Snehalathak: Created page with " {| style="border-spacing:0;" ! Visual Cue ! Narration |- | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;..."

2015-12-11T05:57:21Z

Created page with " {| style="border-spacing:0;" ! <center>Visual Cue</center> ! <center>Narration</center> |- | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;..."

New page

{| style="border-spacing:0;"
! <center>Visual Cue</center>
! <center>Narration</center>

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 1'''

'''Title Slide'''
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Welcome to this tutorial on '''Structure Manipulation '''using Chimera.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 2'''

'''Learning Objectives'''
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| In this tutorial, we will learn to

* Open a structure on the Chimera window.
* Move, rotate and zoom the structure.
* Scale and clip
* And change the display.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 3'''

'''Pre-requisites'''
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To follow this tutorial you should have knowledge of,

Undergraduate Biochemistry

Or must be familiar with Structural Biology

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 4'''

'''System Requirement'''
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To record this tutorial I am using,

Ubuntu Linux OS version. 14.04

Chimera version 1.10.2

Mozilla firefox browser 35.0

Working internet connection.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 5'''

'''UCSF Chimera'''
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| UCSF Chimera is a software for interactive visualization and analysis of molecular structures.

Chimera is developed by the Resource for Biocomputing, Visualization and Informatics at the University of California, San Francisco.

More information is available at the given link.

[http://www.cgl.ucsf.edu/chimera/ http://www.cgl.ucsf.edu/chimera]

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on Chimera icon on the desktop.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To start the Chimera window:

Click or double click on the Chimera icon present on the desktop.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the window.

| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| A Rapid access interface opens.

Rapid access window allows you to access the frequently used data and tools.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click the lightning bolt icon at the bottom right corner of the window.

Cursor on graphics window.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Click the lightning bolt icon at the bottom right corner of the window.

This will display the graphics window.

3D structures and other data are displayed on this window.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click the lightning bolt icon.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Toggle between the two windows by clicking the lightning bolt icon.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on graphic window.

Cursor on the menu bar.

| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Let me now go back to graphics window.

Many tasks in Chimera can be accomplished by two methods.

First one, by making use of '''menu bar''', located at the top of the Chimera window.

Other is by entering '''commands''' on the '''command line'''.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on “Favorites” menu.

Scroll down and click on “command line” option.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To show the command line, click on '''Favorites''' menu.

Scroll down and click on '''command line''' option.

A command dialog box appears at the bottom of the chimera window.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the command line.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| '''Commands''' for a particular task are to be written in the text box.

We will learn more about this feature in the subsequent tutorial.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Drag the corner of the window.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To resize the window, drag any corner of the window.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on “File” menu.

Scroll down and click on “fetch by ID”.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Now let us see how to open a protein structure.

There are 3 ways you can do it.

If you are connected to internet, click on the '''File''' menu.

Scroll down and click on “'''Fetch by ID'''” option.

A dialog box appears on the screen.

You can connect to various databases to fetch the structure.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Select PDB.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| For demonstration, I wish to display a protein structure.

I will select '''PDB '''from the options.

Type the 4 letter '''PDB code''' of the protein molecule you intend to display.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Type 1ZIK

Click on “'''Fetch'''” button.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| I will type '''1zik''', this is the pdb code for '''Leucine zipper '''protein.

Click on '''Fetch '''button.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the panel.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| By default a ribbons display of the protein will appear on the display window.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| In the command line text box type “open 1zik”

Press enter.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| We can also type a command to fetch a structure.

In the command line text box type “'''open 1zik'''”

Press enter to open the structure on the display window.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on “favorites menu”.

Scroll down and click on “model panel”.

In the model panel dialog box,

Click on model id, then click on close option.

Close the model panel.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| If you are not connected to internet, you can open the already downloaded pdb file.

To clear the structure present on the screen:

Scroll down the '''Favorites''' menu and click on '''Model Panel''' option.

A''' Model Panel''' dialog box opens.

Click on model id, then click on close option.

Close the '''model panel '''window.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Scroll down the “file” menu, click on “Fetch by ID”.

A dialog box opens, scroll down to bottom of the page.

Click on “web page” button.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Now I will demonstrate how to download a PDB file.

You need a working internet connection to download the pdb file.

Scroll down the '''File''' menu and click on '''Fetch by ID''' option.

A dialog box opens, scroll down to bottom of the dialog box.

Click on '''web page''' button.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the web page.

Type “'''1zik”''' in the text box.

Click on “Go” button.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| PDB database web page opens in the browser.

If you know the pdb code for the protein, type in the text box provided.

Or type the name of the protein.

I know the pdb code for '''leucine zipper''', so I will type “'''1zik”''' in the text box.

Click on '''Go''' button.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Scroll down the page.

Click on the “Download files” button located on the right-hand corner of the page.

From the dropdown menu click on “PDB-file-text option”
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Scroll down the page.

Click on the '''Download files''' button located on the right-hand corner of the page.

From the drop-down menu click on '''PDB-file-text''' option

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| A dialog box appears, click on “Save file” option. Click on ok button.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| A dialog box appears, click on '''Save file''' option.

Click on '''ok''' button.

The downloaded pdb file will now be saved in the '''Downloads''' folder.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on Chimera window.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Back to the Chimera window.

Close the dialog box.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on “open” option in file menu.

Navigate to the downloads folder.

Select 1zik.pdb file

Click on “Open” button.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To open the already downloaded pdb file:

Click on '''Open '''option in file menu.

Navigate to the downloads folder.

Select '''1zik.pdb''' file

Click on “'''Open'''” button.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on chimera window.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| A model of leucine zipper is displayed on the panel.

By default the two peptide chains are displayed as grey ribbons.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Hold left button and drag.

Move the middle mouse button.

Move the mouse wheel up and down.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Use the mouse buttons to move the structure on the panel.

Left mouse button for rotation.

The middle mouse button controls xy translation.

The right button or the mouse wheel to zoom in or zoom out.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Go to favorites menu and click on “side view” option.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| For interactive scaling and clipping of the structure, use '''Side View''' option from '''Favorites menu.'''

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the “viewing window”

Move the small square using left mouse button.

Move the “clipping planes” the two vertical lines using left mouse button.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| A '''viewing window '''opens.

A tiny version of the structure is shown on the window.

The yellow square on the left represents the viewer's eye position

Try moving the small square using left mouse button.

Dragging it horizontally, adjusts the '''scale factor'''.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Double-click the small yellow box.

Move the “'''clipping planes”''' the two vertical lines using left mouse button.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Double-clicking the eye position shows a menu for changing the camera mode.

Move the '''clipping planes''' that is the two vertical lines using left mouse button.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the window.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| There are more viewing controls on the window, which you can explore.

Close the '''viewing window.'''

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the window.

| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Let us now learn to manipulate this structure.

The first step is to select the part of the structure you want to modify.

For now, I want to show the entire protein structure as atoms.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on select menu in the menu bar.

Scroll down the menu items.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Click on the '''Select''' menu in the menu bar.

'''Select''' menu in the menu bar will allow us to select individual components of the structure.

Such as '''chain, element, residue, ligand''' etc.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the window.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| However, if nothing is selected from the “'''select'''” menu, it means we want to modify the entire structure.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Go to “Actions” menu, and select

“atoms/bonds” from the options.

Click on “show” from the sub-menu.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Now go to '''Actions''' menu, and select '''atoms/bonds''' from the options.

Click on '''show '''from the sub-menu.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on Chimera window.

elect ribbons from the “Action” menu. Then click on “hide”.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| On the screen we see atoms as well as part of the structure as ribbons.

Now to remove ribbons, select ribbons from the '''Action''' menu.

Then click on '''hide''' option.

The entire structure is now shown as sticks display.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the panel.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Let us now proceed with a bit more manipulation of the structure.

The following steps will convert it to the ball and stick display.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on “Actions” menu. Scroll down to atoms/bonds. Select “ball and stick” from the sub-menu.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Click on '''Actions''' menu. Scroll down to atoms/bonds. Select '''ball and stick''' from the sub-menu.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Scroll down the “Tools” menu.

Click on “Structure editing” , from the submenu select “add hydrogens” option.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Notice that the structure is with out hydrogen atoms.

To add hydrogen atoms, scroll down the '''Tools''' menu.

Click on '''Structure Editing''', from the submenu select '''add hydrogens''' option.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| In the dialog box, make selections as shown. Click on '''OK''' button.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| In the dialog box, make selections as shown.

Click on '''OK''' button.

Observe that the structure is now shown with hydrogen atoms.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the panel.

the select menu, select solvent.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Usually the structure of a protein is associated with water molecules.

To hide water molecules, go to '''Select '''menu, scroll down to Residue, click on '''HOH''' option.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the panel.

Go to “Actions” menu scroll down and click on “hide”.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Observe the screen, all the water molecules are highlighted.

Go to '''actions''' menu scroll down to '''Atoms\bonds''' and click on '''hide option.'''

This will hide the water molecules from the structure.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on “presets” option.

Click on “Interactive 1” option.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| The '''Presets''' option in the menu bar has some more options to change the display.

When you click on I'''nteractive 1''' option:

The structure will be displayed as ribbons, and both the peptide chains in different color.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on “Interactive 2” option.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| '''Interactive 2''' will convert the structure to atoms display.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on “Interactive 1” option.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Go back to '''Interactive 1''' display.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Scroll down the “Select” menu and select “chain” and “A” from the sub-menu.

Go to “Actions” menu scroll down to color, select yellow.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| We can also selectively change the color of peptide chains.

Scroll down the '''Select''' menu and select '''chain''' '''A''' from the sub-menu.

Chain A is now highlighted.

Go to '''Actions''' menu scroll down to color, select yellow.

Chain A is now displayed in yellow color.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Hold ctrl key on the key board and click on anywhere on the Chimera window.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To clear the selection, hold CTRL key on the key board and click on the empty space on the Chimera window.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the window.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| We have now come to the end of this tutorial.

To exit the Chimera window, go to '''File '''menu and click on '''quit''' option.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 6'''

Summary
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Let's summarize,

In this tutorial we have learnt to

* Open a structure on the Chimera window.
* And also download the PDB file for the protein.
* Move, rotate and zoom the structure.
* Scale and clip.<br/>

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 7'''

'''Summary'''
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"|* Change the display using menus in the menu bar.
* Remove the water molecules.
* Add hydrogens.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 8'''

Assignment
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| For the Assignment

<nowiki>* </nowiki>Download the pdb file of '''Leucine zipper''' from PDB database.

<nowiki>* Open the pdb file </nowiki>on Chimera window using '''open''' option in file menu.

<nowiki>* </nowiki>Change the display of atoms to '''wire''' and all the aromatic rings as '''disks'''.

Your completed assignment will look as follows.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 9'''

'''Acknowledgement '''
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| The video at the following link summarizes the Spoken Tutorial project.

Please download and watch it.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 10'''

'''Acknowledgement '''
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| The Spoken Tutorial Project Team conducts workshops and gives certificates for those who pass an online test.

For more details, please write to us.

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide number 11'''

'''Acknowledgement '''
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Spoken Tutorial Project is funded by NMEICT, MHRD, Government of India.

More information on this Mission is available at the link shown

|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide number 11'''
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| This is Snehalatha from IIT Bombay signing off. Thank you for joining.

|}

UCSF-Chimera/C2/Structure-Manipulation/English - Revision history

Nancyvarkey at 02:29, 16 December 2015

Snehalathak: Created page with " {| style="border-spacing:0;" ! Visual Cue ! Narration |- | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;..."