RMSF Analysis

The RMSF Analysis tool computes the root-mean-square fluctuation of each atom (or residue) along a trajectory: how much it moves around its mean position. It is the usual way to identify flexible regions (loops, termini) and rigid regions of a protein.

RMSFi = sqrt( < | ri(t) − <ri> |2 > )

The reference is always the mean position of each atom over the analyzed frames. Run Align Trajectory first if the trajectory has not been superposed, otherwise the motion of the whole molecule dominates the result.

To open the tool: Main Menu > Analysis > RMSF Analysis (Figure 1).

• System / Object: the trajectory to analyze. By default every atom of the object is used.

• Limit to current viewer selection: only the atoms currently selected in the 3D view (they must belong to the same object).

• Backbone atoms only (N, CA, C, O): keeps only protein backbone atoms; water, ions and ligands are left out.

• Group by: Atom / Residue: one value per atom, or the average of the atoms of each residue.

• Frames from / to and Step Size: the frame range (-1 = last frame) and the interval between analyzed frames.

• Plot the result: plots RMSF (Å) against the atom index or residue number.

• Save results to text file: writes a tab-separated file (by default rmsf.txt in the working folder of the system) with the same data shown in the results window.

Click Run. The values are listed in a text window and, if selected, plotted (Figure 2).