View source for UCSF-Chimera/C2/Structure-Manipulation/English-timed


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! <center>Time</center>
! <center>Narration</center>

|-
| | 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. 

|}