UCSF-Chimera/C2/Overview-of-UCSF-Chimera/English-timed

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Time Narration
00:01 Welcome to this tutorial on Overview of UCSF Chimera.
00:07 In this tutorial we will learn,

About UCSF Chimera.

00:14 Download and installation of Chimera on Ubuntu Linux operating system.
00:19 Uses and Advantages

Play video clippings of Chimera available on our website.

00:28 To record this tutorial, I am using,

Ubuntu Linux OS version 14.04

00:35 UCSF Chimera version 1.13
00:40 Mozilla Firefox browser version 54.0, and

A Working internet connection.

00:48 About Chimera,

It is a software for 3D visualization and analysis of molecular structures.

00:57 Chimera is developed by the Resource for Biocomputing, Visualization and Informatics at the University of California, San Francisco.
01:08 It can be downloaded free of charge for academic, government, nonprofit and personal use.
01:16 Runs on Windows, Mac and Linux operating systems.
01:21 This software can be used by academic and industry researchers, educators and students.
01:29 More information about this software is available at the following link
01:34 Open this link in any web browser.
01:38 I have opened the link in Firefox web browser.
01:42 Here you will find information about features and uses of the software.
01:48 On the left-side, under Quick Links, links to various pages are available.
01:54 Click on these links to know more about

Documentation, User's Guide, Command Index etc.

02:02 To download Chimera,

Click on Download link.

02:06 A page opens with various download options.

Scroll-down the page.

02:14 Under Current Production Releases, 64-bit Releases,

you will see a table with links to Installers and Instructions for windows, Mac and Linux operating systems.

02:33 Read the instructions carefully and download the required installer file.
02:39 I am using Linux 64-bit machine.
02:44 So I will click on the installer for Linux 64-bit to download.

Software License agreement page opens.

02:54 Please read the agreement carefully.

Scroll down the page.

03:00 Click on Accept button at the end of the page.
03:04 A dialog-box opens which prompts you to save the file.

Click on Save File button.

03:12 The installer downloads to the Downloads folder.
03:16 To open the terminal, press CTRL + ALT and T keys simultaneously
03:22 Navigate to the chimera installer.

At the prompt type, cd space Downloads press Enter.

03:32 Then type the following command,

sudo space chmod space plus symbol x, in lowercase, followed by the name of the installer file.

03:47 The name of the installer file may be different in your case.

Press Enter.

03:54 You will get a message prompting you to type the system password.

Type the password and press Enter.

04:03 At the prompt type, dot forward slash, followed by the name of the

chimera installer file. Press Enter.

04:16 Again press Enter for the default location.
04:21 For the query, Install desktop menu and icon, type yes

Press Enter.

04:30 Do not change the default option to Install symbolic link.

Number (0)is selected by default. Leave it as such.

04:43 Press Enter.
04:47 After Installation is complete, a command appears at the prompt.

Installation is done.

04:55 Press Enter.
04:58 Check the Desktop for the chimera icon.

Double-click on the chimera icon to open the interface.

05:07 Rapid Access interface opens.

Click on the lightning bolt icon at the bottom-right corner of the window, to switch to Graphics window.

05:19 Molecular structures and other 3D data are displayed in the graphics window.
05:25 The graphics window shows a menu bar across the top with menu headings.
05:32 Click on the menu heading to show the list of items under that heading.
05:38 Click on Help menu.
05:41 Extensive help is available for Chimera.
05:45 Help menu contains,

Search Documentation

User's Guide

Commands Index etc.

05:54 There is a Status bar across the bottom of the window.
05:59 It displays status messages, keyboard shortcuts or icons.
06:06 This software offers the following advantages:

It has set of features accessible through both commands and graphical interface.

06:16 Visualize molecular data on all scales, including large molecular assemblies.
06:24 Production of high-quality images and movies for publication and presentation
06:31 It is designed to accommodate outside development of software extensions
06:38 I have created a series of tutorials which describe how to use this software.
06:44 The first tutorial Structure Manipulation shows,

How to open structures on Chimera window and change the display.

06:56 Here is the video clipping of this tutorial.
07:00 ----Add the audio----
07:18 Next tutorial, Picking and selection shows,

How to Select atoms and residues.

07:27 Change display and modify the structure.
07:32 Here is the video clipping of this tutorial.
07:36 ----Add the audio----
07:54 Next tutorial, Writing commands, shows,

How to change display by writing commands.

08:04 Here is the video clipping of this tutorial.
08:08 ---Add the audio---
08:27 Next tutorial tutorial Surface Properties shows,

surfaces for protein and DNA structures.

08:37 Create images of protein surface coloured by

Amino acid hydrophobicity

And Electrostatic Potential

08:46 Here is the video clipping of this tutorial.
08:51 ---Add the audio---
09:10 Next tutorial Build Structures shows,

How to create peptides and DNA fragments.

09:19 Minimize energy and Join models.

Here is the video clipping of this tutorial.

09:27 ----Add the audio-----
09:47 Next tutroial Structure Analysis explains,

Hydrogen bonds, non-polar interactions and rotamers.

09:58 Here is the video clipping of this tutorial.
10:02 ---Add the audio----
10:17 Next tutorial Superimposing and Morphing explains,

How to Superimpose structures and morph conformations.

10:28 Here is the video clipping of this tutorial.
10:32 ---Add the audio---
10:49 Next tutorial is Attributes shows,

How to change attributes, color, B-factor values and kdHydrophobicity for atoms and residues.

11:03 Here is the video clipping of this tutorial.
11:07 ----Add the audio-----
11:25 Next tutorial Animation shows,

How to create animation and record a movie.

11:34 Here is the video clipping of this tutorial.
11:38 -----Add the audio------
11:54 Axes and Planes tutorial, explains,

About 2D labels, draw arrows and clipping tool.

12:04 Here is the video clipping of this tutorial.
12:08 ----Add the audio----
12:25 Let us summarize,

In this tutorial we have learnt, About UCSF Chimera

12:35 Download and install Chimera on Ubuntu Linux operating system.
12:41 About uses and advantages and

Play video clippings of Chimera available on our website.

12:51 As an assignment,

Install Chimera on your PC.

Explore Chimera interface.

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