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

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| |'''Chimera''' is developed by the '''Resource for Biocomputing, Visualization and Informatics at the University of California, San Francisco.
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| |'''Chimera''' is developed by the '''Resource for Biocomputing, Visualization and Informatics''' at the '''University of California, San Francisco'''.
  
 
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| | '''More information is available at the given link.
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| | More information is available at the given link.
  
 
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| |  '''Rapid access''' window allows you to access the frequently used data and tools.
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| |  '''Rapid access''' window allows you to access the frequently used '''data''' and '''tool'''s.
  
 
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| | To resize the window, drag any corner of the window.
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| | To '''resize''' the window, drag any corner of the window.
  
 
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| | 02:30
 
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| | Now let us see how to open a '''protein''' structure.
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| | Now, let us see how to open a '''protein''' structure.
  
 
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| |A dialog box appears on the screen.
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| |A dialog box appears on the '''screen'''.
  
 
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| |You can connect to various databases to fetch the structure.
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| |You can connect to various '''database'''s to fetch the structure.
  
 
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| | I will type '''1zik''' (one z i k)
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| | I will type '''1zik''' (one z i k).
  
 
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| | By default, a ribbons display of the '''protein''' will appear on the display window.
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| | By default, a '''ribbons''' display of the '''protein''' will appear on the display window.
  
 
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| |In the '''command line''' text box type “'''open 1zik'''”  
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| |In the '''command line''' text box, type “'''open 1zik'''”.
  
 
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| | If you are not connected to Internet, you can open the already downloaded '''pdb''' file.
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| | If you are not connected to internet, you can open the already downloaded '''pdb''' file.
  
 
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| |To clear the structure present on the screen:scroll down the '''Favorites''' menu and click on '''Model Panel''' option.
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| |To clear the structure present on the screen: scroll down the '''Favorites''' menu and click on '''Model Panel''' option.
  
 
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| |You need a working Internet connection to download the '''pdb''' file.
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| |You need a working internet connection to download the '''pdb''' file.
  
 
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| |If you know the '''pdb''' code for the '''protein''', type in the text box provided. Or type the name of the '''protein'''.
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| |If you know the '''pdb''' code for the '''protein''', type in the text box provided. Or, type the name of the '''protein'''.
  
 
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| |I know the '''pdb''' code for '''leucine zipper''', so I will type “'''1zik”''' in the text box.
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| |I know the '''pdb''' code for '''leucine zipper'''. So, I will type “'''1zik”''' in the text box.
  
 
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| |From the drop-down menu click on '''PDB-file-text''' option
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| |From the drop-down menu click on '''PDB-file-text''' option.
  
 
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| | A model of '''leucine zipper''' is displayed on the panel.
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| | A model of '''leucine zipper''' is displayed on the '''panel'''.
  
 
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| |By default, the two '''peptide chains''' are displayed as grey ribbons.
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| |By default, the two '''peptide chains''' are displayed as grey '''ribbon'''s.
  
 
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| |  Use the mouse button to move the structure on the panel.  
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| |  Use the '''mouse''' button to move the structure on the panel.  
  
 
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| |Left mouse button for rotation.
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| |Left '''mouse''' button for rotation,
  
 
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| |The middle mouse button controls '''xy translation'''.
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| |the middle mouse button controls '''xy translation'''.
  
 
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| |The yellow square on the left represents the viewer's eye position
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| |The yellow square on the left, represents the viewer's eye position
  
 
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| | Double-clicking the eye position shows a menu for changing the camera mode.
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| | Double-clicking the eye position shows a menu for changing the '''camera mode'''.
  
 
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| | There are more viewing controls on the window, which you can explore.  
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| | There are more viewing controls on the window which you can explore.  
  
 
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| |'''Select''' menu in the menu bar will allow us to select individual components of the structure.
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| |'''Select''' menu in the menu bar will allow us to select individual components of the structure
  
 
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| |Such as '''chain, element, residue, ligand''' etc.
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| |such as '''chain, element, residue, ligand''' etc.
 
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| | On the screen we see atoms as well as part of the structure as ribbons.
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| | On the screen, we see atoms as well as part of the structure as ribbons.
  
 
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| |Scroll down to atoms/bonds.  
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| |Scroll down to '''atoms/bonds'''.  
  
 
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| |From the sub-menu select '''Add hydrogens''' option.
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| |From the sub-menu, select '''Add hydrogens''' option.
  
 
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| |Go to '''actions''' menu scroll down to '''Atoms\bonds''' and click on '''hide''' option.
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| |Go to '''actions''' menu, scroll down to '''Atoms\bonds''' and click on '''hide''' option.
  
 
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| |When you click on '''Interactive 1''' option: the structure will be displayed as ribbons,
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| |When you click on '''Interactive 1''' option: the structure will be displayed as ribbons and both the '''peptide chains''' in different color.
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and both the '''peptide chains''' in different color.
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| |Chain A is now highlighted.
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| |'''Chain A''' is now highlighted.
  
 
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| |Chain A is now displayed in yellow color.
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| |'''Chain A''' is now displayed in yellow color.
  
 
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| | 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.
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| | 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,
−
 
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| | 10:43
 
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| | Move, rotate and zoom the structure. Scale and clip.
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| | move, rotate and zoom the structure, Scale and clip,
  
 
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| | Change the display using menus in the menu bar.
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| | change the display using menus in the menu bar,
 
   
 
   
 
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| |Remove the water molecules. And Add '''hydrogens'''.  
+
| |remove the water molecules, and add '''hydrogens'''.  
  
 
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| |10:57
 
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| | For the Assignment Download the '''pdb''' file of '''Leucine zipper''' from '''PDB''' database.
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| | For the Assignment, download the '''pdb''' file of '''Leucine zipper''' from '''PDB''' database.
  
 
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| | The video at the following link summarizes the Spoken Tutorial project.  
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| | The video at the following link summarizes the '''Spoken Tutorial''' project.  
  
 
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| | Spoken Tutorial Project is funded by NMEICT, MHRD, Government of India.  
+
| | Spoken Tutorial Project is funded by '''NMEICT, MHRD''', Government of India.  
  
 
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| | 11:44
 
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| |More information on this Mission is available at the link shown
+
| |More information on this mission is available at the link shown.
  
 
|-
 
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| |11:48
 
| |11:48
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| | This is Snehalatha from IIT Bombay signing off. Thank you for joining.  
+
| | This is Snehalatha from IIT Bombay,
 +
signing off. Thank you for joining.  
  
 
|}
 
|}

Revision as of 16:43, 25 June 2018

­

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

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