Difference between revisions of "UCSF-Chimera/C2/Structure-Manipulation/English-timed"
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| | 00:01 | | | 00:01 | ||
− | | | Welcome to this tutorial on '''Structure Manipulation '''using Chimera. | + | | | Welcome to this tutorial on '''Structure Manipulation '''using '''Chimera'''. |
|- | |- | ||
| |00:06 | | |00:06 | ||
− | | | In this tutorial, we will learn to | + | | | In this tutorial, we will learn to: open a structure on the '''Chimera window''', |
|- | |- | ||
| |00:12 | | |00:12 | ||
− | | | | + | | | move, rotate and zoom the structure, scale and clip, and change the display of the structure. |
|- | |- | ||
| |00:20 | | |00:20 | ||
− | | | To follow this tutorial you should have knowledge of | + | | | To follow this tutorial, you should have knowledge of undergraduate Biochemistry or |
− | must be familiar with Structural Biology | + | must be familiar with Structural Biology. |
|- | |- | ||
| | 00:29 | | | 00:29 | ||
− | | | To record this tutorial I am using | + | | | 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 | + | '''Mozilla Firefox''' browser 35.0 and a working internet connection. |
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| | 00:55 | | | 00:55 | ||
− | | |'''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'''. |
|- | |- | ||
| |01:05 | | |01:05 | ||
− | | | | + | | | More information is available at the given link. |
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| |01:20 | | |01:20 | ||
− | | | '''Rapid access''' window allows you to access the frequently used data and | + | | | '''Rapid access''' window allows you to access the frequently used '''data''' and '''tool'''s. |
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| |02:25 | | |02:25 | ||
− | | | To resize the window, drag any corner of the window. | + | | | To '''resize''' the window, drag any corner of the window. |
|- | |- | ||
| | 02:30 | | | 02:30 | ||
− | | | Now let us see how to open a '''protein''' structure. | + | | | Now, let us see how to open a '''protein''' structure. |
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| | 02:45 | | | 02:45 | ||
− | | |A dialog box appears on the screen. | + | | |A dialog box appears on the '''screen'''. |
|- | |- | ||
| | 02:48 | | | 02:48 | ||
− | | |You can connect to various | + | | |You can connect to various '''database'''s to fetch the structure. |
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| | 03:08 | | | 03:08 | ||
− | | | I will type '''1zik''' (one z i k) | + | | | I will type '''1zik''' (one z i k). |
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| |03:19 | | |03:19 | ||
− | | | By default, a ribbons display of the '''protein''' will appear on the display window. | + | | | By default, a '''ribbons''' display of the '''protein''' will appear on the display window. |
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| | 03:29 | | | 03:29 | ||
− | | |In the '''command line''' text box type “'''open 1zik'''” | + | | |In the '''command line''' text box, type “'''open 1zik'''”. |
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| | 03:40 | | | 03:40 | ||
− | | | If you are not connected to | + | | | If you are not connected to internet, you can open the already downloaded '''pdb''' file. |
|- | |- | ||
| | 03:46 | | | 03:46 | ||
− | | |To clear the structure present on the screen:scroll down the '''Favorites''' menu and click on '''Model Panel''' option. | + | | |To clear the structure present on the screen: scroll down the '''Favorites''' menu and click on '''Model Panel''' option. |
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| | 04:12 | | | 04:12 | ||
− | | |You need a working | + | | |You need a working internet connection to download the '''pdb''' file. |
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| | 04:37 | | | 04:37 | ||
− | | |If you know the '''pdb''' code for the '''protein''', type in the text box provided. Or type the name of the '''protein'''. | + | | |If you know the '''pdb''' code for the '''protein''', type in the text box provided. Or, type the name of the '''protein'''. |
|- | |- | ||
| | 04:46 | | | 04:46 | ||
− | | |I know the '''pdb''' code for '''leucine zipper''', | + | | |I know the '''pdb''' code for '''leucine zipper'''. So, I will type “'''1zik”''' in the text box. |
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| | 05:06 | | | 05:06 | ||
− | | |From the drop-down menu click on '''PDB-file-text''' option | + | | |From the drop-down menu click on '''PDB-file-text''' option. |
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| | 05:47 | | | 05:47 | ||
− | | | A model of '''leucine zipper''' is displayed on the panel. | + | | | A model of '''leucine zipper''' is displayed on the '''panel'''. |
|- | |- | ||
| | 05:51 | | | 05:51 | ||
− | | |By default, the two '''peptide chains''' are displayed as grey | + | | |By default, the two '''peptide chains''' are displayed as grey '''ribbon'''s. |
|- | |- | ||
| | 05:57 | | | 05:57 | ||
− | | | Use the mouse button to move the structure on the panel. | + | | | Use the '''mouse''' button to move the structure on the panel. |
|- | |- | ||
| | 06:01 | | | 06:01 | ||
− | | |Left mouse button for rotation | + | | |Left '''mouse''' button for rotation, |
|- | |- | ||
| | 06:04 | | | 06:04 | ||
− | | | | + | | |the middle mouse button controls '''xy translation'''. |
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| | 06:27 | | | 06:27 | ||
− | | |The yellow square on the left represents the viewer's eye position | + | | |The yellow square on the left, represents the viewer's eye position |
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| | 06:41 | | | 06:41 | ||
− | | | Double-clicking the eye position shows a menu for changing the camera mode. | + | | | Double-clicking the eye position shows a menu for changing the '''camera mode'''. |
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| | 06:53 | | | 06:53 | ||
− | | | There are more viewing controls on the window | + | | | There are more viewing controls on the window which you can explore. |
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| | 07:19 | | | 07:19 | ||
− | | |'''Select''' menu in the menu bar will allow us to select individual components of the structure | + | | |'''Select''' menu in the menu bar will allow us to select individual components of the structure |
|- | |- | ||
| | 07:25 | | | 07:25 | ||
− | | | | + | | |such as '''chain, element, residue, ligand''' etc. |
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| | 07:31 | | | 07:31 | ||
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| | 07:49 | | | 07:49 | ||
− | | | On the screen we see atoms as well as part of the structure as ribbons. | + | | | On the screen, we see atoms as well as part of the structure as ribbons. |
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| | 08:21 | | | 08:21 | ||
− | | |Scroll down to atoms/bonds. | + | | |Scroll down to '''atoms/bonds'''. |
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| | 08:40 | | | 08:40 | ||
− | | |From the sub-menu select '''Add hydrogens''' option. | + | | |From the sub-menu, select '''Add hydrogens''' option. |
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| | 09:18 | | | 09:18 | ||
− | | |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. |
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| | 09:36 | | | 09:36 | ||
− | | |When you click on '''Interactive 1''' option: the structure will be displayed as ribbons | + | | |When you click on '''Interactive 1''' option: the structure will be displayed as ribbons and both the '''peptide chains''' in different color. |
− | and both the '''peptide chains''' in different color. | + | |
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| | 10:02 | | | 10:02 | ||
− | | |Chain A is now highlighted. | + | | |'''Chain A''' is now highlighted. |
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| | 10:11 | | | 10:11 | ||
− | | |Chain A is now displayed in yellow color. | + | | |'''Chain A''' is now displayed in yellow color. |
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| | 10:32 | | | 10:32 | ||
− | | | Let's summarize | + | | | 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 | | | 10:43 | ||
− | | | | + | | | move, rotate and zoom the structure, Scale and clip, |
|- | |- | ||
| |10:49 | | |10:49 | ||
− | | | | + | | | change the display using menus in the menu bar, |
|- | |- | ||
| | 10:53 | | | 10:53 | ||
− | | | | + | | |remove the water molecules, and add '''hydrogens'''. |
|- | |- | ||
| |10:57 | | |10:57 | ||
− | | | For the Assignment | + | | | For the Assignment, download the '''pdb''' file of '''Leucine zipper''' from '''PDB''' database. |
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| | 11:21 | | | 11:21 | ||
− | | | The video at the following link summarizes the Spoken Tutorial project. | + | | | The video at the following link summarizes the '''Spoken Tutorial''' project. |
|- | |- | ||
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| | 11:38 | | | 11:38 | ||
− | | | Spoken Tutorial Project is funded by NMEICT, MHRD, Government of India. | + | | | Spoken Tutorial Project is funded by '''NMEICT, MHRD''', Government of India. |
|- | |- | ||
| | 11:44 | | | 11:44 | ||
− | | |More information on this | + | | |More information on this mission is available at the link shown. |
|- | |- | ||
| |11:48 | | |11:48 | ||
− | | | This is Snehalatha from IIT Bombay signing off. Thank you for joining. | + | | | This is Snehalatha from IIT Bombay, signing off. |
+ | Thank you for joining. | ||
|} | |} |
Latest revision as of 16:44, 25 June 2018
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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. |