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

Visual Cue	Narration
Slide Number 1 Title Slide	Welcome to this tutorial on Overview of UCSF Chimera.
Slide Number 2 Learning Objectives	In this tutorial we will learn, About UCSF Chimera. Download and installation of Chimera on Ubuntu Linux operating system. Uses and Advantages Play video clippings of Chimera available on our website.
Slide Number 3 System Requirement	To record this tutorial, I am using, Ubuntu Linux OS version 14.04 UCSF Chimera version 1.13 Mozilla Firefox browser version 54.0, and a Working internet connection.
Slide Number 4 About Chimera	About Chimera, It is a software for 3D visualization and analysis of molecular structures. Chimera is developed by the Resource for Biocomputing, Visualization and Informatics at the University of California, San Francisco.
Slide Number 5 About Chimera	It can be downloaded free of charge for academic, government, nonprofit and personal use. Runs on Windows, Mac and Linux operating systems.
Slide Number 6 Important Links http://www.cgl.ucsf.edu/chimera	This software can be used by academic and industry researchers, educators and students. More information about this software is available at the following link https://www.cgl.ucsf.edu/chimera/ Open this link in any web browser.
Open the link on Firefox web browser. Point towards headings on left-side of web-page.	I have opened the link in Firefox web browser. Here you will find information about features and uses of the software. On the left-side, under Quick Links, links to various pages are available. Click on these links to know more about Documentation, User's Guide, Command Index etc.
Click on Download link provided at the left corner of the page.	To download Chimera, Click on Download link. A page opens with various download options. Scroll-down the page.
Cursor on Current Production Releases, in 64-bit Releases table. Point to installers and Instructions for windows, mac and linux OS.	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.
Point to Instructions.	Read the instructions carefully and download the required installer file.
For Linux-64 bit platform, under installer column, Click on chimera-1.13-linux_x86_64.bin	I am using Linux 64-bit machine. I will click on the installer for Linux 64-bit to download. Software License agreement page opens.
Scroll down to requirements page, click Accept button at the end of the page.	Please read the agreement carefully. Scroll down the page. Click on Accept button at the end of the page.
In the dialog-box, Opening chimera-1.13-linux_x86_64.bin , click on Save File option. Show installer file in Downloads folder.	A dialog-box opens which prompts you to save the file. Click on Save File button. The installer downloads to the Downloads folder.
Press CTRL ALT and T keys simultaneously. At the prompt type, cd Downloads press enter.	To open the terminal, press CTRL + ALT and T keys simultaneously Navigate to the chimera installer. At the prompt type, cd space Downloads press Enter.
At the prompt type,sudo chmod +x chimera-1.13-linux_x86_64.bin press enter	Then type the following command, sudo space chmod space plus symbol x, in lowercase, followed by the name of the installer file. The name of the installer file may be different in your case. chimera-1.13-linux_x86_64.bin press Enter.
Type the password and press enter.	You will get a message prompting you to type the system password. Type the password and press Enter.
At the prompt type, ./chimera-1.13-linux_x86_64.bin Press Enter.	At the prompt type, dot forward slash, followed by the name of the chimera installer file. ./chimera-1.13-linux_x86_64.bin Press Enter.
Type, yes and Press enter	Again press Enter for the default location. For the query, Install desktop menu and icon, type yes Press Enter.
Number (0)is selected by default. Leave it as such. Press enter.	Do not change the default option to Install symbolic link. Number (0)is selected by default. Leave it as such. Press Enter.
Press Enter. Highlight Installation is done, press return.	After Installation is complete, a command appears at the prompt. Installation is done. Press Enter.
Point to the Desktop. Double-click on chimera icon.	Check the Desktop for the chimera icon. Double-click on the chimera icon to open the interface.
Click on the lightning bolt icon at the bottom right corner of the window. The main Chimera graphics window opens. Sometimes Rapid Access interface may opens first.	Rapid Access interface opens. Click on the lightning bolt icon at the bottom-right corner of the window, to switch to Graphics window.
Cursor on the graphics window. Cursor on the menu bar. Click on the first menu then, Hover the mouse on each menu.	Molecular structures and other 3D data are displayed in the graphics window. The graphics window shows a menu bar across the top with menu headings. Click on the menu heading to show the list of items under that heading.
Click on Help menu. Scroll down.	Click on Help menu. Extensive help is available for Chimera. Help menu contains, Search Documentation User's Guide Commands Index etc.
Cursor on Status bar and icons.	There is a Status bar across the bottom of the window. It displays status messages, keyboard shortcuts or icons.
Slide Number 7 Advantages	This software offers the following advantages: It has set of features accessible through both commands and graphical interface. Visualize molecular data on all scales, including large molecular assemblies.
Slide Number 8 Advantages	Production of high-quality images and movies for publication and presentation Designed to accommodate outside development of software extensions
Slide Number 9 Video Clippings	I have created a series of tutorials which describe how to use this software.
Slide Number 10 Structure Manipulation Open a structure on the Chimera window. Move, rotate and zoom the structure. Scale and clip And change the display. Show the tutorial clipping of Structure Manipulation video.	The first tutorial Structure Manipulation shows, How to open structures on Chimera window and change the display. Here is the video clipping of this tutorial.
Slide Number 11 Picking and selection Show labels for atoms and residues. Select atoms and residues using Select menu or by Picking. Change the color and display of the residues. Add, delete or change atoms Rotate bonds Show the tutorial clipping of Picking and selection video.	Next tutorial, Picking and selection shows, How to Select atoms and residues. Change display and modify the structure. Here is the video clipping of this tutorial.
Slide Number 12 Writing commands Change the display to atoms. Show and hide ribbons. Change the color of the amino acid residues. Label individual residues. Show the tutorial clipping of Writing commands video.	Next tutorial, Writing commands, shows, How to change display by writing commands. Here is the video clipping of this tutorial.
Slide Number 13 Surface Properties Show surfaces for protein and DNA structures. Create images of protein surface colored by: Amino acid hydrophobicity And Electrostatic Potential Show the tutorial clipping of Surface Properties video.	Next tutorial tutorial Surface Properties shows, surfaces for protein and DNA structures. Create images of protein surface coloured by Amino acid hydrophobicity And Electrostatic Potential Here is the video clipping of this tutorial.
Slide Number 14 Build Structures Create structures of small molecules, peptides and DNA fragments. Modify structure, Minimize energy, and Join models	Next tutorial Build Structures shows, How to create peptides and DNA fragments. Minimize energy and Join models. Here is the video clipping of this tutorial.
Slide Number 15 Structure Analysis Measure distance between atoms in the structure Show Hydrogen bonds Identify non-polar interactions And rotate bonds in the residues to get different rotamers.	Structure Analysis tutorial explains, Hydrogen bonds, non-polar interactions and rotamers. Here is the video clipping of this tutorial.
Slide Number 16 Superimposing and Morphing Superimpose and compare different structures of the same protein. Morph conformations and create a trajectory.	Next tutorial Superimposing and Morphing explains, How to Superimpose structures and morph conformations. Here is the video clipping of this tutorial.
Slide Number 17 Attributes Change attributes of atoms, residues and models. Color atoms in a protein according to B-factor values. Color residues according to kdHydrophobicity values	Next tutorial Attributes shows, how to change attributes, color, B-factor values and kdHydrophobicity for atoms and residues. Here is the video clipping of this tutorial.
Slide Number 18 Animation Adjust background lighting and effects. Create scenes for animation. Place scenes along a timeline. Record a movie of the resulting animation.	Next tutorial Animation shows, How to create animation and record a movie. Here is the video clipping of this tutorial.
Slide Number 19 Axes and Planes Show Axes, Planes and Centroids for structure of Green Fluorescent Protein. Show 2D-Labels. Draw Arrows. Clip a model of Myoglobin using Per-Model clipping tool.	Axes and Planes tutorial, explains, About 2D labels, draw arrows and clipping tool. Here is the video clipping of this tutorial.
Slide Number 20 Summary	Let us summarize, In this tutorial we have learnt, About UCSF Chimera Download and install Chimera on Ubuntu Linux operating system. About uses and advantages and Play video clippings of Chimera available on our website.
Slide Number 21 Assignment	As an assignment, Install Chimera on your PC. Explore Chimera interface.
Slide Number 22 About Spoken Tutorial project	The video at the following link summarizes the Spoken Tutorial project. Please download and watch it.
Slide Number 23 Spoken Tutorial workshops	The Spoken Tutorial Project team: conducts workshops using spoken tutorials and gives certificates on passing online tests.</nowiki> For more details, please write to us.
Slide Number 24 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
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Slide Number 26 Acknowledgement	Spoken Tutorial Project is funded by NMEICT, MHRD, Government of India. More information on this mission is available at this link.
Slide number 26	This is Snehalatha from IIT Bombay. Thank you for joining.

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Snehalathak