Jmol-Application/C2/Overview-of-Jmol-Application/English

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- Explore Jmol Application interface. 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