol Wiki main page opens in the web browser.

Cursor on the page. This page has detailed information about Jmol and Jsmol.


JSmol is a Java independent version of Jmol.

It runs in any HTML5 web browser.

Point to the links.


Point to all the sections.

This page has links to various pages on the left panel.


The page also has various sections for topics such as

  • About Jmol and JSmol,
  • Installation,
  • Development etc.
Cursor on Jmol/JSmol Community section.

Click on Community and Users link.

The section for Jmol Community has links to

Community and Users and Communities.


Click on Community and Users link.

Cursor on Community page.


Community page opens.

On this page you will find the work description of group of Jmol developers and Jmol users.

Cursor on sub-communities.

I will click on Crystal community.


Different web pages for various sub-communities are available here.

I will click on Crystal community.


Here Jmol users can discuss their experiences in using Jmol for displaying crystal structures.

Please explore these pages according to your interest.

Slide number 9

Advantages of Jmol Application

Advantages of Jmol Application.
  • No special hardware is required for high quality 3D-rendering.
  • If you are connected to internet you can directly load models on Jmol panel from
    • PubChem and
    • PDB databases.
Slide Number 10

Uses of Jmol

Jmol can be effectively used to teach certain topics in Chemistry.

For example:

  • Structure and functional groups.
  • Atomic and Molecular orbitals.
  • Stereochemistry
  • Symmetry and point-groups.
  • Crystal structure and Unit cell.
Slide Number 11

Uses of Jmol Application

  • High quality 3D images can be produced, they can be used in publications and presentations
  • View simulated proton and carbon 13 NMR spectra for molecules.
  • This feature is available in Jmol version 14.0 and above.
Slide Number 12

Uses of Jmol Application

Jmol can also be used to study
  • Structure Activity Relationships
  • Molecular modelling
  • Animation of molecules
Slide Number 13

Video Clippings

We have created a series of tutorials which describe how to use this software.
Slide Number 14

Introduction to Jmol Application


Show the tutorial clipping of Introduction to Jmol Application tutorial.

The first tutorial is Introduction to Jmol Application.


It explains various features available on Jmol window.

  • Create models of simple organic molecules.
  • Energy minimization and
  • Save image.

Here is the video clipping.

Slide Number 15

Create and Edit Molecular Models

Show the tutorial clipping of “Create and Edit” tutorial.

Next tutorial Create and Edit Molecular Models explains how to
  • Add functional group
  • Add and delete bonds
  • Add and delete atoms
  • Pop-up-menu.

Here is the video clipping.

Slide Number 16

Modify Display and View

Show the tutorial clipping of Modify Display and View tutorial.

Next tutorial Modify Display and View explains,
  • How to, modify the view.
  • Change the style of the display.
  • Save the image in various file formats.

Here is the video clipping.

Slide Number 17

Measurements and Labeling


Show the tutorial clipping of Measurements and labeling

Next tutorial Measurements and Labeling tutorial explains,
  • How to measure bond lengths, bond angles and dihedral angles for a model.
  • Label atoms with symbols and number.

Here is the video clipping.

Slide Number 18

Script Console and Script Commands


Show the tutorial clipping of Script console and Script commands

Next tutorial Script Console and Script Commands explains
  • How to use script console and write script commands.

Here is the video clipping.

Slide Number 19

Surfaces and Orbitals


Show the tutorial clipping of Surface and orbitals.

Next tutorial Surfaces and Orbitals demonstrates how to-
  • show surfaces, create models of aromatic molecules, atomic orbitals and molecular orbitals.

Here is the video clipping.

Slide number 20

Structures from Database


Show the tutorial clipping of “Structures from Database”

Next tutorial Structures from Database explains-
  • How to load structures directly from chemical structure database such as PubChem.
  • Convert 2D structures drawn in GChemPaint to 3D models in Jmol

Here is the video clipping.

Slide number 21

Crystal structure and Unit Cell


Show the tutorial clipping of

Crystal structure and Unit Cell

Next tutorial Crystal structure and Unit Cell shows demonstration of-
  • Download and open CIF files in Jmol.
  • Display unit cell and unit cell parameters.
  • Display crystal structures of different crystal systems.

Here is the video clipping.

Slide number 22

Proteins and macromolecules

Show the tutorial clipping of Proteins and macromolecules and “3D models of Enzymes”

Next tutorial, Proteins and macromolecules tutorial demonstrates how to
  • Download pdb files from database.
  • View and modify secondary structure of a protein.

Here is the video clipping of this tutorial.

Slide number 23

3D Models of Enzymes


Show the tutorial clipping of “Plane of symmetry and point-groups”

Next tutorial 3D Models of Enzymes explains how to-
  • Modify the display of secondary structure.
  • Highlight amino acid residues and substrate.
  • View Ramachandran plot for proteins.

Here is the video clipping of this tutorial.

Slide number 24

Symmetry and Point Groups

Show the tutorial clipping of Symmetry and Point Groups

Next tutorial Symmetry and Point Groups demonstrates
  • C2 and C3 rotational axes, reflection planes and point group classification.

Here is the video clipping

Slide number 25

Animation using Script Commands


Show the tutorial clipping of Animation using Script Commands

Next tutorial Animation using Script Commands demonstrates
  • Animation using script commands.
  • Save the animation as GIF file.

Here is the video clipping

Slide Number 26

Summary

Let us summarize,

In this tutorial we have learnt,

  • About Jmol Application.
  • Download and run Jmol Application on Linux OS.
  • Uses and advantages.
  • Play video clippings of Jmol Application tutorials available on our website.
Slide Number 27

Assignment

As an assignment-
  1. Explore Jmol Application interface.
  2. On the Jmol Wiki main page, explore Jmol Documentation page.
Slide Number 28

About Spoken Tutorial project

The video at the following link summarizes the Spoken Tutorial project.

Please download and watch it.

Slide Number 29

Spoken Tutorial workshops

The Spoken Tutorial Project team:
  • conducts workshops using spoken tutorials and
  • gives certificates on passing online tests.

For more details, please write to us.

Slide Number 30

Forum for specific questions:

Do you have questions in THIS Spoken Tutorial?
  • Please visit this site.
  • Choose the minute and second where you have the question.
  • Explain your question briefly.
  • Someone from our team will answer them.
Slide Number 31

Forum for specific questions:

The Spoken Tutorial forum is for specific questions on this tutorial.
  • Please do not post unrelated and general questions on them.
  • This will help reduce the clutter.
  • With less clutter, we can use this discussion as instructional material.
Slide Number 32

Acknowledgement

Spoken Tutorial Project is funded by NMEICT, MHRD, Government of India.

More information on this mission is available at

this link.

Slide number 32 This is Snehalatha from IIT Bombay signing off. Thank you for joining.

Contributors and Content Editors

Nancyvarkey, Snehalathak

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