UCSF-Chimera/C2/Structure-Manipulation/English-timed

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Time	Narration
00:01	Welcome to this tutorial on Structure Manipulation using Chimera.
00:06	In this tutorial, we will learn to: open a structure on the Chimera window,
00:12	move, rotate and zoom the structure, scale and clip, and change the display of the structure.
00:20	To follow this tutorial, you should have knowledge of undergraduate Biochemistry or must be familiar with Structural Biology.
00:29	To record this tutorial, I am using: Ubuntu Linux OS version. 14.04, Chimera version 1.10.2, Mozilla Firefox browser 35.0 and a working internet connection.
00:47	UCSF Chimera is a software for interactive visualization and analysis of molecular structures.
00:55	Chimera is developed by the Resource for Biocomputing, Visualization and Informatics at the University of California, San Francisco.
01:05	More information is available at the given link.
01:09	To start the Chimera window, click or double-click on the Chimera icon present on the desktop.
01:16	A Rapid access interface opens.
01:20	Rapid access window allows you to access the frequently used data and tools.
01:27	Click the lightning bolt icon at the bottom right corner of the window.
01:32	This will display the graphics window. 3D structures and other data are displayed on this window.
01:40	Toggle between the two windows by clicking the lightning bolt icon.
01:45	Let me now go back to graphics window.
01:48	Many tasks in Chimera can be accomplished by two methods.
01:53	First one, by making use of menu bar, located at the top of the Chimera window.
01:59	Other is by entering commands on the command line.
02:03	To show the command line, click on Favorites menu.
02:06	Scroll down and click on command line option.
02:10	A command dialog box appears at the bottom of the Chimera window.
02:15	Commands for a particular task are to be written in the text box.
02:21	We will learn more about this feature in the subsequent tutorials.
02:25	To resize the window, drag any corner of the window.
02:30	Now, let us see how to open a protein structure.
02:34	There are 3 ways you can do it. If you are connected to Internet, click on the File menu.
02:40	Scroll down and click on “Fetch by ID” option.
02:45	A dialog box appears on the screen.
02:48	You can connect to various databases to fetch the structure.
02:53	For demonstration, I wish to display a protein structure.
02:58	I will select PDB from the options. Type the 4 letter PDB code of the protein molecule you intend to display.
03:08	I will type 1zik (one z i k).
03:12	This is the pdb code for Leucine zipper protein. Click on Fetch button.
03:19	By default, a ribbons display of the protein will appear on the display window.
03:25	We can also type a command to fetch a structure.
03:29	In the command line text box, type “open 1zik”.
03:35	Press Enter to open the structure on the display window.
03:40	If you are not connected to internet, you can open the already downloaded pdb file.
03:46	To clear the structure present on the screen: scroll down the Favorites menu and click on Model Panel option.
03:55	A Model Panel dialog box opens.
03:58	Click on model id, then click on Close option.
04:04	Close the model panel window.
04:07	Now I will demonstrate how to download a PDB file.
04:12	You need a working internet connection to download the pdb file.
04:17	Scroll down the File menu and click on Fetch by ID option.
04:23	A dialog box opens.
04:26	Scroll down to bottom of the dialog box.
04:30	Click on web page button.
04:33	PDB database web page opens in the browser.
04:37	If you know the pdb code for the protein, type in the text box provided. Or, type the name of the protein.
04:46	I know the pdb code for leucine zipper. So, I will type “1zik” in the text box.
04:54	Click on Go button.
04:57	Scroll down the page.
04:59	Click on the Download files button located on the right-hand corner of the page.
05:06	From the drop-down menu click on PDB-file-text option.
05:12	A dialog box appears.
05:14	Click on Save File option.
05:17	Click on Ok button.
05:20	The downloaded pdb file will now be saved in the Downloads folder.
05:25	Back to the Chimera window.
05:27	Close the dialog box.
05:30	To open the already downloaded pdb file, click on Open option in File.
05:37	Navigate to the Downloads folder. Select 1zik.pdb file.
05:44	Click on “Open” button.
05:47	A model of leucine zipper is displayed on the panel.
05:51	By default, the two peptide chains are displayed as grey ribbons.
05:57	Use the mouse button to move the structure on the panel.
06:01	Left mouse button for rotation,
06:04	the middle mouse button controls xy translation.
06:08	The right button or the mouse wheel to zoom in or zoom out.
06:13	For interactive scaling and clipping of the structure: use Side View option from Favorites menu.
06:20	A viewing window opens.
06:22	A tiny version of the structure is shown on the window.
06:27	The yellow square on the left, represents the viewer's eye position
06:32	Try moving the small square using left mouse button.
06:36	Dragging it horizontally, adjust the scale factor.
06:41	Double-clicking the eye position shows a menu for changing the camera mode.
06:46	Move the clipping planes i.e. the two vertical lines using left mouse button.
06:53	There are more viewing controls on the window which you can explore.
06:58	Close the viewing window.
07:01	Let us now learn to manipulate this structure.
07:04	The first step is to select the part of the structure you want to modify.
07:09	For now, I want to show the entire protein structure as atoms.
07:15	Click on the Select menu in the menu bar.
07:19	Select menu in the menu bar will allow us to select individual components of the structure
07:25	such as chain, element, residue, ligand etc.
07:31	However, if nothing is selected from the “Select” menu, it means we want to modify the entire structure.
07:39	Now go to Actions menu, and select atoms/bonds from the options.
07:46	Click on show from the sub-menu.
07:49	On the screen, we see atoms as well as part of the structure as ribbons.
07:55	Now to remove ribbons, select ribbons from the Action menu.
08:00	Then click on hide option.
08:03	The entire structure is now shown as sticks display.
08:08	Let us now proceed with a bit more manipulation of the structure.
08:13	The following steps will convert it to the ball and stick display.
08:18	Click on Actions menu.
08:21	Scroll down to atoms/bonds.
08:24	Select ball and stick from the sub-menu.
08:28	Notice that the structure is without hydrogen atoms.
08:33	To add hydrogen atoms, scroll down the Tools menu.
08:37	Click on Structure Editing.
08:40	From the sub-menu, select Add hydrogens option.
08:45	In the dialog box, make selections as shown.
08:49	Click on OK button.
08:52	Observe that the structure is now shown with hydrogen atoms.
08:57	Usually the structure of a protein is associated with water molecules.
09:02	To hide water molecules, go to Select menu, scroll down to Residue, click on HOH option.
09:13	Observe the screen; all the water molecules are highlighted.
09:18	Go to actions menu, scroll down to Atoms\bonds and click on hide option.
09:26	This will hide the water molecules from the structure.
09:30	The Presets option in the menu bar has some more options to change the display.
09:36	When you click on Interactive 1 option: the structure will be displayed as ribbons and both the peptide chains in different color.
09:45	Interactive 2 will convert the structure to atoms display.
09:50	Go back to Interactive 1 display.
09:53	We can also selectively change the color of peptide chains.
09:57	Scroll down the Select menu and select chain A from the sub-menu.
10:02	Chain A is now highlighted.
10:05	Go to Actions menu scroll down to color, select yellow.
10:11	Chain A is now displayed in yellow color.
10:15	To clear the selection, hold CTRL key on the key board. And click on the empty space on the Chimera window.
10:23	We have now come to the end of this tutorial.
10:26	To exit the Chimera window, go to File menu and click on Quit option.
10:32	Let's summarize. In this tutorial, we have learnt to" open a structure on the Chimera window and download the PDB file for protein structures,
10:43	move, rotate and zoom the structure, Scale and clip,
10:49	change the display using menus in the menu bar,
10:53	remove the water molecules, and add hydrogens.
10:57	For the Assignment, download the pdb file of Leucine zipper from PDB database.
11:04	Open the pdb file on Chimera window using Open option in the File menu.
11:10	Change the display of atoms to wire and all the aromatic rings as disks.
11:16	Your completed assignment will look as follows.
11:21	The video at the following link summarizes the Spoken Tutorial project.
11:26	Please download and watch it.
11:28	The Spoken Tutorial Project Team conducts workshops and gives certificates for those who pass an online test.
11:34	For more details, please write to us.
11:38	Spoken Tutorial Project is funded by NMEICT, MHRD, Government of India.
11:44	More information on this mission is available at the link shown.
11:48	This is Snehalatha from IIT Bombay, signing off. Thank you for joining.

Contributors and Content Editors

PoojaMoolya, Sandhya.np14