PoojaMoolya: Created page with "{|border=1 ||'''Time''' ||'''Narration''' |- || 00:01 || Welcome to this tutorial on Overview of '''UCSF Chimera'''. |- ||00:07 || In this tutorial we will learn, Ab..."

2019-02-06T05:00:45Z

Created page with "{|border=1 ||'''Time''' ||'''Narration''' |- || 00:01 || Welcome to this tutorial on Overview of '''UCSF Chimera'''. |- ||00:07 || In this tutorial we will learn, Ab..."

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{|border=1
||'''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.

|-
|| 13:19
|| For more details, please write to us.

|-
|| 13:23
|| Do you have questions in THIS Spoken Tutorial?

Please visit this site

|-
|| 13:30
|| Choose the minute and second where you have the question

Explain your question briefly

|-
|| 13:37
|| Someone from our team will answer them

|-
||13:41
|| The Spoken Tutorial forum is for specific questions on this tutorial

|-
|| 13:47
|| Please do not post unrelated and general questions on them

This will help reduce the clutter

|-
|| 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.

More information on this mission is available at this link.

|-
|| 14:13
|| This is Snehalatha from IIT Bombay. Thank you for joining.

|}

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

PoojaMoolya: Created page with "{|border=1 ||'''Time''' ||'''Narration''' |- || 00:01 || Welcome to this tutorial on Overview of '''UCSF Chimera'''. |- ||00:07 || In this tutorial we will learn, Ab..."