Difference between revisions of "UCSF-Chimera/C3/Structure-Analysis/English-timed"

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| | In this tutorial, we will learn to : Measure distance between atoms in the structure.Show Hydrogen bonds,  Identify non-polar interactions.
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| | In this tutorial, we will learn to : measure distance between atoms in the structure, show Hydrogen bonds,  identify non-polar interactions,
  
 
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| | 00:16
 
| | 00:16
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| And rotate bonds in the '''residues''' to get different '''rotamers'''
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| and rotate bonds in the '''residues''' to get different '''rotamers'''.
  
 
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| | 00:21
 
| | 00:21
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| | To follow this tutorial you should be familiar with '''Chimera '''Interface. If not, for relevant tutorials, please visit our website.  
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| | To follow this tutorial, you should be familiar with '''Chimera '''interface. If not, for relevant tutorials, please visit our '''website'''.  
  
 
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| |00:30
 
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| | Here I am using '''Ubuntu''' OS version. 14.04 ,'''Chimera''' version 1.10.2 , '''Mozilla firefox''' browser 42.0 , And a working Internet connection.
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| | Here, I am using '''Ubuntu OS''' version. '''14.04''' ,'''Chimera''' version '''1.10.2''' , '''Mozilla firefox''' browser '''42.0''' and a working internet connection.
  
 
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| | 00:46
 
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| | Here I have opened a '''Chimera''' window.
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| | Here, I have opened a '''Chimera''' window.
  
 
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| | 00:49
 
| | 00:49
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| | Using '''command line''', open a structure of '''Squalene Synthase.''' It is a '''Transferace''' '''enzyme''' with a '''pdb code 3w7f'''.
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| | Using '''command line''', open a structure of '''Squalene Synthase.''' It is a '''Transferace enzyme''' with a '''pdb code 3w7f'''.
  
 
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| | 01:00
 
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| |On the '''command line''', typen''' Open space 3w7f''' Press '''Enter'''.
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| |On the '''command line''', type''' Open space 3w7f'''. Press '''Enter'''.
  
 
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| |Change the display to '''Interactive 1, '''using '''Presets menu'''.
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| |Change the display to '''Interactive 1, '''using '''Presets''' menu.
  
 
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| | 01:21
 
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| |To delete one of the copies, type  '''delete colon dot a''' Press '''Enter'''.
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| |To delete one of the copies, type  '''delete colon dot a''', press '''Enter'''.
  
 
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| | 01:29
 
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| | To delete solvent molecules from the structure, type  '''delete solvent'''Press '''Enter'''.
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| | To delete solvent molecules from the structure, type: '''delete solvent'''. Press '''Enter'''.
  
 
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| | Label the '''ligand residues''' using '''commands'''. Type, '''rlabel '''space''' ligand''' Press '''Enter'''.
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| | Label the '''ligand residues''' using '''commands'''. Type: '''rlabel '''space''' ligand'''. Press '''Enter'''.
  
 
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| | 01:53
 
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| | There are two''' farnesyl thiopyrophosphate:''' that is''', FPS '''for short in this structure.
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| | There are two''' farnesyl thiopyrophosphate,''' that is, '''FPS '''for short in this structure.
  
 
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| | There are several side chains that can donate '''hydrogen bonds''' to '''phosphate oxygens''' of '''FPS'''.
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| | There are several side chains that can donate hydrogen bonds to '''phosphate oxygens''' of '''FPS'''.
  
 
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| |Now, lets measure the distance between  '''oxygen '''of '''Serine 21''': and nearest '''phosphate oxygen''' of '''FPS.'''
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| |Now, let's measure the distance between  oxygen of '''Serine 21''' and nearest '''phosphate oxygen''' of '''FPS.'''
  
 
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| | '''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.  
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| | '''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.  
  
 
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| |Scroll down to residue option, click on '''FPS''' from the sub-menu.  
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| |Scroll down to '''residue''' option, click on '''FPS''' from the sub-menu.  
  
 
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| |Click on '''FindHbond''' in the''' Structure Analysis option.'''
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| |Click on '''FindHbond''' in the''' Structure Analysis''' option.
  
 
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| |Fix the line width to 3.0 for a thicker line.
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| |Fix the '''line width''' to 3.0 for a thicker line.
  
 
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| | And click on '''Write information to reply log'''.
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| | And, click on '''Write information to reply log'''.
  
 
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| | Details of the bonds can viewed on the '''Reply log'''.  
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| | Details of the bonds can be viewed on the '''Reply log'''.  
  
 
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| |Open '''Reply log '''using''' Favorites menu.'''
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| |Open '''Reply log '''using''' Favorites''' menu.
  
 
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| | If you want to remove the '''hydrogen bonds''' from the structure,On the command line type: '''The Tilda symbol '''followed by''' hbond ''' Press '''Enter'''.
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| | If you want to remove the '''hydrogen bonds''' from the structure- on the command line, type: The Tilda symbol followed by '''hbond'''.  Press '''Enter'''.
  
 
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| |05:07
 
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| | There is another feature in the''' Tools''' menu under '''Structure Analysis''' option.
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| | There is another feature in the''' Tools''' menu, under '''Structure Analysis''' option.
  
 
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| |  '''''Clashes''''' are unfavorable interactions where atoms are too close together.
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| |  '''Clashes''' are unfavorable interactions where atoms are too close together.
  
 
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| |'''''Contacts''''' are all direct interactions: polar and non-polar, favorable and unfavorable (including clashes)  
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| |'''Contacts''' are all direct interactions, polar and non-polar, favorable and unfavorable (including clashes).
  
 
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| |Click on '''Designate''' in the '''Find Clashes/Contacts dialog box.'''
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| |Click on '''Designate''' in the '''Find Clashes/Contacts''' dialog box.
  
 
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| | Set the '''Clash/Contact Parameters''' to default '''Contact.'''
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| | Set the '''Clash/Contact''' parameters to default '''Contact.'''
  
 
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| | 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'''
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| | 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'''.
  
 
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| | On the '''command line''' type:  '''focus space colon 248''' Press '''Enter'''.
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| | On the '''command line''', type:  '''focus space colon 248'''. Press '''Enter'''.
  
 
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| |Press up arrow key on the '''keyboard''' to select the entire molecule.
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| |Press up-arrow key on the keyboard to select the entire molecule.
  
 
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| | 07:20
 
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| | Now we will rotate the side-chain '''Tyrosine 248''' interactively and check for '''Clashes'''.
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| | Now, we will rotate the side-chain '''Tyrosine 248''' interactively and check for '''Clashes'''.
  
 
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| |On the '''command line''' type display, '''disp space colon 248 space z less than four. ''' (disp :248 z<4) Press '''Enter'''.
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| |On the '''command line''', type: display, '''disp space colon 248 space z less than four. ''' (disp :248 z<4) Press '''Enter'''.
  
 
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Revision as of 13:11, 27 June 2018

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

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