Investigating Structural Alignment

RMSD per Residue

The ability to graphically display the RMSD per Residue between two proteins is a useful feature for demonstrating how well the proteins align. The root mean square deviation (RMSD) measures the distances in angstroms between the C-alpha atoms of 2 aligned residues.
To begin RMSD per Residue:

1

Go to Tools $\rightarrow$ RMSD Tools $\rightarrow$ RMSD per Residue. A window called RMSD per Residue will pop up with the four proteins listed.

2

Highlight two, three, or four proteins you want to compare by simply clicking on each one.

3

Click the Graph button. Another window, RMSD Per Residue, should appear that displays the graph of the plots.

Figure 21: Dialog

 
If you select two proteins, there will be one line on the graph. If you select three, there will be two lines differentiated by color on the graph.

Figure 22: This graph plots the RMSD between all four molecules. Residues in gaps are assigned an RMSD value of -1.

 
Now that we have examined RMSD per Residue, close both windows.

Pairwise RMSD

Pairwise RMSD prints the average overall RMSD for each pair of aligned proteins. To find the Pairwise RMSD of each molecule in relation to the other:

1

In the main Multiple Alignment window, select Tools $\rightarrow$ RMSD Tools.

2

Then select Pairwise RMSD in the side menu. A new window called Pairwise RMSD will appear printing the results of the RMSD calculations.

Figure 23: Printout of results.

To continue to the next section, close the Pairwise RMSD window.