Difference between revisions of "UCSF-Chimera/C2/Structure-Manipulation/English"

Title Slide

Learning Objectives

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

Pre-requisites

• should have knowledge of Undergraduate Biochemistry or
• must be familiar with Structural Biology

System Requirement

• Ubuntu Linux OS version. 14.04
• Chimera version 1.10.2
• Mozilla Firefox browser 35.0
• Working Internet connection.

UCSF Chimera

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

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

Cursor on graphics window.

This will display the graphics window.

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

Cursor on the menu bar.

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.

Scroll down and click on “command line” option.

Scroll down and click on command line option.

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

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

Scroll down and click on “fetch by ID”.

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.

I will select PDB from the options.

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

Click on “Fetch” button.

This is the pdb code for Leucine zipper protein.

Click on Fetch button.

Press enter.

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

Press Enter to open the structure on the display window.

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.

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.

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

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

Click on “web page” button.

Scroll down to bottom of the dialog box.

Click on web page button.

Type “1zik” in the text box.

Click on “Go” button.

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.

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”

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

Click on Save File option.

Click on Ok button.

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

Close the dialog box.

Navigate to the downloads folder.

Select 1zik.pdb file

Click on “Open” button.

Navigate to the Downloads folder.

Select 1zik.pdb file

Click on “Open” button.

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

Move the middle mouse button.

Move the mouse wheel up and down.

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.

• use Side View option from Favorites menu.

Move the small square using left mouse button.

Move the “clipping planes” the two vertical lines using left mouse button.

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, adjust the scale factor.

Move the “clipping planes” the two vertical lines using left mouse button.

Move the clipping planes i.e. the two vertical lines using left mouse button.

Close the viewing window.

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.

Scroll down the menu items.

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

Such as chain, element, residue, ligand etc.

“atoms/bonds” from the options.

Click on “show” from the sub-menu.

Click on show from the sub-menu.

elect ribbons from the “Action” menu. Then click on “hide”.

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

Then click on hide option.

The entire structure is now shown as sticks display.

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

Scroll down to atoms/bonds.

Select ball and stick from the sub-menu.

Click on “Structure editing” , from the submenu select “add hydrogens” option.

To add hydrogen atoms, scroll down the Tools menu.

Click on Structure Editing.

From the sub-menu select Add hydrogens option.

Click on OK button.

Observe that the structure is now shown with hydrogen atoms.

the select menu, select solvent.

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

Go to “Actions” menu scroll down and click on “hide”.

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

This will hide the water molecules from the structure.

Click on “Interactive 1” option.

When you click on Interactive 1 option:

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

Go to “Actions” menu scroll down to color, select yellow.

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.

And click on the empty space on the Chimera window.

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

Summary

In this tutorial we have learnt to

• Open a structure on the Chimera window.
• And also download the PDB file for protein structures.
• Move, rotate and zoom the structure.
• Scale and clip.
  

Summary

• Change the display using menus in the menu bar.
• Remove the water molecules.
• Add hydrogens.

Assignment

• Download the pdb file of Leucine zipper from PDB database.
• Open the pdb file on Chimera window using Open option in File menu.
• Change the display of atoms to wire and all the aromatic rings as disks.

Your completed assignment will look as follows.

Acknowledgement

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Acknowledgement

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Acknowledgement

More information on this Mission is available at the link shown