UCSF-Chimera/C2/Structure-Manipulation/English
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Slide Number 1
Title Slide |
Welcome to this tutorial on Structure Manipulation using Chimera.
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Slide Number 2
Learning Objectives |
In this tutorial, we will learn to
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Slide Number 3
Pre-requisites |
To follow this tutorial you should have knowledge of,
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Slide Number 4
System Requirement |
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. |
Slide Number 5
UCSF Chimera |
UCSF Chimera is a software for interactive visualization and analysis of molecular structures.
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Click on Chimera icon on the desktop. | To start the Chimera window:
Click or double click on the Chimera icon present on the desktop. |
Cursor on the window.
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A Rapid access interface opens.
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Click the lightning bolt icon at the bottom right corner of the window.
Cursor on graphics window. |
Click the lightning bolt icon at the bottom right corner of the window.
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Click the lightning bolt icon. | Toggle between the two windows by clicking the lightning bolt icon.
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Cursor on graphic window.
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Let me now go back to graphics window.
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Click on “Favorites” menu.
Scroll down and click on “command line” option. |
To show the command line, click on Favorites menu.
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Cursor on the command line. | Commands for a particular task are to be written in the text box.
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Drag the corner of the window. | To resize the window, drag any corner of the window. |
Click on “File” menu.
Scroll down and click on “fetch by ID”. |
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. |
Select PDB. | For demonstration, I wish to display a protein structure.
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Type 1ZIK
Click on “Fetch” button. |
I will type 1zik, this is the pdb code for Leucine zipper protein.
Click on Fetch button. |
Cursor on the panel. | By default a ribbons display of the protein will appear on the display window. |
In the command line text box type “open 1zik”
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We can also type a command to fetch a structure.
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Click on “favorites menu”.
Scroll down and click on “model panel”.
Click on model id, then click on close option. Close the model panel. |
If you are not connected to internet, you can open the already downloaded pdb file.
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Scroll down the “file” menu, click on “Fetch by ID”.
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Now I will demonstrate how to download a PDB file.
Click on web page button. |
Cursor on the web page.
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PDB database web page opens in the browser.
Click on Go button. |
Scroll down the page.
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Scroll down the page.
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A dialog box appears, click on “Save file” option. Click on ok button. | A dialog box appears, click on Save file option.
Click on ok button.
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Cursor on Chimera window. | Back to the Chimera window.
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Click on “open” option in file menu.
Select 1zik.pdb file Click on “Open” button. |
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. |
Cursor on chimera window. | A model of leucine zipper is displayed on the panel.
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Hold left button and drag.
Move the mouse wheel up and down. |
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. |
Go to favorites menu and click on “side view” option. | For interactive scaling and clipping of the structure, use Side View option from Favorites menu.
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Cursor on the “viewing window”
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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.
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Double-click the small yellow box.
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Double-clicking the eye position shows a menu for changing the camera mode.
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Cursor on the window. | There are more viewing controls on the window, which you can explore.
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Cursor on the window.
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Let us now learn to manipulate this structure.
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Click on select menu in the menu bar.
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Click on the Select menu in the menu bar.
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Cursor on the window. | However, if nothing is selected from the “select” menu, it means we want to modify the entire structure.
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Go to “Actions” menu, and select
“atoms/bonds” from the options. Click on “show” from the sub-menu. |
Now go to Actions menu, and select atoms/bonds from the options.
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Cursor on Chimera window.
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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.
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Cursor on the panel. | Let us now proceed with a bit more manipulation of the structure.
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Click on “Actions” menu. Scroll down to atoms/bonds. Select “ball and stick” from the sub-menu. | Click on Actions menu. Scroll down to atoms/bonds. Select ball and stick from the sub-menu. |
Scroll down the “Tools” menu.
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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. |
In the dialog box, make selections as shown. Click on OK button. | In the dialog box, make selections as shown.
Click on OK button.
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Cursor on the panel.
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Usually the structure of a protein is associated with water molecules.
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Cursor on the panel.
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Observe the screen, all the water molecules are highlighted.
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Cursor on “presets” option.
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The Presets option in the menu bar has some more options to change the display.
When you click on Interactive 1 option:
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Click on “Interactive 2” option. | Interactive 2 will convert the structure to atoms display. |
Click on “Interactive 1” option. | Go back to Interactive 1 display. |
Scroll down the “Select” menu and select “chain” and “A” from the sub-menu.
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We can also selectively change the color of peptide chains.
Chain A is now highlighted. Go to Actions menu scroll down to color, select yellow. Chain A is now displayed in yellow color. |
Hold ctrl key on the key board and click on anywhere on the Chimera window. | To clear the selection, hold CTRL key on the key board and click on the empty space on the Chimera window.
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Cursor on the window. | We have now come to the end of this tutorial.
To exit the Chimera window, go to File menu and click on quit option. |
Slide Number 6
Summary |
Let's summarize,
In this tutorial we have learnt to
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Slide Number 7
Summary |
* Change the display using menus in the menu bar.
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Slide Number 8
Assignment |
For the Assignment
* Download the pdb file of Leucine zipper from PDB database.
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Slide Number 9
Acknowledgement |
The video at the following link summarizes the Spoken Tutorial project.
Please download and watch it. |
Slide Number 10
Acknowledgement |
The Spoken Tutorial Project Team conducts workshops and gives certificates for those who pass an online test.
For more details, please write to us. |
Slide number 11
Acknowledgement |
Spoken Tutorial Project is funded by NMEICT, MHRD, Government of India.
More information on this Mission is available at the link shown |
Slide number 11 | This is Snehalatha from IIT Bombay signing off. Thank you for joining. |