Welcome to this tutorial on Overview of Jmol Application.
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.
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
To follow this tutorial you should have knowledge of high school chemistry.
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.
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.
Here is the official website address for Jmol Application.
Open this link in any web browser. A web-page opens.
At the top-right corner of the page we see links for Demonstration pages, Documentation, Wiki, Download and others
To download Jmol Application, click on the Download link.
The Download page opens with headings:
Scroll down to see the details. Downloading Jmol
Requirements
Installing and running Jmol
Subversion Access
Scroll up to the Requirements section.
Please note - standalone Jmol Application requires Java 1.4 or higher.
If you do not have Java installed on your system, click on the link provided here. Follow the instructions.
Also read instructions for Installing and Running Jmol.
Scroll up the page. Under the heading Downloading Jmol, click on download link.
A new page opens. A prompt appears that says download will start in a few seconds.
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.
Jmol binary.zip file gets downloaded to the Downloads directory.
Go to the directory where you have downloaded the file. Then extract the contents of the folder.
Right-click on the zip file, from the context menu select Extract Here.
Double-click on the extracted folder to open it. Scroll down and find Jmol.jar file.
For Windows and Mac, double-click on Jmol.jar file to open the Jmol interface.
I am using Ubuntu Linux operating system. I will show how to run Jmol Application on my system.
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.
Open the terminal by pressing Ctrl, Alt and T keys simultaneously.
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 space hyphen jar space Jmol.jar Press Enter.
Jmol Application interface opens.
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.
Back to Jmol interface. Many features of Jmol are available in the menus on the menu bar and the toolbar.
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.
This page has detailed information about Jmol and Jsmol.
JSmol is a Java independent version of Jmol.
It runs in any HTML5 web browser.
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.
The section for Jmol Community has links to Community and Users and Communities.
Click on Community and Users link.
Community page opens.
On this page you will find the work description of group of Jmol developers and Jmol users.
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.
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.
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.
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.
Jmol can also be used to study Structure Activity Relationships
Molecular modelling and Animation of molecules
We have created a series of tutorials which describe how to use this software.
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.
Next tutorial Create and Edit Molecular Models explains how to Add functional group
Add and delete atoms and bonds.
Pop-up-menu.
Here is the video clipping.
----Add the audio-----
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.
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.
Next tutorial Script Console and Script Commands explains How to use script console and write script commands.
Here is the video clipping.
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.
------Add the audio------
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.
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.
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.
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.
Next tutorial Symmetry and Point Groups demonstrates
C2 and C3 rotational axes, reflection planes and point group classification. Here is the video clipping
Next tutorial Animation using Script Commands demonstrates Animation using script commands. Save the animation as GIF file.
Here is the video clipping
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.
As an assignment- Explore Jmol Application interface.
On the Jmol Wiki main page, explore Jmol Documentation page.
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