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

Sandhya.np14 at 09:28, 28 June 2018

2018-06-28T09:28:10Z

Sandhya.np14 at 09:49, 27 June 2018

2018-06-27T09:49:43Z

Sandhya.np14 at 07:41, 27 June 2018

2018-06-27T07:41:14Z

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PoojaMoolya at 10:54, 27 February 2018

2018-02-27T10:54:22Z

Jyotisolanki: Created page with " {| border=1 || '''Time''' || '''Narration''' |- | | 00:01 | | Welcome to this tutorial on '''Structure Analysis'''. |- | | 00:05 | | In this tutorial, we will learn to : Me..."

2017-11-16T10:18:34Z

Created page with " {| border=1 || '''Time''' || '''Narration''' |- | | 00:01 | | Welcome to this tutorial on '''Structure Analysis'''. |- | | 00:05 | | In this tutorial, we will learn to : Me..."

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{| border=1
|| '''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''', typen''' 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, lets 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 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.

|}

@@ Line 10: / Line 10: @@
 |-
 | | 00:05
-| | In this tutorial, we will learn to : measure distance between atoms in the structure, show Hydrogen bonds,  identify non-polar interactions,
+| | In this tutorial, we will learn to : measure distance between atoms in the structure, show Hydrogen '''bond'''s,  identify non-polar interactions,
 |-

@@ Line 234: / Line 234: @@
 |-
 | |06:06
-| | Set the '''Clash/Contact''' parameters to default '''Contact.'''
+| | Set the '''Clash/Contact Parameters''' to default '''Contact.'''
 |-
@@ Line 310: / Line 310: @@
 |-
 | | 07:59
-| | Set the '''Clash/Contact Parameters''' to '''Clash. ''' . The ''' Treatment of Clash/Contact Atoms''' to  '''Select'''  ,  '''Draw pseudobonds''' , '''If end point atom hidden'''
+| | Set the '''Clash/Contact Parameters''' to '''Clash. ''' . The ''' Treatment of Clash/Contact Atoms''' to  '''Select''',  '''Draw pseudobonds''', '''If end point atom hidden'''.
 |-
@@ Line 322: / Line 322: @@
 |-
 | | 08:18
-| | To rotate the side-chain of '''Tyrosine 248''' interactively;
+| | 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'''.
+| |while pressing '''CTRL''' key, double-click on the '''bond''' that is attached to the '''ribbon'''.
 |-
@@ Line 350: / Line 350: @@
 |-
 | | 08:55
-| | To revert bond back to the original position:  Click the entry under '''Bond'''. Choose '''Revert'''.
+| | To revert bond back to the original position:  click the entry under '''Bond'''. Choose '''Revert'''.
 |-
@@ Line 406: / Line 406: @@
 |-
 | | 10:06
-| | Now to add Hydrogen bonds: Click on '''Columns''', scroll down to '''Add''', and select '''hydrogen bonds.'''
+| | Now, to add Hydrogen bonds: click on '''Columns''', scroll down to '''Add''', and select '''hydrogen bonds.'''
 |-
@@ Line 426: / Line 426: @@
 |-
 | | 10:35
-| | Let's summarize. In this tutorial we have learnt to- Measure distance between atoms in the structure .
+| | 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
+| |show '''Hydrogen bonds''', identify non-polar interactions,
 |-
 | | 10:48
-| |Rotate bonds in the residues to find '''clashes''' and '''contacts'''.  And compare different '''rotamers'''.
+| |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 .'''
+| | For the assignment- open a structure of '''Squalene Synthase''', '''pdb code 3w7f .'''
 |-
@@ Line 446: / Line 446: @@
 |-
 | | 11:11
-| | The video at the following link summarizes the '''Spoken Tutorial project. ''' Please download and watch it.
+| | 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.
+| | 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
+| | 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.
+| | This is Snehalatha from IIT Bombay, signing off. Thank you for joining.
 |}