Starting Multiple Sequence Alignment

From this point forward we will use MultiSeq extensively. In order to align and analyze the structural relationships of the four loaded molecules, we need to open MultiSeq.

1 Within the VMD main window, choose the Extensions menu.

2 In the Extensions menu select Sequence $\rightarrow$ Multiple Sequence Alignment.

A window entitled Multiple Sequence Alignment will appear on your screen. This is the main MultiSeq program window. The rest of the tutorial and exercises will use features from this window, unless otherwise specified.

Figure 4: Multiple Sequence Alignment Window

 

MultiSeq will align all four loaded molecules, unless you delete the molecule(s) in the VMD Main window.