UCSF-Chimera/C2/Structure-Manipulation/English

Visual Cue	Narration
Slide Number 1 Title Slide	Welcome to this tutorial on Structure Manipulation using Chimera.
Slide Number 2 Learning Objectives	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.
Slide Number 3 Pre-requisites	To follow this tutorial you should have knowledge of Undergraduate Biochemistry or must be familiar with Structural Biology
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. 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
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.	A Rapid access interface opens. Rapid access window allows you to access the frequently used data and tools.
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. This will display the graphics window. 3D structures and other data are displayed on this window.
Click the lightning bolt icon.	Toggle between the two windows by clicking the lightning bolt icon.
Cursor on graphic window. Cursor on the menu bar.	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.
Click on “Favorites” menu. Scroll down and click on “command line” option.	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.
Cursor on the command line.	Commands for a particular task are to be written in the text box. We will learn more about this feature in the subsequent tutorials.
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. I will select PDB from the options. Type the 4 letter PDB code of the protein molecule you intend to display.
Type 1ZIK Click on “Fetch” button.	I will type 1zik (one z i k) 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” Press enter.	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.
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.	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.
Scroll down the “file” menu, click on “Fetch by ID”.	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 page. Click on “web page” button.	A dialog box opens. Scroll down to bottom of the dialog box. Click on web page button.
Cursor on the web page. Type “1zik” in the text box. Click on “Go” button.	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.
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”	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
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. The downloaded pdb file will now be saved in the Downloads folder.
Cursor on Chimera window.	Back to the Chimera window. Close the dialog box.
Click on “open” option in file menu. Navigate to the downloads folder. 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. By default, the two peptide chains are displayed as grey ribbons.
Hold left button and drag. Move the middle mouse button. 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.
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.	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, adjust the scale factor.
Double-click the small yellow box. Move the “clipping planes” the two vertical lines using left mouse button.	Double-clicking the eye position shows a menu for changing the camera mode. Move the clipping planes i.e. the two vertical lines using left mouse button.
Cursor on the window.	There are more viewing controls on the window, which you can explore. Close the viewing window.
Cursor on the window.	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.
Click on Select menu in the menu bar. Scroll down the menu items.	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.
Cursor on the window.	However, if nothing is selected from the “Select” menu, it means we want to modify the entire structure.
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. Click on show from the sub-menu.
Cursor on Chimera window. elect ribbons from the “Action” menu. Then click on “hide”.	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.
Cursor on the panel.	Let us now proceed with a bit more manipulation of the structure. The following steps will convert it to the ball and stick display.
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. Click on “Structure editing” , from the submenu select “add hydrogens” option.	Notice that the structure is without hydrogen atoms. To add hydrogen atoms, scroll down the Tools menu. Click on Structure Editing. From the sub-menu 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. Observe that the structure is now shown with hydrogen atoms.
Cursor on the panel. the select menu, select solvent.	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.
Cursor on the panel. Go to “Actions” menu scroll down and click on “hide”.	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.
Cursor on “presets” option. Click on “Interactive 1” option.	The Presets option in the menu bar has some more options to change the display. When you click on Interactive 1 option: the structure will be displayed as ribbons, and both the peptide chains in different color.
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. Go to “Actions” menu scroll down to color, select yellow.	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.
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.
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 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.
Slide Number 7 Summary	Change the display using menus in the menu bar. Remove the water molecules. Add hydrogens.
Slide Number 8 Assignment	For the 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.
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.

Contributors and Content Editors

Nancyvarkey, Snehalathak