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

Snehalathak at 11:53, 6 September 2018

2018-09-06T11:53:39Z

Snehalathak: Created page with "{|border=1 ||'''Visual Cue''' ||'''Narration''' |- || '''Slide Number 1''' '''Title Slide''' || Welcome to this tutorial on Overview of '''UCSF Chimera'''. |- || '''Slide Nu..."

2018-09-06T11:10:42Z

Created page with "{|border=1 ||'''Visual Cue''' ||'''Narration''' |- || '''Slide Number 1''' '''Title Slide''' || Welcome to this tutorial on Overview of '''UCSF Chimera'''. |- || '''Slide Nu..."

New page

{|border=1
||'''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/ 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 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 colored 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

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
|-
|| '''Slide Number 25'''

'''Forum for specific questions:'''
|| The Spoken Tutorial forum is for specific questions on this tutorial

Please do not post unrelated and general questions on them
This will help reduce the clutter
With less clutter, we can use this discussion as instructional material
|-
|| '''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.

|}

@@ Line 2: / Line 2: @@
 ||'''Visual Cue'''
 ||'''Narration'''
 |-
 || '''Slide Number 1'''
@@ Line 44: / Line 43: @@
 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'''.
+'''Chimera''' is developed by the '''Resource for Biocomputing, Visualization and Informatics''' at the '''University of California''', '''San Francisco'''.
 |-
 || '''Slide Number 5'''
@@ Line 60: / Line 59: @@
 || This software can be used by academic and
-industry researchers, educators and students .
+industry researchers, educators and students.
 More information about this software is available at the following link
@@ Line 75: / Line 74: @@
 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.
+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.
+'''Documentation, User's Guide, Command Index''' etc.
 |-
-|| Click on “'''Download'''” link provided at the left corner of the page.
+|| Click on '''Download''' link provided at the left corner of the page.
 || To download Chimera,
@@ Line 90: / Line 89: @@
 Scroll-down the page.
 |-
-|| Cursor on “Current Production Releases” , in 64-bit Releases table.
+|| 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.
+you will see a table with links to '''Installers and Instructions''' for '''windows''', '''Mac''' and '''Linux ''' operating systems.
 |-
 || Point to Instructions.
@@ Line 106: / Line 105: @@
 || I am using '''Linux 64-bit''' machine.
-I will click on the installer for '''Linux 64-bit '''to download.
+I will click on the installer for '''Linux 64-bit''' to download.
-'''Software License agreement '''page opens.
+'''Software License agreement''' page opens.
 |-
 || Scroll down to requirements page, click '''Accept''' button at the end of the page.
@@ Line 118: / Line 117: @@
 |-
-|| In the dialog-box, '''Opening''' '''chimera-1.13-linux_x86_64.bin , '''click on''' Save File '''option.
+|| In the dialog-box, '''Opening chimera-1.13-linux_x86_64.bin''' , click on '''Save File''' option.
 Show installer file in Downloads folder.
@@ Line 183: / Line 182: @@
 || Again press '''Enter''' for the default location.
-For the query, '''install desktop menu and icon''', type '''yes '''
+For the query, '''Install desktop menu and icon''', type '''yes '''
 Press '''Enter.'''
@@ Line 213: / Line 212: @@
 || Check the '''Desktop''' for the chimera icon.
-Double-click on chimera icon to open the interface.
+Double-click on the '''chimera''' icon to open the interface.
 |-
 || Click on the lightning bolt icon at the bottom right corner of the window.
@@ Line 232: / Line 231: @@
 Click on the first menu then, Hover the mouse on each menu.
-|| Molecular structures and other 3D data are displayed in the '''''graphics window'''''.
+|| 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.
@@ Line 245: / Line 242: @@
 || Click on '''Help '''menu.
-Extensive help is available for '''Chimera.'''
+Extensive help is available for '''Chimera'''.
 '''Help''' menu contains,
@@ Line 253: / Line 250: @@
 '''User's Guide '''
-'''Commands Index etc.'''
+'''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'''.
+It displays '''status messages''', '''keyboard shortcuts''' or '''icons'''.
 |-
 || '''Slide Number 7'''
@@ Line 298: / Line 295: @@
 ||The first tutorial '''Structure Manipulation''' shows,
-How to open structures on Chimera window and change the display.
+How to open structures on '''Chimera''' window and change the display.
 Here is the video clipping of this tutorial.
@@ Line 366: / Line 363: @@
 surfaces for protein and '''DNA''' structures.
-Create images of protein surface colored by
+Create images of protein surface coloured by
 '''Amino acid hydrophobicity'''
@@ Line 384: / Line 381: @@
 ||Next tutorial '''Build Structures '''shows,
 How to create '''peptides''' and '''DNA''' fragments.
 '''Minimize energy''' and Join models.
@@ Line 437: / Line 432: @@
 || Next tutorial '''Attributes''' shows,
-how to change '''attributes''', color, '''B-factor values '''and '''kdHydrophobicity '''for '''atoms''' and '''residues'''.
+how to change '''attributes''', color, '''B-factor values '''and '''kdHydrophobicity''' for '''atoms''' and '''residues'''.
 Here is the video clipping of this tutorial.
@@ Line 488: / Line 483: @@
 About UCSF Chimera
-Download and install Chimera on Ubuntu Linux operating system.
+Download and install '''Chimera''' on Ubuntu Linux operating system.
-About uses and advantages
+About uses and advantages and
 Play video clippings of Chimera available on our website.
@@ Line 526: / Line 521: @@
 || Do you have questions in THIS Spoken Tutorial?
-Please visit this site
+* Please visit this site
 Choose the minute and second where you have the question
-Explain your question briefly
+* Choose the minute and second where you have the question
 Someone from our team will answer them
 |-
 || '''Slide Number 25'''
@@ Line 538: / Line 536: @@
 Please do not post unrelated and general questions on them
 This will help reduce the clutter
 With less clutter, we can use this discussion as instructional material
 |-