UCSF-Chimera/C3/Superimposing-and-Morphing/English-timed - Revision history

Sandhya.np14 at 08:20, 28 June 2018

2018-06-28T08:20:17Z

Sandhya.np14 at 07:13, 28 June 2018

2018-06-28T07:13:57Z

Sandhya.np14 at 06:49, 28 June 2018

2018-06-28T06:49:09Z

Devraj at 07:22, 27 March 2018

2018-03-27T07:22:55Z

Jyotisolanki at 06:32, 8 December 2017

2017-12-08T06:32:06Z

Jyotisolanki: Created page with " {| style="border-spacing:0;" ! Time ! Narration |- |00:01 | Welcome to this tutorial on '''Superimposing and Morphing''' |- | 00:06 | In t..."

2017-12-08T06:30:08Z

Created page with " {| style="border-spacing:0;" ! <center>Time</center> ! <center>Narration</center> |- |00:01 | Welcome to this tutorial on '''Superimposing and Morphing''' |- | 00:06 | In t..."

New page

{| style="border-spacing:0;"
! <center>Time</center>
! <center>Narration</center>

|-
|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.

|-
|07:42
| 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.

|}

@@ Line 242: / Line 242: @@
 |-
 |05:13
-| The structures are mostly similar except for the loop at residues 52-54.
+| The structures are mostly similar except for the '''loop''' at '''residues 52-54'''.
 |-
@@ Line 266: / Line 266: @@
 |-
 |05:45
-| This corresponds to the '''non-superimposable''' part of the structure.
+| 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.
+| You can change the color of this non-superimposing parts using '''Actions''' menu.
 |-
@@ Line 290: / Line 290: @@
 |-
 | 06:10
-| Now, let me demonstrate how to morph '''conformations''' and create a trajectory.
+| 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.
+| 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.'''
+| The series of intermediate structures created can be saved as '''Molecular Dynamics Movie,''' in short,''' MD Movie.'''
 |-
@@ Line 310: / Line 310: @@
 |-
 |06:37
-| Click on '''Tools menu scroll down to Structure Comparison.'''
+| Click on '''Tools''' menu, scroll down to '''Structure Comparison'''.
 |-
 |06:42
-| '''Click on Morph conformations '''option.
+| Click on '''Morph conformations '''option.
 |-
@@ Line 326: / Line 326: @@
 |-
 |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.
+| 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'''.
+| Next, click on model number 1, that is, '''2zco'''.
 |-
@@ Line 338: / Line 338: @@
 |-
 |07:16
-| This sequence corresponds to : a morph '''trajectory''' from ligand , bound to the structure to empty structure ,  and then back.
+| This sequence corresponds to a morph '''trajectory''' from '''ligand''', bound to the structure to empty structure and then back.
 |-
@@ Line 350: / Line 350: @@
 |-
 |07:34
-| After a few seconds a''' MD Movie''' is created.
+| After a few seconds, a''' MD Movie''' is created.
 |-
@@ Line 358: / Line 358: @@
 |-
 |07:42
-| The dialog box has buttons to play or pause the movie.
+| The dialog box has buttons to '''play''' or '''pause''' the movie.
 |-
@@ Line 378: / Line 378: @@
 |-
 |08:02
-| Now let's summarize what we have learnt.
+| 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.
+| In this tutorial, we have learnt to: '''superimpose '''and compare different structures of the same protein,
 |-
 |08:12
-| Morph '''conformations''' and create a '''trajectory'''.
+| morph '''conformations''' and create a '''trajectory''',
 |-
 |08:16
-| Save the trajectory as '''Molecular Dynamics Movie.'''
+| '''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'''
+| 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.
+| '''Superimpose''' the structures using '''MatchMaker''' tool.
 |-
@@ Line 410: / Line 410: @@
 |-
 |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.
+| 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
+| '''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.
+| This is '''Snehalatha''' from '''IIT Bombay''', signing off. Thank you for joining.
 |}

@@ Line 70: / Line 70: @@
 |-
 | 01:32
-| This structure is bound to the substrate analog '''Farnesyl thiopyrophosphate'''. '''FPS''' in short.
+| This structure is bound to the '''substrate analog Farnesyl thiopyrophosphate''', '''FPS''' in short.
 |-
@@ Line 78: / Line 78: @@
 |-
 | 01:46
-|For this we will fetch a structure of the same enzyme without substrate.
+|For this, we will fetch a structure of the same enzyme without substrate.
 |-
 | 01:52
-| On the '''command line''' type “'''open 2zco'''” press enter.
+| On the '''command line''', type: “'''open 2zco'''”, press '''Enter'''.
 |-
@@ Line 90: / Line 90: @@
 |-
 | 02:05
-| Now these two structures are ready to be '''superimposed'''.
+| 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.
+| '''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.
+|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.
+| Before we start superimposing, let us place some '''icon'''s in the tool bar.
 |-
 | 02:30
-| Click on '''Favorites menu.'''
+| Click on '''Favorites''' menu.
 |-
 | 02:32
-|'''Scroll down to Add to favorites/Tool bar '''option.
+|Scroll down to '''Add to favorites/Tool bar '''option.
 |-
@@ Line 126: / Line 126: @@
 |-
 | 02:53
-| Check boxes for, '''Command line''' , '''Model Panel''' , '''Side View'''.
+| Check boxes for '''Command line''' , '''Model Panel''' , '''Side View'''.
 |-
 | 02:59
-| Scroll down and click on, '''MatchMaker '''  and '''Match-Align'''
+| Scroll down and click on '''MatchMaker '''  and '''Match-Align'''.
 |-
@@ Line 138: / Line 138: @@
 |-
 | 03:08
-|Select tools according to your requirement.
+|Select '''tool'''s according to your requirement.
 |-
 | 03:12
-| Observe the panel.
+| Observe the '''panel'''.
 |-
@@ Line 170: / Line 170: @@
 |-
 | 03:43
-| Now let us '''superimpose''' the structures using '''MatchMaker''' function.
+| Now, let us '''superimpose''' the structures using '''MatchMaker''' function.
 |-
@@ Line 186: / Line 186: @@
 |-
 |04:01
-|For now, let us continue with the default settings. Press '''OK''' button.
+|For now, let us continue with the '''default setting'''s. Press '''OK''' button.
 |-
@@ Line 194: / Line 194: @@
 |-
 | 04:09
-|The two structures are '''superimposed''' on each other.
+|The two structures are superimposed on each other.
 |-
 |04:13
-| The two structures are almost completely '''superimposable''' with each other.
+| The two structures are almost completely superimposable with each other
 |-
 |04:19
-|Except for a small part which is '''non-superimposable'''.
+|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.
+| The fragment involved in this non-superimposable part starts from the '''amino acid''' number 53 to '''amino acid''' number 57.
 |-
@@ Line 226: / Line 226: @@
 |-
 |04:55
-| To select the chains, click on their '''pdb Ids'''.
+| To select the '''chain'''s, click on their '''pdb Ids'''.
 |-
@@ Line 238: / Line 238: @@
 |-
 |05:05
-| In this box the '''amino acid '''pairs used in the final fit, are shown with light orange boxes.
+| In this box, the '''amino acid '''pairs used in the final fit, are shown with light orange boxes.
 |-

@@ Line 6: / Line 6: @@
 |-
 |00:01
-| Welcome to this tutorial on '''Superimposing and Morphing'''
+| 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.
+| In this tutorial, we will learn to: superimpose and compare different structures of the same protein,
 |-
 | 00:13
-| Morph '''conformations''' and create a '''trajectory'''.
+| morph '''conformations''' and create a '''trajectory'''.
 |-
 | 00:17
-| To follow this tutorial you should be familiar with, '''Chimera''' Interface.
+| To follow this tutorial, you should be familiar with '''Chimera''' interface.
 |-
@@ Line 26: / Line 26: @@
 |-
 | 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.
+| 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.
+| Here, I have opened a '''Chimera''' window.
 |-
@@ Line 38: / Line 38: @@
 |-
 | 00:53
-| The structure of '''Squalin Synthase''' opens on the screen.
+| The structure of '''Squalin Synthase''' opens on the '''screen'''.
 |-
 | 00:57
-|Now let us prepare this structure for '''superimposing'''.
+|Now, let us prepare this structure for superimposing.
 |-
 | 01:01
-| It contains two copies of the same '''protein'''.
+| It contains two copies of the same protein.
 |-
 | 01:05
-|Using the '''command line''' delete one of the chains.
+|Using the '''command line''', delete one of the '''chain'''s.
 |-
 | 01:09
-| I will recall the command by clicking on the command history.
+| I will recall the '''command''' by clicking on the '''command history'''.
 |-
 | 01:14
-| From the command history dialog box, select the command '''“delete:.a”'''
+| From the '''command history''' dialog box, select the command '''“delete:.a”'''.
 |-
@@ Line 66: / Line 66: @@
 |-
 | 01:22
-| Next, to remove '''solvent '''molecules from the structure; I will select the command “'''del solvent'''”. Press '''Enter'''.
+| Next, to remove solvent molecules from the structure, I will select the command “'''del solvent'''”. Press '''Enter'''.
 |-

@@ Line 361: / Line 361: @@
 |-
-|07:42
+|07:46
 | Click on the arrow button to play.

@@ Line 1: / Line 1: @@
-{| style="border-spacing:0;"
+{| border=1
-! <center>Time</center>
+||''' Time '''
-! <center>Narration</center>
+||'''Narration'''
 |-
@@ Line 47: / Line 47: @@
 | 01:01
 | It contains two copies of the same '''protein'''.
 |-
@@ Line 148: / Line 147: @@
 | 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.
 |-