UCSF-Chimera/C3/Structure-Analysis/English-timed

Time	Narration
00:01	Welcome to this tutorial on Structure Analysis.
00:05	In this tutorial, we will learn to : measure distance between atoms in the structure, show Hydrogen bonds, identify non-polar interactions,
00:16	and rotate bonds in the residues to get different rotamers.
00:21	To follow this tutorial, you should be familiar with Chimera interface. If not, for relevant tutorials, please visit our website.
00:30	Here, I am using Ubuntu OS version. 14.04 ,Chimera version 1.10.2 , Mozilla firefox browser 42.0 and a working internet connection.
00:46	Here, I have opened a Chimera window.
00:49	Using command line, open a structure of Squalene Synthase. It is a Transferace enzyme with a pdb code 3w7f.
01:00	On the command line, type Open space 3w7f. Press Enter.
01:09	A model of the enzyme is displayed on the panel.
01:12	Change the display to Interactive 1, using Presets menu.
01:18	The protein is displayed as two copies.
01:21	To delete one of the copies, type delete colon dot a, press Enter.
01:29	To delete solvent molecules from the structure, type: delete solvent. Press Enter.
01:37	In this structure, the ligand is farnesyl thiopyrophosphate.
01:43	Label the ligand residues using commands. Type: rlabel space ligand. Press Enter.
01:53	There are two farnesyl thiopyrophosphate, that is, FPS for short in this structure.
02:01	The structures are shown in sticks display.
02:05	Rotate the structure and zoom-in.
02:08	There are several side chains that can donate hydrogen bonds to phosphate oxygens of FPS.
02:15	Place the cursor over the atoms in the side-chain residues.
02:21	Locate Serine 21 residue.
02:23	Now, let's measure the distance between oxygen of Serine 21 and nearest phosphate oxygen of FPS.
02:32	To measure the distance, select oxygen of Serine 21 residue.
02:37	While pressing the CTRL key, click on the side chain oxygen of Serine 21.
02:43	While pressing CTRL and Shift keys simultaneously, double-click on the nearest phosphate oxygen of FPS.
02:52	Select Show Distance from the context menu.
02:56	Observe the panel. The distance between two atoms is displayed. Clear selection.
03:04	Similarly, measure distance between side-chain oxygen of Tyrosine and the same phosphate oxygen of FPS.
03:15	The distances seem consistent with hydrogen bonds.
03:20	Hydrogen bonds with donor and acceptor distances of 2.2 to 2.5 Angstroms are classified as strong, 2.5 to 3.2 as moderate, 3.2 to 4.0 as weak.
03:36	Now, select the ligand using Select menu.
03:40	Scroll down to residue option, click on FPS from the sub-menu.
03:46	The easy way to find hydrogen bonds formed by FPS is to use Find Hydrogen bond feature from Tools menu.
03:55	Click on FindHbond in the Structure Analysis option.
04:01	A H-Bond Parameters dialog opens.
04:05	Fix the color of the hydrogen bond by clicking on the colored box.
04:09	Fix the line width to 3.0 for a thicker line.
04:13	Click on the check box against Label Hydrogen bond with distance.
04:21	Click on Only find H-bonds with at least one end selected.
04:26	And, click on Write information to reply log.
04:31	Click on OK button.
04:33	Observe the panel. Hydrogen bonds are shown as pseudo-bonds of specified color and line width.
04:42	Details of the bonds can be viewed on the Reply log.
04:45	Open Reply log using Favorites menu.
04:49	Information about each hydrogen bond is given here.
04:53	Close the dialog box.
04:55	If you want to remove the hydrogen bonds from the structure- on the command line, type: The Tilda symbol followed by hbond. Press Enter.
05:07	There is another feature in the Tools menu, under Structure Analysis option.
05:13	It is Findclashes/contacts. A dialog box opens.
05:19	This feature identifies non-polar interactions such as Clashes and Contacts.
05:26	Clashes are unfavorable interactions where atoms are too close together.
05:33	Contacts are all direct interactions, polar and non-polar, favorable and unfavorable (including clashes).
05:43	Let us identify contacts of the FPS residues with all other atoms.
05:48	Select FPS residue using Select menu.
05:52	Click on Designate in the Find Clashes/Contacts dialog box.
05:58	It shows 48 atoms designated.
06:02	Click on the radio button against “All other atoms”.
06:06	Set the Clash/Contact Parameters to default Contact.
06:11	Under Treatment of Clash/Contact Atoms, click on the following check boxes. Select, Draw pseudo-bonds, If endpoint atom hidden, and Write information to reply log.
06:27	Click on OK button. Observe the panel.
06:32	All the contacts of FPS residues are shown.
06:37	Open the Reply Log. . Atom-atom contacts are listed here.
06:44	Close the dialog box.
06:46	Now let's display some clashes.
06:49	Let us focus on the residue Tyrosine 248.
06:54	On the command line, type: focus space colon 248. Press Enter.
07:03	Clear the selection.
07:06	Now select Tyrosine 248 residue.
07:10	While pressing the CTRL key, click on any atom in Tyrosine 248.
07:15	Press up-arrow key on the keyboard to select the entire molecule.
07:20	Now, we will rotate the side-chain Tyrosine 248 interactively and check for Clashes.
07:27	Display residues within 4 Angstroms of Tyrosine 248.
07:32	On the command line, type: display, disp space colon 248 space z less than four. (disp :248 z<4) Press Enter.
07:45	To display the clashes, select FindClashes/Contacts option from the Tools menu.
07:53	click on Designate.
07:55	Click the button against “All other atoms”.
07:59	Set the Clash/Contact Parameters to Clash. . The Treatment of Clash/Contact Atoms to Select, Draw pseudobonds, If end point atom hidden.
08:11	And set the Frequency of Checking to Continuously.
08:15	Hide the dialog box.
08:18	To rotate the side-chain of Tyrosine 248 interactively-
08:22	while pressing CTRL key, double-click on the bond that is attached to the ribbon.
08:29	Choose rotate bond option from the context menu.
08:33	A Build structure dialog opens.
08:36	Rotate the bond by dragging the pointer on the dial.
08:41	Alternatively, click on the black arrowheads to edit the angle values.
08:47	Observe the panel. As the side-chain moves, new pseudo-bonds are formed or disappear.
08:55	To revert bond back to the original position: click the entry under Bond. Choose Revert.
09:03	Again click on the bond then Deactivate to make the bond no longer rotate-able.
09:09	Close the dialog box.
09:11	We can compare all the rotamers of Tyrosine 248 using the option in the Tools menu.
09:18	First select Tryrosine 248.
09:22	Click on Tools menu, scroll down to Structure editing.
09:26	Click on Rotamers option.
09:29	In the Rotamer dialog box, select Dunbrack from the rotamer library.
09:36	Click on OK button.
09:38	The rotamers are shown as wire representation on the panel.
09:43	Another dialog opens. Click on the lines in the dialog box to display the rotamer. Observe the panel.
09:52	We can also detect Clash and hydrogen bonds for the rotamers.
09:58	Click on Columns ,then Add. Select Clashes.
10:03	Click on OK in the dialog box.
10:06	Now, to add Hydrogen bonds: click on Columns, scroll down to Add, and select hydrogen bonds.
10:15	Click on OK in the Hydrogen bonds dialog box.
10:19	Observe the dialog, two new columns are added.
10:24	Now each rotamer forms several Clashes but no hydrogen bonds.
10:30	Try finding rotamers by rotating bonds in a different residue.
10:35	Let's summarize. In this tutorial, we have learnt to- measure distance between atoms in the structure,
10:43	show Hydrogen bonds, identify non-polar interactions,
10:48	rotate bonds in the residues to find clashes and contacts and compare different rotamers.
10:56	For the assignment- open a structure of Squalene Synthase, pdb code 3w7f .
11:03	Rotate bonds in Tyrosine 41, residue to determine Clashes and Contacts. And compare the rotamers.
11:11	The video at the following link summarizes the Spoken Tutorial project. Please download and watch it.
11:17	The Spoken Tutorial project team conducts workshops and gives certificates for those who pass an on line test. For more details, please write to us.
11:27	Spoken Tutorial project is funded by NMEICT, MHRD, Government of India. More information on this mission is available at the link shown.
11:37	This is Snehalatha from IIT Bombay, signing off. Thank you for joining.

Contributors and Content Editors

Jyotisolanki, PoojaMoolya, Sandhya.np14