Difference between revisions of "UCSF-Chimera/C3/Superimposing-and-Morphing/English-timed"

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| 01:32
 
| 01:32
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| This structure is bound to the substrate analog '''Farnesyl thiopyrophosphate'''. '''FPS''' in short.
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| This structure is bound to the '''substrate analog Farnesyl thiopyrophosphate''', '''FPS''' in short.
  
 
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|-
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| 01:46
 
| 01:46
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|For this we will fetch a structure of the same enzyme without substrate.
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|For this, we will fetch a structure of the same enzyme without substrate.
  
 
|-
 
|-
 
| 01:52   
 
| 01:52   
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| On the '''command line''' type “'''open 2zco'''” press enter.
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| On the '''command line''', type: “'''open 2zco'''”, press '''Enter'''.
  
 
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|-
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| 02:05
 
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| Now these two structures are ready to be '''superimposed'''.
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| Now, these two structures are ready to be superimposed.
  
 
|-
 
|-
 
| 02:10
 
| 02:10
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| '''Superimposition or Structural alignment''' is a tool to compare two or more '''protein''' structures.
+
| '''Superimposition''' or '''Structural alignment''' is a tool to compare two or more '''protein''' structures.
  
 
|-
 
|-
 
| 02:18
 
| 02:18
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|The alignment is based on their shape and three-dimensional conformation.
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|The alignment is based on their shape and three-dimensional '''conformation'''.
  
 
|-
 
|-
 
| 02:24
 
| 02:24
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| Before we start '''superimposing''', let us place some icons in the tool bar.  
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| Before we start superimposing, let us place some '''icon'''s in the tool bar.  
  
 
|-
 
|-
 
| 02:30
 
| 02:30
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| Click on '''Favorites menu.'''
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| Click on '''Favorites''' menu.
  
 
|-
 
|-
 
| 02:32
 
| 02:32
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|'''Scroll down to Add to favorites/Tool bar '''option.
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|Scroll down to '''Add to favorites/Tool bar '''option.
  
 
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|-
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| 02:53  
 
| 02:53  
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| Check boxes for, '''Command line''' , '''Model Panel''' , '''Side View'''.
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| Check boxes for '''Command line''' , '''Model Panel''' , '''Side View'''.
  
 
|-
 
|-
 
| 02:59  
 
| 02:59  
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| Scroll down and click on, '''MatchMaker '''  and '''Match-Align'''
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| Scroll down and click on '''MatchMaker '''  and '''Match-Align'''.
  
 
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|-
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| 03:08
 
| 03:08
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|Select tools according to your requirement.
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|Select '''tool'''s according to your requirement.
  
 
|-
 
|-
 
| 03:12
 
| 03:12
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| Observe the panel.  
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| Observe the '''panel'''.  
  
 
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| 03:43   
 
| 03:43   
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| Now let us '''superimpose''' the structures using '''MatchMaker''' function.
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| Now, let us '''superimpose''' the structures using '''MatchMaker''' function.
  
 
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|04:01  
 
|04:01  
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|For now, let us continue with the default settings. Press '''OK''' button.  
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|For now, let us continue with the '''default setting'''s. Press '''OK''' button.  
  
 
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| 04:09
 
| 04:09
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|The two structures are '''superimposed''' on each other.
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|The two structures are superimposed on each other.
  
 
|-
 
|-
 
|04:13
 
|04:13
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| The two structures are almost completely '''superimposable''' with each other.
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| The two structures are almost completely superimposable with each other
  
 
|-
 
|-
 
|04:19
 
|04:19
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|Except for a small part which is '''non-superimposable'''.
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|except for a small part which is non-superimposable.
  
 
|-
 
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|04:23  
 
|04:23  
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| The fragment involved in this '''non-superimposable''' part starts from : The '''amino acid''' number 53 to '''amino acid''' number 57.
+
| The fragment involved in this non-superimposable part starts from the '''amino acid''' number 53 to '''amino acid''' number 57.
  
 
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|04:55   
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| To select the chains, click on their '''pdb Ids'''.
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| To select the '''chain'''s, click on their '''pdb Ids'''.
  
 
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|05:05   
 
|05:05   
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| In this box the '''amino acid '''pairs used in the final fit, are shown with light orange boxes.
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| In this box, the '''amino acid '''pairs used in the final fit, are shown with light orange boxes.
  
 
|-
 
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|05:13
 
|05:13
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| The structures are mostly similar except for the loop at residues 52-54.
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| The structures are mostly similar except for the '''loop''' at '''residues 52-54'''.
  
 
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| This corresponds to the '''non-superimposable''' part of the structure.
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| This corresponds to the non-superimposable part of the structure.
  
 
|-
 
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|05:50  
 
|05:50  
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| You can change the color of this '''non-superimposing''' parts using '''Actions''' menu.
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| You can change the color of this non-superimposing parts using '''Actions''' menu.
  
 
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| Now, let me demonstrate how to morph '''conformations''' and create a trajectory.
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| Now, let me demonstrate how to morph '''conformations''' and create a '''trajectory'''.
  
 
|-
 
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|06:15  
 
|06:15  
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| '''Morphing''' involves calculating a series of intermediate structures between the original input structures.
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| Morphing involves calculating a series of intermediate structures between the original input structures.
  
 
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|06:23  
 
|06:23  
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| The series of intermediate structures created can be saved as '''Molecular Dynamics Movie.'''- in short''' MD Movie.'''
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| The series of intermediate structures created can be saved as '''Molecular Dynamics Movie,''' in short,''' MD Movie.'''
  
 
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| Click on '''Tools menu scroll down to Structure Comparison.'''
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| Click on '''Tools''' menu, scroll down to '''Structure Comparison'''.
  
 
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|06:42   
 
|06:42   
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| '''Click on Morph conformations '''option.
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| Click on '''Morph conformations '''option.
  
 
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| In the resulting list of the models dialog box; double click on model number zero, that is '''3w7f''' to add to the conformations.
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| In the resulting list of the models dialog box, double click on model number zero, that is, '''3w7f''' to add to the conformations.
  
 
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|07:03  
 
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| Next click on model number 1 that is '''2zco'''.
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| Next, click on model number 1, that is, '''2zco'''.
  
 
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| This sequence corresponds to : a morph '''trajectory''' from ligand , bound to the structure to empty structure ,  and then back.
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| This sequence corresponds to a morph '''trajectory''' from '''ligand''', bound to the structure to empty structure and then back.
  
 
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| After a few seconds a''' MD Movie''' is created.  
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| After a few seconds, a''' MD Movie''' is created.  
  
 
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| The dialog box has buttons to play or pause the movie.
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| The dialog box has buttons to '''play''' or '''pause''' the movie.
  
 
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| Now let's summarize what we have learnt.
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| Now, let's summarize what we have learnt.
  
 
|-
 
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|08:05   
 
|08:05   
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| In this tutorial we have learnt to, '''Superimpose '''and compare different structures of the same protein.
+
| In this tutorial, we have learnt to: '''superimpose '''and compare different structures of the same protein,
  
 
|-
 
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|08:12   
 
|08:12   
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| Morph '''conformations''' and create a '''trajectory'''.
+
| morph '''conformations''' and create a '''trajectory''',
  
 
|-
 
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|08:16   
 
|08:16   
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| Save the trajectory as '''Molecular Dynamics Movie.'''
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| '''save''' the trajectory as '''Molecular Dynamics Movie.'''
  
 
|-
 
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|08:20
 
|08:20
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| For the assignment, Open the structures of '''GTP binding '''proteins with the '''PDB code''': '''1TAG''' and '''1TND'''
+
| For the assignment, open the structures of '''GTP binding '''proteins with the '''PDB code''': '''1TAG''' and '''1TND'''
  
 
|-
 
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|08:31  
 
|08:31  
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| Superimpose the structures using '''MatchMaker''' tool.  
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| '''Superimpose''' the structures using '''MatchMaker''' tool.  
  
 
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|08:48  
 
|08:48  
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| The '''Spoken Tutorial Project''' Team conducts workshops and  gives certificates for those who pass an online test.  For more details, please write to us.  
+
| The '''Spoken Tutorial Project''' team conducts workshops and  gives certificates for those who pass an online test.  For more details, please write to us.  
  
 
|-
 
|-
 
| 08:57
 
| 08:57
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| '''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.
  
 
|-
 
|-
 
|09:09  
 
|09:09  
−
| This is '''Snehalatha''' from '''IIT Bombay''' signing off. Thank you for joining.  
+
| This is '''Snehalatha''' from '''IIT Bombay''', signing off. Thank you for joining.  
  
 
|}
 
|}

Latest revision as of 13:50, 28 June 2018

Time Narration
00:01 Welcome to this tutorial on Superimposing and Morphing.
00:06 In this tutorial, we will learn to: superimpose and compare different structures of the same protein,
00:13 morph conformations and create a trajectory.
00:17 To follow this tutorial, you should be familiar with Chimera interface.
00:22 If not, for relevant tutorials, please visit our website.
00:27 Here I am using :Ubuntu OS version 14.04, Chimera version 1.10.2 , Mozilla firefox browser 42.0 and a working internet connection.
00:43 Here, I have opened a Chimera window.
00:46 From the graphic access interface, click on the file 3w7f.
00:53 The structure of Squalin Synthase opens on the screen.
00:57 Now, let us prepare this structure for superimposing.
01:01 It contains two copies of the same protein.
01:05 Using the command line, delete one of the chains.
01:09 I will recall the command by clicking on the command history.
01:14 From the command history dialog box, select the command “delete:.a”.
01:20 Press Enter.
01:22 Next, to remove solvent molecules from the structure, I will select the command “del solvent”. Press Enter.
01:32 This structure is bound to the substrate analog Farnesyl thiopyrophosphate, FPS in short.
01:40 We will superimpose two similar proteins to compare their secondary structures.
01:46 For this, we will fetch a structure of the same enzyme without substrate.
01:52 On the command line, type: “open 2zco”, press Enter.
02:02 The new structure is in blue color.
02:05 Now, these two structures are ready to be superimposed.
02:10 Superimposition or Structural alignment is a tool to compare two or more protein structures.
02:18 The alignment is based on their shape and three-dimensional conformation.
02:24 Before we start superimposing, let us place some icons in the tool bar.
02:30 Click on Favorites menu.
02:32 Scroll down to Add to favorites/Tool bar option.
02:37 A Preferences dialog box opens.
02:40 From the Category drop-down, select Tools.
02:44 Under the heading “Settings”, check boxes under “On Tool bar” column.
02:53 Check boxes for Command line , Model Panel , Side View.
02:59 Scroll down and click on MatchMaker and Match-Align.
03:05 You can customize your own tool bar.
03:08 Select tools according to your requirement.
03:12 Observe the panel.
03:14 Icons have been added to the Tool bar on top of the panel.
03:19 To change the position of the tool bar, click on the Toolbar placement button.
03:25 And select the option from the drop-down menu.
03:29 When you finish adding all icons to the tool bar, click on Save button.
03:35 And click on Close to close the dialog box.
03:39 The structures are now in different positions.
03:43 Now, let us superimpose the structures using MatchMaker function.
03:48 Click on MatchMaker tool on the Tool bar.
03:53 A MatchMaker dialog box opens.
03:56 Click on 3w7f as Reference structure.
04:01 For now, let us continue with the default settings. Press OK button.
04:07 Observe the panel.
04:09 The two structures are superimposed on each other.
04:13 The two structures are almost completely superimposable with each other
04:19 except for a small part which is non-superimposable.
04:23 The fragment involved in this non-superimposable part starts from the amino acid number 53 to amino acid number 57.
04:34 The MatchMaker generates a sequence alignment using residue types and secondary structure.
04:40 And then fits the sequence-aligned residues in 3D.
04:44 Let us now check the Match-Align tool.
04:48 Click on Match-Align tool from the tool bar. A dialog box opens.
04:55 To select the chains, click on their pdb Ids.
04:59 Click on OK button.
05:03 A sequence alignment dialog box opens.
05:05 In this box, the amino acid pairs used in the final fit, are shown with light orange boxes.
05:13 The structures are mostly similar except for the loop at residues 52-54.
05:21 Place the cursor over the corresponding one letter code.
05:25 The residues from 52 to 54 are shifted due to the presence of gaps in the sequence.
05:33 Select this part using the cursor.
05:38 Observe the panel.
05:41 The part of the sequence selected is highlighted.
05:45 This corresponds to the non-superimposable part of the structure.
05:50 You can change the color of this non-superimposing parts using Actions menu.
05:55 Click on Actions menu.
05:57 Scroll down to Color, click on orange-red option.
06:02 Now this part is highlighted.
06:05 Clear the selection and close the dialog box.
06:10 Now, let me demonstrate how to morph conformations and create a trajectory.
06:15 Morphing involves calculating a series of intermediate structures between the original input structures.
06:23 The series of intermediate structures created can be saved as Molecular Dynamics Movie, in short, MD Movie.
06:32 Back to the panel.
06:34 Start the morphing tool from the Tools menu.
06:37 Click on Tools menu, scroll down to Structure Comparison.
06:42 Click on Morph conformations option.
06:46 A Morph conformations dialog box opens.
06:50 Click on Add.
06:52 In the resulting list of the models dialog box, double click on model number zero, that is, 3w7f to add to the conformations.
07:03 Next, click on model number 1, that is, 2zco.
07:10 Then again click on 3w7f, that is model number zero.
07:16 This sequence corresponds to a morph trajectory from ligand, bound to the structure to empty structure and then back.
07:26 Close the model list dialog.
07:29 Click on Create in the Morph conformations dialog box.
07:34 After a few seconds, a MD Movie is created.
07:39 The dialog box appears on the screen.
07:42 The dialog box has buttons to play or pause the movie.
07:46 Click on the arrow button to play.
07:50 Observe the panel.
07:52 The morphing of conformations is being played as a movie.
07:57 Pause the movie and close the MD movie dialog box.
08:02 Now, let's summarize what we have learnt.
08:05 In this tutorial, we have learnt to: superimpose and compare different structures of the same protein,
08:12 morph conformations and create a trajectory,
08:16 save the trajectory as Molecular Dynamics Movie.
08:20 For the assignment, open the structures of GTP binding proteins with the PDB code: 1TAG and 1TND
08:31 Superimpose the structures using MatchMaker tool.
08:34 Using Sequence Alignment tool, find out the regions that are non-identical.
08:41 The video at the following link summarizes the Spoken Tutorial project. Please download and watch it.
08:48 The Spoken Tutorial Project team conducts workshops and gives certificates for those who pass an online test. For more details, please write to us.
08:57 Spoken Tutorial project is funded by NMEICT, MHRD, Government of India. More information on this mission is available at the link shown.
09:09 This is Snehalatha from IIT Bombay, signing off. Thank you for joining.

Contributors and Content Editors

Devraj, Jyotisolanki, Sandhya.np14

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