UCSF-Chimera/C2/Picking-and-Selection/English-timed

Time	Narration
00:01	Welcome to this tutorial on Picking and Selection using Chimera.
00:06	In this tutorial, we will learn to: show labels for atoms and residues,
00:12	select atoms and residues using Select menu or by Picking,
00:17	change the color and display of the residues,
00:21	add, delete or change atoms , rotate bonds,
00:27	open more than one model on the display window, select and move the model.
00:34	To follow this tutorial, you should have knowledge of undergraduate Biochemistry.
00:40	Or familiar with structural biology. For relevant tutorials, please visit our website.
00:47	To record this tutorial, I am using: Ubuntu Operating System version 14.04,
00:52	Chimera version 1.10.2,
00:57	Mozilla firefox browser 35.0,
01:01	and a working internet connection.
01:04	Here I have opened a Chimera window.
01:07	On the rapid access window, click on 1zik from the list of recently accessed data.
01:15	A model of Leucine zipper opens on the graphics window.
01:20	Individual components of the structure such as: residues, atoms, bonds etc. can be modified using tools available in Chimera.
01:31	The first step is to make selection.
01:34	There are different ways to make a selection: using the Select menu in the menu bar,
01:40	Picking from the graphics window,
01:43	typing commands on the command line, Or by selecting Model Panel and Sequence option present in the Favorites menu.
01:53	Back to the Chimera window.
01:55	Leucine zipper motif consists of periodic repetition of leucine residues.
02:02	I will now demonstrate how to highlight the leucine residues present in this structure.
02:08	From the presets menu, choose interactive 2 option.
02:12	This will convert the structure to atoms display. From the Select menu, choose Residue option.
02:20	The sub-menu has many options.
02:23	The Amino acid category menu has amino acids grouped as aliphatic, aromatic, hydrophobic, polar etc.
02:34	Standard amino acid menu has list of amino acid residues present in the structure. Click on leucine.
02:42	All the leucine residues are now highlighted.
02:46	Click on actions menu, select color.
02:49	I will choose yellow from the list of colors. All the leucines are now displayed in yellow color.
02:57	To clear the selection, click on Select menu. Then click on Clear selection option.
03:03	Leucine being hydrophobic, is packed into the hydrophobic core of the protein.
03:09	Now, change the display to ribbons using presets option. Click on Interactive 1.
03:17	To pick a residue from the screen, hover the cursor over the structure.
03:22	A pop-up balloon appears with identifying information.
03:26	It has information such as residue name, residue number and chain.
03:32	The balloon disappears when you move the cursor.
03:36	Bring the cursor to the first residue on chain A, that is arginine.
03:41	Press and hold the CTRL key on the keyboard and click the left mouse button. Release the CTRL key.
03:49	The outline of the residue is highlighted. By default, the selection is outlined in green.
03:57	If you want to select more than one residue: press and hold both CTRL and shift key on the key board.
04:04	Hover the mouse over the peptide chain. Click on the residues you want to pick.
04:10	Release the CTRL and Shift keys from the keyboard.
04:14	Now you have picked the residues for modification.
04:18	Choose an option from the Actions menu. Click on Actions menu.
04:23	For example: to display atoms, choose atoms/bonds. Click on Show.
04:30	The selected residues are now seen in atoms display. Clear the selection.
04:36	We can also modify atoms or bonds present in the structure by Picking.
04:42	Place the cursor over an object such as an atom or bond.
04:47	This will show its label information in an atomspec balloon.
04:52	Atomspec balloon for an atom has information such as Residue name, number, chain and atom name.
05:01	To select an atom, press and hold the CTRL key on the keyboard.
05:06	While holding the CTRL key, click on the atom you want to change.
05:11	The atom is now highlighted. To modify the atom, double-click on the atom while holding the CTRL key.
05:20	A context menu opens with options.
05:24	Click on Modify-atom option. Release the CTRL key.
05:30	A Build Structure window opens.
05:33	Let us change the selected atom, that is Nitrogen, to a methyl group.
05:38	In the Build Structure window, select Element as carbon, Bonds as 4 and click on Apply button.
05:49	Observe the panel.
05:51	A methyl group is now added to the existing structure. Close the window.
05:57	There is also an option to rotate bonds.
06:00	Hover the cursor over the bond you want to rotate.
06:04	Information regarding the bond appears in the atomspec balloon.
06:09	To select a bond, place the cursor on the bond.
06:13	Press and hold the CTRL key. Click the left mouse button.
06:18	The selected bond is now highlighted. While still holding the CTRL key, double click on the bond.
06:26	Release the CTRL key on the key board.
06:29	A context-menu opens. Click on rotate bond option.
06:35	A Build Structure dialog box appears on the screen.
06:39	Click and rotate the rotating tool that is present in the dialog box.
06:46	Observe the panel. The selected bond is now rotating.
06:51	Stop rotating when you reach the desired angle. Close the dialog box.
06:57	Clear the selection. We can also use Sequence option in the tools menu to highlight the chains.
07:05	Scroll down the tools menu and click on Sequence option.
07:10	Choose Sequence from the sub-menu.
07:13	A Show model sequence dialog box appears.
07:17	Click on chain A if you want to select chain A. Then click on show.
07:23	Another dialog box appears on screen with the amino acid sequence.
07:28	The amino acid residues are represented as single letter abbreviations.
07:34	Click on the sequence to select.
07:37	Observe the panel, Chain A is now highlighted.
07:41	Click on quit to close the window.
07:44	Go to Actions menu, scroll down to Color. Click on yellow option.
07:50	Chain A is now in yellow color. Clear the selection.
07:55	We can open more than one structure on the Chimera window.
07:59	To open a second structure: scroll down the file menu.
08:03	Click on Fetch by ID.
08:06	A Fetch structure by ID dialog box opens.
08:11	Select PDB option. Then type the 4 letter PDB code. For example: to fetch human insulin, type 4ex1.
08:23	Click on fetch button.
08:25	The two protein structures are overlapped on the panel.
08:29	To separate the two overlapping structures, we have to selectively move one model on the panel.
08:36	Open the Command line using favorites menu.
08:39	The Command line appears at the bottom of the window.
08:43	Click to uncheck model zero, which represents leucine zipper.
08:48	Bring the cursor to the insulin structure, hold the center mouse button.
08:54	Then drag to move the insulin model to the desired location on the panel. Release the mouse button.
09:01	To selectively remove model from the screen: open the Model panel using Favorites menu.
09:08	A Model Panel dialog box appears.
09:11	Select the model you want to remove, by clicking on the model ID.
09:16	For example, I want to remove the insulin model from the screen.
09:21	Click on the model ID. Click on close option.
09:26	Observe the panel. The model of insulin is now removed from the screen.
09:32	Close the model panel window.
09:34	We have reached the end of this tutorial.
09:37	Let's summarize what we have learnt.
09:40	In this tutorial, we have learnt to: show labels for atoms and residues,
09:46	select atoms and residues using Select menu or by Picking,
09:51	change the color and display of the residues,
09:55	add, delete or change atoms , rotate bonds,
10:00	open more than one model on the display window, select and move the model.
10:06	For the assignment: open a structure of human insulin, pdb code 4ex1 on the Chimera window.
10:14	Color all the hydrophobic amino acid residues in blue.
10:19	Color all polar residues in red.
10:23	Your completed assignment should look as follows.
10:29	The video at the following link summarizes the Spoken Tutorial project. Please download and watch it.
10:36	The Spoken Tutorial project team conducts workshops and gives certificates for those who pass an online test. For more details, please write to us.
10:45	Spoken Tutorial Project is funded by NMEICT, MHRD, Government of India. More information on this mission is available at the link shown.
10:55	This is Snehalatha from IIT Bombay, signing off. Thank you for joining.

Contributors and Content Editors

Jyotisolanki, PoojaMoolya, Sandhya.np14