The RMSD Calculator menu is used to calculate RMS distances between molecules.
The upper left corner of the menu is where you specify which atoms are to be used in the calculation. In the input field, type the atom selection text just as you would in the Graphics form. The checkbox below the input field entitled "Backbone only" restricts whatever atom selection you typed to just the backbone atoms of the selection; in effect, it adds "and backbone" to the atom selection text.
The upper right corner of the menu has a button labeled "RMSD". Its effect depends on which of the two radio buttons, "Top" or "Average", is pressed down. If "Top" is pressed, VMD calculates the RMS distance between the top molecule (which is usually the last molecule loaded) and every other molecule. If "Average" is pressed, VMD first computes the average x, y, z coordinates of the selected atoms in each molecule, then computes the RMS distance of each molecule from that average structure.
Results of the RMS calculations for each molecule are shown in the browser in the bottom half of the menu. Note that this list is not updated until you presse the RMSD button, so the effects of loading/deleting molecules will not be immediately reflected. The "Total RMSD" label at the bottom of the menu shows the average RMSD for all molecules listed.
