Difference between revisions of "UCSF-Chimera/C2/Overview-of-UCSF-Chimera/English"
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||'''Visual Cue''' | ||'''Visual Cue''' | ||
||'''Narration''' | ||'''Narration''' | ||
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|| '''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''' | ||
| Line 60: | Line 59: | ||
|| 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 | ||
| Line 75: | Line 74: | ||
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 | + | 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 | + | || Click on '''Download''' link provided at the left corner of the page. |
|| To download Chimera, | || To download Chimera, | ||
| Line 90: | Line 89: | ||
Scroll-down the page. | Scroll-down the page. | ||
|- | |- | ||
| − | || Cursor on | + | || 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 | + | you will see a table with links to '''Installers and Instructions''' for '''windows''', '''Mac''' and '''Linux ''' operating systems. |
|- | |- | ||
|| Point to Instructions. | || Point to Instructions. | ||
| Line 106: | Line 105: | ||
|| 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. | ||
| Line 118: | Line 117: | ||
|- | |- | ||
| − | || In the dialog-box, '''Opening | + | || 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. | ||
| Line 183: | Line 182: | ||
|| Again press '''Enter''' for the default location. | || Again press '''Enter''' for the default location. | ||
| − | For the query, ''' | + | For the query, '''Install desktop menu and icon''', type '''yes ''' |
Press '''Enter.''' | Press '''Enter.''' | ||
| Line 213: | Line 212: | ||
|| 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. | ||
| Line 232: | Line 231: | ||
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 | + | || 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. | ||
| Line 245: | Line 242: | ||
|| 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, | ||
| Line 253: | Line 250: | ||
'''User's Guide ''' | '''User's Guide ''' | ||
| − | '''Commands Index | + | '''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''' | ||
| Line 298: | Line 295: | ||
||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. | ||
| Line 366: | Line 363: | ||
surfaces for protein and '''DNA''' structures. | surfaces for protein and '''DNA''' structures. | ||
| − | Create images of protein surface | + | Create images of protein surface coloured by |
'''Amino acid hydrophobicity''' | '''Amino acid hydrophobicity''' | ||
| Line 384: | Line 381: | ||
||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. | ||
| Line 437: | Line 432: | ||
|| 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. | ||
| Line 488: | Line 483: | ||
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''' | ||
| Line 538: | Line 536: | ||
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 |
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,
The name of the installer file may be different in your case.
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.
|
| 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
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
|
| 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?
|
| 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. |
