VMD User's Guide

of loading/deleting molecules will not be immediately reflected. The Total RMSD label at thebottom of the menu shows the average RMSD for all molecules listed.RMS AlignmentThe RMS Alignment button fits molecules based on selected groups of atoms. Whereas the RMSDcalculator button finds the RMS distance between molecules without disturbing their coordinates,the RMS Alignment button actually moves molecules to new positions.This button is quite simple: Enter an atom selection in the input field, and press Align toalign the molecules based on the atoms in that selection. If you recompute the RMSD betweenmolecules with the RMSD calculator button, you will probably find that the values are different;this is because the calculation is made based on the current positions of the atoms.11.4.2 RMS and scriptingThe same actions can be taken on the scripting level. The Text interface also gives you moreflexibility through the atom selection mechanism allowing to choose the atoms to fit/compare.RMSD ComputationThere are two atom selections needed to do an RMSD computation, the list of atoms to comparein both molecules. The first atom of the first selection is compared to the first atom of the secondselection, fifth to fifth, and so on. The actual order is identical to the order from the input PDBfile.Once the two selections are made, the RMSD calculation is a matter of calling the measurermsd function. Here’s an example:set sel1 [atomselect 0 "backbone"]set sel2 [atomselect 1 "backbone"]measure rmsd $sel1 $sel2Info) 10.403014This prints the RMSD between the backbone atoms of molecule 0 with those of molecule 1.You could also use a weighting factor in these calculations. The best way to understand how to dothis is to see another example:set weighted_rmsd [measure rmsd $sel1 $sel2 weight mass]Info) 10.403022In this case, the weight is determined by the mass of each atom. Actually, the term is reallyone of the standard keywords available to an atom selection. Other ones include index and resid(which would both be rather strange to use) as well as charge, beta and occupancy. These lastterms useful if you want to specify your own values for the weighting factors.Computing the AlignmentThe best-fit alignment is done in two steps. The first is to compute the 4×4 matrix transformationthat takes one set of coordinates onto the other. This is done with the measure fit command.Assuming the same selections as before:166