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

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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.


Downloading Jmol

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.
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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.

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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.

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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.

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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.

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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.

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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.
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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
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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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Contributors and Content Editors

PoojaMoolya, Pratik kamble, Sandhya.np14