UCSF-Chimera/C3/Superimposing-and-Morphing/English
|
|
---|---|
Slide Number 1
Title Slide |
Welcome to this tutorial on Superimposing and Morphing |
Slide Number 2
Learning Objectives |
In this tutorial, we will learn to
|
Slide Number 3
Pre-requisites
|
To follow this tutorial you should be familiar with, Chimera Interface.
|
Slide Number 4
System Requirement |
Here I am using
|
Double-click on the Chimera | Here I have opened a Chimera window. |
Click on the file 3w7f from the side panel. | From the graphic access interface, click on the file 3w7f. |
Cursor on the panel. | The structure of Squalin Synthase opens on the screen.
|
Cursor on the panel. | It contains two copies of the same protein.
|
Click on the small back triangle at the end of the command line. | I will recall the command by clicking on the command history. |
Scroll down the command history dialog box.
|
From the command history dialog box, select the command “delete:.a”
|
Select the command “del solvent” from command history.
press enter. |
Next, to remove solvent molecules from the structure;
I will select the command “del solvent”. Press Enter. |
Cursor on the panel. | This structure is bound to the substrate analog Farnesyl thiopyrophosphate. FPS in short.
|
On the command line type “open 2zco” press enter. | On the command line type “open 2zco” press enter.
|
Cursor on the panel. | Now these two structures are ready to be superimposed. |
Slide Number 5
Structural alignment |
Superimposition or Structural alignment is a tool to compare two or more protein structures.
|
Cursor on the panel. | Before we start superimposing, let us place some icons in the tool bar. |
Click on Favorites menu >>Add to favorites. | Click on Favorites menu.
|
Cursor on preferences dialog box.
Model Panel Side View MatchMaker Match-Align |
From the Category drop-down, select Tools.
|
Cursor on the panel. | You can customize your own tool bar.
|
Cursor pointing tool bar.
|
Observe the panel.
Icons have been added to the Tool bar on top of the panel.
|
Click on Save button.
Close the window. |
When you finish adding all icons to the tool bar, click on Save button.
|
Hold the mouse button and drag on the panel. | The structures are now in different positions. |
Cursor on the panel. | Now let us superimpose the structures using MatchMaker function. |
Click on MatchMaker tool on the Tool bar. | Click on MatchMaker tool on the Tool bar.
|
Cursor on MatchMaker dialog box.
|
Click on 3w7f as Reference structure.
|
Cursor on the panel. | Observe the panel.
The two structures are superimposed on each other. |
Cursor on the panel. | The two structures are almost completely superimposable with each other.
|
Cursor on amino acids 53 and 57. | The fragment involved in this non-superimposable part starts from :
|
Cursor on the panel. | The MatchMaker generates a sequence alignment using residue types and secondary structure.
|
Click on Match-Align tool.
|
Let us now check the Match-Align tool.
A dialog box opens.
|
Click on OK button.
|
Click on OK button.
A sequence alignment dialog box opens.
|
Cursor on the sequence alignment dialog box. | The structures are mostly similar except for the loop at residues 52-54. |
Hover the cursor over one letter code. | Place the cursor over the corresponding one letter code. |
Cursor on the sequence alignment dialog box.
|
The residues from 52 to 54 are shifted due to the presence of gaps in the sequence.
|
Click on Actions menu, Scroll down to Color.
|
Observe the panel.
The part of the sequence selected is highlighted.
|
Click on Actions menu, scroll down to Color, click on orange-red option. | Click on Actions menu.
Scroll down to Color, click on orange-red option.
|
Cursor on the panel. | Now, let me demonstrate how to morph conformations and create a trajectory. |
Slide Number 6
Morphing |
Morphing involves calculating a series of intermediate structures between the original input structures.
|
Click on Tools menu >> Structure Comparison >> Morph conformations. | Back to the panel.
Start the morphing tool from the Tools menu. Click on Tools menu scroll down to Structure Comparison. Click on Morph conformations option. |
Cursor on the Morph conformations dialog box. | A Morph conformations dialog box opens. |
Click on Add button.
|
Click on Add.
Then again click on 3w7f, that is model number zero. |
Cursor on the Morph conformations dialog box.
|
This sequence corresponds to
|
Click on x button. | Close the model list dialog. |
Click on Create in the Morph conformations dialog. | Click on Create in the Morph conformations dialog box. |
Cursor on the dialog box. | After a few seconds a MD Movie is created.
|
Click on arrow button. | Click on the arrow button to play.
|
Cursor on the panel. | The morphing of conformations is being played as a movie.
Pause the movie and close the MD movie dialog box. |
Slide Number 7
Summary |
Now let's summarize what we have learnt.
|
Slide Number 8
Assignment |
For the assignment,
|
Slide Number 9
Acknowledgement |
The video at the following link summarizes the Spoken Tutorial project.
Please download and watch it. |
Slide Number 10 | The Spoken Tutorial Project Team
For more details, please write to us. |
Slide number 11 | Spoken Tutorial Project is funded by NMEICT, MHRD, Government of India.
More information on this Mission is available at the link shown |
This is Snehalatha from IIT Bombay signing off. Thank you for joining. |