UCSF-Chimera/C2/Writing-Commands/English-timed

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Time
Narration
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.

Contributors and Content Editors

PoojaMoolya, Sandhya.np14