Jmol-Application/C2/Overview-of-Jmol-Application/English-timed
| Time | Narration |
| 00:01 | Welcome to this tutorial on Overview of Jmol Application. |
| 00:06 | In this tutorial we will learn,
About Jmol Application. |
| 00:12 | Download and run Jmol Application on Linux Operating System. |
| 00:18 | Uses and advantages. |
| 00:21 | Play video clippings of Jmol Application tutorials available on our website. |
| 00:28 | To record this tutorial, I am using,
Ubuntu Linux OS version 14.04 |
| 00:35 | Java (JVM) version 1. 8 |
| 00:38 | Firefox web browser 54.0 and A working internet connection |
| 00:45 | To follow this tutorial you should have knowledge of high school chemistry. |
| 00:50 | About Jmol Application.
Jmol is an open source 3D viewer for: Chemical structures, Biomolecules, Crystal structures and Materials. |
| 01:02 | It runs on Windows, Mac, Linux operating systems and Android devices. |
| 01:09 | It can be used to create and edit models of chemical structures. |
| 01:15 | Jmol is used by students, educators, and researchers in the fields of Chemistry and Biochemistry. |
| 01:23 | Here is the official website address for Jmol Application. |
| 01:28 | Open this link in any web browser.
A web-page opens. |
| 01:35 | At the top-right corner of the page we see links for
Demonstration pages, Documentation, Wiki, Download and others |
| 01:48 | To download Jmol Application, click on the Download link. |
| 01:53 | The Download page opens with headings: |
| 01:57 | Scroll down to see the details.
|
| 02:02 | Requirements |
| 02:04 | Installing and running Jmol |
| 02:08 | Subversion Access |
| 02:11 | Scroll up to the Requirements section. |
| 02:14 | Please note - standalone Jmol Application requires Java 1.4 or higher. |
| 02:21 | If you do not have Java installed on your system, click on the link provided here.
Follow the instructions. |
| 02:30 | Also read instructions for Installing and Running Jmol. |
| 02:36 | Scroll up the page.
Under the heading Downloading Jmol, click on download link. |
| 02:44 | A new page opens.
A prompt appears that says download will start in a few seconds. |
| 02:53 | After this, a dialog box appears which prompts you to save the file. |
| 02:59 | Click on Save file option.
Then click on OK button. |
| 03:05 | Depending on the Internet speed, It may take a few minutes to complete the download. |
| 03:12 | Jmol binary.zip file gets downloaded to the Downloads directory. |
| 03:18 | Go to the directory where you have downloaded the file. Then extract the contents of the folder. |
| 03:25 | Right-click on the zip file, from the context menu select Extract Here. |
| 03:33 | Double-click on the extracted folder to open it.
Scroll down and find Jmol.jar file. |
| 03:42 | For Windows and Mac, double-click on Jmol.jar file to open the Jmol interface. |
| 03:50 | I am using Ubuntu Linux operating system.
I will show how to run Jmol Application on my system. |
| 03:59 | Right-click on Jmol.jar file. A context menu opens with options. |
| 04:07 | I have already installed Java 8 Runtime Environment on my system. |
| 04:13 | Fom the options in the context menu, I will select Open with Oracle Java 8 Runtime.
Jmol Application interface opens. |
| 04:25 | Another method to open Jmol interface is through terminal. |
| 04:30 | Open the terminal by pressing Ctrl, Alt and T keys simultaneously. |
| 04:36 | Navigate to Jmol folder which we had downloaded and extracted earlier. |
| 04:42 | To do so, at the prompt type cd space Downloads, press Enter. |
| 04:50 | Then type cd space and the name of the Jmol folder. |
| 04:56 | In my case, it is Jmol hyphen fourteen dot twenty-nine dot four two |
| 05:03 | You may have a different name depending on the version you have downloaded.
Press Enter. |
| 05:10 | Then type java space hyphen jar space Jmol.jar
Press Enter. |
| 05:19 | Jmol Application interface opens. |
| 05:24 | Linux users can also install Jmol using Ubuntu Software Center or Synaptic Package Manager. |
| 05:32 | For information on how to use these, please see the Linux series on this website. |
| 05:39 | Back to Jmol interface.
Many features of Jmol are available in the menus on the menu bar and the toolbar. |
| 05:52 | Click on Help menu. |
| 05:54 | Here we have link for Jmol Wiki main page.
Click on Jmol Wiki. |
| 06:02 | If you are connected to the internet Jmol Wiki main page opens in the web browser. |
| 06:08 | This page has detailed information about Jmol and Jsmol. |
| 06:14 | JSmol is a Java independent version of Jmol. |
| 06:19 | It runs in any HTML5 web browser. |
| 06:24 | This page has links to various pages on the left panel. |
| 06:29 | The page also has various sections for topics such as
About Jmol and JSmol, Installation, Development etc. |
| 06:40 | The section for Jmol Community has links to
Community and Users and Communities. |
| 06:47 | Click on Community and Users link. |
| 06:51 | Community page opens. |
| 06:54 | On this page you will find the work description of group of Jmol developers and Jmol users. |
| 07:02 | Different web pages for various sub-communities are available here.
I will click on Crystal community. |
| 07:10 | Here Jmol users can discuss their experiences in using Jmol for displaying crystal structures. |
| 07:19 | Please explore these pages according to your interest. |
| 07:25 | Advantages of Jmol Application.
No special hardware is required for high quality 3D-rendering. |
| 07:35 | If you are connected to internet you can directly load models on Jmol panel from
PubChem and PDB databases. |
| 07:44 | Jmol can be effectively used to teach certain topics in Chemistry. |
| 07:49 | For example: Structure and functional groups. |
| 07:53 | Atomic and Molecular orbitals. |
| 07:56 | Stereochemistry |
| 07:58 | Symmetry and point-groups. |
| 08:01 | Crystal structure and Unit cell. |
| 08:04 | High quality 3D images can be produced, they can be used in publications and presentations |
| 08:13 | View simulated proton and carbon 13 NMR spectra for molecules. |
| 08:19 | This feature is available in Jmol version 14.0 and above. |
| 08:25 | Jmol can also be used to study
Structure Activity Relationships |
| 08:31 | Molecular modelling
and Animation of molecules |
| 08:36 | We have created a series of tutorials which describe how to use this software. |
| 08:42 | The first tutorial is Introduction to Jmol Application. |
| 08:47 | It explains various features available on Jmol window. |
| 08:52 | Create models of simple organic molecules.
Energy minimization and Save image. |
| 09:01 | Here is the video clipping. |
| -----Add the audio---- | |
| 09:21 | Next tutorial Create and Edit Molecular Models explains how to
Add functional group |
| 09:29 | Add and delete atoms and bonds. |
| 09:32 | Pop-up-menu. |
| 09:33 | Here is the video clipping. |
| 09:37 | ----Add the audio----- |
| 09:51 | Next tutorial Modify Display and View explains,
How to, modify the view. |
| 09:59 | Change the style of the display. |
| 10:02 | Save the image in various file formats.
Here is the video clipping. |
| -----Add the audio------ | |
| 10:28 | Next tutorial Measurements and Labeling tutorial explains, |
| 10:33 | How to measure bond lengths, bond angles and dihedral angles for a model. |
| 10:39 | Label atoms with symbols and number.
Here is the video clipping. |
| -----Add the audio----- | |
| 11:04 | Next tutorial Script Console and Script Commands explains
How to use script console and write script commands. |
| 11:14 | Here is the video clipping. |
| 11:34 | Next tutorial Surfaces and Orbitals demonstrates how to-
Show surfaces, create models of aromatic molecules, atomic orbitals and molecular orbitals. |
| 11:46 | Here is the video clipping. |
| 11:49 | ------Add the audio------ |
| 12:02 | Next tutorial Structures from Database explains-
How to load structures directly from chemical structure database such as PubChem. |
| 12:13 | Convert 2D structures drawn in GChemPaint to 3D models in Jmol
Here is the video clipping. |
| -----Add the audio------ | |
| 12:42 | Next tutorial Crystal structure and Unit Cell shows demonstration of-
Download and open CIF files in Jmol. |
| 12:52 | Display unit cell and unit cell parameters. |
| 12:56 | Display crystal structures of different crystal systems.
Here is the video clipping. |
| ----Add the audio----- | |
| 13:20 | Next tutorial, Proteins and macromolecules tutorial demonstrates how to
Download pdb files from database. |
| 13:29 | View and modify secondary structure of a protein.
Here is the video clipping of this tutorial. |
| ---Add the Audio---- | |
| 13:52 | Next tutorial 3D Models of Enzymes explains how to-
Modify the display of secondary structure. |
| 14:00 | Highlight amino acid residues and substrate. |
| 14:04 | View Ramachandran plot for proteins. |
| 14:08 | Here is the video clipping. |
| -----Add the audio----- | |
| 14:22 | Next tutorial Symmetry and Point Groups demonstrates |
| 14:27 | C2 and C3 rotational axes, reflection planes and point group classification.
Here is the video clipping |
| 14:51 | Next tutorial Animation using Script Commands demonstrates
Animation using script commands. Save the animation as GIF file. |
| 15:02 | Here is the video clipping |
| ----Add the Audio-------- | |
| 15:23 | Let us summarize,
In this tutorial we have learnt, About Jmol Application. |
| 15:30 | Download and run Jmol Application on Linux OS.
Uses and advantages. |
| 15:38 | Play video clippings of Jmol Application tutorials available on our website. |
| 15:44 | As an assignment- Explore Jmol Application interface. |
| 15:50 | On the Jmol Wiki main page, explore Jmol Documentation page. |
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