Exercise 1: Investigating Structure Conservation

For this exercise, we will first examine structure conservation. Make sure Molecule Coloring is set to Q per residue.

1 In the main MultiSeq window top pull-down, select Tools $\rightarrow$ Residue Selection $\rightarrow$ Q Value. 2 A new window entitled Q Value will appear. Select Greater than 3 To the right, you can select a value between 0.0 to 1.0. Select 0.5 for a value. 4 Then, click on the Select button.

Figure 12: Exercise 1

Look in the OpenGL Display window and see what happens to the molecule. Since you selected the Q Value to be greater than or equal to 0.5, the majority of the molecule will be yellow. Also, the Sequence Display, in the MultiSeq window, will have the majority of the molecules highlighted. Why is this? By selecting the Q Value to be greater than or equal to 0.5, you have selected structural conservation at Q=0.5 or greater. In other words, you have demonstrated where the Q Value, structural conservation, is at a moderate to high level in all 4 aligned molecules - almost obscuring where high levels of conservation occur. Due to the high level of conservation, the Bond highlighting style is not very informative.

Figure 13: Q$\ge$0.5 with Bonds Highlight Style

 


You can change this by accessing the main MultiSeq window top pull-down menu:

5 Clicking on View $\rightarrow$ Highlight Style.

6 A side menu will appear alongside Highlight Style. Select Trace for the highlighting style.

Figure 14: Q$\ge$0.5 with Trace Highlight Style

As you can see, the areas with high levels of conservation are easily discerned using the Trace style. Now go back to the Q Value window and click on the Close Window button.