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

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 abreviation 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