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

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'''Title Slide'''
 
'''Title Slide'''
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Welcome to this tutorial on '''Structure Manipulation '''using Chimera.
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Welcome to this tutorial on '''Structure Manipulation '''using Chimera.
 
  
 
|-
 
|-
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'''Learning Objectives'''
 
'''Learning Objectives'''
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| In this tutorial, we will learn to
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| In this tutorial, we will learn to
 
  
 
* Open a structure on the Chimera window.
 
* Open a structure on the Chimera window.
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'''Pre-requisites'''
 
'''Pre-requisites'''
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To follow this tutorial you should have knowledge of,
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To follow this tutorial you  
 
+
*should have knowledge of Undergraduate Biochemistry or
 
+
*must be familiar with Structural Biology  
Undergraduate Biochemistry  
+
 
+
 
+
Or must be familiar with Structural Biology  
+
 
+
  
 
|-
 
|-
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| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To record this tutorial I am using,  
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To record this tutorial I am using,  
  
Ubuntu Linux OS version. 14.04
+
*'''Ubuntu Linux''' OS version. 14.04
 
+
*'''Chimera''' version 1.10.2
Chimera version 1.10.2
+
*'''Mozilla Firefox''' browser 35.0
 
+
*Working Internet connection.
Mozilla firefox browser 35.0
+
 
+
Working internet connection.
+
  
 
|-
 
|-
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'''UCSF Chimera'''
 
'''UCSF Chimera'''
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| UCSF Chimera is a software for interactive visualization and analysis of molecular structures.
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| '''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.
+
'''Chimera''' is developed by the '''Resource for Biocomputing, Visualization and Informatics at the University of California, San Francisco.'''
  
  
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|-
 
|-
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on Chimera icon on the desktop.
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on Chimera icon on the desktop.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To start the Chimera window:
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To start the '''Chimera''' window, click or double-click on the '''Chimera''' icon present on the desktop.  
 
+
Click or double click on the Chimera icon present on the desktop.  
+
  
 
|-
 
|-
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| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| A Rapid access interface opens.
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| A '''Rapid access''' interface opens.
 
+
  
Rapid access window allows you to access the frequently used data and tools.
 
  
 +
'''Rapid access''' window allows you to access the frequently used data and tools.
  
 
|-
 
|-
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This will display the graphics window.
+
This will display the '''graphics''' window.
  
  
3D structures and other data are displayed on this window.  
+
'''3D structures''' and other data are displayed on this window.  
  
 
|-
 
|-
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click the lightning bolt icon.
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click the lightning bolt icon.
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Toggle between the two windows by clicking the lightning bolt icon.  
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Toggle between the two windows by clicking the lightning bolt icon.  
 
  
 
|-
 
|-
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Cursor on the menu bar.
 
Cursor on the menu bar.
  
 +
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Let me now go back to '''graphics''' window.
  
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Let me now go back to graphics window.
 
  
 +
Many tasks in '''Chimera''' can be accomplished by two methods.
  
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.
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'''.
 
Other is by entering '''commands''' on the '''command line'''.
 
  
 
|-
 
|-
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Scroll down and click on “command line” option.
 
Scroll down and click on “command line” option.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To show the command line, click on '''Favorites''' menu.
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To show the '''command line''', click on '''Favorites''' menu.
  
  
Line 127: Line 111:
  
  
A command dialog box appears at the bottom of the chimera window.
+
A '''command''' dialog box appears at the bottom of the '''Chimera''' window.
  
 
|-
 
|-
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We will learn more about this feature in the subsequent tutorial.
+
We will learn more about this feature in the subsequent tutorials.
  
 
|-
 
|-
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Scroll down and click on “fetch by ID”.
 
Scroll down and click on “fetch by ID”.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Now let us see how to open a protein structure.
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Now let us see how to open a '''protein''' structure.
  
 
There are 3 ways you can do it.
 
There are 3 ways you can do it.
  
If you are connected to internet, click on the '''File''' menu.  
+
If you are connected to Internet, click on the '''File''' menu.  
  
 
Scroll down and click on “'''Fetch by ID'''” option.
 
Scroll down and click on “'''Fetch by ID'''” option.
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|-
 
|-
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Select PDB.
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Select PDB.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| For demonstration, I wish to display a protein structure.  
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| For demonstration, I wish to display a '''protein''' structure.  
  
  
Line 164: Line 148:
  
  
Type the 4 letter '''PDB code''' of the protein molecule you intend to display.
+
Type the 4 letter '''PDB code''' of the '''protein''' molecule you intend to display.
  
 
|-
 
|-
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Click on “'''Fetch'''” button.
 
Click on “'''Fetch'''” button.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| I will type '''1zik''', this is the pdb code for '''Leucine zipper '''protein.
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| I will type '''1zik''' (one z i k)
 +
 
 +
 
 +
This is the '''pdb''' code for '''Leucine zipper '''protein.
  
 
Click on '''Fetch '''button.
 
Click on '''Fetch '''button.
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|-
 
|-
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the panel.
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the panel.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| By default a ribbons display of the protein will appear on the display window.
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| By default, a ribbons display of the '''protein''' will appear on the display window.
  
 
|-
 
|-
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Press enter.  
 
Press enter.  
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| We can also type a command to fetch a structure.
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| We can also type a '''command''' to fetch a structure.
  
  
In the command line text box type “'''open 1zik'''”  
+
In the '''command line''' text box type “'''open 1zik'''”  
  
  
Press enter to open the structure on the display window.
+
Press '''Enter''' to open the structure on the display window.
 
+
  
 
|-
 
|-
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In the model panel dialog box,  
+
In the model panel dialog box, click on model id, then click on close option.
 
+
Click on model id, then click on close option.
+
  
 
Close the model panel.
 
Close the model panel.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| If you are not connected to internet, you can open the already downloaded pdb file.
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| If you are not connected to Internet, you can open the already downloaded '''pdb''' file.
  
  
 
To clear the structure present on the screen:
 
To clear the structure present on the screen:
 
+
*scroll down the '''Favorites''' menu  
 
+
*and click on '''Model Panel''' option.
Scroll down the '''Favorites''' menu and click on '''Model Panel''' option.
+
  
  
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Click on model id, then click on close option.
+
Click on '''model id''', then click on '''Close''' option.
  
  
 
Close the '''model panel '''window.
 
Close the '''model panel '''window.
 
  
 
|-
 
|-
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Scroll down the “file” menu, click on “Fetch by ID”.
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Scroll down the “file” menu, click on “Fetch by ID”.
  
 +
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Now I will demonstrate how to download a '''PDB''' file.
  
A dialog box opens, scroll down to bottom of the page.
 
  
 +
You need a working Internet connection to download the '''pdb''' file.
  
Click on “web page” button.
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Now I will demonstrate how to download a PDB file.
 
  
 +
Scroll down the '''File''' menu and click on '''Fetch by ID''' option.
  
You need a working internet connection to download the pdb file.
+
|-
 +
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| A dialog box opens, scroll down to bottom of the page.
  
  
Scroll down the '''File''' menu and click on '''Fetch by ID''' option.
+
Click on “web page” button.  
  
 +
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"|A dialog box opens.
  
A dialog box opens, scroll down to bottom of the dialog box.
+
Scroll down to bottom of the dialog box.
  
 
Click on '''web page''' button.  
 
Click on '''web page''' button.  
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Click on “Go” button.
 
Click on “Go” button.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| PDB database web page opens in the browser.
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| '''PDB database''' web page opens in the browser.
  
  
If you know the pdb code for the protein, type in the text box provided.
+
If you know the '''pdb''' code for the '''protein''', type in the text box provided.
  
  
Or type the name of the protein.
+
Or type the name of the '''protein'''.
  
  
I know the pdb code for '''leucine zipper''', so I will type “'''1zik”''' in the text box.
+
I know the '''pdb''' code for '''leucine zipper''', so I will type “'''1zik”''' in the text box.
  
 
Click on '''Go''' button.
 
Click on '''Go''' button.
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|-
 
|-
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| A dialog box appears, click on “Save file” option. Click on ok button.
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| A dialog box appears, click on “Save file” option. Click on ok button.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| A dialog box appears, click on '''Save file''' option.  
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| A dialog box appears.
 +
 
 +
Click on '''Save File''' option.  
  
Click on '''ok''' button.
+
Click on '''Ok''' button.
  
  
The downloaded pdb file will now be saved in the '''Downloads''' folder.
+
The downloaded '''pdb''' file will now be saved in the '''Downloads''' folder.
  
 
|-
 
|-
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on Chimera window.
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on Chimera window.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Back to the Chimera window.
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Back to the '''Chimera''' window.
  
  
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Click on “Open” button.  
 
Click on “Open” button.  
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To open the already downloaded pdb file:
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To open the already downloaded '''pdb''' file, click on '''Open '''option in '''File''' menu.
  
Click on '''Open '''option in file menu.
+
Navigate to the '''Downloads''' folder.
 
+
Navigate to the downloads folder.
+
  
 
Select '''1zik.pdb''' file
 
Select '''1zik.pdb''' file
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|-
 
|-
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on chimera window.
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on chimera window.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| A model of leucine zipper is displayed on the panel.
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| A model of '''leucine zipper''' is displayed on the panel.
  
  
By default the two peptide chains are displayed as grey ribbons.
+
By default, the two '''peptide chains''' are displayed as grey ribbons.
  
 
|-
 
|-
Line 332: Line 316:
 
Left mouse button for rotation.
 
Left mouse button for rotation.
  
The middle mouse button controls xy translation.
+
The middle mouse button controls '''xy translation'''.
  
 
The right button or the mouse wheel to zoom in or zoom out.
 
The right button or the mouse wheel to zoom in or zoom out.
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|-
 
|-
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Go to favorites menu and click on “side view” option.
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Go to favorites menu and click on “side view” option.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| For interactive scaling and clipping of the structure, use '''Side View''' option from '''Favorites menu.'''
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| For interactive scaling and clipping of the structure:
 
+
* use '''Side View''' option from '''Favorites menu.'''
  
 
|-
 
|-
Line 357: Line 341:
 
Try moving the small square using left mouse button.
 
Try moving the small square using left mouse button.
  
Dragging it horizontally, adjusts the '''scale factor'''.
+
Dragging it horizontally, adjust the '''scale factor'''.
 
+
  
 
|-
 
|-
Line 368: Line 351:
  
  
Move the '''clipping planes''' that is the two vertical lines using left mouse button.
+
Move the '''clipping planes''' i.e. the two vertical lines using left mouse button.
  
 
|-
 
|-
Line 387: Line 370:
  
  
For now, I want to show the entire protein structure as atoms.
+
For now, I want to show the entire '''protein''' structure as '''atoms'''.
  
 
|-
 
|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on select menu in the menu bar.
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on '''Select''' menu in the menu bar.
  
  
Line 404: Line 387:
 
|-
 
|-
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the window.
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the window.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| However, if nothing is selected from the “'''select'''” menu, it means we want to modify the entire structure.
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| However, if nothing is selected from the “'''Select'''” menu, it means we want to modify the entire structure.
 
+
  
 
|-
 
|-
Line 417: Line 399:
  
 
Click on '''show '''from the sub-menu.
 
Click on '''show '''from the sub-menu.
 
  
 
|-
 
|-
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|-
 
|-
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on “Actions” menu. Scroll down to atoms/bonds. Select “ball and stick” from the sub-menu.
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on “Actions” menu. Scroll down to atoms/bonds. Select “ball and stick” from the sub-menu.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Click on '''Actions''' menu. Scroll down to atoms/bonds. Select '''ball and stick''' from the sub-menu.
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Click on '''Actions''' menu.  
 +
 
 +
Scroll down to atoms/bonds.  
 +
 
 +
 
 +
Select '''ball and stick''' from the sub-menu.
  
 
|-
 
|-
Line 449: Line 435:
  
 
Click on “Structure editing” , from the submenu select “add hydrogens” option.
 
Click on “Structure editing” , from the submenu select “add hydrogens” option.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Notice that the structure is with out hydrogen atoms.
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Notice that the structure is without '''hydrogen''' atoms.
  
 
To add hydrogen atoms, scroll down the '''Tools''' menu.
 
To add hydrogen atoms, scroll down the '''Tools''' menu.
  
Click on '''Structure Editing''', from the submenu select '''add hydrogens''' option.
+
Click on '''Structure Editing'''.
 +
 
 +
From the sub-menu select '''Add hydrogens''' option.
  
 
|-
 
|-
Line 462: Line 450:
  
  
Observe that the structure is now shown with hydrogen atoms.
+
Observe that the structure is now shown with '''hydrogen''' atoms.
  
 
|-
 
|-
Line 469: Line 457:
  
 
the select menu, select solvent.
 
the select menu, select solvent.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Usually the structure of a protein is associated with water molecules.
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| 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.
+
To hide water molecules, go to '''Select '''menu, scroll down to '''Residue''', click on '''HOH''' option.
  
 
|-
 
|-
Line 479: Line 467:
  
 
Go to “Actions” menu scroll down and click on “hide”.
 
Go to “Actions” menu scroll down and click on “hide”.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Observe the screen, all the water molecules are highlighted.
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Observe the screen; all the water molecules are highlighted.
  
  
Go to '''actions''' menu scroll down to '''Atoms\bonds''' and click on '''hide option.'''
+
Go to '''actions''' menu scroll down to '''Atoms\bonds''' and click on '''hide''' option.
  
  
Line 494: Line 482:
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| The '''Presets''' option in the menu bar has some more options to change the display.
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| The '''Presets''' option in the menu bar has some more options to change the display.
  
When you click on I'''nteractive 1''' option:
+
When you click on '''Interactive 1''' option:
 
+
*the structure will be displayed as ribbons,  
 
+
*and both the '''peptide chains''' in different color.
The structure will be displayed as ribbons, and both the peptide chains in different color.
+
  
 
|-
 
|-
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on “Interactive 2” option.
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on “Interactive 2” option.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| '''Interactive 2''' will convert the structure to atoms display.
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| '''Interactive 2''' will convert the structure to '''atoms''' display.
  
 
|-
 
|-
Line 512: Line 499:
  
 
Go to “Actions” menu scroll down to color, select yellow.
 
Go to “Actions” menu scroll down to color, select yellow.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| We can also selectively change the color of peptide chains.
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| We can also selectively change the color of '''peptide chains'''.
  
  
Scroll down the '''Select''' menu and select '''chain''' '''A''' from the sub-menu.
+
Scroll down the '''Select''' menu and select '''chain A''' from the sub-menu.
  
 
Chain A is now highlighted.
 
Chain A is now highlighted.
Line 525: Line 512:
 
|-
 
|-
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Hold ctrl key on the key board and click on anywhere on the Chimera window.  
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Hold ctrl key on the key board and click on anywhere on the Chimera window.  
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To clear the selection, hold CTRL key on the key board and click on the empty space on the Chimera window.  
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To clear the selection, hold '''CTRL''' key on the key board.
  
 +
 +
And click on the empty space on the '''Chimera''' window.
  
 
|-
 
|-
Line 532: Line 521:
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| We have now come to the end of this tutorial.
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| We have now come to the end of this tutorial.
  
To exit the Chimera window, go to '''File '''menu and click on '''quit''' option.
+
To exit the '''Chimera''' window, go to '''File '''menu and click on '''Quit''' option.
  
 
|-
 
|-
Line 542: Line 531:
 
In this tutorial we have learnt to
 
In this tutorial we have learnt to
  
* Open a structure on the Chimera window.
+
* Open a structure on the '''Chimera''' window.
* And also download the PDB file for the protein.
+
* And also download the '''PDB''' file for '''protein''' structures.
 
* Move, rotate and zoom the structure.  
 
* Move, rotate and zoom the structure.  
 
* Scale and clip.<br/>  
 
* Scale and clip.<br/>  
 
  
 
|-
 
|-
Line 552: Line 540:
  
 
'''Summary'''
 
'''Summary'''
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"|* Change the display using menus in the menu bar.
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"|
 +
* Change the display using menus in the menu bar.
 
* Remove the water molecules.
 
* Remove the water molecules.
* Add hydrogens.  
+
* Add '''hydrogens'''.  
 
+
  
 
|-
 
|-
Line 563: Line 551:
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| For the Assignment
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| For the Assignment
  
<nowiki>* </nowiki>Download the pdb file of '''Leucine zipper''' from PDB database.
+
*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'''.
<nowiki>* Open the pdb file </nowiki>on Chimera window using '''open''' option in file menu.
+
 
+
 
+
<nowiki>* </nowiki>Change the display of atoms to '''wire''' and all the aromatic rings as '''disks'''.
+
  
  

Latest revision as of 07:59, 16 December 2015

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