UCSF-Chimera/C2/Overview-of-UCSF-Chimera/English-timed
| 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. |
| 13:02 | The video at the following link summarizes the Spoken Tutorial project.
Please download and watch it. |
| 13:10 | The Spoken Tutorial Project team:
conducts workshops using spoken tutorials and gives certificates on passing online tests. |
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| 13:55 | With less clutter, we can use this discussion as instructional material |
| 14:01 | Spoken Tutorial Project is funded by NMEICT, MHRD, Government of India.
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| 14:13 | This is Snehalatha from IIT Bombay. Thank you for joining. |
