UCSF-Chimera/C2/Writing-Commands/English-timed
From Script | Spoken-Tutorial
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| 00:01 | Welcome to this tutorial on Writing Commands in Chimera. |
| 00:06 | In this tutorial, we will type commands to- change the display to atoms, |
| 00:12 | show and hide ribbons, |
| 00:14 | change the color of the amino acid residues, |
| 00:18 | label individual residues, |
| 00:21 | remove solvent molecules and save the image in different file formats. |
| 00:28 | To follow this tutorial, you should have knowledge of- undergraduate Biochemistry, |
| 00:34 | must be familiar with Structural Biology and Chimera interface. |
| 00:40 | For relevant tutorials, please visit our website. |
| 00:44 | To record this tutorial, I am using Ubuntu OS version 14.04, |
| 00:50 | Chimera version 1.10.2, |
| 00:53 | Mozilla firefox browser 42.0 and a working internet connection. |
| 01:00 | Double-click on the Chimera icon to open the Chimera window. |
| 01:06 | Click on the lightning bolt icon to open the graphics window. |
| 01:10 | In this tutorial, I will demonstrate how to use commands to manipulate the structure. |
| 01:16 | Open the Command Line using Favorites menu. |
| 01:20 | A command text box appears at the bottom of the Chimera window. |
| 01:25 | Tasks performed with menus can be carried out using commands. |
| 01:31 | About Chimera Commands- |
| 01:34 | Chimera commands are entered at the Command line. |
| 01:38 | Multiple commands can be combined into one line with semicolon separators. |
| 01:43 | Press Enter key to execute the command. |
| 01:47 | Previous commands can be accessed from command History. |
| 01:51 | More information about commands is given at the link shown. |
| 01:56 | Back to the Chimera window. Let us open a model of leucine zipper by typing a command. |
| 02:03 | The command starts with a command word. |
| 02:06 | On the command line text box, type- "open space 1zik". |
| 02:13 | You need a working internet connection for this step. |
| 02:17 | Press Enter to execute the command. |
| 02:20 | The structure appears on the screen. |
| 02:23 | To change the ribbons display to atoms- in the command line text box, type the command word display . Press Enter. |
| 02:34 | We now have the structure of the protein in atoms display. |
| 02:38 | The structure is partially represented as ribbons. |
| 02:42 | To hide the ribbons- type the wave symbol, also known as tilda, followed by the command word ribbon. |
| 02:51 | A command with a tilda indicates the reverse function. |
| 02:55 | Here, tilda symbol followed by ribbon keyword hides the ribbons.
Press Enter. |
| 03:03 | We can use color command to set colors to atoms, bonds, surfaces etc. |
| 03:10 | For example, to change the color of all leucines, type:
color space yellow space colon followed by the three letter abbreviation for the amino acid. |
| 03:24 | For leucine, I will type leu. |
| 03:28 | Here, color is command word with argument as yellow and the target is all leucines in the structure. |
| 03:37 | If you do not specify a target, the entire structure will be colored in yellow.
Press Enter. |
| 03:45 | Observe the panel. All the leucines are now colored yellow. |
| 03:51 | We can specifically color an amino acid present at a particular location. |
| 03:56 | For example, to change the color of histidine, present at position 18 on chain B, type -
color space red space colon18.B. Press Enter. |
| 04:13 | Observe the panel. histidine is now colored in red. |
| 04:19 | To change the display of the entire structure to CPK spacefill, type rep . |
| 04:26 | rep is the truncated version for the keyword represent. rep space sphere ; press Enter. |
| 04:37 | Observe the panel. |
| 04:39 | To bring back the structure to stick display, again type rep space stick
Press Enter |
| 04:50 | To hide the solvent molecules from the structure, type - del (for delete) space solvent
Press Enter. |
| 05:02 | To activate residues for selection, use select command word. |
| 05:08 | On the command line text box type: select space colon followed by the number and chain of the residue. |
| 05:18 | For example, to activate the lysine present at the position 28, on chain B, type:select space colon followed by 28 dot B . Press Enter. |
| 05:34 | Now, to show the label for the residue selected, type: rlabel space sel
Press Enter. |
| 05:44 | Observe the panel. The residue label for the selected residue is displayed. |
| 05:51 | To de-select the residue which we have selected earlier, press up-arrow key to get the select command. |
| 05:59 | Type the tilda symbol at the beginning of the command. Press Enter. |
| 06:05 | A list of keywords and command index is available in the Help menu. |
| 06:09 | Click on the Help menu, scroll down and click on Commands index. |
| 06:16 | A web-page opens with the list of keywords to write commands. |
| 06:22 | Back to the Chimera window. |
| 06:25 | If you want to change the background color from black to blue, type: background space solid space blue
Press Enter. |
| 06:38 | The panel is now blue in color. |
| 06:41 | To view the Command history, click on the black triangle present at the right side of the Command line. |
| 06:48 | The Command history lists previously used commands. |
| 06:53 | Commands can be re-executed by clicking on the command. |
| 06:57 | To hide the command line, click on Hide command line option in the drop-down. |
| 07:03 | There are many options to save the structure you have created. Open the File menu. |
| 07:09 | You can: Restore a Session, Save a Session, |
| 07:14 | save the image in JPEG or PNG formats, |
| 07:19 | save the image as PDB or Mol2 files, Export the scene etc. |
| 07:27 | For demonstration, let me save the image in JPEG format. |
| 07:33 | Click on Save image option. A Save image dialog box opens. |
| 07:40 | Select the file location as Desktop. |
| 07:44 | Type the File name as 1zik. Choose the File type as JPEG. |
| 07:52 | Fix the image size according to your requirement. |
| 07:56 | For demonstration, I will type 800 as width and 600 as height. |
| 08:05 | Click on Save button. The image is saved as 1zik.jpg on the Desktop. |
| 08:15 | Let's summarize what we have learnt. |
| 08:17 | In this tutorial, we typed commands to: change the display to atoms, |
| 08:22 | show and hide ribbons, |
| 08:25 | change the color of the amino acid residues, |
| 08:28 | label individual residues, |
| 08:31 | remove solvent molecules, save the image in different file formats. |
| 08:38 | Now for the assignment:
Type commands to- load the structure of Human oxy-hemoglobin (PDB code: 2dn1). |
| 08:48 | Change the display to atoms and hide ribbons. |
| 08:52 | Color all histidine residues in green. |
| 08:56 | Remove the solvent molecules and save the image in JPEG format. |
| 09:03 | Your completed assignment should look as follows. |
| 09:12 | The video at the following link summarizes the Spoken Tutorial project.
Please download and watch it. |
| 09:19 | The Spoken Tutorial Project team conducts workshops and gives certificates for those who pass an online test.
For more details, please write to us. |
| 09:29 | Spoken Tutorial Project is funded by NMEICT, MHRD, Government of India. |
| 09:35 | More information on this mission is available at the link shown. |
| 09:40 | This is Snehalatha from IIT Bombay, signing off. Thank you for joining. |
