Difference between revisions of "UCSF-Chimera/C2/Overview-of-UCSF-Chimera/English"

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(Created page with "{|border=1 ||'''Visual Cue''' ||'''Narration''' |- || '''Slide Number 1''' '''Title Slide''' || Welcome to this tutorial on Overview of '''UCSF Chimera'''. |- || '''Slide Nu...")
 
 
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||'''Visual Cue'''
 
||'''Visual Cue'''
 
||'''Narration'''
 
||'''Narration'''
 
 
|-
 
|-
 
|| '''Slide Number 1'''
 
|| '''Slide Number 1'''
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It is a software for 3D visualization and analysis of molecular structures.
 
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'''
 
|| '''Slide Number 5'''
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|| This software can be used by academic and  
 
|| 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
 
More information about this software is available at the following link
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Here you will find information about features and uses of the software.
 
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  
 
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,
 
|| To download Chimera,
  
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Scroll-down the page.
 
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.
 
Point to installers and Instructions for windows, mac and linux OS.
 
|| Under '''Current Production Releases''', '''64-bit Releases''',  
 
|| 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.
 
|| Point to Instructions.
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|| I am using '''Linux 64-bit''' machine.
 
|| 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.
 
|| Scroll down to requirements page, click '''Accept''' button at the end of the page.
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|-
 
|-
|| 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.
 
Show installer file in Downloads folder.
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|| Again press '''Enter''' for the default location.
 
|| 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.'''
 
Press '''Enter.'''
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|| Check the '''Desktop''' for the chimera icon.
 
|| 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.
 
|| Click on the lightning bolt icon at the bottom right corner of the window.
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Click on the first menu then, Hover the mouse on each menu.
 
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.
 
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 the menu heading to show the list of items under that heading.
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|| Click on '''Help '''menu.
 
|| Click on '''Help '''menu.
  
Extensive help is available for '''Chimera.'''
+
Extensive help is available for '''Chimera'''.
  
 
'''Help''' menu contains,
 
'''Help''' menu contains,
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'''User's Guide '''
 
'''User's Guide '''
  
'''Commands Index etc.'''
+
'''Commands Index''' etc.
 
|-
 
|-
 
|| Cursor on Status bar and icons.
 
|| Cursor on Status bar and icons.
 
|| There is a Status bar across the bottom of the window.
 
|| 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'''
 
|| '''Slide Number 7'''
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||The first tutorial '''Structure Manipulation''' shows,
 
||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.  
 
Here is the video clipping of this tutorial.  
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surfaces for protein and '''DNA''' structures.  
 
surfaces for protein and '''DNA''' structures.  
  
Create images of protein surface colored by
+
Create images of protein surface coloured by
  
 
'''Amino acid hydrophobicity'''  
 
'''Amino acid hydrophobicity'''  
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||Next tutorial '''Build Structures '''shows,
 
||Next tutorial '''Build Structures '''shows,
 
  
 
How to create '''peptides''' and '''DNA''' fragments.  
 
How to create '''peptides''' and '''DNA''' fragments.  
 
  
 
'''Minimize energy''' and Join models.  
 
'''Minimize energy''' and Join models.  
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|| Next tutorial '''Attributes''' shows,
 
|| 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.
 
Here is the video clipping of this tutorial.
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About UCSF Chimera
 
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.
 
Play video clippings of Chimera available on our website.
Line 526: Line 521:
 
|| Do you have questions in THIS Spoken Tutorial?
 
|| 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
+
 
 +
* Explain your question briefly
 +
 
 +
* Someone from our team will answer them
 
|-
 
|-
 
|| '''Slide Number 25'''
 
|| '''Slide Number 25'''
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Please do not post unrelated and general questions on them
 
Please do not post unrelated and general questions on them
 
This will help reduce the clutter
 
This will help reduce the clutter
 +
 
With less clutter, we can use this discussion as instructional material
 
With less clutter, we can use this discussion as instructional material
 
|-
 
|-

Latest revision as of 17:23, 6 September 2018

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
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.

Contributors and Content Editors

Snehalathak