Normally a rigid superposition which minimizes the RMSD is performed, and this minimum is returned. Given two sets of points and , the RMSD is defined as follows:
$\begin{align*} \mathrm{RMSD}(\mathbf v,\mathbf w)&=\sqrt{\frac1{n}\sum_{i=1}^n\|v_i-w_i\|^2}\\ &=\sqrt{\frac1{n}\sum_{i=1}^n\left((v_{ix}-w_{ix})^2+(v_{iy}-w_{iy})^2+(v_{iz}-w_{iz})^2\right)} \end{align*}$
Those descriptions are from wikipedia(bioinformatics). Could you explain what the equations mean?
And What does $\|\cdot\|$ mean above?