UCSF-Chimera/C2/Writing-Commands/English

Visual Cue	Narration
Slide Number 1 Title Slide	Welcome to this tutorial on Writing Commands in Chimera.
Slide Number 2 Learning Objectives	In this tutorial, we will type commands to- Change the display to atoms. Show and hide ribbons. Change the color of the amino acid residues. Label individual residues.
Slide Number 3 Learning Objectives	Remove solvent molecules. And save the image in different file formats.
Slide Number 4 Pre-requisites	To follow this tutorial you should have knowledge of- Undergraduate Biochemistry Must be familiar with, Structural Biology and Chimera interface. For relevant tutorials, please visit our website.
Slide Number 5 System Requirement	To record this tutorial, I am using Ubuntu OS version. 14.04 Chimera version 1.10.2 Mozilla firefox browser 42.0 And a working Internet connection.
Click on the Chimera icon.	Double-click on the Chimera icon to open the Chimera window.
Click on the lightning bolt icon.	Click on the lightning bolt icon to open the graphics window.
Cursor on the panel. Click on Favorites menu, scroll down. Click on Command line option.	In this tutorial, I will demonstrate how to use commands to manipulate the structure. Open the Command Line using Favorites menu.
Point to the command Cursor on the Command line.	A command text box appears at the bottom of the Chimera window. Tasks performed with menus can be carried out using commands.
Slide Number 6 Chimera Commands	About Chimera Commands. Chimera commands are entered at the Command line. Multiple commands can be combined into one line with semicolon separators. Press Enter key to execute the command.
Slide number 7 Chimera Commands	Previous commands can be accessed from command History. More information about commands is given at the link shown. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/framecore.html
Cursor on the command line.	Back to the Chimera window. Let us open a model of leucine zipper by typing a command.
On the command line text box type open 1zik.	The command starts with a command word. On the command line text box, type- open space 1zik. You need a working Internet connection for this step.
Press enter.	Press Enter to execute the command. The structure appears on the screen.
Type: display Press enter.	To change the ribbons display to atoms, in the command line text box type: The command word display Press Enter.
Cursor on the panel.	We now have the structure of the protein in atoms display. The structure is partially represented as ribbons.
Type: ~ ribbon Press enter.	To hide the ribbons- Type, the wave symbol, also known as tilda, followed by the command word ribbon. A command with a tilda indicates the reverse function. Here, tilda symbol followed by ribbon keyword hides the ribbons. Press Enter.
Cursor on the panel.	We can use color command to set colors to atoms, bonds, surfaces etc.
Type: color yellow :leu	For example, to change the color of all leucines, type: Color space yellow space colon : followed by the three letter abreviation for the amino acid. For leucine, I will type leu. Here color is command word with argument as yellow and the target is all leucines in the structure.
Cursor on the command line.	If you do not specify a target, the entire structure will be colored in yellow. Press Enter. Observe the panel. All the leucines are now colored yellow.
Cursor on the command line. Type color red :18.A Press enter	We can specifically color an amino acid present at a particular location. For example to change the color of histidine, present at position 18 on chain B, type - color space red space colon18.B Press Enter.
Cursor on the panel.	Observe the panel. histidine is now colored in red.
Type rep sphere Press enter	To change the display of the entire structure to CPK spacefill, type rep rep is the truncated version for the keyword represent. rep space sphere ; press Enter. Observe the panel.
Type, rep stick press enter.	To bring back the structure to stick display, again type rep space stick Press Enter
Type del solvent Press enter	To hide the solvent molecules from the structure, type - del (for delete) space solvent Press Enter.
Type, Select :18.A Press enter Type, select :28.B	To activate residues for selection, use select command word. On the command line text box type, select space colon followed by the number and chain of the residue. 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.
Type rlabel sel Press enter	Now to show the label for the residue selected, type rlabel space sel Press Enter.
Cursor on the panel.	Observe the panel. The residue label for the selected residue is displayed.
press up arrow key to get the select command(select :28.B) Type, ~select :28.B	To de-select the residue which we have selected earlier, press up arrow key to get the select command. Type the tilda symbol at the beginning of the command. Press Enter.
Scroll down the commands index page.	A list of keywords and command index is available in the Help menu. Click on the Help menu, scroll down and click on Commands index. A web-page opens with the list of keywords to write commands.
Type: background solid blue Press enter.	Back to the Chimera window. If you want to change the background color from black to blue, type: background space solid space blue Press Enter.
Cursor on the panel.	The panel is now in blue color.
Click on the black triangle present at the right side of the Command line.	To view the Command history, click on the black triangle present at the right side of the Command line.
Cursor on the Command history. Click on any command.	The Command history lists previously used commands. Commands can be re-executed by clicking on the command.
Click on Hide command line option.	To hide the command line, click on Hide command line option in the drop down.
Click on File menu. Scroll down.	There are many options to save the structure you have created. Open the File menu.
Scroll down the File menu.	You can: Restore a Session Save a Session Save the image in JPEG or PNG formats Save the image as PDB or Mol2 files Export the scene etc.
Click on Save Image option.	For demonstration, let me save the image in JPEG format.
Double click on “Desktop”. Type the file name as 1zik. File type as JPEG.	Click on Save image option. A Save image dialog box opens. Select the file location as Desktop. Type the File name as 1zik. Choose the File type as JPEG.
Type, 800 as image width and 600 as height. Click on save button.	Fix the image size according to your requirement. For demonstration, I will type 800 as width and 600 as height. Click on Save button. The image is saved as 1zik.jpg on the Desktop.
Cursor on the panel.	Let's summarize what we have learnt.
Slide Number 8 Summary	In this tutorial we typed commands to, Change the display to atoms. Show and hide ribbons. Change the color of the amino acid residues. Label individual residues.
Slide Number 9 Summary	Remove solvent molecules. Save the image in different file formats.
Slide Number 10 Assignment	Now for the Assignment Type commands to, Load the structure of Human oxy-hemoglobin (PDB code: 2dn1) Change the display to atoms and hide ribbons. Color all histidine residues in green. Remove the solvent molecules. Save the image in JPEG format. Your completed assignment should look as follows.
Slide Number 11 Acknowledgement	The video at the following link summarizes the Spoken Tutorial project. Please download and watch it.
Slide Number 12	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 13	Spoken Tutorial Project is funded by NMEICT, MHRD, Government of India. More information on this Mission is available at the link shown.
	This is Snehalatha from IIT Bombay signing off. Thank you for joining.

Contributors and Content Editors

Nancyvarkey, Snehalathak