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

Visual Cue	Narration
Slide Number 1 Title Slide	Welcome to this Overview tutorial on Jmol Application series.
Slide Number 2 Learning Objectives	In this tutorial we will go through, Important features of Jmol Application. Information regarding download and installation on various operating systems. Uses of Jmol Application. We will Play clippings of video tutorials available in Jmol Application series at our website.
Slide Number 3 Pre-requisites	To follow this tutorial you should have knowledge of, High School chemistry Or Basic Organic Chemistry
Slide Number 4 System Requirement	To record this tutorial, I am using, Ubuntu OS version 12.10 Jmol version 14.1.11 Java version 7 and Mozilla Firefox Browser 35.0
Slide Number 5 What is Jmol Application?	About Jmol Application, Jmol is a molecular viewer for three-dimensional chemical structures and macromolecules. Jmol can be used to create and edit 3D models of chemical structures. This software can be used by students, educators, and researchers in chemistry and biochemistry.
Slide Number 6 Important Features	Here are some important features of Jmol. It is a Free and Open Source Software. Works on Windows, Mac Operating System, Linux and also on android devices. It supports all major web browsers. No special hardware is required for high quality 3D-rendering.
Slide Number 7 Important Features	Images can be exported to various file formats: Such as jpg, png, gif, pdf etc. Reads various file formats such as pdb, cif, mol, cml, xyz etc If you are connected to internet you can directly loads models on Jmol panel: From databases such as pubchem for chemical structures. And PDB database for proteins and macromolecules.
Slide Number 8 Important Links	More information about this software is available at the following links. http://jmol.sourceforge.net/ http://www.jmol.org/
Slide Number 9 Uses of Jmol	Uses of Jmol. Jmol can be used: as a teaching tool to explain concepts in chemistry. And for producing high quality 3D images that can be used in print media: such as journals, publications and books. And also for presentations in classrooms and lectures.
Slide Number 10 Uses of Jmol	Jmol can also be used for molecular modelling. And producing animation movies.
Open the below link http://www.umass.edu/molvis/bme3d/ materials/jtat_080510/_docs/slides.htm	Here is the webpage that describes how to incorporate Jmol images in powerpoint presentations.
Slide Number 11 Teaching Chemistry using Jmol.	Jmol can be effectively used to teach certain topics in chemistry which require 3D visualization. At Basic level, topics such as: Structure and functional groups. Atomic and Molecular orbitals.
Slide Number 12 Teaching Chemistry using Jmol.	At advanced levels Jmol can be used to teach topics such as Stereochemistry which involves the study of spatial arrangement of atoms in a molecule. Symmetry and point-groups. Crystal Structure and Unit cell. And Predict proton NMR spectrum for molecules. This feature available in Jmol version 14.0 and above. Jmol can be used to study Structure Activity Relationships.
Slide Number 13 Download and Installation	Lets see how to download and install Jmol. Jmol can be installed on Windows, Mac operating system and on Linux systems. A special version of Jmol for Android devices is available at the link shown below. http://wiki.jmol.org/index.php/Support/Android
Slide number 14 Download and Installation on Linux OS	For Linux operating systems, download using Ubuntu software center or Synaptic package manager. Follow this tutorial in the linux series on our website.
Slide number 15 Download and Installation for	For Windows and Mac operating systems: Open the given link in any web browser. www.jmol.sourceforge.net I will open this link and quickly go through the contents given on the web-page.
Cursor on web-page. Scroll down the page.	This web-page gives a lot of general information about Jmol. Scroll down the page. It gives information about the overview, demonstration pages, features. To download Jmol click on the downloads page. Follow the instructions given on the page to download. Information about installing and running Jmol is also given on this page.
Slide Number 16 Video Clippings	I have created a series of tutorials which describe how to use this software.
Cursor on menu bar and tool bar. Click on the modelkit menu. Show the tutorial clipping of “Introduction to Jmol Application” tutorial.	The first tutorial “Introduction to Jmol Application” has information regarding the various features available on Jmol window. Here is the video clipping of that video.
Show the tutorial clipping of “Create and Edit” tutorial.	To create and edit molecular models, follow the tutorial “Create and Edit”. Here is the clipping.
Show the tutorial clipping of “Measurements and labeling”	We can Measure bond lengths, bond angles and dihedral angles. Here is the video clipping.
Show the tutorial clipping of “Surface and orbitals”	Using Jmol we can show surfaces and create atomic and molecular orbitals. Here is the video clipping.
Show the tutorial clipping of “Plane of symmetry and point-groups”	This video explains how to show Plane of symmetry and point-groups. Here is the video clipping.
Show the tutorial clipping of “Crystal structure and Unit Cell”	Crystal structures and unit cell can be viewed using Jmol.Here is the video clipping.
Show the tutorial clipping of “Proteins and macromolecules”	Here is the video clipping to show proteins and macromolecules in Jmol.
Slide number 17 Simulated H NMR	A simulated H NMR spectrum can be displayed for all the molecules listed in chemical structure database: Starting from Jmol version 14.0 Let me open Jmol window and demonstrate this feature.
Cursor on the panel Go to tools menu, scroll down to “spectra”, then click on “proton spectra”. Scroll down the file menu, click on “add simulation”. In the dialog box, type “nitrobenzene”. Click on ok button.	To view simulated proton NMR: Go to tools menu. Scroll down to “spectra” and click on “spectrum”. The Jspecview window opens. Scroll down the file menu, click on “add simulation” In the dialog box enter the name of the molecule. Let us type “nitrobenzene”, click on ok button. A proton NMR spectrum of nitrobenzene is displayed on the panel. Atoms on the structure are correlated with signals in the spectrum.
Slide Number 18 Animating Vibrations	Certain files include information about molecular vibrations, such as GAMESS .log files and Spartan output files. We can open these files in Jmol and view vibrations.
Open the file CO2-DZV-hess.log	Let me open a log file showing vibrations in carbondioxide molecule.
Open the file C6H6.smol	Here is an animation, showing vibrations in benzene molecule.
Open the file cyclohexane_movie.xyz	Here is the animation showing conformations in cyclohexane molecule.
Slide Number 19 Summary	Let us summarize, In this tutorial we have learnt, Important features of Jmol Application. Information regarding Installation on various operating systems. Uses of Jmol Application.
Slide Number 20 Summary	We have also seen clippings of video tutorials in Jmol Application series. And some animation videos showing vibrations and conformations of cyclohexane.
Slide Number 21 Acknowledgement	The video at the following link summarizes the Spoken Tutorial project. Please download and watch it.
Slide Number 22	The Spoken Tutorial Project Team conducts workshops and gives certificates for those who pass an online test. For more details, please write to us.
Slide number 23	Spoken Tutorial Project is funded by NMEICT, MHRD, Government of India. More information on this Mission is available at the link shown.
Slide number 23	This is Snehalatha from IIT Bombay signing off. Thank you for joining.

Contributors and Content Editors

Nancyvarkey, Snehalathak