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.

 


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